diff --git a/.gitignore b/.gitignore index e6cef7a73..25e23fcdf 100644 --- a/.gitignore +++ b/.gitignore @@ -62,6 +62,9 @@ docs/_build/ # PyBuilder target/ +# PyCharm +*.idea/vcs.xml + # Ipython notebook checkpoints *.ipynb_checkpoints/ diff --git a/.travis.yml b/.travis.yml index bc2ba07c4..e9c1d46f8 100644 --- a/.travis.yml +++ b/.travis.yml @@ -1,57 +1,101 @@ language: python -sudo: false +# Run jobs on container-based infrastructure, can be overridden per job +dist: xenial + +# Run builds for both master and topology (and PRs to each) branches: only: - - master + - master + - topology -install: - - source devtools/travis-ci/install.sh - - export PYTHONUNBUFFERED=true +matrix: + include: + # Test osx with RDKit + - os: osx + language: generic + env: PYTHON_VER=3.6 RDKIT=true + - os: osx + language: generic + env: PYTHON_VER=3.7 RDKIT=true + + # Test RDKit compatibility + - os: linux + python: 3.6 + env: PYTHON_VER=3.6 RDKIT=true + - os: linux + python: 3.7 + sudo: required + env: PYTHON_VER=3.7 RDKIT=true + + # Test OpenEye compatibility + - os: linux + python: 3.6 + env: PYTHON_VER=3.6 OPENEYE=true + - os: linux + sudo: required + python: 3.7 + env: PYTHON_VER=3.7 OPENEYE=true + + # Test case where both OpenEye and RDKit are installed + - os: linux + python: 3.6 + env: PYTHON_VER=3.6 OPENEYE=true RDKIT=true + - os: linux + sudo: required + python: 3.7 + env: PYTHON_VER=3.7 OPENEYE=true RDKIT=true + +env: + global: + - OE_LICENSE="$HOME/oe_license.txt" + +before_install: + # Additional info about the build + - uname -a + - df -h + - ulimit -a + + # Install the Python environemt + - source devtools/travis-ci/before_install.sh + - python -V # Unpack encrypted OpenEye license file - if [ "$TRAVIS_SECURE_ENV_VARS" == true ]; then openssl aes-256-cbc -K $encrypted_a4fdffb2b55a_key -iv $encrypted_a4fdffb2b55a_iv -in oe_license.txt.enc -out $OE_LICENSE -d; fi - - if [ "$TRAVIS_SECURE_ENV_VARS" == false ]; then echo "OpenEye license will not be installed in forks."; fi + - if [[ "$OPENEYE" == true && "$TRAVIS_SECURE_ENV_VARS" == false ]]; then echo "OpenEye license will not be installed in forks."; fi -script: - # Add omnia and conda-forge channel - - conda config --add channels ${ORGNAME} - - conda config --add channels conda-forge - # Create and activate test environment - - conda create --yes -n test python=$python +install: + # Create test environment for package + - conda create -n test python=$PYTHON_VER pip pytest pytest-cov nbval - source activate test - # Install OpenEye toolkit - #- pip install $OPENEYE_CHANNEL openeye-toolkits && python -c "import openeye; print(openeye.__version__)" + + # TODO: Do we still need the beta version or can we do simply -c openeye openeye-toolkits? # Use beta version for partial bond orders - - pip install --pre -i https://pypi.anaconda.org/openeye/simple openeye-toolkits && python -c "import openeye; print(openeye.__version__)" + # TODO: Reactivate conda install instead of pip install once OpenEye is released for python 3.7 on conda-forge. + # - if [[ "$OPENEYE" == true ]]; then conda install --yes -c openeye/label/Orion openeye-toolkits oeommtools && python -c "import openeye; print(openeye.__version__)"; fi + # Install RDKit - - conda install --yes -c rdkit rdkit - # Build the recipe - - conda build devtools/conda-recipe - # Use oeommtools for improper test - - conda install --yes -c openeye/label/Orion oeommtools -c omnia - # Install - - conda install --yes --use-local openforcefield - # Run tests - - conda install --yes nose nose-timer - - cd devtools && nosetests -vv --nocapture --with-timer $PACKAGENAME && cd .. + - if [[ "$RDKIT" == true ]]; then conda install --yes -c rdkit rdkit; fi + - if [[ "$RDKIT" == true ]]; then conda install --yes -c omnia ambertools; fi -env: - matrix: - - python=3.5 CONDA_PY=35 - - python=3.6 CONDA_PY=36 + # Install pip only modules + - pip install codecov + - pip install coverage==4.4 + # TODO: Go back to conda install once OpenEye is released for python 3.7 on conda-forge. + - pip install -i https://pypi.anaconda.org/openeye/simple openeye-toolkits - global: - - ORGNAME="omnia" - - PACKAGENAME="openforcefield" - # OpenEye toolkit - - OE_LICENSE="$HOME/oe_license.txt" - - OPENEYE_CHANNEL="-i https://pypi.anaconda.org/openeye/channel/main/simple" - # encrypted BINSTAR_TOKEN for push of dev package to binstar - - secure: "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" - # encrypted AWS_ACCESS_KEY_ID and AWS_SECRET_ACCESS_KEY - #- secure: "SrSd1JoI8dBXQxDAX0xBTYBinTusRBQoPETnxHrBAgKdoty1pkzaghTKNMsrGsk78iwkkj1hAyttIY9trdFQkmx+OTx0fLKFmDHsMkgko4RzTtrgLgoxuRIs/gruID2cN1XKEbxlhRmQF14+q8/X1q6iGGdYMrxo51JcYPuEOSo=" - #- secure: "br6QRMYXhHltYTEh/d+zejxcunT3GsqwQvxxLmqnLxi+LIxX4j7eymR6p4fPBd5mCRxyvkQEjnSZxF6e7JlEKxWVcMG28I/dBWzVIRW3EKQQNRmyI+JL1dfNaqj68kHJD+FknBwHK9LD238JPcyqXPdVrm9iPkDijPczvPBxvDs=" - -#after_success: -# - echo "after_success" -# - if [ "$TRAVIS_SECURE_ENV_VARS" == true ]; then ./devtools/travis-ci/after_success.sh; fi + # Build and install package + - conda build --python=$PYTHON_VER devtools/conda-recipe + - conda install --use-local openforcefield + +script: + # Run doctests only if both RDKit and OpenEye are installed. + - if [[ "$RDKIT" == true && "$OPENEYE" == true ]]; + then pytest -v --ignore=utilities --ignore=examples/deprecated --ignore=docs --doctest-modules --nbval-lax --cov=openforcefield; + else pytest -v --ignore=utilities --ignore=examples/deprecated --nbval-lax --cov=openforcefield; + fi + +notifications: + email: false + +after_success: + - codecov diff --git a/Chemical-starting-points.md b/FAQ.md similarity index 96% rename from Chemical-starting-points.md rename to FAQ.md index ec7301aa9..ab0ece21c 100644 --- a/Chemical-starting-points.md +++ b/FAQ.md @@ -1,10 +1,12 @@ -# Appropriate starting points for applying a SMIRNOFF +# Frequently asked questions (FAQ) + +## Input files for applying SMIRNOFF parameters SMIRNOFF force fields use direct chemical perception meaning that, unlike many molecular mechanics (MM) force fields, they apply parameters based on substructure searches acting directly on molecules. This creates unique opportunities and allows them to encode a great deal of chemistry quite simply, but it also means that the *starting point* for parameter assignment must be well-defined chemically, giving not just the elements and connectivity for all of the atoms of all of the components of your system, but also providing the formal charges and bond orders. Specifically, to apply SMIRNOFF to a system, you must either: -1. Provide molecules (currently `OEMol` objects, but an RDKit version is in development) corresponding to the components of your system, or +1. Provide Open Force Field Toolkit `Molecule` objects corresponding to the components of your system, or 2. Provide an OpenMM `Topology` which includes bond orders and thus can be converted to molecules corresponding to the components of your system Without this information, our direct chemical perception cannot be applied to your molecule, as it requires the chemical identity of the molecules in your system -- that is, bond order and formal charge as well as atoms and connectivity. diff --git a/LICENSE b/LICENSE index 803d5d474..d94730706 100644 --- a/LICENSE +++ b/LICENSE @@ -1,4 +1,14 @@ -Copyright (c) 2016, Open Forcefield Group +This software is distributed under the MIT License. + +More information on this license can be found at the Open Source Initiative + +https://opensource.org/licenses/MIT + +The complete license text is reproduced below: + +--- + +Copyright (c) 2016-2018, Open Force Field Initiative Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/README.md b/README.md index 1cc7870aa..9408cd462 100644 --- a/README.md +++ b/README.md @@ -1,95 +1,85 @@ [![Build Status](https://travis-ci.org/openforcefield/openforcefield.svg?branch=master)](https://travis-ci.org/openforcefield/openforcefield?branch=master) -[![Documentation Status](https://readthedocs.org/projects/open-forcefield-toolkit/badge/?version=latest)](http://open-forcefield-toolkit.readthedocs.io/en/latest/?badge=latest) +[![Documentation](https://readthedocs.org/projects/open-forcefield-toolkit/badge/?version=latest)](http://open-forcefield-toolkit.readthedocs.io/en/latest/?badge=latest) +[![Language grade: Python](https://img.shields.io/lgtm/grade/python/g/openforcefield/openforcefield.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/openforcefield/openforcefield/context:python) +[![codecov](https://codecov.io/gh/openforcefield/openforcefield/branch/master/graph/badge.svg)](https://codecov.io/gh/openforcefield/openforcefield) +[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT) +[![Install with Conda](https://anaconda.org/omnia/openforcefield/badges/installer/conda.svg)](https://anaconda.org/omnia/openforcefield) +[![Anaconda Cloud platforms](https://anaconda.org/omnia/openforcefield/badges/platforms.svg)](https://anaconda.org/omnia/openforcefield) +[![Anaconda Cloud downloads](https://anaconda.org/omnia/openforcefield/badges/downloads.svg)](https://anaconda.org/openforcefield/openforcefield) +[![Funding](https://img.shields.io/badge/Funding-Open%20Force%20Field%20Consortium-brightgreen.svg)](http://openforcefield.org) -# Open Forcefield Group toolkit +# The Open Force Field toolkit -This repository contains a number of tools from the [Open Forcefield Consortium](http://github.com/openforcefield) for the development and use of modern molecular mechanics forcefields based on direct chemical perception and parameterized with rigorous statistical methods. +This repository contains a number of tools from the [Open Force Field Initiative](http://openforcefield.org) for the development and use of modern molecular mechanics forcefields based on direct chemical perception and parameterized with rigorous statistical methods. This repository hosts tools that we have committed to stably maintain throughout their lifetimes: -* The [SMIRKS Native Open Force Field (SMIRNOFF)](https://github.com/openforcefield/openforcefield/blob/master/The-SMIRNOFF-force-field-format.md) direct chemical perception forcefield specification language +* Tools for using the [SMIRKS Native Open Force Field (SMIRNOFF) specification](https://open-forcefield-toolkit.readthedocs.io/en/latest/smirnoff.html) * Tools for direct chemical environment perception and manipulation +## Documentation + +[Documentation](https://open-forcefield-toolkit.readthedocs.io/en/latest/) for the `openforcefield` toolkit is hosted at [readthedocs](https://open-forcefield-toolkit.readthedocs.io/en/latest). + ## Installation -We currently support Python 2.7, 3.5 and 3.6. - -We recommend the [miniconda](http://conda.pydata.org/miniconda.html) Python distribution. -To install `miniconda` on `osx` with `bash`, this is: -```bash -wget https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -bash Miniconda3-latest-MacOSX-x86_64.sh -b -p $HOME/miniconda3 -export PATH="$HOME/miniconda3/bin:${PATH}" -``` -These tools currently require the OpenEye toolkit (which requires a [license](https://www.eyesopen.com/licensing-philosophy) that is free for academics indenting to rapidly release results into the public domain): -```bash -pip install -i https://pypi.anaconda.org/OpenEye/simple OpenEye-toolkits -``` -Install `openforcefield` tools via conda: -```bash -conda install --yes -c conda-forge -c omnia openforcefield -``` -# Tools +`openforcefield` is a Python toolkit, and supports Python 3.6 and 3.7. + +### Installing via conda + +Detailed installation instructions can be found [here](https://open-forcefield-toolkit.readthedocs.io/en/latest/installation.html). + +### Installing from source + +If you need to install via source, see the build and run package requirements listed in the [development conda recipe](https://github.com/openforcefield/openforcefield/blob/master/devtools/conda-recipe/meta.yaml). + +# Features of the `openforcefield` toolkit -## `SMIRNOFF`: SMIRKS Native Open Force Field +## The SMIRKS Native Open Force Field (SMIRNOFF) format -This repository houses the SMIRNOFF SMIRKS-based force field format, along with classes to parameterize OpenMM systems given [SMIRNOFF `.offxml` format files](https://github.com/openforcefield/openforcefield/blob/master/The-SMIRNOFF-force-field-format.md). +This repository provides tools for using the [SMIRKS Native Open Force Field (SMIRNOFF) specification](https://open-forcefield-toolkit.readthedocs.io/en/latest/smirnoff.html), which currently supports an XML representation for force field definition files. -The SMIRNOFF force field format is documented [here](https://github.com/openforcefield/smirnoff/blob/master/The-SMIRNOFF-force-field-format.md). +By convention, files containing [XML representations](https://en.wikipedia.org/wiki/XML) of SMIRNOFF force fields carry `.offxml` extensions. -The SMIRNOFF forcefield format is available in sample form under `data/forcefield`, and is handled by `forcefield.py`. - An example comparing SMIRNOFF versus AMBER energies for the parm@frosst forcefield is provided under -examples/SMIRNOFF_comparison, where two scripts can compare energies for a single molecule or for the entire AlkEthOH set. -Note that two forcefields are currently available in this format, `Frosst_AlkEthOH.offxml`, -the parm@frosst forcefield as it should have been for this set, and `Frosst_AlkEthOH_parmAtFrosst.offxml`, -the forcefield as it was actually implemented (containing several bugs as noted in the file itself). +Example SMIRNOFF `.offxml` force field definitions can be found in [`openforcefield/data/forcefield`](https://github.com/openforcefield/openforcefield/tree/master/openforcefield/data/forcefield). -It can also be of interest to know what SMIRNOFF parameters would be applied to particular molecules. Utility functionality for this is provided under `forcefield_labeler.py`, which has generally similar structure to `forcefield.py` but instead of providing OpenMM systems with parameters, it can be applied to specific molecules and returns information about what parameters would be applied. +### Working with SMIRNOFF parameter sets -### Example usage +The SMIRNOFF `ForceField` class is essentially a drop-in replacement for the [OpenMM `ForceField` class](http://docs.openmm.org/latest/api-python/generated/simtk.openmm.app.forcefield.ForceField.html#simtk.openmm.app.forcefield.ForceField). -The SMIRNOFF `ForceField` class is essentially a drop-in replacement for the [OpenMM `ForceField` class](http://docs.openmm.org/latest/api-python/generated/simtk.openmm.app.forcefield.ForceField.html#simtk.openmm.app.forcefield.ForceField), with the additional requirement that an OpenEye `OEMol`-compatible object must also be provided to allow for chemical environment perception (and optionally charges). -For example, if we have an `OEMol` named `mol`, we can create an OpenMM `System` object with the following code: ```python -# Import the SMIRNOFF forcefield engine and some useful tools -from openforcefield.typing.engines.smirnoff import ForceField -from openforcefield.utils import read_molecules, get_data_filename, generateTopologyFromOEMol +# Load a molecule into the openforcefield Molecule object +from openforcefield.topology import Molecule +from openforcefield.utils import get_data_filename +sdf_file_path = get_data_filename('molecules/ethanol.sdf') +molecule = Molecule.from_file(sdf_file_path) -# read in molecule from file in openforcefield/data/molecules/ -mols = read_molecules('benzene.mol2') +# Create an openforcefield Topology object from the molecule +from openforcefield.topology import Topology +topology = Topology.from_molecules(molecule) -# Get positions and topology in OpenMM-compatible format -topology = generateTopologyFromOEMol(mols[0]) +# Load the smirnoff99Frosst SMIRNOFF force field definition +from openforcefield.typing.engines.smirnoff import ForceField +forcefield = ForceField('smirnoff99Frosst.offxml') -# Load a SMIRNOFF small molecule forcefield for alkanes, ethers, and alcohols -FF_filename = get_data_filename('forcefield/Frosst_AlkEthOH_parmAtFrosst.offxml') -forcefield = ForceField(FF_filename) +# Create an OpenMM system representing the molecule with SMIRNOFF-applied parameters +openmm_system = forcefield.create_openmm_system(topology) -# Create the OpenMM system, additionally specifying a list of OEMol objects for the unique molecules in the system -system = forcefield.createSystem(topology, mols) +# Load a SMIRNOFF small molecule forcefield for alkanes, ethers, and alcohols +forcefield = ForceField('Frosst_AlkEthOH_parmAtFrosst.offxml') ``` -See `examples/SMIRNOFF_simulation/` for a complete example of how SMIRNOFF can be used for small molecule vacuum simulations, and `examples/mixedFF_structure` for how to set up a system which uses an AMBER forcefield (in this case, AMBER99SB-ILDN) for a protein in combination with SMIRNOFF for a small molecules. Via ParmEd, this can be translated into GROMACS, AMBER, or CHARMM formats for use elsewhere (and additional formats via InterMol). -**For an especially complete worked example, see complete setup of a host-guest simulation in water with SMIRNOFF**, including docking, 2D and 3D visualization, etc., in `examples/host_guest_simulation/smirnoff_host_guest.ipynb` (Jupyter notebook). +Detailed examples of using SMIRNOFF with the toolkit can be found [in the documentation](https://open-forcefield-toolkit.readthedocs.io/en/latest/examples.html). -### FAQs: -See [`Chemical-starting-points.md`](Chemical-starting-points.md) for answers to a variety of common problems, such as: -- Why do I need to provide molecules corresponding to the components of my system, or a Topology with bond orders? -- Can I use an AMBER (or GROMACS) topology/coordinate file as a starting point for applying a SMIRNOFF force field? -- What about starting from a PDB file? +## Chemical environments: Tools for chemical environment perception and manipulation -## `ChemicalEnvironment`: Tools for chemical environment perception and manipulation +The `ChemicalEnvironments` class can be used to parse and manipulate [tagged SMARTS strings](http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html) or single-fragment [SMIRKS strings](http://www.daylight.com/dayhtml/doc/theory/theory.smirks.html) representing chemical environments with tagged atoms. -ChemicalEnvironments are a python class used to parse and manipulate SMIRKS strings. -They were created with the goal of being able to automatically sample over chemical perceptions space. -Someday they will be used to generate SMIRKS patterns for SMIRKS Native-Open Force Fields parameters. -These are initiated with SMIRKS strings for single molecules fragements`*` and then the information is stored for each atom and bond in the initial fragment. - -`*` NOTE SMIRKS can be used to show how a reaction would happen between fragments in different molecules. This is done with `'.'` between molecules and `'>>'` to indicate a reaction. Chemical Environments can only parse SMIRKS strings for fragments of a single molecule. +### Working with chemical environments ```python from openforcefield.typing.chemistry import environment smirks = "[#6X3,#7:1]~;@[#8;r:2]~;@[#6X3,#7:3]" -angle = environment.AngleChemicalEnvironment(smirks = smirks) +angle = environment.AngleChemicalEnvironment(smirks=smirks) print(angle.asSMIRKS()) # "[#6X3,#7:1]~;@[#8;r:2]~;@[#6X3,#7:3]" @@ -103,23 +93,14 @@ print(alpha.asSMIRKS()) # smirks for atom only print(angle.asSMIRKS()) # "[#6X3,#7:1]~;@[#8;r:2]~;@[#6X3,#7:3]~;!@[#8X2]" ``` -If you are not familiar with the SMIRKS language, take a look at these Daylight resources: -* [SMILES](http://www.daylight.com/dayhtml_tutorials/languages/smiles/index.html) -* [SMARTS](http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html) -* [SMIRKS](http://www.daylight.com/dayhtml_tutorials/languages/smirks/index.html) - -For more detailed examples see README and `using_environment.ipynb` in `examples/chemicalEnvironments/` - -# Manifest - -* `examples/` - some examples - look here to get started; see especially `host_guest_simulation` for a detailed worked example of SMIRNOFF simulation of host-guest binding. -* `openforcefield/` - openforcefield tools -* `devtools/` - continuous integration and packaging scripts and utilities -* `utilities/` - utilities; scripts to convert parm@frosst modified `frcmod` files to SMIRNOFF XML -* `oe_license.txt.enc` - encrypted OpenEye license for continuous integration testing -* `.travis.yml` - travis-ci continuous integration file -* `The-SMIRNOFF-force-field-format.md` - specifications for the SMIRNOFF force field format -* `Chemical-starting-points.md` - discussion of appropriate starting points for applying a SMIRNOFF force field to a system +Daylight provides detailed specifications of the [SMILES](http://www.daylight.com/dayhtml_tutorials/languages/smiles/index.html), [SMARTS](http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html), and [SMIRKS](http://www.daylight.com/dayhtml_tutorials/languages/smirks/index.html) languages. + +# Frequently asked questions (FAQ) + +See [`Chemical-starting-points.md`](Chemical-starting-points.md) for answers to a variety of common problems, such as: +* Why do I need to provide molecules corresponding to the components of my system, or a `Topology` with bond orders? +* Can I use an AMBER, CHARMM, or gromacs topology/coordinate file as a starting point for applying a SMIRNOFF force field? +* What if I am starting from a PDB file? # Contributors diff --git a/The-SMIRNOFF-force-field-format.md b/The-SMIRNOFF-force-field-format.md index 263cb0a92..7bea5926f 100644 --- a/The-SMIRNOFF-force-field-format.md +++ b/The-SMIRNOFF-force-field-format.md @@ -1,129 +1,457 @@ -# The SMIRKS Native Open Force Field (SMIRNOFF) v0.1 +# The SMIRks Native Open Force Field (SMIRNOFF) specification v0.2 -The SMIRNOFF format is based on the [`OpenMM`](http://openmm.org) [`ForceField`](http://docs.openmm.org/7.0.0/api-python/generated/simtk.openmm.app.forcefield.ForceField.html#simtk.openmm.app.forcefield.ForceField) class and provides an XML format for encoding force fields based on [SMIRKS](http://www.daylight.com/dayhtml/doc/theory/theory.smirks.html)-based chemical perception. -While designed for [`OpenMM`](http://openmm.org), parameters encoded in this format can be applied to systems and then these systems converted via [`ParmEd`](http://parmed.github.io/ParmEd) and [`InterMol`](https://github.com/shirtsgroup/InterMol) for simulations in a variety of other simulation packages. +SMIRNOFF is a specification for encoding molecular mechanics force fields from the [Open Force Field Initiative](http://openforcefield.org) based on direct chemical perception using the broadly-supported [SMARTS](http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html) language, utilizing atom tagging extensions from [SMIRKS](http://www.daylight.com/dayhtml/doc/theory/theory.smirks.html). + +## Authors and acknowledgments + +The SMIRNOFF specification was designed by the [Open Force Field Initiative](http://openforcefield.org). + +Primary contributors include: +* Caitlin C. Bannan (University of California, Irvine) `` +* Christopher I. Bayly (OpenEye Software) `` +* John D. Chodera (Memorial Sloan Kettering Cancer Center) `` +* David L. Mobley (University of California, Irvine) `` + +SMIRNOFF and its reference implementation in the `openforcefield` toolkit was heavily inspired by the [ForceField class](http://docs.openmm.org/latest/api-python/generated/simtk.openmm.app.forcefield.ForceField.html#simtk.openmm.app.forcefield.ForceField) from the [OpenMM](http://openmm.org) molecular simulation package, and its associated [XML format](http://docs.openmm.org/latest/userguide/application.html#writing-the-xml-file), developed by [Peter K. Eastman](https://en.wikipedia.org/wiki/Peter_Eastman) (Stanford University). + +## Representations and encodings + +A force field in the SMIRNOFF format can be encoded in multiple representations. +Currently, only an [XML](https://en.wikipedia.org/wiki/XML) representation is supported by the reference implementation of the [openforcefield toolkit](http://github.com/openforcefield/openforcefield). + +### XML representation + +A SMIRNOFF force field can be described in an [XML](https://en.wikipedia.org/wiki/XML) representation, which provides a human- and machine-readable form for encoding the parameter set and its typing rules. +This document focuses on describing the XML representation of the force field. + +* By convention, XML-encoded SMIRNOFF force fields use an `.offxml` extension if written to a file to prevent confusion with other file formats. +* In XML, numeric quantities appear as strings, like `"1"` or `"2.3"`. +* Integers should always be written without a decimal point, such as `"1"`, `"9"`. +* Non-integral numbers, such as parameter values, should be written with a decimal point, such as `"1.23"`, `"2."`. +* In XML, certain special characters that occur in valid SMARTS/SMIRKS patterns (such as ampersand symbols `&`) must be specially encoded. +See [this list of XML and HTML character entity references](https://en.wikipedia.org/wiki/List_of_XML_and_HTML_character_entity_references) for more details. + +### Future representations: JSON, MessagePack, YAML, and TOML + +We are considering supporting [JSON](https://www.json.org/), [MessagePack](https://msgpack.org/index.html), [YAML](http://yaml.org/), and [TOML](https://github.com/toml-lang/toml) representations as well. + +## Reference implementation + +A reference implementation of the SMIRNOFF XML specification is provided in the [openforcefield toolkit](http://github.com/openforcefield/openforcefield). + +## Support for molecular simulation packages + +The reference implementation currently generates parameterized molecular mechanics systems for the GPU-accelerated [OpenMM](http://openmm.org) molecular simulation toolkit. +Parameterized systems can subsequently be converted for use in other popular molecular dynamics simulation packages (including [AMBER](http://ambermd.org/), [CHARMM](https://www.charmm.org), [NAMD](http://www.ks.uiuc.edu/Research/namd/), [Desmond](https://www.deshawresearch.com/resources_desmond.html), and [LAMMPS](http://lammps.sandia.gov/)) via [ParmEd](http://parmed.github.io/ParmEd) and [InterMol](https://github.com/shirtsgroup/InterMol). +See [Converting SMIRNOFF parameterized systems to other simulation packages](https://open-forcefield-toolkit.readthedocs.io/en/latest/converting.html) for more details. ## Basic structure -The SMIRNOFF format provides XML `ffxml` files that are parseable by the `ForceField` class of the `openforcefield.typing.smirnoff` module. -These encode parameters for a force field based on a SMIRKS-based specification of the chemical environment the parameters are to be applied to. -The file has tags corresponding to OpenMM force terms (`HarmonicBondForce`, `HarmonicAngleForce`, `PeriodicTorsionForce`, etc., as discussed in more detail below); these specify units used for the different constants provided for individual force terms, for example (see the [AlkEthOH example ffxml](https://github.com/openforcefield/openforcefield/blob/master/openforcefield/data/forcefield/Frosst_AlkEthOH.offxml)): +A reference implementation of a SMIRNOFF force field parser that can process XML representations (denoted by `.offxml` file extensions) can be found in the `ForceField` class of the `openforcefield.typing.engines.smirnoff` module. + +Below, we describe the main structure of such an XML representation. + +### The enclosing `` tag + +A SMIRNOFF forcefield XML specification always is enclosed in a `` tag, with certain required attributes provided. ```XML - + +... + +``` + +#### Versioning + +The SMIRNOFF force field format supports versioning via the `version` attribute to the root `` tag, e.g.: +```XML + +... + +``` +The version format is `x.y`, where `x` denotes the major version and `y` denotes the minor version. +SMIRNOFF versions are guaranteed to be backward-compatible within the *same major version number series*, but it is possible major version increments will break backwards-compatibility. + +#### Aromaticity model + +The `aromaticity_model` specifies the aromaticity model used for chemical perception (here, `OEAroModel_MDL`). + +Currently, the only supported model is `OEAroModel_MDL`, which is implemented in both the RDKit and the OpenEye Toolkit. + +.. note :: Add link to complete open specification of `OEAroModel_MDL` aromaticity model. + +### Metadata + +Typically, date and author information is included: +```XML +2016-05-25 +J. D. Chodera (MSKCC) charge increment tests +``` +The `` tag should conform to [ISO 8601 date formatting guidelines](https://en.wikipedia.org/wiki/ISO_8601), such as `2018-07-14` or `2018-07-14T08:50:48+00:00` (UTC time). + +.. todo :: Should we have a separate `` or `` section that users can add whatever they want to? This would minimize the potential for accidentally colliding with other tags we add in the future. + +### Parameter generators + +Within the `` tag, top-level tags encode parameters for a force field based on a SMARTS/SMIRKS-based specification describing the chemical environment the parameters are to be applied to. +The file has tags corresponding to OpenMM force terms (`Bonds`, `Angles`, `TorsionForce`, etc., as discussed in more detail below); these specify units used for the different constants provided for individual force terms. +```XML + + ... + ``` which introduces following `Angle` terms which will use units of degrees for the angle and kilocalories per mole per square radian for the force constant. +### Specifying parameters + Under each of these force terms, there are tags for individual parameter lines such as these: ```XML + + ``` -The first of these specifies the `[a,A:1]-[#6X4:2]-[a,A:3]` SMIRKS pattern for an angle, with a tetravalent carbon at the center with single bonds to two atoms of any type. -Atoms are labeled 1, 2, and 3, with 2 being the central atom. Equilibrium angle values are provided, along with force constants (with units as given above). +The first of these specifies the `smirks` attribute as `[a,A:1]-[#6X4:2]-[a,A:3]`, specifying a SMIRKS pattern that matches three connected atoms specifying an angle. +This particular SMIRKS pattern matches a tetravalent carbon at the center with single bonds to two atoms of any type. +This pattern is essentially a [SMARTS](http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html) string with numerical atom tags commonly used in [SMIRKS](http://www.daylight.com/dayhtml/doc/theory/theory.smirks.html) to identify atoms in chemically unique environments---these can be thought of as tagged regular expressions for identifying chemical environments, and atoms within those environments. +Here, `[a,A]` denotes any atom---either aromatic (`a`) or aliphatic (`A`), while `[#6X4]` denotes a carbon by element number (`#6`) that with four substituents (`X4`). +The symbol `-` joining these groups denotes a single bond. +The strings `:1`, `:2`, and `:2` label these atoms as indices 1, 2, and 3, with 2 being the central atom. +Equilibrium angles are provided as the `angle` attribute, along with force constants as the `k` attribute (with corresponding units as given above by `angle_unit` and `k_unit`, respectively). + +.. note :: + + The XML parser ignores attributes in the XML that it does not know how to process. + For example, providing an `` tag that also specifies a second force constant `k2` will simply result in `k2` being silently ignored. -**SMIRNOFF parameters are hierarchical** in that parameters which come later in a file override those which come earlier if they match the same pattern. - This can be seen in the example above, where the first line provides a generic angle parameter for any tetravalent carbon (single bond) angle, and the second line overrides this for the specific case of a hydrogen-(tetravalent carbon)-hydrogen angle. +### SMIRNOFF parameter specification is hierarchical +Parameters that appear later in a SMIRNOFF specification override those which come earlier if they match the same pattern. +This can be seen in the example above, where the first line provides a generic angle parameter for any tetravalent carbon (single bond) angle, and the second line overrides this for the specific case of a hydrogen-(tetravalent carbon)-hydrogen angle. This hierarchical structure means that a typical parameter file will tend to have generic parameters early in the section for each force type, with more specialized parameters assigned later. -**Technical note**: Because this is an XML format, certain special characters that occur in valid SMIRKS patterns (such as ampersand symbols `&`) must be treated specially to process. +### Multiple SMIRNOFF representations can be processed in sequence -## Functional forms, etc. +Multiple SMIRNOFF `.offxml` files can be loaded by the openforcefield `ForceField` in sequence. +If these files each contain unique top-level tags (such as ``, ``, etc.), the resulting forcefield will be independent of the order in which the files are loaded. +If, however, the same tag occurs in multiple files, the contents of the tags are merged, with the tags read later taking precedence over the parameters read earlier, provided the top-level tags have compatible attributes. +The resulting force field will therefore depend on the order in which parameters are read. -**Functional form**: The SMIRNOFF format specifies parameters; once specified, these are processed by the SMIRNOFF `ForceField` class and used to assign parameters to OpenMM Forces. -This means that specific forces are generally implemented as discussed in the [OpenMM Documentation](http://docs.openmm.org/7.0.0/userguide/theory.html), see especially [Section 19 on Standard Forces](http://docs.openmm.org/7.0.0/userguide/theory.html#standard-forces) for functional forms. In some cases, typically for consistency with the AMBER force field philosophy motivating some of the authors, we do some manipulation of parameters from these files as discussed below in "Parameter sections". +This behavior is intended for limited use in appending very specific parameters, such as parameters specifying solvent models, to override standard parameters. -**Charges**: In keeping with the AMBER force field philosophy, especially as implemented in small molecule force fields such as [GAFF](http://ambermd.org/antechamber/gaff.html), [GAFF2](https://mulan.swmed.edu/group/gaff.php), and [parm@Frosst](http://www.ccl.net/cca/data/parm_at_Frosst/), we at least initially treat partial charges as something to be obtained separately from the rest of the force field (bonds, angles, impropers, torsions [BAIT] and vdW terms), typically via QM calculations or a method such as Bayly's [AM1-BCC](https://dx.doi.org/10.1002/jcc.10128) approach, thus, for system setup we provide the option of specifying a charging method, though charges are not normally specified in the FFXML itself. - For other force fields with "library"-style charges, we could introduce a new section providing specific charges via SMIRKS pattern, though this is not yet implemented. Bond charge corrections, however, are supported as we discuss below. +## Units + +To minimize the potential for [unit conversion errors](https://en.wikipedia.org/wiki/Mars_Climate_Orbiter#Cause_of_failure), SMIRNOFF forcefields explicitly specify units in a form readable to both humans and computers for all unit-bearing quantities. +Allowed values for units are given in [simtk.unit](https://github.com/pandegroup/openmm/blob/topology/wrappers/python/simtk/unit/unit_definitions.py). +For example, for the `angle` (equilibrium angle) and `k` (force constant) parameters in the `` example block above, the `angle_unit` and `k_unit` top-level attributes specify the corresponding units: +```XML + +... + +``` +For more information, see the [standard OpenMM unit system](http://docs.openmm.org/latest/userguide/theory.html#units). + +## SMIRNOFF independently applies parameters to each class of potential energy terms + +The SMIRNOFF uses direct chemical perception to assign parameters for potential energy terms independently for each term. +Rather than first applying atom typing rules and then looking up combinations of the resulting atom types for each force term, the rules for directly applying parameters to atoms is compartmentalized in separate sections. +The file consists of multiple top-level tags defining individual components of the potential energy (in addition to charge models or modifiers), with each section specifying the typing rules used to assign parameters for that potential term: +```XML + + + + ... + + + + + + ... + +``` +Each top-level tag specifying a class of potential energy terms has an attribute `potential` for specifying the functional form for the interaction. +Common defaults are defined, but the goal is to eventually allow these to be overridden by alternative choices or even algebraic expressions in the future, once more molecular simulation packages support general expressions. +We distinguish between functional forms available in all common molecular simulation packages (specified by keywords) and support for general functional forms available in a few packages (especially OpenMM, which supports a flexible set of custom forces defined by algebraic expressions) with an **EXPERIMENTAL** label. + +Many of the specific forces are implemented as discussed in the [OpenMM Documentation](http://docs.openmm.org/latest/userguide/theory.html); see especially [Section 19 on Standard Forces](http://docs.openmm.org/latest/userguide/theory.html#standard-forces) for mathematical descriptions of these functional forms. +Some top-level tags provide attributes that modify the functional form used to be consistent with packages such as AMBER or CHARMM. + +## Partial charge and electrostatics models + +SMIRNOFF supports several approaches to specifying electrostatic models. +Currently, only classical fixed point charge models are supported, but future extensions to the specification will support point multipoles, point polarizable dipoles, Drude oscillators, charge equilibration methods, and so on. + +### ``: Library charges for polymeric residues and special solvent models + +.. warning:: This functionality is not yet implemented and will appear in a future version of the toolkit + +A mechanism is provided for specifying library charges that can be applied to molecules or residues that match provided templates. +Library charges are applied first, and atoms for which library charges are applied will be excluded from alternative charging schemes listed below. + +For example, to assign partial charges for a non-terminal ALA residue from the [AMBER ff14SB](http://doi.org/10.1021/acs.jctc.5b00255) parameter set: +```XML + + + + ... + +``` +In this case, a SMIRKS string defining the residue tags each atom that should receive a partial charge, with the charges specified by attributes `charge1`, `charge2`, etc. +The `name` attribute is optional. +Note that, for a given template, chemically equivalent atoms should be assigned the same charge to avoid undefined behavior. +If the template matches multiple non-overlapping sets of atoms, all such matches will be assigned the provided charges. +If multiple templates match the same set of atoms, the last template specified will be used. + +Solvent models or excipients can also have partial charges specified via the `` tag. +For example, to ensure water molecules are assigned partial charges for [TIP3P](http://www.sklogwiki.org/SklogWiki/index.php/TIP3P_model_of_water) water, we can specify a library charge entry: +```XML + + + + +``` + +### ``: Small molecule and fragment charges + +.. warning:: This functionality is not yet implemented and will appear in a future version of the toolkit. This area of the SMIRNOFF spec is under further consideration. Please see [Issue 208 on the Open Force Field Toolkit issue tracker](https://github.com/openforcefield/openforcefield/issues/208). + +In keeping with the AMBER force field philosophy, especially as implemented in small molecule force fields such as [GAFF](http://ambermd.org/antechamber/gaff.html), [GAFF2](https://mulan.swmed.edu/group/gaff.php), and [parm@Frosst](http://www.ccl.net/cca/data/parm_at_Frosst/), partial charges for small molecules are usually assigned using a quantum chemical method (usually a semiempirical method such as [AM1](https://en.wikipedia.org/wiki/Austin_Model_1)) and a [partial charge determination scheme](https://en.wikipedia.org/wiki/Partial_charge) (such as [CM2](http://doi.org/10.1021/jp972682r) or [RESP](http://doi.org/10.1021/ja00074a030)), then subsequently corrected via charge increment rules, as in the highly successful [AM1-BCC](https://dx.doi.org/10.1002/jcc.10128) approach. + +Here is an example: +```XML + + + + + + + + +``` +The sum of formal charges for the molecule or fragment will be used to determine the total charge the molecule or fragment will possess. + +`` provides several optional attributes to control its behavior: +* The `number_of_conformers` attribute (default: `"10"`) is used to specify how many conformers will be generated for the molecule (or capped fragment) prior to charging. +* The `quantum_chemical_method` attribute (default: `"AM1"`) is used to specify the quantum chemical method applied to the molecule or capped fragment. +* The `partial_charge_method` attribute (default: `"CM2"`) is used to specify how uncorrected partial charges are to be generated from the quantum chemical wavefunction. Later additions will add restrained electrostatic potential fitting (RESP) capabilities. + +The `` tags specify how the quantum chemical derived charges are to be corrected to produce the final charges. +The `charge#increment` attribute specify how much the charge on the associated tagged atom index (replacing `#`) should be modified. +The sum of charge increments should equal zero. + +Note that atoms for which library charges have already been applied are excluded from charging via ``. + +Future additions will provide options for intelligently fragmenting large molecules and biopolymers, as well as a `capping` attribute to specify how fragments with dangling bonds are to be capped to allow these groups to be charged. + +### Prespecified charges (reference implementation only) + +In our reference implementation of SMIRNOFF in the `openforcefield` toolkit, we also provide a method for specifying user-defined partial charges during system creation. +This functionality is accessed by using the `charge_from_molecules` optional argument during system creation, such as in `ForceField.create_openmm_system(topology, charge_from_molecules=molecule_list)`. When this optional keyword is provided, all matching molecules will have their charges set by the entries in `molecule_list`. +This method is provided solely for convenience in developing and exploring alternative charging schemes; actual force field releases for distribution will use one of the other mechanisms specified above. ## Parameter sections -For this section it will help to have on hand an example SMIRNOFF file, such as that the [AlkEthOH example ffxml](https://github.com/openforcefield/openforcefield/blob/master/openforcefield/data/forcefield/Frosst_AlkEthOH.offxml) or the larger prototype [SMIRNOFF99Frosst ffxml](https://github.com/openforcefield/SMIRNOFF99Frosst/blob/master/SMIRNOFF99Frosst.offxml). +A SMIRNOFF force field consists of one or more force field term definition sections. +For the most part, these sections independently define how a specific component of the potential energy function for a molecular system is supposed to be computed (such as bond stretch energies, or Lennard-Jones interactions), as well as how parameters are to be assigned for this particular term. +This decoupling of how parameters are assigned for each term provides a great deal of flexibility in composing new force fields while allowing a minimal number of parameters to be used to achieve accurate modeling of intramolecular forces. + +Below, we describe the specification for each force field term definition using the XML representation of a SMIRNOFF force field. -Before getting in to individual sections, it's worth noting that the XML parser ignores attributes in the XML that it does not understand, so providing a parameter line for an angle that specifies (for example) a second force constant `k2` will lead to no effect. +As an example of a complete SMIRNOFF force field specification, see the prototype [SMIRNOFF99Frosst offxml](https://github.com/openforcefield/openforcefield/blob/master/openforcefield/data/forcefield/smirnoff99Frosst.offxml). -### NONBONDED PARAMETERS (E.G. LENNARD-JONES) +.. note :: Not all parameter sections *must* be specified in a SMIRNOFF force field. A wide variety of force field terms are provided in the specification, but a particular force field only needs to define a subset of those terms. -Nonbonded parameters (currently, Lennard-Jones parameters) are specified via the [`NonbondedForce`](http://docs.openmm.org/7.0.0/userguide/theory.html#nonbondedforce) tag with sub-tags for individual `Atom` entries, such as: +### `` + +van der Waals force parameters, which include repulsive forces arising from Pauli exclusion and attractive forces arising from dispersion, are specified via the `` tag with sub-tags for individual `Atom` entries, such as: ```XML - - - + + + ... - + ``` -Scaling terms for 1-4 interactions should be specified in attributes for the `NonbondedForce` tag, along with units. +For standard Lennard-Jones 12-6 potentials (specified via `potential="Lennard-Jones-12-6"`), the `epsilon` parameter denotes the well depth, while the size property can be specified either via providing the `sigma` attribute, such as `sigma="1.3"`, or via the `r_0/2` (`rmin/2`) values used in AMBER force fields (here denoted `rmin_half` as in the example above). +The two are related by `r0 = 2^(1/6)*sigma` and conversion is done internally in `ForceField` into the `sigma` values used in OpenMM. +Note that, if `rmin_half` is specified instead of `sigma`, `rmin_half_unit` should be specified; both can be used in the same block if desired. -For compatibility, the size property of an atom can be specified either via providing the `sigma` attribute, such as `sigma="1.3"`, or via the `r_0/2` (`rmin/2`) values used in AMBER force fields (here denoted `rmin_half` as in the example above). The two are related by `r0 = 2^(1/6)*sigma` and conversion is done internally in `ForceField` into the `sigma` values used in OpenMM. `epsilon` denotes the well depth. +Attributes in the `` tag specify the scaling terms applied to the energies of 1-2 (`scale12`, default: 0), 1-3 (`scale13`, default: 0), 1-4 (`scale14`, default: 0.5), and 1-5 (`scale15`, default: 1.0) interactions, +as well as the distance at which a switching function is applied (`switch_width`, default: `"1.0"` angstroms), the cutoff (`cutoff`, default: `"9.0"` angstroms), and long-range dispersion treatment scheme (`long_range_dispersion`, default: `"isotropic"`). -### BOND PARAMETERS +The `potential` attribute (default: `"none"`) specifies the potential energy function to use. +Currently, only `potential="Lennard-Jones-12-6"` is supported: +``` +U(r) = 4*epsilon*((sigma/r)^12 - (sigma/r)^6) +``` +The `combining_rules` attribute (default: `"none"`) currently only supports `"Lorentz-Berthelot"`, which specifies the geometric mean of `epsilon` and arithmetic mean of `sigma`. +Support for [other Lennard-Jones mixing schemes](https://en.wikipedia.org/wiki/Combining_rules) will be added later: `Waldman-Hagler`, `Fender-Halsey`, `Kong`, `Tang-Toennies`, `Pena`, `Hudson-McCoubrey`, `Sikora`. -Bond parameters are specified via the [`HarmonicBondForce`](http://docs.openmm.org/7.0.0/userguide/theory.html#harmonicbondforce) tag with individual `Bond` tags providing equilibrium bond length `length` and force constant `k` values for specific bonds, for example: +Later revisions will add support for additional potential types (e.g., `Buckingham-exp-6`), as well as the ability to support arbitrary algebraic functional forms using a scheme such as ```XML - + + + + + + + + ... + +``` +If the `` tag is provided, it overrides the `combining_rules` attribute. + +Later revisions will also provide support for special interactions using the `` tag: +```XML + + + ... + +``` + +### `` + +Electrostatic interactions are specified via the `` tag. +```XML + +``` +The `method` attribute specifies the manner in which electrostatic interactions are to be computed: +* `PME` - [particle mesh Ewald](http://docs.openmm.org/latest/userguide/theory.html#coulomb-interaction-with-particle-mesh-ewald) should be used (DEFAULT); can only apply to periodic systems +* `reaction-field` - [reaction-field electrostatics](http://docs.openmm.org/latest/userguide/theory.html#coulomb-interaction-with-cutoff) should be used; can only apply to periodic systems +* `Coulomb` - direct Coulomb interactions (with no reaction-field attenuation) should be used + +The interaction scaling parameters applied to atoms connected by a few bonds are +* `scale12` (default: 0) specifies the scaling applied to 1-2 bonds +* `scale13` (default: 0) specifies the scaling applied to 1-3 bonds +* `scale14` (default: 0.833333) specifies the scaling applied to 1-4 bonds +* `scale15` (default: 1.0) specifies the scaling applied to 1-5 bonds + +Currently, no child tags are used because the charge model is specified via different means (currently library charges or BCCs). + +For methods where the cutoff is not simply an implementation detail but determines the potential energy of the system (`reaction-field` and `Coulomb`), the `cutoff` distance must also be specified, and a `switch_width` if a switching function is to be used. + +### `` + +Bond parameters are specified via a `...` block, with individual `` tags containing attributes specifying the equilibrium bond length (`length`) and force constant (`k`) values for specific bonds. +For example: +```XML + -... - + ... + +``` +Currently, only `potential="harmonic"` is supported, where we utilize the standard harmonic functional form: +``` +U(r) = (k/2)*(r-length)^2 ``` +Later revisions will add support for additional potential types and the ability to support arbitrary algebraic functional forms. +If the `potential` attribute is omitted, it defaults to `harmonic`. -**AMBER functional forms define the force constant `k` in a manner that differs by a factor of two---we do not use that convention here, electing to use the standard harmonic definition `U(r) = (k/2)*(r-length)^2` instead.** -Thus, comparing a SMIRNOFF file to a corresponding AMBER parameter file or `.frcmod` will make it appear that force constants here are twice as large as they ought to be. +**Note that AMBER and CHARMM define a modified functional form**, such that `U(r) = k*(r-length)^2`, so that force constants would need to be multiplied by two in order to be used in the SMIRNOFF format. -### ANGLE PARAMETERS +Constrained bonds are handled by a separate `` tag, which can either specify constraint distances or draw them from equilibrium distances specified in ``. -Angle parameters are specified via the [`HarmonicAngleForce`](http://docs.openmm.org/7.0.0/userguide/theory.html#harmonicangleforce) tag with individual `Angle` tags providing parameters (equilibrium angle `angle` and force constant `k`), as in this example: +#### Fractional bond orders (EXPERIMENTAL) + +.. warning:: This functionality is not yet implemented and will appear in a future version of the toolkit. + +Fractional bond orders can be used to allow interpolation of bond parameters. +For example, these parameters: ```XML - + + + + + ... +``` +can be replaced by a single parameter line by first invoking the `fractional_bondorder_method` attribute to specify a method for computing the fractional bond order and `fractional_bondorder_interpolation` for specifying the procedure for interpolating parameters between specified integral bond orders: +```XML + + + ... +``` +This allows specification of force constants and lengths for bond orders 1 and 2, and then interpolation between those based on the partial bond order. +* `fractional_bondorder_method` defaults to `none`, but the `Wiberg` method is supported. +* `fractional_bondorder_interpolation` defaults to `linear`, which is the only supported scheme for now. + +### `` + +Angle parameters are specified via an `...` block, with individual `` tags containing attributes specifying the equilibrium angle (`angle`) and force constant (`k`), as in this example: +```XML + -... - + ... + +``` +Currently, only `potential="harmonic"` is supported, where we utilize the standard harmonic functional form: ``` +U(r) = (k/2)*(theta-angle)^2 +``` +Later revisions will add support for additional potential types and the ability to support arbitrary algebraic functional forms. +If the `potential` attribute is omitted, it defaults to `harmonic`. -**AMBER functional forms drop the factor of 2 in the angle energy term, which we elect not to do here.** -Thus, comparing a SMIRNOFF file to a corresponding AMBER parameter file or .frcmod will make it appear that force constants here are twice as large as they ought to be. +**Note that AMBER and CHARMM define a modified functional form**, such that `U(r) = k*(theta-angle)^2`, so that force constants would need to be multiplied by two in order to be used in the SMIRNOFF format. -### PROPER TORSIONS +### `` -Torsions are implemented as a [`PeriodicTorsionForce`](http://docs.openmm.org/7.0.0/userguide/theory.html#periodictorsionforce) tag with child tags for `Proper` (discussed here) and `Improper` (discussed below) parameters, for example: +Proper torsions are specified via a `...` block, with individual `` tags containing attributes specifying the periodicity (`periodicity#`), phase (`phase#`), and barrier height (`k#`). ```XML - + -... -... - + ... + ``` - Here, child `Proper` tags specify at least `k1`, `phase1`, and `periodicity1` attributes for the corresponding parameters of the first force term applied to this torsion. -However, additional values are allowed in the form kN, phaseN, and periodicityN, where all N values must be consecutive (e.g. no `k1` and `k3` values without a `k2` value) but `N` can go as high as necessary. +However, additional values are allowed in the form `k#`, `phase#`, and `periodicity#`, where all `#` values must be consecutive (e.g., it is impermissible to specify `k1` and `k3` values without a `k2` value) but `#` can go as high as necessary. -Optionally, an `idivfN` attribute may be specified for each torsional term (for easier compatibility with AMBER files); this specifies a numerical value (in AMBER, always an integer) which is used as a divisor for the barrier height when assigning the torsion; i.e., a torsion with `idivf1="9"` is assigned a barrier height `k1` that is 1/9th the specified value. -If `idivfN` is not specified, the barrier height is applied as stated. +For convenience, and optional attribute specifies a torsion multiplicity by which the barrier height should be divided (`idivf#`). +The default behavior of this attribute can be controlled by the top-level attribute `default_idivf` (default: `"auto"`) for ``, which can be an integer (such as `"1"`) controlling the value of `idivf` if not specified or `"auto"` if the barrier height should be divided by the number of torsions impinging on the central bond. +For example: +```XML + + + ... + +``` + +Currently, only `potential="charmm"` is supported, where we utilize the functional form: +``` +U = \sum_{i=1}^N k_i * (1 + cos(periodicity_i * phi - phase_i)) +``` -In the future, we may switch to a model where torsional barriers are [automatically divided by the number of torsions along a bond](https://github.com/openforcefield/smarty/issues/131), effectively resulting in the torsional barrier being the average of all barriers applied to that bond, rather than the current model where barriers are summed. -(Barrier heights would need to be increased accordingly.) -This would result in better handling of some cases where a small change in a molecule (such as a change in tautomer) could currently (as in AMBER) result in a dramatically different applied barrier height because of a change in the number of torsions passing through that bond. -The averaging approach would make it easier to avoid this problem without requiring as many different torsional terms. +.. note:: **AMBER defines a modified functional form**, such that `U = \sum_{i=1}^N (k_i/2) * (1 + cos(periodicity_i * phi - phase_i))`, so that barrier heights would need to be divided by two in order to be used in the SMIRNOFF format. -### IMPROPER TORSIONS +If the `potential` attribute is omitted, it defaults to `charmm`. -Impropers are applied in the same manner as proper torsions, via `PeriodicTorsionForce`, but with the `Improper` tag, as in: +### `` + +Improper torsions are specified via an `...` block, with individual `` tags containing attributes that specify the same properties as ``: ```XML - -... + + + ... + +``` +Currently, only `potential="charmm"` is supported, where we utilize the functional form: ``` +U = \sum_{i=1}^N k_i * (1 + cos(periodicity_i * phi - phase_i)) +``` + +.. note:: **AMBER defines a modified functional form**, such that `U = \sum_{i=1}^N (k_i/2) * (1 + cos(periodicity_i * phi - phase_i))`, so that barrier heights would need to be divided by two in order to be used in the SMIRNOFF format. +If the `potential` attribute is omitted, it defaults to `charmm`. + +The improper torsion energy is computed as the average over all three impropers (all with the same handedness) in a [trefoil](https://upload.wikimedia.org/wikipedia/commons/thumb/5/5c/Trefoil_knot_left.svg/2000px-Trefoil_knot_left.svg.png). +This avoids the dependence on arbitrary atom orderings that occur in more traditional typing engines such as those used in AMBER. +The *second* atom in an improper (in the example above, the trivalent carbon) is the central atom in the trefoil. -**Improper torsions deviate profoundly from AMBER handling of impropers** in two ways. -First, to eliminate ambiguity, we treat impropers as a [trefoil](https://upload.wikimedia.org/wikipedia/commons/thumb/5/5c/Trefoil_knot_left.svg/2000px-Trefoil_knot_left.svg.png) and apply the same set of parameters to all three paths around the trefoil that have the same handedness. -*Because of this, all barrier heights are divided by three before we apply them*, for consistency with AMBER force fields. Second, the *second* atom in an improper (in the example above, the trivalent carbon) is the central atom in the trefoil. +### `` -### GBSA parameters +.. warning:: This functionality is not yet implemented and will appear in a future version of the toolkit. -Generalized-Born surface area (GBSA) implicit solvent parameters can also be specified in a manner similar to `NonbondedForce`: +Generalized-Born surface area (GBSA) implicit solvent parameters are optionally specified via a `...` using `` tags with GBSA model specific attributes: ```XML - + @@ -136,56 +464,48 @@ Generalized-Born surface area (GBSA) implicit solvent parameters can also be spe - + ``` -#### GB model -In the `` tag, `gb_model` selects which GB model is used. -Currently, this can be selected from a subset of the [GBSA models available in OpenMM's `simtk.openmm.app`](http://docs.openmm.org/7.1.0/userguide/application.html#amber-implicit-solvent): -* `HCT`: [Hawkins-Cramer-Truhlar](http://docs.openmm.org/7.1.0/userguide/zbibliography.html#hawkins1995) (corresponding to `igb=1` in AMBER): requires `[radius, scale]` -* `OBC1`: [Onufriev-Bashford-Case](http://docs.openmm.org/7.1.0/userguide/zbibliography.html#onufriev2004) using the GB(OBC)I parameters (corresponding to `igb=2` in AMBER): requires `[radius, scale]` -* `OBC2`: [Onufriev-Bashford-Case](http://docs.openmm.org/7.1.0/userguide/zbibliography.html#onufriev2004) using the GB(OBC)II parameters (corresponding to `igb=5` in AMBER): requires `[radius, scale]` -Each GB model can possess several attributes, which may be unitless (`1.0`, `78.5`) or unit-bearing quantities (`1.4*angstrom`, `5.4*calories/mole/angstrom**2`). +#### Supported Generalized Born (GB) models +In the `` tag, `gb_model` selects which GB model is used. +Currently, this can be selected from a subset of the [GBSA models available in OpenMM's `simtk.openmm.app`](http://docs.openmm.org/latest/userguide/application.html#amber-implicit-solvent): +* `HCT`: [Hawkins-Cramer-Truhlar](http://docs.openmm.org/latest/userguide/zbibliography.html#hawkins1995) (corresponding to `igb=1` in AMBER): requires `[radius, scale]` +* `OBC1`: [Onufriev-Bashford-Case](http://docs.openmm.org/latest/userguide/zbibliography.html#onufriev2004) using the GB(OBC)I parameters (corresponding to `igb=2` in AMBER): requires `[radius, scale]` +* `OBC2`: [Onufriev-Bashford-Case](http://docs.openmm.org/latest/userguide/zbibliography.html#onufriev2004) using the GB(OBC)II parameters (corresponding to `igb=5` in AMBER): requires `[radius, scale]` + +If the `gb_model` attribute is omitted, it defaults to `OBC1`. + The attributes `solvent_dielectric` and `solute_dielectric` specify solvent and solute dielectric constants used by the GB model. In this example, `radius` and `scale` are per-particle parameters of the `OBC1` GB model supported by OpenMM. -Units are for these per-particle parameters (such as `radius_units`) optionally specified in the `` tag. +Units are for these per-particle parameters (such as `radius_units`) specified in the `` tag. -#### SA model +#### Surface area (SA) penalty model The `sa_model` attribute specifies the solvent-accessible surface area model ("SA" part of GBSA) if one should be included; if omitted, no SA term is included. -Currently, only the [analytical continuum electrostatics (ACE) model](http://docs.openmm.org/7.1.0/userguide/theory.html#surface-area-term), designated `ACE`, can be specified, but there are plans to add more models in the future, such as the Gaussian solvation energy component of [EEF1](https://www.ncbi.nlm.nih.gov/pubmed/10223287). -The `ACE` model permits two additional parameters to be specified: -* The `surface_area_penalty` attribute specifies the surface area penalty for the `ACE` model (defaults to `5.4*calories/mole/angstroms**2`). -* The `solvent_radius` attribute specifies the solvent radius, which defaults to `1.4*angstroms`. +Currently, only the [analytical continuum electrostatics (ACE) model](http://docs.openmm.org/latest/userguide/theory.html#surface-area-term), designated `ACE`, can be specified, but there are plans to add more models in the future, such as the Gaussian solvation energy component of [EEF1](https://www.ncbi.nlm.nih.gov/pubmed/10223287). +If `sa_model` is not specified, it defaults to `ACE`. -### SPECIAL SECTIONS - -**Bond charge corrections** -Bond charge corrections (along the lines of Christopher Bayly's bond charge corrections in [AM1-BCC](https://dx.doi.org/10.1002/jcc.10128)) can be applied via a `BondChargeCorrections` tag with children specifying specific `BondChargeCorrection` terms. -Here is an example not intended for actual use: -```XML - - - - - -``` -The charge model specified must be a method understood by the OpenEye toolkits, and the charge correction `increment` (in units of proton charge) will be applied on top of this by subtracting `increment` from the atom tagged as 1 and adding it to the atom tagged as 2. +The `ACE` model permits two additional parameters to be specified: +* The `surface_area_penalty` attribute specifies the surface area penalty for the `ACE` model. (Default: `5.4 calories/mole/angstroms**2`) +* The `solvent_radius` attribute specifies the solvent radius. (Default: `1.4 angstroms`) -### CONSTRAINTS +### `` -Bond length constraints can be specified through a `` block, which can constrain bonds to their equilibrium lengths or specify an interatomic constraint distance. -Two atoms must be tagged in the `smirks` attribute of each `` record. +Bond length or angle constraints can be specified through a `` block, which can constrain bonds to their equilibrium lengths or specify an interatomic constraint distance. +Two atoms must be tagged in the `smirks` attribute of each `` record. -To constrain two atoms to their equilibrium bond length, it is critical that a `` record be specified for those atoms: +To constrain the separation between two atoms to their equilibrium bond length, it is critical that a `` record be specified for those atoms: ```XML ``` -However, this constraint distance can be overridden, or two atoms that are not directly bonded constrained, by specifying the `distance` attribute (and optional `distance_unit` attribute for the `` tag): +Note that the two atoms must be bonded in the specified `Topology` for the equilibrium bond length to be used. + +To specify the constraint distance, or constrain two atoms that are not directly bonded (such as the hydrogens in rigid water models), specify the `distance` attribute (and optional `distance_unit` attribute for the `` tag): ```XML @@ -209,145 +529,151 @@ Typical molecular simulation practice is to constrain all bonds to hydrogen to t Standard usage is expected to rely primarily on the features documented above and potentially new features. However, some advanced features are also currently supported. -### Versioning +### ``: Virtual sites for off-atom charges -The SMIRNOFF forcefield format supports versioning via the `version` attribute to the root `` tag, e.g.: -```XML - -... - -``` -The version format is `x.y`, where `x` denotes the major version and `y` denotes the minor version. -SMIRNOFF versions are guaranteed to be backward-compatible within the *same major version number series*, but it is possible major version increments will break backwards-compatibility. +.. warning:: This functionality is not yet implemented and will appear in a future version of the toolkit -### Partial bond orders -Partial bond orders can be used to allow interpolation of parameters. For example, these parameters: -```XML - -... - - - -... -``` -can be replaced by a single parameter line: +We have implemented experimental support for placement of off-atom (off-center) charges in a variety of contexts which may be chemically important in order to allow easy exploration of when these will be warranted. +Currently we support the following different types or geometries of off-center charges (as diagrammed below): +- `BondCharge`: This supports placement of a virtual site `S` along a vector between two specified atoms, e.g. to allow for a sigma hole for halogens or similar contexts. With positive values of the distance, the virtual site lies outside the first indexed atom (green in this image). +![Bond charge virtual site](figures/vsite_bondcharge.jpg) +- `MonovalentLonePair`: This is originally intended for situations like a carbonyl, and allows placement of a virtual site `S` at a specified distance `d`, `inPlaneAngle` (theta 1 in the diagram), and `outOfPlaneAngle` (theta 2 in the diagram) relative to a central atom and two connected atoms. +![Monovalent lone pair virtual site](figures/vsite_monovalent.jpg) +- `DivalentLonePair`: This is suitable for cases like four-point and five-point water models as well as pyrimidine; a charge site `S` lies a specified distance `d` from the central atom among three atoms (blue) along the bisector of the angle between the atoms (if `outOfPlaneAngle` is zero) or out of the plane by the specified angle (if `outOfPlaneAngle` is nonzero) with its projection along the bisector. For positive values fo the distance `d` the virtual site lies outside the 2-1-3 angle and for negative values it lies inside. +![Divalent lone pair virtual site](figures/vsite_divalent.jpg) +- `TrivalentLonePair`: This is suitable for planar or tetrahedral nitrogen lone pairs; a charge site `S` lies above the central atom (e.g. nitrogen, blue) a distance `d` along the vector perpendicular to the plane of the three connected atoms (2,3,4). With positive values of `d` the site lies above the nitrogen and with negative values it lies below the nitrogen. +![Trivalent lone pair virtual site](figures/vsite_trivalent.jpg) + +Each virtual site receives charge which is transferred from the desired atoms specified in the SMIRKS pattern via a `chargeincrement#` parameter, e.g., if `chargeincrement1=+0.1` then the virtual site will receive a charge of -0.1 and the atom labeled `1` will have its charge adjusted upwards by +0.1. +N may index any indexed atom. +Increments which are left unspecified default to zero. +Additionally, each virtual site can bear Lennard-Jones parameters, specified by `sigma` and `epsilon` or `rmin_half` and `epsilon`. +If unspecified these also default to zero. + +In the SMIRNOFF format, these are encoded as: ```XML - -... - -... + + + + + + + + + + + + + + + + + + + + + ``` -This allows specification of force constants and lengths for bond orders 1 and 2, and then interpolation between those based on the partial bond order. -Currently the Wiberg bond order is used, which will be obtained automatically from an AM1-based charge calculation using the OpenEye toolkits if a beta version (or later) of the October 2016 toolkits is used. - -Important usage notes: -* An interpolation scheme must be specified in the `HarmonicBondForce` attributes; currently only `interpolate-linear` is supported, though a spline interpolation may be preferable (this needs to be explored) -* If it is desired to use fractional bond orders, the introductory SMIRNOFF tag for the file must specify that the force field will use these via `` or similar. Otherwise, no partial bond orders will be obtained for possible later use. -* This feature is only implemented for bonds at present, though it needs to be extended to angles and torsions; possibly also it may have value for vdW parameters (which could vary depending on bond order) though this needs to be explored ### Aromaticity models -Before conduct SMIRKS substructure searches, molecules are prepared by applying one of OpenEye's aromaticity models, with the default model used unless otherwise requested. -Alternate aromaticity models can be requested by the force field, such as -`` used by SMIRNOFF99Frosst (a choice by Christopher Bayly to simplify handling of certain heteroaromatic compounds). -Any of the names of the [aromaticity models available in the OpenEye toolkit](https://docs.eyesopen.com/toolkits/python/oechemtk/aromaticity.html) can be used. - -### Future advanced features - -At present, the SMIRNOFF format basically defaults to AMBER- or OpenMM-style decisions on many issues. -For example, AMBER-style (Lorentz-Berthelot) combining rules are used, and the AMBER force field functional form. -Angles potentials are assumed to be harmonic. -However, we have plans to support other combination rules, functional forms, and angle potentials. -In keeping with the above, whole-force field decisions will be handled as attributes of the SMIRNOFF tag. -For example, alternate combination rules or functional forms might be handled as follows: -* Geometric mean combining rule: `` -* A Halgren buffered 14-7 potential for vdW could be handled as `` -* Selection of the type of angle force applied would be handled in a similar manner, via an `AngleForce="harmonic"` tag or similar. [This feature is being planned.](https://github.com/openforcefield/smarty/issues/179) +Before conduct SMIRKS substructure searches, molecules are prepared using one of the supported aromaticity models, which must be specified with the `aromaticity_model` attribute. +The only aromaticity model currently widely supported (by both the [OpenEye toolkit](https://docs.eyesopen.com/toolkits/python/oechemtk/aromaticity.html) and [RDKit](http://www.rdkit.org/docs/RDKit_Book.html)) is the `OEAroModel_MDL` model. +### Additional plans for future development -[Generalized Born parameters and models will also be supported](https://github.com/openforcefield/smarty/issues/165) and implementation is being planned. +See the [openforcefield GitHub issue tracker](https://github.com/openforcefield/openforcefield/issues) to propose changes to this specification, or read through proposed changes currently being discussed. +## The `openforcefield` reference implementation -### Additional plans for future development +A Python reference implementation of a parameterization engine implementing the SMIRNOFF force field specification can be found [online](http://github.com/openforcefield/openforcefield). +This implementation can use either the free-for-academics (but commercially supported) [OpenEye toolkit](https://docs.eyesopen.com/toolkits/python/index.html) or the free and open source [RDKit cheminformatics toolkit](http://www.rdkit.org/). +See the [installation instructions](https://open-forcefield-toolkit.readthedocs.io/en/latest/installation.html) for information on how to install this implementation and its dependencies. -See the Issue tracker for a more thorough list, though some major areas are highlighted here: -* Exploring how use of partial bond order can simplify the environments needed -* Implementing partial bond order use for other parameter types -* Modifications discussed above to handling of torsions -* Possible modifications to make it easier to support other force field families -* [Off-atom charges](https://github.com/openforcefield/smarty/issues/132) -* Additional functional forms for vdW interactions +### Examples -## Use for parameterization of systems +A relatively extensive set of examples is made available on the [reference implementation repository](http://github.com/openforcefield/openforcefield) under [examples/](https://github.com/openforcefield/openforcefield/tree/master/examples). -A relatively extensive set of examples is available under [`examples/`](https://github.com/openforcefield/openforcefield/tree/master/examples). Basic usage works as follows in python, however: +### Parameterizing a system +Consider parameterizing a simple system containing a the drug imatinib. ```python -from simtk import openmm, unit -import numpy as np -import oechem -mol = oechem.OEGraphMol() -ifs = oechem.oemolistream(mol_filename) -flavor = oechem.OEIFlavor_Generic_Default | oechem.OEIFlavor_MOL2_Default | oechem.OEIFlavor_MOL2_Forcefield -ifs.SetFlavor(oechem.OEFormat_MOL2, flavor) -oechem.OEReadMolecule(ifs, mol) -oechem.OETriposAtomNames(mol) +# Create a molecule from a mol2 file +from openforcefield.topology import Molecule +molecule = Molecule.from_file('imatinib.mol2') -# Load forcefield -from openforcefield.typing import smirnoff -from openforcefield.utils import get_data_filename -forcefield = smirnoff.ForceField(get_data_filename('forcefield/Frosst_AlkEthOH_parmAtFrosst.offxml')) +# Create a Topology specifying the system to be parameterized containing just the molecule +topology = molecule.to_topology() -# Generate an OpenMM Topology and create an OpenMM System -import openforcefield.tools -topology = openforcefield.tools.generateTopologyFromOEMol(mol) -system = forcefield.createSystem(topology, [mol]) -``` -This example can essentially trivially be extended to handle the case of beginning from a SMILES string rather than a `.mol2` file. +# Load the smirnoff99Frosst forcefield +from openforcefield.typing.engines import smirnoff +forcefield = smirnoff.ForceField('smirnoff99Frosst.offxml') -The SMIRNOFF_simulation example in the examples directory shows how to extend the example above to simulate this molecule in the gas phase. - -`createSystem()` can also handle a system consisting of a mixture of molecules; we've tested it on cyclohexane/ethanol and propane/methanol/butanol mixtures for example. -As input it is necessary to provide a Topology file representing the system, and a list of OpenEye molecules for the components of that Topology. -So, for example, one can read a PDB file describing a mixture and provide OpenEye molecules for the components (generated by the Mobleylab's [SolvationToolkit](https://github.com/MobleyLab/SolvationToolkit), for example) and create a system from that. +# Create an OpenMM System from the topology +system = forcefield.create_openmm_system(topology) +``` +See `examples/SMIRNOFF_simulation/` for an extension of this example illustrating to simulate this molecule in the gas phase. -`createSystem()` allows the user to specify a choice of charge model, among other properties. Consult its help in python for more information. +The `topology` object provided to `create_openmm_system()` can contain any number of molecules of different types, including biopolymers, ions, buffer molecules, or solvent molecules. +The openforcefield toolkit provides a number of convenient methods for importing or constructing topologies given PDB files, Sybyl mol2 files, SDF files, SMILES strings, and IUPAC names; see the [toolkit documentation](https://open-forcefield-toolkit.readthedocs.io/) for more information. +Notably, this `topology` object differs from those found in [OpenMM](http://docs.openmm.org/latest/api-python/generated/simtk.openmm.app.topology.Topology.html#simtk.openmm.app.topology.Topology) or [MDTraj](http://mdtraj.org/1.9.0/api/generated/mdtraj.Topology.html#mdtraj.Topology) in that it contains information on the *chemical identity* of the molecules constituting the system, rather than this atomic elements and covalent connectivity; this additional chemical information is required for the [direct chemical perception](https://doi.org/10.1101/286542) features of SMIRNOFF typing. -One important note is that the OpenEye molecules currently must have atom names, hence the [`OETriposAtomNames`](https://docs.eyesopen.com/toolkits/python/oechemtk/OEChemFunctions/OETriposAtomNames.html) above. +### Using SMIRNOFF small molecule forcefields with traditional biopolymer force fields -**Use with protein force fields**: While SMIRNOFF format force fields can cover a wide range of biological systems, an initial focus is on small molecule force fields, meaning that users may have considerable interest in combining SMIRNOFF small molecule parameters to systems in combination with traditional biopolymer parameters from conventional force fields, such as the AMBER family of protein/nucleic acid force fields. -Thus, we provide an example of setting up a mixed system in [`examples/mixedFF_structure`](examples/mixedFF_structure), where an AMBER family force field is used for a protein and smirnoff99Frosst for a small molecule. +While SMIRNOFF format force fields can cover a wide range of biological systems, our initial focus is on gneral small molecule force fields, meaning that users may have considerable interest in combining SMIRNOFF small molecule parameters to systems in combination with traditional biopolymer parameters from conventional force fields, such as the AMBER family of protein/nucleic acid force fields. +Thus, we provide an example of setting up a mixed protein-ligand system in [examples/mixedFF_structure](examples/mixedFF_structure), where an AMBER family force field is used for a protein and smirnoff99Frosst for a small molecule. -### `id` and other XML attributes +### The optional `id` and `parent_id` attributes and other XML attributes -In general, other XML attributes can be specified and will be ignored by `ForceField` unless they are specifically handled by the parser (and specified in this document). +In general, additional optional XML attributes can be specified and will be ignored by `ForceField` unless they are specifically handled by the parser (and specified in this document). -One attribute we have found helpful in actual parsing is the `id` attribute for a specific parameter line, and we *recommend* that SMIRNOFF forcefields utilize this as effectively a parameter serial number, such as in: +One attribute we have found helpful in parameter file development is the `id` attribute for a specific parameter line, and we *recommend* that SMIRNOFF force fields utilize this as effectively a parameter serial number, such as in: ```XML ``` Some functionality in `ForceField`, such as `ForceField.labelMolecules`, looks for the `id` attribute. -Without this attribute, there is no way to uniquely identify a specific parameter line in the XML file without referring to it by its smirks string, and since some smirks strings can become long and relatively unwieldly (especially for torsions) this provides a more human- and search-friendly way of referring to specific sets of parameters. +Without this attribute, there is no way to uniquely identify a specific parameter line in the XML file without referring to it by its smirks string, and since some smirks strings can become long and relatively unwieldy (especially for torsions) this provides a more human- and search-friendly way of referring to specific sets of parameters. + +The `parent_id` attribute is also frequently used to denote parameters from which the current parameter is derived in some manner. ### A remark about parameter availability `ForceField` will currently raise an exception if any parameters are missing where expected for your system---i.e. if a bond is assigned no parameters, an exception will be raised. -However, use of generic parameters (i.e. `[*:1]~[*:2]` for a bond) in your FFXML will result in parameters being assigned everywhere, bypassing this exception. -So use generics sparingly unless it is your intention to provide generics that should be used. +However, use of generic parameters (i.e. `[*:1]~[*:2]` for a bond) in your `.offxml` will result in parameters being assigned everywhere, bypassing this exception. +We recommend generics be used sparingly unless it is your intention to provide true universal generic parameters. ## Version history +### 0.2 + +This is a backwards-incompatible overhaul of the SMIRNOFF 0.1 draft specification along with `ForceField` implementation refactor: +* Aromaticity model now defaults to `OEAroModel_MDL`, and aromaticity model names drop OpenEye-specific prefixes +* Top-level tags are now required to specify units for any unit-bearing quantities to avoid the potential for mistakes from implied units. +* Potential energy component definitions were renamed to be more general: + * `` was renamed to `` + * `` was renamed to `` + * `` was renamed to `` + * `` was renamed to `` and generalized to accommodate an arbitrary number of tagged atoms + * `` was renamed to `` +* `` was split into `` and `` +* `` now specifies 1-2, 1-3, 1-4, and 1-5 scaling factors via `scale12` (default: 0), `scale13` (default: 0), `scale14` (default: 0.5), and `scale15` (default 1.0) attributes. It also specifies the long-range vdW method to use, currently supporting `cutoff` (default) and `PME`. Coulomb scaling parameters have been removed from `StericsForce`. +* Added the `` tag to separately specify 1-2, 1-3, 1-4, and 1-5 scaling factors for electrostatics, as well as the method used to compute electrostatics (`PME`, `reaction-field`, `Coulomb`) since this has a huge effect on the energetics of the system. +* Made it clear that `` entries do not have to be between bonded atoms. +* `` has been added, and the specification of charge increments harmonized with `` +* The `potential` attribute was added to most forces to allow flexibility in extending forces to additional functional forms (or algebraic expressions) in the future. `potential` defaults to the current recommended scheme if omitted. +* `` now has defaults specified for `gb_method` and `sa_method` +* Changes to how fractional bond orders are handled: + * Use of fractional bond order is now are specified at the force tag level, rather than the root level + * The fractional bond order method is specified via the `fractional_bondorder_method` attribute + * The fractional bond order interpolation scheme is specified via the `fractional_bondorder_interpolation` +* Section heading names were cleaned up. +* Example was updated to reflect use of the new `openforcefield.topology.Topology` class +* Eliminated "Requirements" section, since it specified requirements for the software, rather than described an aspect of the SMIRNOFF specification +* Fractional bond orders are described in ``, since they currently only apply to this term. + ### 0.1 Initial draft specification. -## Requirements -Currently, [OpenEye toolkits](http://www.eyesopen.com/toolkit-development) (free for academic use, but they require a license) are utilized for most of our chemistry. -[OpenMM](http://openmm.org) is also required, as are a variety of other relatively standard python packages and other toolkits available via [`conda`](http://conda.pydata.org/docs/building/meta-yaml.html). -The easiest way to install SMIRNOFF along with its dependencies is via `conda`: -```bash -conda config --add channels omnia -conda install --yes openforcefield -``` diff --git a/devtools/conda-recipe/meta.yaml b/devtools/conda-recipe/meta.yaml index 6af47ee6b..4f970caf3 100755 --- a/devtools/conda-recipe/meta.yaml +++ b/devtools/conda-recipe/meta.yaml @@ -13,25 +13,23 @@ requirements: build: - python - setuptools - - pandas run: - python - numpy - networkx - - lxml - - icu 58* # This is a lxml dependency but sometimes conda installs version 56 - - openmoltools >=0.7.3 - parmed - - matplotlib - - pandas - -test: - requires: - - nose - - nose-timer - imports: - - openforcefield + - rdkit + - ambermini + - packaging + # Should we require this? It's useful for tests and examples, but not strictly required + - openmmtools + # Serialization: Should these be optional? + - pyyaml + - toml + - bson + - msgpack-python + - xmltodict about: home: https://github.com/openforcefield/openforcefield diff --git a/devtools/travis-ci/after_success.sh b/devtools/travis-ci/after_success.sh deleted file mode 100755 index b8dc4a93a..000000000 --- a/devtools/travis-ci/after_success.sh +++ /dev/null @@ -1,43 +0,0 @@ -#!/bin/bash -# Must be invoked with $PACKAGENAME - -echo $TRAVIS_PULL_REQUEST $TRAVIS_BRANCH -PUSH_DOCS_TO_S3=false - -if [ "$TRAVIS_PULL_REQUEST" = true ]; then - echo "This is a pull request. No deployment will be done."; exit 0 -fi - - -if [ "$TRAVIS_BRANCH" != "master" ]; then - echo "No deployment on BRANCH='$TRAVIS_BRANCH'"; exit 0 -fi - - -# Deploy to binstar -conda install --yes anaconda-client jinja2 -pushd . -cd $HOME/miniconda/conda-bld -FILES=*/${PACKAGENAME}-dev-*.tar.bz2 -for filename in $FILES; do - anaconda -t $BINSTAR_TOKEN remove --force ${ORGNAME}/${PACKAGENAME}-dev/${filename} - anaconda -t $BINSTAR_TOKEN upload --force -u ${ORGNAME} -p ${PACKAGENAME}-dev ${filename} -done -popd - -if [ $PUSH_DOCS_TO_S3 = true ]; then - # Create the docs and push them to S3 - # ----------------------------------- - conda install --yes pip - conda config --add channels $ORGNAME - conda install --yes `conda build devtools/conda-recipe --output` - pip install numpydoc s3cmd msmb_theme - conda install --yes `cat docs/requirements.txt | xargs` - - conda list -e - - (cd docs && make html && cd -) - ls -lt docs/_build - pwd - python devtools/ci/push-docs-to-s3.py -fi diff --git a/devtools/travis-ci/before_install.sh b/devtools/travis-ci/before_install.sh new file mode 100644 index 000000000..f2207470d --- /dev/null +++ b/devtools/travis-ci/before_install.sh @@ -0,0 +1,35 @@ +# Temporarily change directory to $HOME to install software +pushd . +cd $HOME +# Install Miniconda +if [ "$TRAVIS_OS_NAME" == "osx" ]; then + # Make OSX md5 mimic md5sum from linux, alias does not work + md5sum () { + command md5 -r "$@" + } + MINICONDA=Miniconda3-latest-MacOSX-x86_64.sh +else + MINICONDA=Miniconda3-latest-Linux-x86_64.sh + export PYTHON_VER=$TRAVIS_PYTHON_VERSION +fi +MINICONDA_HOME=$HOME/miniconda +MINICONDA_MD5=$(curl -s https://repo.continuum.io/miniconda/ | grep -A3 $MINICONDA | sed -n '4p' | sed -n 's/ *\(.*\)<\/td> */\1/p') +wget -q https://repo.continuum.io/miniconda/$MINICONDA +if [[ $MINICONDA_MD5 != $(md5sum $MINICONDA | cut -d ' ' -f 1) ]]; then + echo "Miniconda MD5 mismatch" + exit 1 +fi +bash $MINICONDA -b -p $MINICONDA_HOME + +# Configure miniconda +export PIP_ARGS="-U" +export PATH=$MINICONDA_HOME/bin:$PATH +conda config --add channels openeye +conda config --add channels omnia +conda config --add channels conda-forge +conda config --set always_yes yes +conda install conda conda-build jinja2 anaconda-client +conda update --quiet --all + +# Restore original directory +popd diff --git a/devtools/travis-ci/index.html b/devtools/travis-ci/index.html deleted file mode 100755 index 576994b0d..000000000 --- a/devtools/travis-ci/index.html +++ /dev/null @@ -1 +0,0 @@ - diff --git a/devtools/travis-ci/install.sh b/devtools/travis-ci/install.sh deleted file mode 100755 index 119ab7258..000000000 --- a/devtools/travis-ci/install.sh +++ /dev/null @@ -1,27 +0,0 @@ -# Temporarily change directory to $HOME to install software -pushd . -cd $HOME - -# Install Miniconda -MINICONDA=Miniconda2-latest-Linux-x86_64.sh -MINICONDA_HOME=$HOME/miniconda -MINICONDA_MD5=$(curl -s https://repo.continuum.io/miniconda/ | grep -A3 $MINICONDA | sed -n '4p' | sed -n 's/ *\(.*\)<\/td> */\1/p') -wget -q http://repo.continuum.io/miniconda/$MINICONDA -if [[ $MINICONDA_MD5 != $(md5sum $MINICONDA | cut -d ' ' -f 1) ]]; then - echo "Miniconda MD5 mismatch" - exit 1 -fi -bash $MINICONDA -b -p $MINICONDA_HOME - -# Configure miniconda -export PIP_ARGS="-U" -export PATH=$MINICONDA_HOME/bin:$PATH -conda update --yes conda -conda install --yes conda-build jinja2 anaconda-client pip -conda install --yes -c omnia openmoltools -conda install --yes -c omnia parmed -conda install --yes -c matplotlib -conda install --yes pandas - -# Restore original directory -popd diff --git a/devtools/travis-ci/push-docs-to-s3.py b/devtools/travis-ci/push-docs-to-s3.py deleted file mode 100755 index 478305091..000000000 --- a/devtools/travis-ci/push-docs-to-s3.py +++ /dev/null @@ -1,48 +0,0 @@ -#!/usr/bin/env python - -""" -Must have the vollowing environment variables defined: -* BUCKET_NAME : AWS bucket name -* PREFIX : 'latest' or other version number - -""" - -import os -import pip -import tempfile -import subprocess -import thermopyl.version - - -BUCKET_NAME = 'thermopyl.org' -if not thermopyl.version.release: - PREFIX = 'latest' -else: - PREFIX = thermopyl.version.short_version - -if not any(d.project_name == 's3cmd' for d in pip.get_installed_distributions()): - raise ImportError('The s3cmd pacakge is required. try $ pip install s3cmd') -# The secret key is available as a secure environment variable -# on travis-ci to push the build documentation to Amazon S3. -with tempfile.NamedTemporaryFile('w') as f: - f.write('''[default] -access_key = {AWS_ACCESS_KEY_ID} -secret_key = {AWS_SECRET_ACCESS_KEY} -'''.format(**os.environ)) - f.flush() - - template = ('s3cmd --guess-mime-type --config {config} ' - 'sync docs/_build/ s3://{bucket}/{prefix}/') - cmd = template.format( - config=f.name, - bucket=BUCKET_NAME, - prefix=PREFIX) - return_val = subprocess.call(cmd.split()) - - # Sync index file. - template = ('s3cmd --guess-mime-type --config {config} ' - 'sync devtools/ci/index.html s3://{bucket}/') - cmd = template.format( - config=f.name, - bucket=BUCKET_NAME) - return_val = subprocess.call(cmd.split()) diff --git a/docs/conf.py b/docs/conf.py index df2863b4d..798052fa3 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -20,11 +20,12 @@ import os import sys sys.path.insert(0, os.path.abspath('.')) -#import openforcefield # bootstrap theme import sphinx_bootstrap_theme +import openforcefield + # -- General configuration ------------------------------------------------ # If your documentation needs a minimal Sphinx version, state it here. @@ -36,17 +37,22 @@ # ones. extensions = [ 'sphinx.ext.autodoc', - 'sphinx.ext.autosummary', + #'sphinx.ext.napoleon', 'numpydoc', + 'sphinx.ext.autosummary', 'sphinx.ext.doctest', 'sphinx.ext.todo', 'sphinx.ext.mathjax', 'sphinx.ext.viewcode', - 'nbsphinx' + 'sphinx.ext.intersphinx', + 'nbsphinx', + 'm2r', # render markdown ] autosummary_generate = True autodoc_default_flags = ['members', 'inherited-members'] +autodoc_member_order = 'bysource' # preserve ordering in source +#autoclass_content = 'both' # Disable NumPy style attributes/methods expecting every method to have its own docs page numpydoc_class_members_toctree = False @@ -61,30 +67,35 @@ # Add any paths that contain templates here, relative to this directory. templates_path = ['_templates'] +# Source parsers +#source_parsers = { +# '.md': 'recommonmark.parser.CommonMarkParser', +#} + # The suffix(es) of source filenames. # You can specify multiple suffix as a list of string: # -# source_suffix = ['.rst', '.md'] -source_suffix = '.rst' +source_suffix = ['.rst', '.md'] +#source_suffix = '.rst' # The master toctree document. master_doc = 'index' # General information about the project. project = 'openforcefield' -copyright = '2016-2017 Open Forcefield Consortium' -author = 'Open Forcefield Consortium' +copyright = '2016-2019 Open Force Field Initiative' +author = 'Open Force Field Initiative' # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the # built documents. # # The short X.Y version. -#version = openforcefield.__version__ -version = '0.0.4' +version = openforcefield.__version__ +#version = '0.2.0' # The full version, including alpha/beta/rc tags. -#release = openforcefield.__version__ -release = '0.0.4' +release = openforcefield.__version__ +#release = '0.2.0' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. @@ -99,8 +110,8 @@ exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] # The name of the Pygments (syntax highlighting) style to use. -#pygments_style = 'sphinx' -pygments_style = 'paraiso-dark' +pygments_style = 'sphinx' +#pygments_style = 'paraiso-dark' # If true, `todo` and `todoList` produce output, else they produce nothing. todo_include_todos = True @@ -129,10 +140,10 @@ # theme further. html_theme_options = { # Navigation bar title. (Default: ``project`` value) - 'navbar_title': "Open Forcefield Toolkit", + 'navbar_title': "Open Force Field Toolkit", # Tab name for entire site. (Default: "Site") - 'navbar_site_name': "Open Forcefield Toolkit", + 'navbar_site_name': "Open Force Field Toolkit", # A list of tuples containing pages or urls to link to. # Valid tuples should be in the following forms: @@ -142,8 +153,8 @@ # Note the "1" or "True" value above as the third argument to indicate # an arbitrary url. 'navbar_links': [ - ("Examples", "https://github.com/openforcefield/openforcefield/tree/master/examples", True), - ("Open Forcefield Consortium", "http://openforcefield.org", True), + #("Examples", "https://github.com/openforcefield/openforcefield/tree/master/examples", True), + ("Open Force Field Initiative", "http://openforcefield.org", True), ], # Render the next and previous page links in navbar. (Default: true) @@ -184,7 +195,9 @@ # # Options are nothing (default) or the name of a valid theme # such as "cosmo" or "sandstone". - 'bootswatch_theme': "cosmo", + #'bootswatch_theme': "cosmo", + #'bootswatch_theme': "united", + 'bootswatch_theme': "yeti", # Choose Bootstrap version. # Values: "3" (default) or "2" (in quotes) @@ -222,15 +235,18 @@ latex_elements = { # The paper size ('letterpaper' or 'a4paper'). # - # 'papersize': 'letterpaper', + 'papersize': 'letterpaper', # The font size ('10pt', '11pt' or '12pt'). # - # 'pointsize': '10pt', + 'pointsize': '10pt', # Additional stuff for the LaTeX preamble. - # - # 'preamble': '', + 'preamble': r''' + \usepackage{charter} + \usepackage[defaultsans]{lato} + \usepackage{inconsolata} + ''', # Latex figure (float) alignment # @@ -242,7 +258,7 @@ # author, documentclass [howto, manual, or own class]). latex_documents = [ (master_doc, 'openforcefield.tex', 'openforcefield Documentation', - 'Open Forcefield Consortium', 'manual'), + 'Open Force Field Consortium', 'manual'), ] @@ -251,7 +267,7 @@ # One entry per manual page. List of tuples # (source start file, name, description, authors, manual section). man_pages = [ - (master_doc, 'openforcefield', 'openforcefield Documentation', + (master_doc, 'openforcefield', 'openforcefield documentation', [author], 1) ] @@ -262,7 +278,7 @@ # (source start file, target name, title, author, # dir menu entry, description, category) texinfo_documents = [ - (master_doc, 'openforcefield', 'openforcefield Documentation', + (master_doc, 'openforcefield', 'openforcefield documentation', author, 'openforcefield', 'One line description of project.', 'Miscellaneous'), ] diff --git a/docs/developing.rst b/docs/developing.rst new file mode 100644 index 000000000..3231752a3 --- /dev/null +++ b/docs/developing.rst @@ -0,0 +1,20 @@ +.. _developing: + +Developing for the toolkit +************************** + +Style guide +""""""""""" + +Development for the ``openforcefield`` toolkit conforms to the recommendations given by the `Software Development Best Practices for Computational Chemistry `_ guide. + +Contributing +"""""""""""" + +We always welcome `GitHub pull requests `_. +For bug fixes, major feature additions, or refactoring, please raise an issue on the `GitHub issue tracker `_ first to ensure the design will be amenable to current developer plans. + +How can I become a developer? +""""""""""""""""""""""""""""" + +If you would like to contribute, please post an issue on the `GitHub issue tracker `_ describing the contribution you would like to make to start a discussion. diff --git a/docs/environment.yml b/docs/environment.yml index 2c1312bd2..e70729ede 100644 --- a/docs/environment.yml +++ b/docs/environment.yml @@ -2,23 +2,19 @@ name: openforcefield channels: - omnia - conda-forge + - rdkit dependencies: - - python - - cython + - python ==3.6 - numpy - - scipy - setuptools - - six - openmm - parmed - numpydoc - - netCDF4 - - pyyaml - - python - networkx - lxml - openmoltools >=0.7.3 - - matplotlib - - pandas - nbsphinx - sphinx_bootstrap_theme + - m2r >=0.2.1 + - rdkit + - testpath =0.3.1 diff --git a/docs/examples.rst b/docs/examples.rst index e69de29bb..3d794efbd 100644 --- a/docs/examples.rst +++ b/docs/examples.rst @@ -0,0 +1,3 @@ +.. _examples: + +.. mdinclude:: ../examples/README.md diff --git a/docs/faq.rst b/docs/faq.rst new file mode 100644 index 000000000..97e1ee6d2 --- /dev/null +++ b/docs/faq.rst @@ -0,0 +1 @@ +.. mdinclude:: ../FAQ.md diff --git a/docs/figures/vsite_bondcharge.jpg b/docs/figures/vsite_bondcharge.jpg new file mode 100644 index 000000000..c19a572a1 Binary files /dev/null and b/docs/figures/vsite_bondcharge.jpg differ diff --git a/docs/figures/vsite_bondcharge.pdf b/docs/figures/vsite_bondcharge.pdf new file mode 100644 index 000000000..ecdf92888 Binary files /dev/null and b/docs/figures/vsite_bondcharge.pdf differ diff --git a/docs/figures/vsite_divalent.jpg b/docs/figures/vsite_divalent.jpg new file mode 100644 index 000000000..a05f00677 Binary files /dev/null and b/docs/figures/vsite_divalent.jpg differ diff --git a/docs/figures/vsite_divalent.pdf b/docs/figures/vsite_divalent.pdf new file mode 100644 index 000000000..8e01b96d4 Binary files /dev/null and b/docs/figures/vsite_divalent.pdf differ diff --git a/docs/figures/vsite_monovalent.jpg b/docs/figures/vsite_monovalent.jpg new file mode 100644 index 000000000..8734338f8 Binary files /dev/null and b/docs/figures/vsite_monovalent.jpg differ diff --git a/docs/figures/vsite_trivalent.jpg b/docs/figures/vsite_trivalent.jpg new file mode 100644 index 000000000..45da11b25 Binary files /dev/null and b/docs/figures/vsite_trivalent.jpg differ diff --git a/docs/figures/vsite_trivalent.pdf b/docs/figures/vsite_trivalent.pdf new file mode 100644 index 000000000..b33982756 Binary files /dev/null and b/docs/figures/vsite_trivalent.pdf differ diff --git a/docs/index.rst b/docs/index.rst index be1ee15a0..5bb6b0d40 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -3,23 +3,30 @@ You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. -Open Forcefield Toolkit +Open Force Field Toolkit ======================= -A modern, extensible library for molecular mechanics forcefield science. +A modern, extensible library for molecular mechanics force field science from the `Open Force Field Initiative `_ + +User Guide +---------- .. toctree:: - :maxdepth: 2 - :caption: Contents: + :maxdepth: 1 installation releasehistory + smirnoff + examples + developing + faq -Modules -------- +API documentation +----------------- .. toctree:: - :maxdepth: 2 + :maxdepth: 1 + topology typing utils diff --git a/docs/installation.rst b/docs/installation.rst index 65b39013d..ee22c4c82 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -19,20 +19,46 @@ On ``linux``, you can install the Python 3 version into ``$HOME/miniconda3`` wit $ wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh $ bash ./Miniconda3-latest-Linux-x86_64.sh -b -p $HOME/miniconda3 - $ export PATH="$HOME/miniconda3/bin:$PATH" + $ source ~/miniconda3/etc/profile.d/conda.sh + $ conda activate base + On ``osx``, you want to use the ``osx`` binary .. code-block:: bash $ wget https://repo.continuum.io/miniconda/Miniconda2-latest-MacOSX-x86_64.sh - $ bash ./Miniconda3-latest-Linux-x86_64.sh -b -p $HOME/miniconda3 - $ export PATH="$HOME/miniconda3/bin:$PATH" + $ bash ./Miniconda2-latest-MacOSX-x86_64.sh -b -p $HOME/miniconda3 + $ source ~/miniconda3/etc/profile.d/conda.sh + $ conda activate base + + +You may want to add the new ``source ~/miniconda3/etc/profile.d/conda.sh`` line to your ``~/.bashrc`` file to ensure Anaconda Python can enabled in subsequent terminal sessions. +``conda activate base`` will need to be run in each subsequent terminal session to return to the environment where the toolkit will be installed. + -You may want to add the new ```$PATH`` extension to your ``~/.bashrc`` file to ensure Anaconda Python is used by default. Note that ``openforcefield`` will be installed into this local Python installation, so that you will not need to worry about disrupting existing Python installations. -.. note:: ``conda`` installation is the preferred method since all dependencies are automatically fetched and installed for you. +.. note:: Installation via the conda package manager is the preferred method since all dependencies are automatically fetched and installed for you. + +| + +Required dependencies +======================= + +The ``openforcefield`` toolkit makes use of the `Omnia `_ and `Conda Forge `_ free and open source community package repositories: + +.. code-block:: bash + + $ conda config --add channels omnia --add channels conda-forge + $ conda update --all + +This only needs to be done once. + +.. note :: + + If automation is required, provide the ``--yes`` argument to ``conda update`` and ``conda install`` comamnds. + More information on the ``conda`` command-line API can be found in the `conda online documentation `_. | @@ -48,7 +74,7 @@ You can install the latest stable release build of ``openforcefield`` via the `` This version is recommended for all users not actively developing new forcefield parameterization algorithms. -.. note:: ``conda`` will automatically dependencies from binary packages automatically, including difficult-to-install packages such as OpenMM, numpy, and scipy. This is really the easiest way to get started. +.. note:: The conda package manager will install dependencies from binary packages automatically, including difficult-to-install packages such as OpenMM, numpy, and scipy. This is really the easiest way to get started. | @@ -62,3 +88,20 @@ To update an earlier ``conda`` installation of ``openforcefield`` to the latest $ conda update openforcefield | + +Optional dependencies +--------------------- + +This toolkit can optionally make use of the `OpenEye toolkit `_ if the user has a license key installed. +Academic laboratories intending to release results into the public domain can `obtain a free license key `_, while other users (including academics intending to use the software for purposes of generating protected intellectual property) must `pay to obtain a license `_. + +To install the OpenEye toolkits (provided you have a valid license file): + +.. code-block:: none + + $ conda install --yes -c openeye openeye-toolkits + +No essential ``openforcefield`` release capabilities *require* the OpenEye toolkit, but the Open Force Field developers make use of it in parameterizing new open source force fields. +It is known that there are certain differences in toolkit behavior between RDKit and OpenEye when reading a small fraction of molecules, and we encourage you to report any unexpected behavior that may be caused by toolkit differences to our `issue tracker `_. + + diff --git a/docs/readthedocs.yml b/docs/readthedocs.yml index 5d3b36c79..a66990c6a 100644 --- a/docs/readthedocs.yml +++ b/docs/readthedocs.yml @@ -1,2 +1,5 @@ conda: - file: environment.yml + file: environment.yml +python: + setup_py_install: true + version: 3.5 diff --git a/docs/releasehistory.rst b/docs/releasehistory.rst index 81232d2f9..df2f186fb 100644 --- a/docs/releasehistory.rst +++ b/docs/releasehistory.rst @@ -1,2 +1,46 @@ Release History =============== + +Releases follow the ``major.minor.micro`` scheme recommended by `PEP440 `_, where + +* ``major`` increments denote a change that may break API compatibility with previous ``major`` releases +* ``minor`` increments add features but do not break API compatibility +* ``micro`` increments represent bugfix releases or improvements in documentation + +0.2.0 +----- + +This version of the toolkit introduces many new features on the way to a 1.0.0 release. + +New features +"""""""""""" + +* Major overhaul, resulting in the creation of the `0.2 SMIRNOFF specification `_ and its XML representation +* Updated API and infrastructure for reference SMIRNOFF :class:`ForceField` implementation +* Implementation of modular :class:`ParameterHandler` classes which process the topology to add all necessary forces to the system.. +* Implementation of modular :class:`ParameterIOHandler` classes for reading/writing different serialized SMIRNOFF forcefield representations +* Introduction of :class:`Molecule` and :class:`Topology` classes for representing molecules and biomolecular systems +* New :class:`ToolkitWrapper` interface to RDKit, OpenEye, and AmberTools toolkits, managed by :class:`ToolkitRegistry` +* API improvements to more closely follow `PEP8 `_ guidelines +* Improved documentation and examples + +0.1.0 +----- + +This is an early preview release of the toolkit that matches the functionality described in the preprint describing the SMIRNOFF v0.1 force field format: `[DOI] `_. + +New features +"""""""""""" + +This release features additional documentation, code comments, and support for automated testing. + +Bugfixes +"""""""" + +Treatment of improper torsions +'''''''''''''''''''''''''''''' + +A significant (though currently unused) problem in handling of improper torsions was corrected. +Previously, non-planar impropers did not behave correctly, as six-fold impropers have two potential chiralities. +To remedy this, SMIRNOFF impropers are now implemented as three-fold impropers with consistent chirality. +However, current force fields in the SMIRNOFF format had no non-planar impropers, so this change is mainly aimed at future work. diff --git a/docs/smirnoff.rst b/docs/smirnoff.rst new file mode 100644 index 000000000..ff87bad3a --- /dev/null +++ b/docs/smirnoff.rst @@ -0,0 +1 @@ +.. mdinclude:: ../The-SMIRNOFF-force-field-format.md diff --git a/docs/topology.rst b/docs/topology.rst new file mode 100644 index 000000000..bb378f210 --- /dev/null +++ b/docs/topology.rst @@ -0,0 +1,34 @@ +.. _topology :: + +Molecular topology representations +================================== + +This module provides pure-Python classes for representing molecules and molecular systems. +These classes offer several advantages over corresponding ``Topology`` objects in `OpenMM `_ and `MDTraj `_, +including offering serialization to a variety of standard formats (including `XML `_, `JSON `_, `YAML `_, `BSON `_, `TOML `_, and `MessagePack `_). + + +Primary objects +--------------- + +.. currentmodule:: openforcefield.topology +.. autosummary:: + :nosignatures: + :toctree: api/generated/ + + FrozenMolecule + Molecule + Topology + +Secondary objects +----------------- + +.. currentmodule:: openforcefield.topology +.. autosummary:: + :nosignatures: + :toctree: api/generated/ + + Particle + Atom + Bond + VirtualSite diff --git a/docs/typing.rst b/docs/typing.rst index e128812e1..69e7e29c0 100644 --- a/docs/typing.rst +++ b/docs/typing.rst @@ -1,4 +1,4 @@ -.. _typing:: +.. _typing :: Forcefield typing tools ======================= @@ -8,6 +8,9 @@ Chemical environments Tools for representing and operating on chemical environments + .. warning :: This class is largely redundant with the same one in the Chemper package, and will likely be removed. + + .. currentmodule:: openforcefield.typing.chemistry .. autosummary:: :nosignatures: @@ -21,9 +24,75 @@ Forcefield typing engines Engines for applying parameters to chemical systems +The SMIRks-Native Open Force Field (SMIRNOFF) +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +A reference implementation of the SMIRNOFF specification for parameterizing biomolecular systems + +ForceField +~~~~~~~~~~ + +The ``ForceField`` class is a primary part of the top-level toolkit API. +``ForceField`` objects are initialized from SMIRNOFF data sources (e.g. an ``OFFXML`` file). +For a basic example of system creation using a ``ForceField``, see ``examples/SMIRNOFF_simulation``. + + .. currentmodule:: openforcefield.typing.engines.smirnoff.forcefield .. autosummary:: :nosignatures: :toctree: api/generated/ ForceField + +Parameter Type +~~~~~~~~~~~~~~ + +``ParameterType`` objects are representations of individual SMIRKS-based SMIRNOFF parameters. +These are usually initialized during ``ForceField`` creation, and can be inspected and modified by users via the Python API. +For more information, see ``examples/forcefield_modification``. + +.. currentmodule:: openforcefield.typing.engines.smirnoff.parameters +.. autosummary:: + :nosignatures: + :toctree: api/generated/ + + ParameterType + BondHandler.BondType + AngleHandler.AngleType + ProperTorsionHandler.ProperTorsionType + ImproperTorsionHandler.ImproperTorsionType + vdWHandler.vdWType + +Parameter Handlers +~~~~~~~~~~~~~~~~~~ + +Each ``ForceField`` primarily consists of several ``ParameterHandler`` objects, which each contain the machinery to add one energy component to a system. +During system creation, each ``ParameterHandler`` registered to a ``ForceField`` has its ``assign_parameters()`` function called.. + +.. currentmodule:: openforcefield.typing.engines.smirnoff.parameters +.. autosummary:: + :nosignatures: + :toctree: api/generated/ + + ParameterList + ParameterHandler + BondHandler + AngleHandler + ProperTorsionHandler + ImproperTorsionHandler + vdWHandler + ElectrostaticsHandler + ToolkitAM1BCCHandler + +Parameter I/O Handlers +~~~~~~~~~~~~~~~~~~~~~~ + +``ParameterIOHandler`` objects handle reading and writing of serialzied SMIRNOFF data sources. + +.. currentmodule:: openforcefield.typing.engines.smirnoff.io +.. autosummary:: + :nosignatures: + :toctree: api/generated/ + + ParameterIOHandler + XMLParameterIOHandler \ No newline at end of file diff --git a/docs/utils.rst b/docs/utils.rst new file mode 100644 index 000000000..6f56f7309 --- /dev/null +++ b/docs/utils.rst @@ -0,0 +1,103 @@ +.. _utils :: + +Utilities +========= + +Toolkit wrappers +---------------- + +The toolkit wrappers provide a simple uniform API for accessing minimal functionality of cheminformatics toolkits. + +These toolkit wrappers are generally used through a :class:`ToolkitRegistry`, which can be constructed with a desired precedence of toolkits: + +.. code-block:: python + + from openforcefield.utils.toolkits import ToolkitRegistry + toolkit_registry = ToolkitRegistry() + toolkit_precedence = [OpenEyeToolkitWrapper, RDKitToolkitWrapper, AmberToolsToolkitWrapper] + [ toolkit_registry.register(toolkit) for toolkit in toolkit_precedence if toolkit.is_available() ] + +Alternatively, the global toolkit registry (which will attempt to register any available toolkits) can be used: + +.. code-block:: python + + from openforcefield.utils.toolkits import DEFAULT_TOOLKIT_REGISTRY as toolkit_registry + +The toolkit wrappers can then be accessed through the registry: + +.. code-block:: python + + molecule = Molecule.from_smiles('Cc1ccccc1') + smiles = toolkit_registry.call('to_smiles', molecule) + +.. currentmodule:: openforcefield.utils.toolkits +.. autosummary:: + :nosignatures: + :toctree: api/generated/ + + ToolkitRegistry + ToolkitWrapper + OpenEyeToolkitWrapper + RDKitToolkitWrapper + AmberToolsToolkitWrapper + +Serialization support +--------------------- + +.. currentmodule:: openforcefield.utils.serialization +.. autosummary:: + :nosignatures: + :toctree: api/generated/ + + Serializable + +Structure tools +--------------- + +Tools for manipulating molecules and structures + +.. todo :: + + These methods are deprecated and will be removed. + We recommend that no new code makes use of these functions. + +.. currentmodule:: openforcefield.utils.structure +.. autosummary:: + :nosignatures: + :toctree: api/generated/ + + generateSMIRNOFFStructure + generateProteinStructure + combinePositions + mergeStructure + generateTopologyFromOEMol + get_testdata_filename + normalize_molecules + read_molecules + setPositionsInOEMol + extractPositionsFromOEMol + read_typelist + positions_from_oemol + check_energy_is_finite + get_energy + get_molecule_parameterIDs + getMolParamIDToAtomIndex + merge_system + save_system_to_amber + save_system_to_gromacs + +Miscellaneous utilities +----------------------- + +Miscellaneous utility functions. + +.. currentmodule:: openforcefield.utils.utils +.. autosummary:: + :nosignatures: + :toctree: api/generated/ + + inherit_docstrings + all_subclasses + temporary_cd + temporary_directory + get_data_filename diff --git a/examples/README.md b/examples/README.md index 7b80909ab..f58618278 100644 --- a/examples/README.md +++ b/examples/README.md @@ -1,12 +1,11 @@ -# Examples for `openforcefield` tools +# Examples using SMIRNOFF with the toolkit -## Manifest +The following examples are available in [the openforcefield toolkit repository](https://github.com/openforcefield/openforcefield/tree/master/examples): -* `SMIRNOFF_simulation/` - simulation of a molecule in the gas phase with the SMIRNOFF forcefield format -* `SMIRNOFF_comparison/` - compare molecule energies from SMIRNOFF/OpenMM and AMBER -* `forcefield_modification/` - Jupyter notebook example of modifying a forcefield parameter and evaluating how it changes an energy -* `chemicalEnvironments/` - example and documentation of using chemical environment objects to manipulate environment being considered, generate example SMIRKS, etc. Also contains IPython notebook using the chemical environment for depiction. -* `mixedFF_structure` - example of how to use SMIRNOFF forcefields for small molecules in combination with more conventional force fields for proteins and other components of your system. -* `partial_bondorder/` - example of using partial bond orders for parameterizing molecules, and showing how the SMIRNOFF format extends; see https://github.com/openforcefield/smarty/issues/53 -* `host_guest_simulation/` - example of setting up a basic MD simulation for a host-guest system using the SMIRNOFF force fields. -* `label_molecule/` - example showing how to check which parameters are used in which molecules, do parameter usage statistics, etc. +### Index of provided examples + +* [SMIRNOFF_simulation](https://github.com/openforcefield/openforcefield/tree/master/examples/SMIRNOFF_simulation) - simulation of a molecule in the gas phase with the SMIRNOFF forcefield format +* [forcefield_modification](https://github.com/openforcefield/openforcefield/tree/master/examples/forcefield_modification) - modify forcefield parameters and evaluate how system energy changes +* [using_smirnoff_in_amber_or_gromacs](https://github.com/openforcefield/openforcefield/tree/master/examples/using_smirnoff_in_amber_or_gromacs) - convert a System generated with the Open Forcefield Toolkit, which can be simulated natively with OpenMM, into AMBER prmtop/inpcrd and GROMACS top/gro input files through the ParmEd library. +* [inspect_assigned_parameters](https://github.com/openforcefield/openforcefield/tree/master/examples/inspect_assigned_parameters) - check which parameters are used in which molecules and generate parameter usage statistics. +* [using_smirnoff_with_amber_protein_forcefield](https://github.com/openforcefield/openforcefield/tree/master/examples/using_smirnoff_with_amber_protein_forcefield) - use SMIRNOFF parameters for small molecules in combination with more conventional force fields for proteins and other components of your system (using ParmEd to combine parameterized structures) diff --git a/examples/SMIRNOFF_comparison/AlkEthOH_inputfiles.tar.gz b/examples/SMIRNOFF_comparison/AlkEthOH_inputfiles.tar.gz deleted file mode 100644 index d7c55b425..000000000 Binary files a/examples/SMIRNOFF_comparison/AlkEthOH_inputfiles.tar.gz and /dev/null differ diff --git a/examples/SMIRNOFF_comparison/compare_molecule_energies.py b/examples/SMIRNOFF_comparison/compare_molecule_energies.py deleted file mode 100644 index 47f350955..000000000 --- a/examples/SMIRNOFF_comparison/compare_molecule_energies.py +++ /dev/null @@ -1,37 +0,0 @@ -#!/bin/env python - -from openeye import oechem -from openforcefield.utils import get_data_filename -from openforcefield.typing.engines.smirnoff import ForceField, compare_molecule_energies - -import os - -# Cross-check energies of molecules from AlkEthOH set using SMIRNOFF xml file -# versus energies from AMBER .prmtop and .crd files (parm@frosst params) - -datapath = './AlkEthOH_inputfiles/AlkEthOH_rings_filt1' -#molname = 'AlkEthOH_r0' #That fails, but it's complicated. Try cyclobutane -molname = 'AlkEthOH_r51' -mol_filename = os.path.join( datapath, molname+'.mol2') - -# Check if we have this data file; if not we have to extract the archive -if not os.path.isfile( mol_filename): - print "Extracting archived molecule files." - tarfile = 'AlkEthOH_inputfiles.tar.gz' - os.system('tar -xf AlkEthOH_inputfiles.tar.gz') - -# Load OEMol -mol = oechem.OEGraphMol() -ifs = oechem.oemolistream(mol_filename) -flavor = oechem.OEIFlavor_Generic_Default | oechem.OEIFlavor_MOL2_Default | oechem.OEIFlavor_MOL2_Forcefield -ifs.SetFlavor( oechem.OEFormat_MOL2, flavor) -oechem.OEReadMolecule(ifs, mol ) -oechem.OETriposAtomNames(mol) - -# Load forcefield -forcefield = ForceField(get_data_filename('forcefield/Frosst_AlkEthOH_parmAtFrosst.offxml')) - -# Compare energies -prmtop = os.path.join( datapath, molname+'.top') -crd = os.path.join( datapath, molname+'.crd') -results = compare_molecule_energies( prmtop, crd, forcefield, mol) diff --git a/examples/SMIRNOFF_comparison/compare_set_energies.py b/examples/SMIRNOFF_comparison/compare_set_energies.py deleted file mode 100644 index 0ca0daf2d..000000000 --- a/examples/SMIRNOFF_comparison/compare_set_energies.py +++ /dev/null @@ -1,45 +0,0 @@ -#!/bin/env python - -from openeye import oechem -from openforcefield.utils import get_data_filename -from openforcefield.typing.engines.smirnoff import ForceField, compare_molecule_energies - -import os -import glob - -# Cross-check energies of molecules from AlkEthOH set using SMIRNOFF xml file -# versus energies from AMBER .prmtop and .crd files (parm@frosst params) - -#datapath = './AlkEthOH_inputfiles/AlkEthOH_chain_filt1' -datapath = './AlkEthOH_inputfiles/AlkEthOH_rings_filt1' - -#Check if this is a directory, if not, extract it -# Check if we have this data file; if not we have to extract the archive -if not os.path.isdir( datapath ): - print "Extracting archived molecule files." - tarfile = 'AlkEthOH_inputfiles.tar.gz' - os.system('tar -xf AlkEthOH_inputfiles.tar.gz') - -#Obtain list of molecules -mol_filenames = glob.glob( datapath+'/*.mol2') -mol_filenames = [ fnm for fnm in mol_filenames if not 'c1302' in fnm ] #Skip water - -for mol_filename in mol_filenames: - molname = os.path.basename( mol_filename).replace('.mol2','') - print("Comparing %s (%s/%s)..." % (molname, mol_filenames.index(mol_filename), len(mol_filenames) ) ) - - # Load OEMol - mol = oechem.OEGraphMol() - ifs = oechem.oemolistream(mol_filename) - flavor = oechem.OEIFlavor_Generic_Default | oechem.OEIFlavor_MOL2_Default | oechem.OEIFlavor_MOL2_Forcefield - ifs.SetFlavor( oechem.OEFormat_MOL2, flavor) - oechem.OEReadMolecule(ifs, mol ) - oechem.OETriposAtomNames(mol) - - # Load forcefield - forcefield = ForceField(get_data_filename('forcefield/Frosst_AlkEthOH_parmAtFrosst.offxml')) - - # Compare energies - prmtop = os.path.join( datapath, molname+'.top') - crd = os.path.join( datapath, molname+'.crd') - results = compare_molecule_energies( prmtop, crd, forcefield, mol) diff --git a/examples/SMIRNOFF_simulation/AlkEthOH_r51.mol2 b/examples/SMIRNOFF_simulation/AlkEthOH_r51.mol2 deleted file mode 100644 index 02b639fe8..000000000 --- a/examples/SMIRNOFF_simulation/AlkEthOH_r51.mol2 +++ /dev/null @@ -1,34 +0,0 @@ -@MOLECULE -AlkEthOH_r51 - 12 12 1 0 0 -SMALL -USER_CHARGES - -@ATOM - 1 C1 0.7739 -0.6328 -0.4493 CT 1 <0> -0.09541 - 2 C2 0.7841 -2.0794 0.0876 CT 1 <0> -0.09537 - 3 C3 0.3765 -1.2249 -1.8175 CT 1 <0> -0.09537 - 4 C4 -0.2080 -2.4242 -1.0427 CT 1 <0> -0.09537 - 5 H1 -0.0002 -0.0002 -0.0000 HC 1 <0> 0.04769 - 6 H2 1.7307 -0.1060 -0.4177 HC 1 <0> 0.04769 - 7 H3 1.7548 -2.5795 -0.0089 HC 1 <0> 0.04769 - 8 H4 0.4116 -2.2126 1.1060 HC 1 <0> 0.04769 - 9 H5 -0.3391 -0.6397 -2.4004 HC 1 <0> 0.04769 - 10 H6 1.2316 -1.4835 -2.4524 HC 1 <0> 0.04769 - 11 H7 -0.0764 -3.4034 -1.5100 HC 1 <0> 0.04769 - 12 H8 -1.2597 -2.2984 -0.7614 HC 1 <0> 0.04769 -@BOND - 1 1 2 1 - 2 1 3 1 - 3 2 4 1 - 4 3 4 1 - 5 1 5 1 - 6 1 6 1 - 7 2 7 1 - 8 2 8 1 - 9 3 9 1 - 10 3 10 1 - 11 4 11 1 - 12 4 12 1 -@SUBSTRUCTURE - 1 <0> 1 GROUP 0 A **** diff --git a/examples/SMIRNOFF_simulation/README.md b/examples/SMIRNOFF_simulation/README.md index 0dade8393..989c78df1 100644 --- a/examples/SMIRNOFF_simulation/README.md +++ b/examples/SMIRNOFF_simulation/README.md @@ -1,8 +1,3 @@ -# Simulate a molecule in the gas phase using SMIRNOFF forcefield format +## Simulate a system parametrized with the Open Force Field toolkit -This example shows how to simulate a molecule in the gas phase using the SMIRNOFF forcefield format. - -To run: -```bash -python run_molecule.py -``` +The notebook `run_simulation.ipynb` shows how to use the Open Force Field Toolkit to create a parametrized `System` object that can be used to run a molecular dynamic simulation with OpenMM. diff --git a/examples/SMIRNOFF_simulation/run_molecule.py b/examples/SMIRNOFF_simulation/run_molecule.py deleted file mode 100644 index bcaf4ca19..000000000 --- a/examples/SMIRNOFF_simulation/run_molecule.py +++ /dev/null @@ -1,65 +0,0 @@ -#!/bin/env python - -import time -import numpy as np - -# Import OpenMM tools -from simtk import openmm, unit -from simtk.openmm import app, Platform - -# Use MDTraj to write simulation trajectories -from mdtraj.reporters import NetCDFReporter - -# Import the SMIRNOFF forcefield engine and some useful tools -from openforcefield.typing.engines.smirnoff import ForceField -from openforcefield.utils import get_data_filename, extractPositionsFromOEMol, generateTopologyFromOEMol - -# Import the OpenEye toolkit -from openeye import oechem - -# Define what molecule to work on, and a few simulation parameters -mol_filename = 'AlkEthOH_r51.mol2' -time_step = 2*unit.femtoseconds # simulation timestep -temperature = 300*unit.kelvin # simulation temperature -friction = 1/unit.picosecond # collision rate -num_steps = 100000 # number of steps to run -trj_freq = 1000 # number of steps per written trajectory frame -data_freq = 1000 # number of steps per written simulation statistics - -# Load molecule using OpenEye tools -mol = oechem.OEGraphMol() -ifs = oechem.oemolistream(mol_filename) -flavor = oechem.OEIFlavor_Generic_Default | oechem.OEIFlavor_MOL2_Default | oechem.OEIFlavor_MOL2_Forcefield -ifs.SetFlavor( oechem.OEFormat_MOL2, flavor) -oechem.OEReadMolecule(ifs, mol ) -oechem.OETriposAtomNames(mol) - -# Get positions in OpenMM-compatible format -positions = extractPositionsFromOEMol(mol) - -# Load a SMIRNOFF small molecule forcefield for alkanes, ethers, and alcohols -forcefield = ForceField(get_data_filename('forcefield/Frosst_AlkEthOH_parmAtFrosst.offxml')) - -# Create the OpenMM system -topology = generateTopologyFromOEMol(mol) -system = forcefield.createSystem(topology, [mol]) - -# Set up an OpenMM simulation -integrator = openmm.LangevinIntegrator(temperature, friction, time_step) -platform = openmm.Platform.getPlatformByName('Reference') -simulation = app.Simulation(topology, system, integrator) -simulation.context.setPositions(positions) -simulation.context.setVelocitiesToTemperature(temperature) -netcdf_reporter = NetCDFReporter('trajectory.nc', trj_freq) -simulation.reporters.append(netcdf_reporter) -simulation.reporters.append(app.StateDataReporter('data.csv', data_freq, step=True, potentialEnergy=True, temperature=True, density=True)) - -# Run the simulation -print("Starting simulation") -start = time.clock() -simulation.step(num_steps) -end = time.clock() - -print("Elapsed time %.2f seconds" % (end-start)) -netcdf_reporter.close() -print("Done!") diff --git a/examples/SMIRNOFF_simulation/run_simulation.ipynb b/examples/SMIRNOFF_simulation/run_simulation.ipynb new file mode 100644 index 000000000..914b24fe1 --- /dev/null +++ b/examples/SMIRNOFF_simulation/run_simulation.ipynb @@ -0,0 +1,230 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Running a simulation of a System parametrized with a SMIRNOFF force field\n", + "\n", + "This example shows how to use the Open Force Field Toolkit to create a parametrized `System` object that can be used to run a molecular dynamic simulation with OpenMM. If you want to run MD with a different engine, see the example in `examples/conversion_amber_gromacs/`." + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Create an OpenMM System\n", + "\n", + "We start by loading a PDB file containing one copy of ethanol and cyclohexane. Our goal is to create an OFF `Topology` object describing this system that we can parametrize with the smirnoff99Frosst force field.\n", + "\n", + "The two `Molecule` objects created from the SMILES strings can contain information such as partial charges and stereochemistry that is not included in an OpenMM topology. In this example, partial charges are not explicitly given, and `ForceField` will assign AM1/BCC charges as specified by the smirnoff99Frosst force field." + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [], + "source": [ + "from simtk.openmm.app import PDBFile\n", + "from openforcefield.utils import get_data_filename" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "We use the `get_data_filename` utility function to easily access the data installed with the toolkit. Here you have the option to load example systems of increasing complexity. For speed, we recommend that you begin by loading a system with a single ethanol and a single cyclohexane." + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [], + "source": [ + "# 1 molecule of ethanol and 1 of cyclohexane.\n", + "pdb_file_path = get_data_filename('systems/test_systems/1_cyclohexane_1_ethanol.pdb')\n", + "\n", + "# 40%-60% cyclohexane-ethanol mixture.\n", + "# pdb_file_path = get_data_filename('systems/packmol_boxes/cyclohexane_ethanol_0.4_0.6.pdb')\n", + "\n", + "pdbfile = PDBFile(pdb_file_path)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "PDB files are not a reliable source of bond orders, so the toolkit requires users to supply a more detailed description of the molecule and its connectivity (currently either a SMILES, sdf, or mol2 file)." + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [], + "source": [ + "from openforcefield.topology import Molecule\n", + "ethanol = Molecule.from_smiles('CCO')\n", + "cyclohexane = Molecule.from_smiles('C1CCCCC1')" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Alternatively, if you have `sdf` files of the molecules, or if you have OpenEye installed and `mol2` files available, you can get the same results as above by loading the detailed molecule information from the files." + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [], + "source": [ + "from openforcefield.utils.toolkits import OpenEyeToolkitWrapper\n", + "if OpenEyeToolkitWrapper.is_available():\n", + " ethanol = Molecule.from_file(get_data_filename('molecules/ethanol.mol2'))\n", + " cyclohexane = Molecule.from_file(get_data_filename('molecules/cyclohexane.mol2'))" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "We now create the Open Force Field `Topology` describing the system from an OpenMM `Topology` object. The OFF `Topology` include more information (supplied by the two `Molecule` objects) than the OpenMM `Topology` such as (optionally) partial charges and stereochemistry. In this example, partial charges are not explicitly given, and `ForceField` will assign AM1/BCC charges as specified by the smirnoff99Frosst force field.\n", + "\n", + "
\n", + " Note on partial charges: The full 1.0.0 release will implement support for the definition of semiempirical partial charge treatment directly into the SMIRNOFF force field file (for details, see https://open-forcefield-toolkit.readthedocs.io/en/latest/smirnoff.html#partial-charge-and-electrostatics-models). Moreover, it will be possible to import charges directly from sdf and mol2 files.\n", + "
" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [], + "source": [ + "from openforcefield.topology import Topology\n", + "from openforcefield.typing.engines.smirnoff import ForceField\n", + "\n", + "# Create the Open Force Field Topology from an OpenMM Topology object.\n", + "omm_topology = pdbfile.topology\n", + "off_topology = Topology.from_openmm(omm_topology, unique_molecules=[ethanol, cyclohexane])\n", + "\n", + "# Load the smirnof99Frosst force field.\n", + "forcefield = ForceField('smirnoff99Frosst.offxml')\n", + "\n", + "# Parametrize the topology and create an OpenMM System.\n", + "system = forcefield.create_openmm_system(off_topology)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Run a simulation\n", + "\n", + "We can now use the `System` object to run molecular dynamics trajectories with OpenMM." + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [], + "source": [ + "from simtk import openmm, unit\n", + "\n", + "# Propagate the System with Langevin dynamics.\n", + "time_step = 2*unit.femtoseconds # simulation timestep\n", + "temperature = 300*unit.kelvin # simulation temperature\n", + "friction = 1/unit.picosecond # collision rate\n", + "integrator = openmm.LangevinIntegrator(temperature, friction, time_step)\n", + "\n", + "# Length of the simulation.\n", + "num_steps = 1000 # number of integration steps to run\n", + "\n", + "# Logging options.\n", + "trj_freq = 1 # number of steps per written trajectory frame\n", + "data_freq = 1 # number of steps per written simulation statistics\n", + "\n", + "# Set up an OpenMM simulation.\n", + "simulation = openmm.app.Simulation(omm_topology, system, integrator)\n", + "\n", + "# Set the initial positions.\n", + "positions = pdbfile.getPositions() \n", + "simulation.context.setPositions(positions)\n", + "\n", + "# Randomize the velocities from a Boltzmann distribution at a given temperature.\n", + "simulation.context.setVelocitiesToTemperature(temperature)\n", + "\n", + "# Configure the information in the output files.\n", + "pdb_reporter = openmm.app.PDBReporter('trajectory.pdb', trj_freq)\n", + "state_data_reporter = openmm.app.StateDataReporter('data.csv', data_freq, step=True,\n", + " potentialEnergy=True, temperature=True,\n", + " density=True)\n", + "simulation.reporters.append(pdb_reporter)\n", + "simulation.reporters.append(state_data_reporter)" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Starting simulation\n", + "Elapsed time 5.25 seconds\n", + "Done!\n" + ] + } + ], + "source": [ + "import time\n", + "\n", + "print(\"Starting simulation\")\n", + "start = time.clock()\n", + "\n", + "# Run the simulation\n", + "simulation.step(num_steps)\n", + "\n", + "end = time.clock()\n", + "print(\"Elapsed time %.2f seconds\" % (end-start))\n", + "print(\"Done!\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "If successful, the directory where your jupyter notebook is running should contain a `trajectory.pdb` file that you can visualize and a `data.csv` file including potential energy, density, and temperature of each frame." + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.6.8" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/examples/deprecated/SMIRNOFF_comparison/README.md b/examples/deprecated/SMIRNOFF_comparison/README.md new file mode 100644 index 000000000..25a5e4e1a --- /dev/null +++ b/examples/deprecated/SMIRNOFF_comparison/README.md @@ -0,0 +1,22 @@ +## Compare small molecule parm@frosst energies between SMIRNOFF and AMBER `prmtop/inpcrd` + +This example demonstrates how to compare parm@frosst energies of molecules from the AlkEthOH set between systems generated from a SMIRNOFF `.offxml` file and systems generated from AMBER `prmtop/inpcrd` files. + +* [compare_molecule_energies.py](https://github.com/openforcefield/openforcefield/blob/master/examples/SMIRNOFF_comparison/compare_molecule_energies.py): compare energies for a single molecule +* [compare_set_energies.py](https://github.com/openforcefield/openforcefield/blob/master/examples/SMIRNOFF_comparison/compare_set_energies.py): compare energies across a set of molecules + +The key idea here is to use the utility `compare_system_energies` to compare the molecule parameterized by `ForceField` with a corresponding system constructed via an AMBER `prmtop/inpcrd` pair: + +```python +# Load molecule +from openmmtools.topology import Molecule +molecule = Molecule.from_file(mol_filename) + +# Load forcefield +from openforcefield.typing.engines.smirnoff import ForceField +forcefield = ForceField(offxml_filename) + +# Compare energies +from openforcefield.tests.utils import compare_molecule_energies +energies = compare_amber_smirnoff(prmtop_filename, inpcrd_filename, forcefield, molecule) +``` diff --git a/examples/deprecated/SMIRNOFF_comparison/compare_molecule_energies.py b/examples/deprecated/SMIRNOFF_comparison/compare_molecule_energies.py new file mode 100644 index 000000000..2146d5169 --- /dev/null +++ b/examples/deprecated/SMIRNOFF_comparison/compare_molecule_energies.py @@ -0,0 +1,48 @@ +#!/usr/bin/env python + +""" +Cross-check energies of molecules from AlkEthOH set using SMIRNOFF xml file +versus energies from AMBER .prmtop and .crd files (parm@frosst params). +""" + +import os + +# datapath = './AlkEthOH_tripos/AlkEthOH_chain_filt1' +# datapath = './AlkEthOH_tripos/AlkEthOH_rings_filt1' +datapath = './AlkEthOH_tripos/AlkEthOH_test_filt1' + +molname = 'AlkEthOH_r22' + +mol_filepath = os.path.join(datapath, molname + '_tripos.mol2') +prmtop_filepath = os.path.join(datapath, molname + '.top') +inpcrd_filepath = os.path.join(datapath, molname + '.crd') + +# Check if we have this data file; if not we have to extract the archive. +if not os.path.isdir(datapath): + print("Extracting archived molecule files.") + # Extract the AlkEthOH dataset shipped with the toolkit in data/molecules/ in the working directory. + from openforcefield.tests.utils import get_data_filename + tarfile_path = os.path.join(get_data_filename('molecules'), 'AlkEthOH_tripos.tar.gz') + import tarfile + with tarfile.open(tarfile_path, 'r:gz') as tar: + tar.extractall() + +# Load molecule +from openforcefield.topology import Molecule +molecule = Molecule.from_file(mol_filepath) + +# Load forcefield +from openforcefield.typing.engines.smirnoff import ForceField +forcefield = ForceField('Frosst_AlkEthOH_parmAtFrosst.offxml') + +# Compare energies +from openforcefield.tests.utils import compare_amber_smirnoff +# We ignore the charges as they are not included in the force field. +# TODO: Reactivate this check when we'll be able to load charges from the file. +energies = compare_amber_smirnoff(prmtop_filepath, inpcrd_filepath, + forcefield, molecule, + ignore_charges=True) + +# Pretty-print the result. +from pprint import pprint +pprint(energies) diff --git a/examples/deprecated/SMIRNOFF_comparison/compare_set_energies.py b/examples/deprecated/SMIRNOFF_comparison/compare_set_energies.py new file mode 100644 index 000000000..a2470c4b8 --- /dev/null +++ b/examples/deprecated/SMIRNOFF_comparison/compare_set_energies.py @@ -0,0 +1,58 @@ +#!/usr/bin/env python + +""" +Cross-check energies of molecules from AlkEthOH set using SMIRNOFF xml file +versus energies from AMBER .prmtop and .crd files (parm@frosst params). +""" + +import os +import glob + +# datapath = './AlkEthOH_tripos/AlkEthOH_chain_filt1' +# datapath = './AlkEthOH_tripos/AlkEthOH_rings_filt1' +datapath = './AlkEthOH_tripos/AlkEthOH_test_filt1' + +# Check if we have this data file; if not we have to extract the archive. +if not os.path.isdir(datapath): + print("Extracting archived molecule files.") + # Extract the AlkEthOH dataset shipped with the toolkit in data/molecules/ in the working directory. + from openforcefield.tests.utils import get_data_filename + tarfile_path = os.path.join(get_data_filename('molecules'), 'AlkEthOH_tripos.tar.gz') + import tarfile + with tarfile.open(tarfile_path, 'r:gz') as tar: + tar.extractall() + +#Obtain list of molecules +mol_filepaths = glob.glob(datapath+'/*tripos.mol2') +mol_filepaths = [fnm for fnm in mol_filepaths if not 'c1302' in fnm] # Skip water. + +print('Found {} files to test'.format(len(mol_filepaths))) + +# Load forcefield +from openforcefield.typing.engines.smirnoff import ForceField +forcefield = ForceField('Frosst_AlkEthOH_parmAtFrosst.offxml') + +from openforcefield.topology import Molecule +for mol_idx, mol_filepath in enumerate(mol_filepaths): + # Load molecule. + molecule = Molecule.from_file(mol_filepath) + + molname = os.path.basename(mol_filepath).replace('_tripos.mol2','') + print("Comparing {} ({}/{})...".format(molname, mol_idx+1, len(mol_filepaths))) + + prmtop_filepath = os.path.join(datapath, molname+'.top') + inpcrd_filepath = os.path.join(datapath, molname+'.crd') + + # Compare energies + from openforcefield.tests.utils import compare_amber_smirnoff + from openforcefield.tests.utils import FailedParameterComparisonError, FailedEnergyComparisonError + try: + # We ignore the charges as they are not included in the force field. + # TODO: Reactivate this check when we'll be able to load charges from the file. + energies = compare_amber_smirnoff(prmtop_filepath, inpcrd_filepath, + forcefield, molecule, + ignore_charges=True) + except FailedParameterComparisonError as e: + print(e) + except FailedEnergyComparisonError as e: + print(e) diff --git a/examples/chemicalEnvironments/AlkEthOH_dvrs1.oeb b/examples/deprecated/chemicalEnvironments/AlkEthOH_dvrs1.oeb similarity index 100% rename from examples/chemicalEnvironments/AlkEthOH_dvrs1.oeb rename to examples/deprecated/chemicalEnvironments/AlkEthOH_dvrs1.oeb diff --git a/examples/chemicalEnvironments/README.md b/examples/deprecated/chemicalEnvironments/README.md similarity index 74% rename from examples/chemicalEnvironments/README.md rename to examples/deprecated/chemicalEnvironments/README.md index 3af284a0c..eb36f2816 100644 --- a/examples/chemicalEnvironments/README.md +++ b/examples/deprecated/chemicalEnvironments/README.md @@ -1,15 +1,20 @@ -# Chemical Environment usage examples +## `ChemicalEnvironment` usage examples -This directory shows how to use Chemical Environments. First we will outline how they are structured with some example code snippets. -For a more hands on tutorial you can look at the jupyter notebook `using_environments.py`. +Here, we show how to use `ChemicalEnvironments` in detail. +First, we will outline how they are structured with some example code snippets. -### Initiating ChemicalEnvironments +### Demo jupyter notebook -All Chemical Environments can be initated using SMIRKS strings. -If a `ChemicalEnvironment` is initiated with no SMIRKS pattern, it is an empty structure. -However, there are 5 subtypes of `ChemicalEnvironments` that match the types of parameters found in the SMIRNOFF format. -If they are initiated with no SMIRKS pattern, their structure matches a generic for that parameter type, for example `[*:1]~[*:2]` for a bond (that is any atom connected to any other atom by any bond). -The 5 subtypes are listed below with their expected number of indexed atoms and the corresponding SMIRKS structure: +The [using_environments.ipynb](https://github.com/openforcefield/openforcefield/blob/master/examples/chemicalEnvironments/using_environments.ipynb) jupyter notebook should be your first stop for interactively understanding and using `ChemicalEnvironment`. +It includes all of the examples shown above and more in a jupyter notebook so you can play with the different method options. + +### Creating a `ChemicalEnvironment` + +A `ChemicalEnvironment` can be creatied using SMIRKS strings. +If a `ChemicalEnvironment` is created with no SMIRKS pattern, it is an empty structure. +There are five subtypes of `ChemicalEnvironment` that match the types of parameters found in the SMIRNOFF format. +If they are created with no SMIRKS pattern, their structure matches a generic for that parameter type---for example, `[*:1]~[*:2]` for a bond (that is any atom connected to any other atom by any bond). +The five subtypes are listed below with their expected number of indexed atoms and the corresponding SMIRKS structure: * `AtomChemicalEnvironment` - expects 1 indexed atom @@ -111,9 +116,10 @@ print("Updated SMIRKS string: %s" % angle.asSMIRKS()) # print("Updated SMIRKS string: %s" % angle.asSMIRKS()) ``` -### Other ChemicalEnvironment Methods +### Other `ChemicalEnvironment` Methods + +Selecting atoms and bonds -0. Selecting atoms and bonds ```python # when given an integer selectAtom or selectBond returns that atom or bond with that index # otherwise it returns a random atom or bond that meets the specified requirement @@ -123,7 +129,8 @@ atom4 = angle.selectAtom(4) # None, angle has 3 indexed atoms beta_bond = angle.selectBond('beta') # bond between an alpha and beta atom ``` -1. Getting information about an atom or bond in an environment (i.e. isAlpha returns a boolean) +Getting information about an atom or bond in an environment (i.e. `isAlpha()` returns a boolean) + ```python # Check if the alpha atom above is any of the following angle.isIndexed(alpha) # False @@ -132,7 +139,9 @@ angle.isAlpha(alpha) # True angle.isBeta(alpha) # False # NOTE - These methods can take an atom or a bond as an argument ``` -2. Get atoms or bonds in each type of position, for example getIndexedAtoms or getAlphaBonds + +Get atoms or bonds in each type of position, for example `getIndexedAtoms()` or `getAlphaBonds()` + ```python # We will print the SMIRKS for each indexed atom: all_atoms = angle.getAtoms() @@ -142,20 +151,25 @@ alpha_list = angle.getAlphaAtoms() beta_list = angle.getBetaAtoms # Note - Atoms can be replaced with Bonds in each of the above examples ``` -3. Report the minimum order of a bond with Bond.getOrder -SMIRKS strings can match multiple types of bonds, for example `"[*]-,;,=[*]"` describes any two atoms -connected by a single, aromatic, or double bond. The getOrder function returns the minimum order for the bond, 1, in this case. + +Report the minimum order of a bond with `Bond.getOrder`. +SMIRKS strings can match multiple types of bonds, for example `"[*]-,;,=[*]"` describes any two atoms connected by a single, aromatic, or double bond. The getOrder function returns the minimum order for the bond, 1, in this case. + ```python bond1 = angle.selectBond(1) bond1.getOrder() # returns 1 ``` -4. Report the valence and bond order around an atom can be reported with getValence and getBondORder + +Report the valence and bond order around an atom can be reported with `getValence()` and `getBondOrder()`. + ```python atom3 = angle.selectAtom(3) angle.getValence(atom3) # number of neighbors atom 3 has angle.getBondOrder(atom3) # total bond order around atom 3 ``` -5. Get a bond between two atoms (or determine if the atoms are bonded) with getBond(atom1, atom2) + +Get a bond between two atoms (or determine if the atoms are bonded) with `getBond(atom1, atom2)`: + ```python # Check for bonds between each pair of indexed atoms A = 1 @@ -164,29 +178,26 @@ atomA = angle.selectAtom(A) atomB = angle.selectAtom(B) bondAB = angle.getBond(atomA, atomB) # returns None if no bond found ``` -6. Get atoms bound to a specified atom with getNeighbors + +Get atoms bound to a specified atom with `getNeighbors()`: + ```python # get the neighbors for each indexed atom atomA = angle.selectAtom(A) neighbor_list = angle.getNeighbors(atomA) ``` -### Not yet covered +### Aspects of SMIRKS not yet implemented -Types of SMIRKS patterns that cannot be read into `ChemicalEnvironments`: +Types of SMIRKS patterns that cannot be read into `ChemicalEnvironment`: -* SMIRKS for multiple molecules. The symbol `'.'` can be used in SMIRKS to denote fragments in separate molecules, `ChemicalEnvironments` will fail if the given pattern has multiple molecules. -* Similarly, SMIRKS for reactions are not parseable into `ChemicalEnvironments`. These are denoted with `'>>'` to indicate the fragment changing in a reaction. - - -### `using_environments.ipynb` - -This notebook should be your first stop for interactively understanding and using `ChemicalEnvironments`. -It includes all of the examples shown above and more in a jupyter notebook so you can play with the different method options. +* SMIRKS for multiple molecules. The symbol `'.'` can be used in SMIRKS to denote fragments in separate molecules, `ChemicalEnvironment` will fail if the given pattern has multiple molecules. +* Similarly, SMIRKS for reactions are not parseable into `ChemicalEnvironment`. These are denoted with `'>>'` to indicate the fragment changing in a reaction. -### Making moves with Chemical Environments +### Making Monte Carlo proposals in chemical perception space with `ChemicalEnvironment` -Here our goal is to show how to use Chemical Environments to make "moves" in chemical perception space. First a list of weighted moves were generated and saved to output files. Then, a seconds notebook is used to make these moves in chemical space. +Here, our goal is to show how to use `ChemicalEnvironment` to make "moves" in chemical perception space. +First, a list of weighted moves were generated and saved to output files. Then, a seconds notebook is used to make these moves in chemical space. These notebooks were generated in the early planning stages for smirky, the first attempt at sampling chemical perception for SMIRNOFF parameter types. diff --git a/examples/chemicalEnvironments/create_move_types_and_weights.ipynb b/examples/deprecated/chemicalEnvironments/create_move_types_and_weights.ipynb similarity index 97% rename from examples/chemicalEnvironments/create_move_types_and_weights.ipynb rename to examples/deprecated/chemicalEnvironments/create_move_types_and_weights.ipynb index 126255e84..af5799d1d 100644 --- a/examples/chemicalEnvironments/create_move_types_and_weights.ipynb +++ b/examples/deprecated/chemicalEnvironments/create_move_types_and_weights.ipynb @@ -20,12 +20,9 @@ { "cell_type": "code", "execution_count": 1, - "metadata": { - "collapsed": false - }, + "metadata": {}, "outputs": [], "source": [ - "#!/usr/bin/env python\n", "# generic scientific/ipython header\n", "from __future__ import print_function\n", "from __future__ import division\n", @@ -104,9 +101,7 @@ { "cell_type": "code", "execution_count": 4, - "metadata": { - "collapsed": false - }, + "metadata": {}, "outputs": [], "source": [ "# make 'moves with weights' dictionary for vdW\n", @@ -179,9 +174,7 @@ { "cell_type": "code", "execution_count": 9, - "metadata": { - "collapsed": false - }, + "metadata": {}, "outputs": [ { "name": "stdout", @@ -211,9 +204,7 @@ { "cell_type": "code", "execution_count": 10, - "metadata": { - "collapsed": false - }, + "metadata": {}, "outputs": [], "source": [ "# 'VdW', 'Bond', 'Angle', 'Torsion', 'Improper'\n", @@ -256,9 +247,7 @@ { "cell_type": "code", "execution_count": 12, - "metadata": { - "collapsed": false - }, + "metadata": {}, "outputs": [ { "name": "stdout", @@ -272,6 +261,7 @@ } ], "source": [ + "# NBVAL_SKIP\n", "movesWithWeightsTest = movesWithWeightsMaster['Torsion']\n", "key = np.random.choice( movesWithWeightsTest.keys() )\n", "nSamples = 10000\n", @@ -320,9 +310,7 @@ { "cell_type": "code", "execution_count": 14, - "metadata": { - "collapsed": false - }, + "metadata": {}, "outputs": [], "source": [ "def GenerateMoveTree( parameterType):\n", @@ -366,9 +354,7 @@ { "cell_type": "code", "execution_count": 15, - "metadata": { - "collapsed": false - }, + "metadata": {}, "outputs": [ { "name": "stdout", @@ -407,9 +393,7 @@ { "cell_type": "code", "execution_count": 16, - "metadata": { - "collapsed": false - }, + "metadata": {}, "outputs": [], "source": [ "parameterType = 'Torsion'\n", @@ -451,9 +435,9 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.6.0" + "version": "3.6.8" } }, "nbformat": 4, - "nbformat_minor": 0 + "nbformat_minor": 1 } diff --git a/examples/chemicalEnvironments/moveTrees.uniq.Angle.txt b/examples/deprecated/chemicalEnvironments/moveTrees.uniq.Angle.txt similarity index 100% rename from examples/chemicalEnvironments/moveTrees.uniq.Angle.txt rename to examples/deprecated/chemicalEnvironments/moveTrees.uniq.Angle.txt diff --git a/examples/chemicalEnvironments/moveTrees.uniq.Bond.txt b/examples/deprecated/chemicalEnvironments/moveTrees.uniq.Bond.txt similarity index 100% rename from examples/chemicalEnvironments/moveTrees.uniq.Bond.txt rename to examples/deprecated/chemicalEnvironments/moveTrees.uniq.Bond.txt diff --git a/examples/chemicalEnvironments/moveTrees.uniq.Improper.txt b/examples/deprecated/chemicalEnvironments/moveTrees.uniq.Improper.txt similarity index 100% rename from examples/chemicalEnvironments/moveTrees.uniq.Improper.txt rename to examples/deprecated/chemicalEnvironments/moveTrees.uniq.Improper.txt diff --git a/examples/chemicalEnvironments/moveTrees.uniq.Torsion.txt b/examples/deprecated/chemicalEnvironments/moveTrees.uniq.Torsion.txt similarity index 100% rename from examples/chemicalEnvironments/moveTrees.uniq.Torsion.txt rename to examples/deprecated/chemicalEnvironments/moveTrees.uniq.Torsion.txt diff --git a/examples/chemicalEnvironments/moveTrees.uniq.VdW.txt b/examples/deprecated/chemicalEnvironments/moveTrees.uniq.VdW.txt similarity index 100% rename from examples/chemicalEnvironments/moveTrees.uniq.VdW.txt rename to examples/deprecated/chemicalEnvironments/moveTrees.uniq.VdW.txt diff --git a/examples/chemicalEnvironments/moves_using_environments.ipynb b/examples/deprecated/chemicalEnvironments/moves_using_environments.ipynb similarity index 100% rename from examples/chemicalEnvironments/moves_using_environments.ipynb rename to examples/deprecated/chemicalEnvironments/moves_using_environments.ipynb diff --git a/examples/chemicalEnvironments/using_environments.ipynb b/examples/deprecated/chemicalEnvironments/using_environments.ipynb similarity index 97% rename from examples/chemicalEnvironments/using_environments.ipynb rename to examples/deprecated/chemicalEnvironments/using_environments.ipynb index 4fef686de..de1247aad 100644 --- a/examples/chemicalEnvironments/using_environments.ipynb +++ b/examples/deprecated/chemicalEnvironments/using_environments.ipynb @@ -34,9 +34,7 @@ { "cell_type": "code", "execution_count": 1, - "metadata": { - "collapsed": false - }, + "metadata": {}, "outputs": [], "source": [ "# import necessary functions\n", @@ -79,7 +77,6 @@ "cell_type": "code", "execution_count": 2, "metadata": { - "collapsed": false, "scrolled": true }, "outputs": [ @@ -97,6 +94,7 @@ } ], "source": [ + "# NBVAL_SKIP\n", "Env = env.ChemicalEnvironment()\n", "atomEnv = env.AtomChemicalEnvironment()\n", "bondEnv = env.BondChemicalEnvironment()\n", @@ -132,7 +130,6 @@ "cell_type": "code", "execution_count": 3, "metadata": { - "collapsed": false, "scrolled": false }, "outputs": [ @@ -172,6 +169,7 @@ } ], "source": [ + "# NBVAL_SKIP\n", "# define the two replacements strings\n", "replacements = [ ('ewg1', '[#7!-1,#8!-1,#16!-1,#9,#17,#35,#53]'),\n", " ('ewg2', '[#7!-1,#8,#16]')]\n", @@ -261,9 +259,7 @@ { "cell_type": "code", "execution_count": 4, - "metadata": { - "collapsed": false - }, + "metadata": {}, "outputs": [ { "name": "stdout", @@ -308,9 +304,7 @@ }, { "cell_type": "markdown", - "metadata": { - "collapsed": false - }, + "metadata": {}, "source": [ "## Changing ORtypes and ANDtypes\n", "\n", @@ -329,9 +323,7 @@ { "cell_type": "code", "execution_count": 5, - "metadata": { - "collapsed": false - }, + "metadata": {}, "outputs": [ { "name": "stdout", @@ -397,9 +389,7 @@ { "cell_type": "code", "execution_count": 6, - "metadata": { - "collapsed": false - }, + "metadata": {}, "outputs": [ { "name": "stdout", @@ -452,9 +442,7 @@ { "cell_type": "code", "execution_count": 7, - "metadata": { - "collapsed": false - }, + "metadata": {}, "outputs": [ { "name": "stdout", @@ -499,9 +487,7 @@ { "cell_type": "code", "execution_count": 8, - "metadata": { - "collapsed": false - }, + "metadata": {}, "outputs": [ { "name": "stdout", @@ -529,9 +515,7 @@ { "cell_type": "code", "execution_count": 9, - "metadata": { - "collapsed": false - }, + "metadata": {}, "outputs": [ { "name": "stdout", @@ -567,9 +551,7 @@ { "cell_type": "code", "execution_count": 10, - "metadata": { - "collapsed": false - }, + "metadata": {}, "outputs": [ { "name": "stdout", @@ -588,9 +570,7 @@ { "cell_type": "code", "execution_count": 11, - "metadata": { - "collapsed": false - }, + "metadata": {}, "outputs": [ { "name": "stdout", @@ -611,9 +591,7 @@ { "cell_type": "code", "execution_count": 13, - "metadata": { - "collapsed": false - }, + "metadata": {}, "outputs": [ { "name": "stdout", @@ -644,9 +622,7 @@ { "cell_type": "code", "execution_count": 17, - "metadata": { - "collapsed": false - }, + "metadata": {}, "outputs": [ { "name": "stdout", @@ -703,9 +679,9 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.6.0" + "version": "3.6.8" } }, "nbformat": 4, - "nbformat_minor": 0 + "nbformat_minor": 1 } diff --git a/examples/host_guest_simulation/OA.mol2 b/examples/deprecated/host_guest_simulation/OA.mol2 similarity index 100% rename from examples/host_guest_simulation/OA.mol2 rename to examples/deprecated/host_guest_simulation/OA.mol2 diff --git a/examples/deprecated/host_guest_simulation/README.md b/examples/deprecated/host_guest_simulation/README.md new file mode 100644 index 000000000..c35edda4a --- /dev/null +++ b/examples/deprecated/host_guest_simulation/README.md @@ -0,0 +1,16 @@ +## Setting up a host-guest simulation using SMIRNOFF parameters + +This example illustrates how easy it is to set up rather nontrivial simulations with SMIRNOFF force fields. +In this case, we will begin with a guest SMILES string and a 3D structure of a host, dock the host into the guest, solvate, and proceed to simulations. + +### Authorship + +This example was provided by David Mobley (UCI) + +### Source materials +- Based in part on a host-guest [docking Jupyter notebook](https://github.com/MobleyLab/SAMPL6/blob/master/host_guest/GenerateInputs.ipynb) I constructed for SAMPL6 + +### Example files +* [smirnoff_host_guest.ipynb](https://github.com/openforcefield/openforcefield/blob/master/examples/host_guest_simulation/smirnoff_host_guest.ipynb): Jupyter notebook illustrating setup of the host-guest system +* [hbonds.offxml](https://github.com/openforcefield/openforcefield/blob/master/examples/host_guest_simulation/hbonds.ffxml): Force field XML file for constraining hbonds (from https://github.com/MobleyLab/SMIRNOFF_paper_code/blob/master/scripts/hbonds.offxml, courtesy Andrea Rizzi) +* `OA.mol2`: mol2 file of Octa Acid with AM1-BCC charges, as distributed with SAMPL5 (where it was labeled `OAH.mol2`). Atom types converted from GAFF to SYBYL via Antechember. diff --git a/examples/host_guest_simulation/hbonds.ffxml b/examples/deprecated/host_guest_simulation/hbonds.ffxml similarity index 100% rename from examples/host_guest_simulation/hbonds.ffxml rename to examples/deprecated/host_guest_simulation/hbonds.ffxml diff --git a/examples/host_guest_simulation/smirnoff_host_guest.ipynb b/examples/deprecated/host_guest_simulation/smirnoff_host_guest.ipynb similarity index 98% rename from examples/host_guest_simulation/smirnoff_host_guest.ipynb rename to examples/deprecated/host_guest_simulation/smirnoff_host_guest.ipynb index 55b8eb7c4..e2e4eb159 100644 --- a/examples/host_guest_simulation/smirnoff_host_guest.ipynb +++ b/examples/deprecated/host_guest_simulation/smirnoff_host_guest.ipynb @@ -45,6 +45,7 @@ }, "outputs": [], "source": [ + "# NBVAL_SKIP\n", "from openeye import oechem # OpenEye Python toolkits\n", "import oenotebook as oenb\n", "# Check license\n", @@ -113,6 +114,7 @@ }, "outputs": [], "source": [ + "# NBVAL_SKIP\n", "# Create empty OEMol\n", "mol = oechem.OEMol()\n", "# Convert SMILES\n", @@ -139,6 +141,7 @@ }, "outputs": [], "source": [ + "# NBVAL_SKIP\n", "# Output host and guest files\n", "hostfile = os.path.join(datadir, 'host.mol2')\n", "guestfile = os.path.join(datadir, 'guest.mol2')\n", @@ -173,6 +176,7 @@ }, "outputs": [], "source": [ + "# NBVAL_SKIP\n", "# Read in host file\n", "ifile = oechem.oemolistream(hostfile)\n", "host = oechem.OEMol()\n", @@ -203,6 +207,7 @@ }, "outputs": [], "source": [ + "# NBVAL_SKIP\n", "#initialize omega for conformer generation\n", "omega = oeomega.OEOmega()\n", "omega.SetMaxConfs(100) #Generate up to 100 conformers since we'll use for docking\n", @@ -277,6 +282,7 @@ }, "outputs": [], "source": [ + "# NBVAL_SKIP\n", "# Import modules\n", "import nglview\n", "import mdtraj\n", @@ -317,6 +323,7 @@ }, "outputs": [], "source": [ + "# NBVAL_SKIP\n", "# Join OEMols into complex\n", "complex = host.CreateCopy()\n", "oechem.OEAddMols( complex, outmol)\n", @@ -411,6 +418,7 @@ }, "outputs": [], "source": [ + "# NBVAL_SKIP\n", "# Keep a list of OEMols of our components\n", "oemols = [] \n", "\n", @@ -454,9 +462,10 @@ }, "outputs": [], "source": [ + "# NBVAL_SKIP\n", "# Load force fields for small molecules (plus default ions), water, and (temporarily) hydrogen bonds.\n", "# TODO add HBonds constraint through createSystem when openforcefield#32 is implemented, alleviating need for constraints here\n", - "ff = ForceField('forcefield/smirnoff99Frosst.offxml', 'hbonds.offxml', 'forcefield/tip3p.offxml') \n", + "ff = ForceField('smirnoff99Frosst.offxml', 'hbonds.offxml', 'tip3p.offxml') \n", "\n", "# Set up system\n", "# This draws to some extent on Andrea Rizzi's code at https://github.com/MobleyLab/SMIRNOFF_paper_code/blob/master/scripts/create_input_files.py\n", @@ -490,6 +499,7 @@ }, "outputs": [], "source": [ + "# NBVAL_SKIP\n", "# Even though we're just going to minimize, we still have to set up an integrator, since a Simulation needs one\n", "integrator = openmm.VerletIntegrator(2.0*unit.femtoseconds)\n", "# Prep the Simulation using the parameterized system, the integrator, and the topology\n", @@ -525,6 +535,7 @@ }, "outputs": [], "source": [ + "# NBVAL_SKIP\n", "# Set up NetCDF reporter for storing trajectory; prep for Langevin dynamics\n", "from mdtraj.reporters import NetCDFReporter\n", "integrator = openmm.LangevinIntegrator(300*unit.kelvin, 1./unit.picosecond, 2.*unit.femtoseconds)\n", @@ -562,6 +573,7 @@ }, "outputs": [], "source": [ + "# NBVAL_SKIP\n", "# Load stored trajectory using MDTraj; the trajectory doesn't contain chemistry info so we also load a PDB\n", "traj= mdtraj.load(os.path.join(datadir, 'trajectory.nc'), top=os.path.join(datadir, 'complex_solvated.pdb'))\n", "\n", @@ -586,6 +598,7 @@ }, "outputs": [], "source": [ + "# NBVAL_SKIP\n", "# Save centered trajectory for viewing elsewhere\n", "traj.save_netcdf(os.path.join(datadir, 'trajectory_centered.nc'))" ] @@ -608,7 +621,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.6.2" + "version": "3.6.8" }, "toc": { "nav_menu": {}, diff --git a/examples/liquid_box/ETH-box.pdb b/examples/deprecated/liquid_box/ETH-box.pdb similarity index 100% rename from examples/liquid_box/ETH-box.pdb rename to examples/deprecated/liquid_box/ETH-box.pdb diff --git a/examples/liquid_box/ETH.mol2 b/examples/deprecated/liquid_box/ETH.mol2 similarity index 100% rename from examples/liquid_box/ETH.mol2 rename to examples/deprecated/liquid_box/ETH.mol2 diff --git a/examples/liquid_box/create_mol2_pdb/README.md b/examples/deprecated/liquid_box/create_mol2_pdb/README.md similarity index 100% rename from examples/liquid_box/create_mol2_pdb/README.md rename to examples/deprecated/liquid_box/create_mol2_pdb/README.md diff --git a/examples/liquid_box/create_mol2_pdb/create_mol2_pdb.py b/examples/deprecated/liquid_box/create_mol2_pdb/create_mol2_pdb.py similarity index 100% rename from examples/liquid_box/create_mol2_pdb/create_mol2_pdb.py rename to examples/deprecated/liquid_box/create_mol2_pdb/create_mol2_pdb.py diff --git a/examples/liquid_box/create_mol2_pdb/input.smi b/examples/deprecated/liquid_box/create_mol2_pdb/input.smi similarity index 100% rename from examples/liquid_box/create_mol2_pdb/input.smi rename to examples/deprecated/liquid_box/create_mol2_pdb/input.smi diff --git a/examples/liquid_box/openff_simulation.py b/examples/deprecated/liquid_box/openff_simulation.py similarity index 100% rename from examples/liquid_box/openff_simulation.py rename to examples/deprecated/liquid_box/openff_simulation.py diff --git a/examples/deprecated/mixedFF_structure/README.md b/examples/deprecated/mixedFF_structure/README.md new file mode 100644 index 000000000..6c3725497 --- /dev/null +++ b/examples/deprecated/mixedFF_structure/README.md @@ -0,0 +1,45 @@ +## Combining a SMIRNOFF parameterized small molecule with an AMBER parameterized protein using ParmEd + +This example illustrates how the [ParmEd](http://parmed.github.io/ParmEd/html/index.html) utility can be used to merge a small molecule parameterized by SMIRNOFF with a traditionally parameterized protein (or other biopolymer) to create a fully parameterized protein-ligand system. + +The essential idea is to first create a ParmEd structure from the SMIRNOFF parameterized small molecule +```python +# Load the small molecule +from openforcefield.utils import get_data_filename +ligand_filename = get_data_filename('molecules/toluene.mol2') +molecule = Molecule.from_file(ligand_filename) + +# Load the smirnoff99Frosst force field +from openforcefield.typing.engines import smirnoff +forcefield = smirnoff.ForceField('smirnoff99Frosst.offxml') + +# Create a ParmEd structure for the molecule +molecule_structure = forcefield.create_parmed_structure(topology=molecule.to_topology(), positions=molecule.positions) +``` +Next, a ParmEd structure is created for the protein (parameterized with AMBER using the OpenMM `app.ForceField` implementation): +```python +# Load the protein topology +from openforcefield.utils import generate_protein_structure +protein_pdb_filename = get_data_filename('proteins/T4-protein.pdb') +protein_pdbfile = app.PDBFile(protein_pdb_filename) + +# Load the AMBER protein force field, along with a solvent force field +from simtk.openmm import app +protein_forcefield = 'amber99sbildn.xml' +solvent_forcefield = 'tip3p.xml' +forcefield = app.ForceField(protein_forcefield, solvent_forcefield) + +# Parameterize the protein +# TODO: Can we create an OpenMM ffxml file for the ligand? +protein_system = forcefield.createSystem(proteinpdb.topology) + +# Create a ParmEd Structure for the protein +protein_structure = parmed.openmm.load_topology(proteinpdb.topology, + protein_system, + xyz=proteinpdb.positions) +``` +Finally, the two ParmEd `Structure` objects can be combined by concatenation: +```python +# Combine the ParmEd Structure objects to produce a fully parameterized complex +complex_structure = protein_structure + molecule_structure +``` diff --git a/examples/deprecated/mixedFF_structure/generate_mixedFF_complex.py b/examples/deprecated/mixedFF_structure/generate_mixedFF_complex.py new file mode 100644 index 000000000..8fa15ae50 --- /dev/null +++ b/examples/deprecated/mixedFF_structure/generate_mixedFF_complex.py @@ -0,0 +1,57 @@ +#!/bin/env python + +""" +Illustrate how to combine a SMIRNOFF parameterized small molecule with an AMBER parameterized protein using ParmEd. + +""" + +# +# Load and parameterize the small molecule +# + +# Load the small molecule +from openforcefield.utils import get_data_filename +ligand_filename = get_data_filename('molecules/toluene.mol2') +molecule = Molecule.from_file(ligand_filename) + +# Load the smirnoff99Frosst force field +from openforcefield.typing.engines import smirnoff +forcefield = smirnoff.ForceField('smirnoff99Frosst.offxml') + +# Create a ParmEd structure for the molecule +molecule_structure = forcefield.create_parmed_structure(topology=molecule.to_topology(), positions=molecule.positions) +print('Molecule:', molecule_structure) + +# +# Load and parameterize the protein +# + +# Load the protein topology +from openforcefield.utils import generate_protein_structure +protein_pdb_filename = get_data_filename('proteins/T4-protein.pdb') +protein_pdbfile = app.PDBFile(protein_pdb_filename) + +# Load the AMBER protein force field, along with a solvent force field +from simtk.openmm import app +protein_forcefield = 'amber99sbildn.xml' +solvent_forcefield = 'tip3p.xml' +forcefield = app.ForceField(protein_forcefield, solvent_forcefield) + +# Parameterize the protein +protein_system = forcefield.createSystem(proteinpdb.topology) + +# Create a ParmEd Structure for the protein +protein_structure = parmed.openmm.load_topology(proteinpdb.topology, + protein_system, + xyz=proteinpdb.positions) +print('Protein:', protein_structure) + +# Combine the ParmEd Structure objects to produce a fully parameterized complex +# that can now be exported to AMBER, CHARMM, OpenMM, and other packages +# Note that the addition should always add the small molecule second so the box vectors if the first item (the protein) are to be preserved +complex_structure = protein_structure + molecule_structure +print('Complex:', complex_structure) + +# TODO: How can we add solvent while ensuring the ligand doesn't overlap with solvent molecules? +# TODO: Can we have SMIRNOFF ForceField create an OpenMM ffxml file for the ligand, and then use the OpenMM pipeline? +# TODO: Or can OpenMM just use dummy parameters? diff --git a/examples/partial_bondorder/Frosst_AlkEthOH_extracarbons.ffxml b/examples/deprecated/partial_bondorder/Frosst_AlkEthOH_extracarbons.ffxml similarity index 84% rename from examples/partial_bondorder/Frosst_AlkEthOH_extracarbons.ffxml rename to examples/deprecated/partial_bondorder/Frosst_AlkEthOH_extracarbons.ffxml index c765fdc5b..927d51538 100644 --- a/examples/partial_bondorder/Frosst_AlkEthOH_extracarbons.ffxml +++ b/examples/deprecated/partial_bondorder/Frosst_AlkEthOH_extracarbons.ffxml @@ -1,27 +1,27 @@ - + -Date: Sept 2, 2016 +2016-09-02 C. I. Bayly, OpenEye Scientific Software and David Mobley, UCI - + - - - + + + - + @@ -31,8 +31,8 @@ - - + + @@ -46,14 +46,16 @@ - - + + - + + + - + - + @@ -66,6 +68,6 @@ - + diff --git a/examples/deprecated/partial_bondorder/README.md b/examples/deprecated/partial_bondorder/README.md new file mode 100644 index 000000000..028c1e23b --- /dev/null +++ b/examples/deprecated/partial_bondorder/README.md @@ -0,0 +1,15 @@ +## Using partial bond orders + +In this example, we demonstrate how a SMIRNOFF force field can use partial bond order information to assign bond parameters relevant for benzene as well as singly and doubly-bonded trivalent carbon, all with a single bond entry. + +The file `Frosst_AlkEthOH_extracarbons.offxml` is a SMIRNOFF FFXML file adding extra carbon parameters to cover benzene (adapted from work by Christopher Bayly) and uses partial bond orders to compress the `[#6X3]-[#6X3]` , `[#6X3]:[#6X3]` , and `[#6X3]=[#6X3]` bond parameters to a single line. + +The `` section contains +```XML + + ... + + + +``` +The jupyter notebook [test_partialbondorder.ipynb](https://github.com/openforcefield/openforcefield/blob/master/examples/partial_bondorder/test_partialbondorder.ipynb) illustrates the application of these parameters to benzene, and inspection of the resulting bonded parameters. diff --git a/examples/partial_bondorder/test_partialbondorder.ipynb b/examples/deprecated/partial_bondorder/test_partialbondorder.ipynb similarity index 99% rename from examples/partial_bondorder/test_partialbondorder.ipynb rename to examples/deprecated/partial_bondorder/test_partialbondorder.ipynb index b977f05c8..5e26fb9ee 100644 --- a/examples/partial_bondorder/test_partialbondorder.ipynb +++ b/examples/deprecated/partial_bondorder/test_partialbondorder.ipynb @@ -30,6 +30,7 @@ "metadata": {}, "outputs": [], "source": [ + "# NBVAL_SKIP\n", "# Load our forcefield from this directory. Use of partial bond orders here means there is only one [#6X3]~[#6X3] \n", "# bond parameter line rather than three which otherwise would be required\n", "ffxml = 'Frosst_AlkEthOH_extracarbons.offxml'\n", @@ -133,6 +134,7 @@ } ], "source": [ + "# NBVAL_SKIP\n", "topology = generateTopologyFromOEMol(mol)\n", "system = ff.createSystem(topology, [mol], chargeMethod = 'OECharges_AM1BCCSym', verbose = True)" ] @@ -163,7 +165,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.5.3" + "version": "3.6.8" } }, "nbformat": 4, diff --git a/examples/deprecated/rdkit_openeye_comparison/compare_rdk_oe_mol_loading.ipynb b/examples/deprecated/rdkit_openeye_comparison/compare_rdk_oe_mol_loading.ipynb new file mode 100644 index 000000000..1aee851f1 --- /dev/null +++ b/examples/deprecated/rdkit_openeye_comparison/compare_rdk_oe_mol_loading.ipynb @@ -0,0 +1,718 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Jeff's initial writeup -- 2019_01_21\n", + "## Comparing molecule loading using RDKit and OpenEye\n", + "\n", + "It's really important that both RDKitToolkitWrapper and OpenEyeToolkitWrapper load the same file to equivalent OFFMol objects. If the ToolkitWrappers don't create the same OFFMol from a single file/external molecule representation, it's possible that the OpenForceField toolkit will assign the same molecule different parameters depending on whether OE or RDK is running on the backend(1). This notebook is designed to help us see which molecule formats can be reliably loaded using both toolkits.\n", + "\n", + "\n", + "The first test that is performed is loading from 3D. We have OpenEye load `MiniDrugBank_tripos.mol2`. RDKit can not load mol2, but can load SDF, so I've used openbabel(2) to convert `MiniDrugBank_tripos.mol2` to SDF (`MiniDrugBank.sdf`), and then we have RDKit load that.\n", + "\n", + "### How do we compare whether two OFFMols are equivalent?\n", + "\n", + "This is, surprisingly, an unresolved question. \"Equivalent\" for our purposes means \"would have the same SMIRKS-based parameters applied, for any valid SMIRKS\". Since we don't have an `offxml` file containing parameters for all valid SMIRKS (because there are infinity valid SMIRKS, and because we'd also need an infinitely large molecule test set to contain representatives of all those infinity substructures), I'd like to find some sort of test other than SMIRKS matching that will answer this question. \n", + "\n", + "This notebook uses three comparison methods:\n", + "\n", + "\n", + "1. **graph isomorphism**: Convert the molecules to NetworkX graphs where nodes are atoms (described by element, is_aromatic, stereochemistry) and the edges are bonds (described by order, is_aromatic, stereochemistry). Then test to see if the graphs are isomorphic. \n", + "2. **SMILES comparison using OpenEye**: Convert each OFFMol to an OEMol, and then write them to canonical, isomeric, explicit hydrogen SMILES(3). Test for string equality.\n", + "3. **SMILES comparison using RDKit**: Convert each OFFMol to an RDMol, and then write them to canonical, isomeric, explicit hydrogen SMILES. Test for string equality.\n", + "\n", + "_As a note for future efforts, it's possible that, since each SMILES is also a valid SMIRKS, we could test for equality between OFFMol_1 and OFFMol_2 by seeing if OFFMol_1's SMILES is found in a SMIRKS substructure search of OFFMol_2, and vice versa._\n", + "\n", + "Each of these has some weaknesses. \n", + "* Graph isomorphism may be too strict -- eg. a toolkit may mess with the kekule structure around aromatic systems, selecting different resonance forms of bond networks. This would result in a chemically equivalent structure that fails an isomorphism test involving bond orders.\n", + "* SMILES mismatches are hard to debug. Are the original OFFMols really meaningfully different? Or is our `to_rdkit`. or `to_openeye` function not implemented correctly? Or is the mismatch due to some strange toolkit quirk or quiet sanitization that goes on?\n", + "\n", + "\n", + "### What if RDK and OE get different representations when loading from 3D?\n", + "\n", + "This isn't the end of the world. We'd just remove SDF from RDKit's `ALLOWED_READ_FORMATS` list(4). RDKit's main input method would then just be SMILES. But actually we should ensure that...\n", + "\n", + "### At a minimum, RDKit and OpenEye should be able to get the same OFFMol from the same SMILES\n", + "\n", + "My initial thought here is that we could have both toolkits load molecules from a SMILES database. \"I converted `MiniDrugBank_tripos.mol2` to SDF so RDKit could read it, why not convert it to SMILES too?\". \n", + "\n", + "**But conversion from 3D to SMILES requires either OpenEye or RDKit**, which relies on their 3D molecule interpretation being correct... which is what we're testing here in the first place!\n", + "\n", + "So, I couldn't think of a clear resolution to this problem. \n", + "\n", + "For background, Shuzhe Wang did some really good foundational work on toolkit molecule perception equivalence earlier in this project. Shuzhe's successful test of forcefield parameter application equivalence (5) used OE to load a test databse, convert the molecules to SMILES, and then had RDKit load those SMILES. It then tested whether the OE-loaded molecule and the RDKit-loaded molecule got identical forcefield parameters assigned. But this didn't test whether RDKit can load from 3D, just from SMILES. And not just any SMILES -- SMILES that came from OpenEye (including any sneaky sanitizaton that it could have done when loading from 3D). And since we didn't have a toolkit-independent molecule representation then (no OFFMols), he tested whether both molecules got the same forcefield parameters applied, which suffers from the \"our current SMIRKS may not be fine-grained enough to catch all meaningful molecule differences\" problem. \n", + "\n", + "Shuzhe's approach does highlight one way to get a test database of SMILES -- Load a 3D database using OpenEyeToolkitWrapper, then write all the resulting OFFMols to SMILES, and then have RDKitToolkitWrapper read all the SMILES and create OFFMols, then test whether both sets of OFFMols are identical.\n", + "\n", + "And, in case OE's molecule santiization is making us end up with unusually clean SMILES, we can do the same test in reverse -- that is, use RDKitToolkitWrapper to load a 3D SDF, write the resulting OFFMols to SMILES, and then have OpenEyeToolkitWrapper read the SMILES, and compare the resulting OFFMols.\n", + "\n", + "## What this notebook does\n", + "\n", + "#### This notebook creates four OFFMol test sets:\n", + "\n", + "1. **`oe_mols_from 3d`**: The results of calling `OFFMol.from_file('MiniDrugBank_tripos.mol2', toolkit_registry=an_oe_toolkit_wrapper)`.\n", + "\n", + "2. **`rdk_mols_from 3d`**: The results of calling `OFFMol.from_file('MiniDrugBank.sdf', toolkit_registry=a_rdk_toolkit_wrapper)`.\n", + "\n", + "3. **`rdk_mols_from_smiles_from_oe_mols_from_3d`**: The result of taking `oe_mols_from_3d`, converting them all to SMILES using OpenEyeToolkitWrapper, then reading SMILES to OFFMols using RDKitToolkitWrapper.\n", + "\n", + "4. **`oe_mols_from_smiles_from_rdk_mols_from_3d`**: The result of taking `rdk_mols_from_3d`, converting them all to SMILES using RDKitToolkitWrapper, then reading SMILES to OFFMols using OpenEyeToolkitWrapper.\n", + "\n", + "\n", + "\n", + "#### This notebook then compares the OFFMol test sets using three methods (same as above):\n", + "\n", + "1. Graph isomorphism\n", + "\n", + "2. OFFMol.to_smiles() using OpenEyeToolkitWrapper\n", + "\n", + "3. OFFMol.to_smiles using RDKitToolkitWrapper\n", + "\n", + "\n", + "## Results\n", + "\n", + "When the notebook is run using the current codebase, the important outputs are as follows:\n", + "\n", + "```\n", + "In comparing oe_mols_from_3d to rdk_mols_from_3d, I found 284 graph matches, 293 OE SMILES matches (26 comparisons errored), and 293 RDKit SMILES matches (7 comparisons errored) out of 346 molecules\n", + "```\n", + "\n", + "This is the core test that we wanted to do (loading the same molecules from 3D), and these are pretty good results. We pass the strictest test (graph isomorphism) for 284 out of 346 molecules. We see the the SMILES tests are a little more forgiving, both giving 293/346 successes.\n", + "\n", + "```\n", + "In comparing oe_mols_from_3d to rdk_mols_from_smiles_from_oe_mols_from_3d, I found 293 graph matches, 293 OE SMILES matches (26 comparisons errored), and 332 RDKit SMILES matches (0 comparisons errored) out of 365 molecules\n", + "```\n", + "\n", + "\n", + "\n", + "```\n", + "In comparing oe_mols_from_smiles_from_rdk_mols_from_3d to rdk_mols_from_3d, I found 310 graph matches, 219 OE SMILES matches (0 comparisons errored), and 304 RDKit SMILES matches (7 comparisons errored) out of 319 molecules\n", + "```\n", + "\n", + "\n", + "\n", + "## Conclusions\n", + "\n", + "Based on this test, we can expect identical parameterization between RDKit and OpenEye ToolkitWrappers at least 82% (284/346) of the time. The real number is likely to be higher, as the SMILES comparisons are more realistic measures of identity. Also, this limit assumes infinitely specific SMIRKS.\n", + "\n", + "Passing molecules **FROM** rdkit **TO** OE is troublesome largely because rdkit won't recognize stereo around trivalent nitrogens, whereas OE will. See discussion about \"how much stereochemistry info do we want specified\" here: https://github.com/openforcefield/openforcefield/issues/146\n", + "\n", + "\n", + "\n", + "\n", + "## Further work\n", + "\n", + "There is low-hanging fruit that will improve reliability.\n", + "\n", + "To continue debugging differences between OE and RDK, consider setting the \"verbose\" argument to `compare_mols_using_smiles` to True in the final cell of this workbook. Or, look at the molecule loading errors during dataset construction and add logic to catch those cases. \n", + "\n", + "\n", + "#### Footnotes\n", + "\n", + "\n", + "(1) Some molecule perception differences will be covered up by the fact that our SMIRKSes are somewhat coarse-grained currently (one SMIRKS can cover a lot of chemical space). But, this won't always be the case, as we may add finer-grained SMIRKS later. So, taking care of toolkit perception differences now can keep us from getting \"surprised\" in the future.\n", + "\n", + "(2)`conda list` --> `openbabel 1!2.4.0 py37_2 omnia`\n", + "\n", + "(3) `OFFMol.to_smiles()` actually operates by converting the OFFMol to an OEMol or RDMol (depending on which toolkit is available), and then uses the respective toolkit to create a SMILES. You can control which toolkit is used by instantialing an `openforcefield.utils.toolkits.OpenEyeToolkitWrapper` or `RDKitToolkitWrapper`, and passing it as the `toolkit_registry` argument to `to_smiles` (eg. `OFFMol.to_smiles(toolkit_registry=my_toolkit_wrapper)`)\n", + "\n", + "(4) If they really wanted to load from SDF using RDKit, a determined OFF toolkit user could just make an RDMol manually from SDK (`Chem.MolSupplierFromFile()` or something like that), and then run the molecules through `RDKitToolkitWrapper.from_rdkit()` to get OFFMol. However, this would put the burden of correct chemical perception _on them_.\n", + "\n", + "(5) https://github.com/openforcefield/openforcefield/blob/swang/examples/forcefield_modification/RDKitComparison.ipynb, search for `molecules =`" + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [], + "source": [ + "from openforcefield.utils.toolkits import RDKitToolkitWrapper, OpenEyeToolkitWrapper, UndefinedStereochemistryError\n", + "from openforcefield.utils import get_data_filename\n", + "import difflib\n", + "\n", + "OETKW = OpenEyeToolkitWrapper()\n", + "RDKTKW = RDKitToolkitWrapper()" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Load molecules from SDF using RDKit" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "DrugBank_2799 Sanitization error: Explicit valence for atom # 21 N, 4, is greater than permitted\n", + "DrugBank_5415 Sanitization error: Explicit valence for atom # 12 N, 4, is greater than permitted\n", + "DrugBank_3046 Sanitization error: Explicit valence for atom # 3 N, 4, is greater than permitted\n", + "DrugBank_472 Sanitization error: Explicit valence for atom # 16 N, 4, is greater than permitted\n", + "WARNING: RDMol has unspecified stereochemistry\n", + "RDMol name: DrugBank_5847\n", + "DrugBank_794 Sanitization error: Explicit valence for atom # 10 N, 4, is greater than permitted\n", + "DrugBank_3655 Sanitization error: Explicit valence for atom # 4 N, 4, is greater than permitted\n", + "DrugBank_3739 Sanitization error: Explicit valence for atom # 16 N, 4, is greater than permitted\n", + "Unable to check stereochemistry for DrugBank_3787. Original error:\n", + "Pre-condition Violation\n", + "\tStereo atoms should be specified before specifying CIS/TRANS bond stereochemistry\n", + "\tViolation occurred on line 285 in file Code/GraphMol/Bond.h\n", + "\tFailed Expression: what <= STEREOE || getStereoAtoms().size() == 2\n", + "\tRDKIT: 2018.09.1\n", + "\tBOOST: 1_65_1\n", + "\n", + "WARNING: RDMol has unspecified stereochemistry\n", + "RDMol name: DrugBank_3787\n", + "DrugBank_6353 Sanitization error: Explicit valence for atom # 18 N, 4, is greater than permitted\n", + "DrugBank_1570 Sanitization error: Explicit valence for atom # 6 N, 4, is greater than permitted\n", + "DrugBank_1594 Sanitization error: Explicit valence for atom # 5 N, 4, is greater than permitted\n", + "DrugBank_1659 Sanitization error: Explicit valence for atom # 28 N, 4, is greater than permitted\n", + "DrugBank_1661 Sanitization error: Explicit valence for atom # 7 N, 4, is greater than permitted\n", + "DrugBank_4346 Sanitization error: Explicit valence for atom # 35 O, 3, is greater than permitted\n", + "DrugBank_1802 Sanitization error: Explicit valence for atom # 36 N, 4, is greater than permitted\n", + "DrugBank_6947 Sanitization error: Explicit valence for atom # 6 N, 4, is greater than permitted\n", + "WARNING: RDMol has unspecified stereochemistry\n", + "RDMol name: DrugBank_4662\n", + "DrugBank_7049 Sanitization error: Explicit valence for atom # 11 N, 4, is greater than permitted\n", + "DrugBank_4865 Sanitization error: Explicit valence for atom # 10 N, 4, is greater than permitted\n", + "DrugBank_2465 Sanitization error: Explicit valence for atom # 7 N, 4, is greater than permitted\n", + "DrugBank_2467 Sanitization error: Explicit valence for atom # 19 N, 4, is greater than permitted\n", + "Unable to check stereochemistry for DrugBank_2684. Original error:\n", + "Pre-condition Violation\n", + "\tStereo atoms should be specified before specifying CIS/TRANS bond stereochemistry\n", + "\tViolation occurred on line 285 in file Code/GraphMol/Bond.h\n", + "\tFailed Expression: what <= STEREOE || getStereoAtoms().size() == 2\n", + "\tRDKIT: 2018.09.1\n", + "\tBOOST: 1_65_1\n", + "\n", + "WARNING: RDMol has unspecified stereochemistry\n", + "RDMol name: DrugBank_2684\n" + ] + } + ], + "source": [ + "from openforcefield.topology.molecule import Molecule\n", + "from rdkit import Chem\n", + "\n", + "\n", + "rdk_mols_from_3d = Molecule.from_file(get_data_filename('molecules/MiniDrugBank.sdf'), \n", + " toolkit_registry = RDKTKW,\n", + " file_format='sdf',\n", + " allow_undefined_stereo=True)\n", + "\n", + "# Known loading problems (numbers mean X: \"DrugBank_X\"):\n", + "# Pre-condition violations (\"Stereo atoms should be specified...\") for 3787 and 2684 are due to R-C=C=C-R motifs\n", + "# Sanitization errors: \n", + "# Nitro : 2799, 5415, 472, 794, 3739, 1570, 1802, 4865, 2465\n", + "# C#N : 3046, 3655, 1594, 6947, 2467\n", + "# C-N(=O)(C) : 6353\n", + "# Complicated aromatic situation with nitrogen?: 1659, 1661(?), 7049\n", + "# Unknown: 4346" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Load 3D molecules from Mol2 using OpenEye" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Unable to make OFFMol from OEMol: OEMol has unspecified stereochemistry. oemol.GetTitle(): DrugBank_2987\n", + "Problematic atoms are:\n", + "Atom atomic num: 7, name: N4, idx: 20, aromatic: False, chiral: True with bonds:\n", + "bond order: 1, chiral: False to atom atomic num: 6, name: C5, idx: 4, aromatic: True, chiral: False\n", + "bond order: 1, chiral: False to atom atomic num: 6, name: C17, idx: 16, aromatic: False, chiral: True\n", + "bond order: 1, chiral: False to atom atomic num: 8, name: O8, idx: 28, aromatic: False, chiral: False\n", + "\n", + "Unable to make OFFMol from OEMol: OEMol has unspecified stereochemistry. oemol.GetTitle(): DrugBank_3502\n", + "Problematic atoms are:\n", + "Atom atomic num: 7, name: N4, idx: 20, aromatic: False, chiral: True with bonds:\n", + "bond order: 1, chiral: False to atom atomic num: 6, name: C5, idx: 4, aromatic: True, chiral: False\n", + "bond order: 1, chiral: False to atom atomic num: 6, name: C17, idx: 16, aromatic: False, chiral: True\n", + "bond order: 1, chiral: False to atom atomic num: 8, name: O8, idx: 28, aromatic: False, chiral: False\n", + "\n", + "Unable to make OFFMol from OEMol: OEMol has unspecified stereochemistry. oemol.GetTitle(): DrugBank_4161\n", + "Problematic atoms are:\n", + "Atom atomic num: 7, name: N6, idx: 21, aromatic: False, chiral: True with bonds:\n", + "bond order: 1, chiral: False to atom atomic num: 6, name: C13, idx: 12, aromatic: True, chiral: False\n", + "bond order: 1, chiral: False to atom atomic num: 6, name: C16, idx: 15, aromatic: False, chiral: False\n", + "bond order: 1, chiral: False to atom atomic num: 7, name: N4, idx: 19, aromatic: False, chiral: False\n", + "\n", + "Unable to make OFFMol from OEMol: OEMol has unspecified stereochemistry. oemol.GetTitle(): DrugBank_4162\n", + "Problematic atoms are:\n", + "Atom atomic num: 7, name: N6, idx: 21, aromatic: False, chiral: True with bonds:\n", + "bond order: 1, chiral: False to atom atomic num: 6, name: C14, idx: 13, aromatic: True, chiral: False\n", + "bond order: 1, chiral: False to atom atomic num: 6, name: C16, idx: 15, aromatic: False, chiral: False\n", + "bond order: 1, chiral: False to atom atomic num: 7, name: N4, idx: 19, aromatic: False, chiral: False\n", + "\n", + "Unable to make OFFMol from OEMol: OEMol has unspecified stereochemistry. oemol.GetTitle(): DrugBank_6531\n", + "Problematic atoms are:\n", + "Atom atomic num: 7, name: N5, idx: 23, aromatic: False, chiral: True with bonds:\n", + "bond order: 1, chiral: False to atom atomic num: 6, name: C3, idx: 2, aromatic: True, chiral: False\n", + "bond order: 1, chiral: False to atom atomic num: 6, name: C15, idx: 14, aromatic: False, chiral: False\n", + "bond order: 1, chiral: False to atom atomic num: 6, name: C19, idx: 18, aromatic: False, chiral: False\n", + "\n", + "Unable to make OFFMol from OEMol: OEMol has unspecified stereochemistry. oemol.GetTitle(): DrugBank_1700\n", + "Problematic atoms are:\n", + "Atom atomic num: 7, name: N1, idx: 9, aromatic: False, chiral: True with bonds:\n", + "bond order: 1, chiral: False to atom atomic num: 6, name: C2, idx: 1, aromatic: False, chiral: False\n", + "bond order: 1, chiral: False to atom atomic num: 6, name: C4, idx: 3, aromatic: False, chiral: False\n", + "bond order: 1, chiral: False to atom atomic num: 6, name: C8, idx: 7, aromatic: False, chiral: True\n", + "\n" + ] + } + ], + "source": [ + "# NBVAL_SKIP\n", + "from openforcefield.topology import Molecule\n", + "\n", + "#molecules = Molecule.from_file(get_data_filename('molecules/MiniDrugBank.sdf'), \n", + "oe_mols_from_3d = Molecule.from_file(get_data_filename('molecules/MiniDrugBank_tripos.mol2'), \n", + " toolkit_registry = OETKW,\n", + " file_format='sdf',\n", + " allow_undefined_stereo=False)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Convert each OE-derived OFFMol to SMILES, and then use RDKitToolkitWrapper to read the SMILES." + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [], + "source": [ + "# NBVAL_SKIP\n", + "rdk_mols_from_smiles_from_oe_mols_from_3d = []\n", + "for oe_mol in oe_mols_from_3d:\n", + " if oe_mol is None:\n", + " continue\n", + " smiles = oe_mol.to_smiles(toolkit_registry=OETKW)\n", + " try:\n", + " new_mol = Molecule.from_smiles(smiles, \n", + " toolkit_registry=RDKTKW,\n", + " hydrogens_are_explicit=True\n", + " )\n", + " new_mol.name = oe_mol.name\n", + " rdk_mols_from_smiles_from_oe_mols_from_3d.append(new_mol)\n", + " except Exception as e:\n", + " print(smiles)\n", + " print(e)\n", + " print()\n", + " pass" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Convert each RDKit-derived OFFMol to SMILES, and then use OpeneyeToolkitWrapper to read the SMILES." + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[H][O][C](=[O])[C]([H])([H])[N]([H])[C](=[O])[C@]([H])([N]([H])[C](=[O])[C]([H])([H])[C]([H])([H])[C@@]([H])([C](=[O])[O][H])[N]([H])[H])[C]([H])([H])[S][C@]([H])([O][H])[N]([O][H])[C]1=[C]([H])[C]([H])=[C]([I])[C]([H])=[C]1[H]\n", + "(UndefinedStereochemistryError(...), 'Unable to make OFFMol from OEMol: OEMol has unspecified stereochemistry. oemol.GetTitle(): \\nProblematic atoms are:\\nAtom atomic num: 7, name: , idx: 40, aromatic: False, chiral: True with bonds:\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 36, aromatic: False, chiral: True\\nbond order: 1, chiral: False to atom atomic num: 8, name: , idx: 41, aromatic: False, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 43, aromatic: True, chiral: False\\n')\n", + "\n", + "[H][C]1=[C]([H])[C]2=[C]([C]([H])=[C]1[Cl])[C]([H])=[C]([C](=[O])[N]([H])[C@@]1([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[C@@]1([H])[N]([H])[C](=[O])[C]1=[N][C]3=[C]([S]1)[C]([H])([H])[N]([C]([H])([H])[H])[C]([H])([H])[C]3([H])[H])[N]2[H]\n", + "(UndefinedStereochemistryError(...), 'Unable to make OFFMol from OEMol: OEMol has unspecified stereochemistry. oemol.GetTitle(): \\nProblematic atoms are:\\nAtom atomic num: 7, name: , idx: 45, aromatic: False, chiral: True with bonds:\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 42, aromatic: False, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 46, aromatic: False, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 50, aromatic: False, chiral: False\\n')\n", + "\n", + "[H][O][C](=[O])[C]([H])([H])[N]([H])[C](=[O])[C@]([H])([N]([H])[C](=[O])[C]([H])([H])[C]([H])([H])[C@@]([H])([C](=[O])[O][H])[N]([H])[H])[C]([H])([H])[S][C@]([H])([O][H])[N]([O][H])[C]1=[C]([H])[C]([H])=[C]([Br])[C]([H])=[C]1[H]\n", + "(UndefinedStereochemistryError(...), 'Unable to make OFFMol from OEMol: OEMol has unspecified stereochemistry. oemol.GetTitle(): \\nProblematic atoms are:\\nAtom atomic num: 7, name: , idx: 40, aromatic: False, chiral: True with bonds:\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 36, aromatic: False, chiral: True\\nbond order: 1, chiral: False to atom atomic num: 8, name: , idx: 41, aromatic: False, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 43, aromatic: True, chiral: False\\n')\n", + "\n", + "[H][O][C](=[O])[C]([H])([H])[C@]([H])([O][H])[C]([H])([H])[C@]([H])([O][H])/[C]([H])=[C](\\[H])[C]1=[C]([C]2=[C]([H])[C]([H])=[C]([F])[C]([H])=[C]2[H])[N]=[C]([N]([C]([H])([H])[H])[S](=[O])(=[O])[C]([H])([H])[H])[N]=[C]1[C]([H])([C]([H])([H])[H])[C]([H])([H])[H]\n", + "(UndefinedStereochemistryError(...), 'Unable to make OFFMol from OEMol: OEMol has unspecified stereochemistry. oemol.GetTitle(): \\nProblematic atoms are:\\nAtom atomic num: 7, name: , idx: 37, aromatic: False, chiral: True with bonds:\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 36, aromatic: True, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 38, aromatic: False, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 16, name: , idx: 42, aromatic: False, chiral: False\\n')\n", + "\n", + "[H][O][C@]1([H])[C]2=[C]([S][C]([S](=[O])(=[O])[N]([H])[H])=[C]2[H])[S](=[O])(=[O])[N]([C]([H])([H])[C]2=[C]([H])[C]([H])=[C]([H])[S]2)[C]1([H])[H]\n", + "(UndefinedStereochemistryError(...), 'Unable to make OFFMol from OEMol: OEMol has unspecified stereochemistry. oemol.GetTitle(): \\nProblematic atoms are:\\nAtom atomic num: 7, name: , idx: 19, aromatic: False, chiral: True with bonds:\\nbond order: 1, chiral: False to atom atomic num: 16, name: , idx: 16, aromatic: False, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 20, aromatic: False, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 31, aromatic: False, chiral: False\\n')\n", + "\n", + "[H][C]1=[C]([H])[C]([S](=[O])(=[O])[N]([H])[H])=[C]([H])[C]([H])=[C]1[N]1[C]([H])([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[S]1(=[O])=[O]\n", + "(UndefinedStereochemistryError(...), 'Unable to make OFFMol from OEMol: OEMol has unspecified stereochemistry. oemol.GetTitle(): \\nProblematic atoms are:\\nAtom atomic num: 7, name: , idx: 16, aromatic: False, chiral: True with bonds:\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 15, aromatic: True, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 16, name: , idx: 29, aromatic: False, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 17, aromatic: False, chiral: False\\n')\n", + "\n", + "[H][O][C]1=[C]([H])[C]([H])=[C]([H])[C]([H])=[C]1[O][C]1=[N][C]([H])=[C]([H])[C]([C]2=[C]([C]3=[C]([H])[C]([H])=[C]([F])[C]([H])=[C]3[H])[C](=[O])[O][N]2[C]([H])([H])[O][C]([H])([H])[C]([H])([H])[H])=[N]1\n", + "(UndefinedStereochemistryError(...), 'Unable to make OFFMol from OEMol: OEMol has unspecified stereochemistry. oemol.GetTitle(): \\nProblematic atoms are:\\nAtom atomic num: 7, name: , idx: 36, aromatic: False, chiral: True with bonds:\\nbond order: 1, chiral: False to atom atomic num: 8, name: , idx: 35, aromatic: False, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 20, aromatic: False, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 37, aromatic: False, chiral: False\\n')\n", + "\n", + "[H][C]1=[C]([H])[C]([C](=[O])[C]2=[C]([H])[C]([H])=[C]([O][C]([H])([H])/[C]([H])=[C](\\[H])[C]([H])([H])[N]([C]([H])([H])[H])[C]3([H])[C]([H])([H])[C]3([H])[H])[C]([H])=[C]2[H])=[C]([H])[C]([H])=[C]1[Br]\n", + "(UndefinedStereochemistryError(...), 'Unable to make OFFMol from OEMol: OEMol has unspecified stereochemistry. oemol.GetTitle(): \\nProblematic atoms are:\\nAtom atomic num: 7, name: , idx: 24, aromatic: False, chiral: True with bonds:\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 21, aromatic: False, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 25, aromatic: False, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 29, aromatic: False, chiral: False\\n')\n", + "\n", + "[H][O][N]([H])[C](=[O])[C@]([H])([N]([C]([H])([H])[C]1=[C]([H])[C]([H])=[C]([H])[C]([H])=[C]1[H])[P@](=[O])([C]1=[C]([H])[C]([H])=[C]([H])[C]([H])=[C]1[H])[C]([H])([H])[H])[C]([H])([H])[C]([H])([C]([H])([H])[H])[C]([H])([H])[H]\n", + "(UndefinedStereochemistryError(...), 'Unable to make OFFMol from OEMol: OEMol has unspecified stereochemistry. oemol.GetTitle(): \\nProblematic atoms are:\\nAtom atomic num: 7, name: , idx: 8, aromatic: False, chiral: True with bonds:\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 6, aromatic: False, chiral: True\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 9, aromatic: False, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 15, name: , idx: 23, aromatic: False, chiral: True\\n')\n", + "\n", + "[H][C]1=[N][N]=[C]([H])[N]1[N]([C]1=[C]([H])[C]([H])=[C]([C]#[N])[C]([H])=[C]1[H])[C]([H])([H])[C]1=[C]([H])[C]([Br])=[C]([O][S](=[O])(=[O])[N]([H])[H])[C]([H])=[C]1[H]\n", + "(UndefinedStereochemistryError(...), 'Unable to make OFFMol from OEMol: OEMol has unspecified stereochemistry. oemol.GetTitle(): \\nProblematic atoms are:\\nAtom atomic num: 7, name: , idx: 7, aromatic: False, chiral: True with bonds:\\nbond order: 1, chiral: False to atom atomic num: 7, name: , idx: 6, aromatic: False, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 8, aromatic: True, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 20, aromatic: False, chiral: False\\n')\n", + "\n", + "[H][C]1=[N][N]=[C]([H])[N]1[N]([C]1=[C]([H])[C]([H])=[C]([C]#[N])[C]([H])=[C]1[H])[C]([H])([H])[C]1=[C]([H])[C]([H])=[C]([O][S](=[O])(=[O])[N]([H])[H])[C]([H])=[C]1[H]\n", + "(UndefinedStereochemistryError(...), 'Unable to make OFFMol from OEMol: OEMol has unspecified stereochemistry. oemol.GetTitle(): \\nProblematic atoms are:\\nAtom atomic num: 7, name: , idx: 7, aromatic: False, chiral: True with bonds:\\nbond order: 1, chiral: False to atom atomic num: 7, name: , idx: 6, aromatic: False, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 8, aromatic: True, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 20, aromatic: False, chiral: False\\n')\n", + "\n", + "[H][O][P@](=[O])([O][C@@]1([H])[C]([H])([H])[C@@]2([H])[N]([C]([H])([H])[H])[C@]([H])([C]([H])([H])[C]2([H])[H])[C@@]1([H])[C](=[O])[O][C]([H])([H])[H])[C]1=[C]([H])[C]([H])=[C]([H])[C]([H])=[C]1[H]\n", + "(UndefinedStereochemistryError(...), 'Unable to make OFFMol from OEMol: OEMol has unspecified stereochemistry. oemol.GetTitle(): \\nProblematic atoms are:\\nAtom atomic num: 7, name: , idx: 12, aromatic: False, chiral: True with bonds:\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 10, aromatic: False, chiral: True\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 13, aromatic: False, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 17, aromatic: False, chiral: True\\n')\n", + "\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[H][C]1=[C]([O][C]([H])([H])[H])[C]([O][C]([H])([H])[H])=[C]([O][C]([H])([H])[H])[C]([H])=[C]1[N]([C]([H])([H])[H])[C]([H])([H])[C@]1([H])[C]([H])([H])[C]2=[C]([N]([H])[C@@]([H])([N]([H])[H])[N]=[C]2[N]([H])[H])[C]([H])([H])[C]1([H])[H]\n", + "(UndefinedStereochemistryError(...), 'Unable to make OFFMol from OEMol: OEMol has unspecified stereochemistry. oemol.GetTitle(): \\nProblematic atoms are:\\nAtom atomic num: 7, name: , idx: 23, aromatic: False, chiral: True with bonds:\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 22, aromatic: True, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 24, aromatic: False, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 28, aromatic: False, chiral: False\\n')\n", + "\n", + "[H][O][C@@]1([H])[C@]([H])([C]([H])([H])[O][P](=[O])([OH])[OH])[O][C@@]([H])([N]2[C]([OH])=[C]([C](=[O])[N]([H])[H])[N+]([H])([H])[C]2([H])[H])[C@]1([H])[O][H]\n", + "(UndefinedStereochemistryError(...), 'Unable to make OFFMol from OEMol: OEMol has unspecified stereochemistry. oemol.GetTitle(): \\nProblematic atoms are:\\nAtom atomic num: 7, name: , idx: 17, aromatic: False, chiral: True with bonds:\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 15, aromatic: False, chiral: True\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 29, aromatic: False, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 18, aromatic: False, chiral: False\\n')\n", + "\n", + "[H][C]1=[C]([H])[C]([H])=[C]2[C](=[C]1[H])[C]1=[C]([N]2[C]([H])([H])[C]([H])([H])[C]([H])([H])[N]([H])[S](=[O])(=[O])[C]([H])([C]([H])([H])[H])[C]([H])([H])[H])[C@@]2([H])[N]([C]([H])([H])[C]1=[O])[C]([H])([H])[C]([H])([H])[C]([H])([H])[C]2([H])[H]\n", + "(UndefinedStereochemistryError(...), 'Unable to make OFFMol from OEMol: OEMol has unspecified stereochemistry. oemol.GetTitle(): \\nProblematic atoms are:\\nAtom atomic num: 7, name: , idx: 39, aromatic: False, chiral: True with bonds:\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 37, aromatic: False, chiral: True\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 40, aromatic: False, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 45, aromatic: False, chiral: False\\n')\n", + "\n", + "[H][C]1=[N][C]([H])=[C]([H])[C]([C]2=[C]([H])[C]([N]3[C]([H])([H])[C]([H])([H])[N]([H])[C@@]([H])([C]([H])([H])[C]4=[C]([H])[C]([H])=[C]([H])[C]([H])=[C]4[H])[C]3([H])[H])=[N][N]=[C]2[C]2=[C]([H])[C]3=[C]([H])[C]([H])=[C]([H])[C]([H])=[C]3[C]([H])=[C]2[H])=[C]1[H]\n", + "(UndefinedStereochemistryError(...), 'Unable to make OFFMol from OEMol: OEMol has unspecified stereochemistry. oemol.GetTitle(): \\nProblematic atoms are:\\nAtom atomic num: 7, name: , idx: 12, aromatic: False, chiral: True with bonds:\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 11, aromatic: True, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 37, aromatic: False, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 13, aromatic: False, chiral: False\\n')\n", + "\n", + "[H][O][C]1=[C]([C](=[O])/[N]=[C]2\\[C]([H])=[C]([C]([H])([H])[H])[O][N]2[H])[N]([C]([H])([H])[H])[S](=[O])(=[O])[C]2=[C]([H])[C]([H])=[C]([H])[C]([H])=[C]12\n", + "(UndefinedStereochemistryError(...), 'Unable to make OFFMol from OEMol: OEMol has unspecified stereochemistry. oemol.GetTitle(): \\nProblematic atoms are:\\nAtom atomic num: 7, name: , idx: 18, aromatic: False, chiral: True with bonds:\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 3, aromatic: False, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 19, aromatic: False, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 16, name: , idx: 23, aromatic: False, chiral: False\\n')\n", + "\n", + "[H][O][C]1([H])[N]([C]([H])([H])[C]2=[C]([H])[C]([N]([H])[H])=[C]([H])[C]([H])=[C]2[H])[C@@]([H])([C]([H])([H])[C]2=[C]([H])[C]([H])=[C]([H])[C]([H])=[C]2[H])[C@]([H])([O][H])[C@@]([H])([O][H])[C@]([H])([C]([H])([H])[C]2=[C]([H])[C]([H])=[C]([H])[C]([H])=[C]2[H])[N]1[C]([H])([H])[C]1=[C]([H])[C]([N]([H])[H])=[C]([H])[C]([H])=[C]1[H]\n", + "(UndefinedStereochemistryError(...), 'Unable to make OFFMol from OEMol: OEMol has unspecified stereochemistry. oemol.GetTitle(): \\nProblematic atoms are:\\nAtom atomic num: 7, name: , idx: 4, aromatic: False, chiral: True with bonds:\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 2, aromatic: False, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 5, aromatic: False, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 21, aromatic: False, chiral: True\\nAtom atomic num: 7, name: , idx: 61, aromatic: False, chiral: True with bonds:\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 45, aromatic: False, chiral: True\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 2, aromatic: False, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 62, aromatic: False, chiral: False\\n')\n", + "\n", + "[H][C]1=[C]([H])[C]([H])=[C]([C]([H])([H])[N]2[C](=[O])[C]([H])([H])[O][C@@]([H])([C]3=[C]([H])[C]4=[C]([C]([H])=[C]3[H])[N]([C]([H])([H])[H])[S](=[O])(=[O])[C]4([H])[H])[C]2([H])[H])[C]([H])=[C]1[H]\n", + "(UndefinedStereochemistryError(...), 'Unable to make OFFMol from OEMol: OEMol has unspecified stereochemistry. oemol.GetTitle(): \\nProblematic atoms are:\\nAtom atomic num: 7, name: , idx: 28, aromatic: False, chiral: True with bonds:\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 23, aromatic: True, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 29, aromatic: False, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 16, name: , idx: 33, aromatic: False, chiral: False\\n')\n", + "\n", + "[H][C]1=[C]([Cl])[C]([H])=[C]([H])[C]([N]([H])[C](=[O])[C](=[O])[N]([H])[C@@]2([H])[C]([H])([H])[C]([H])([H])[C@]([H])([C](=[O])[N]([C]([H])([H])[H])[C]([H])([H])[H])[C]([H])([H])[C@@]2([H])[N]([H])[C](=[O])[C]2=[N][C]3=[C]([S]2)[C]([H])([H])[N]([C]([H])([H])[H])[C]([H])([H])[C]3([H])[H])=[N]1\n", + "(UndefinedStereochemistryError(...), 'Unable to make OFFMol from OEMol: OEMol has unspecified stereochemistry. oemol.GetTitle(): \\nProblematic atoms are:\\nAtom atomic num: 7, name: , idx: 55, aromatic: False, chiral: True with bonds:\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 52, aromatic: False, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 56, aromatic: False, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 60, aromatic: False, chiral: False\\n')\n", + "\n", + "[H][N]([C](=[O])[N]([N]([C]([H])([H])[C]([H])([H])[Cl])[S](=[O])(=[O])[C]([H])([H])[H])[S](=[O])(=[O])[C]([H])([H])[H])[C]([H])([H])[H]\n", + "(UndefinedStereochemistryError(...), 'Unable to make OFFMol from OEMol: OEMol has unspecified stereochemistry. oemol.GetTitle(): \\nProblematic atoms are:\\nAtom atomic num: 7, name: , idx: 5, aromatic: False, chiral: True with bonds:\\nbond order: 1, chiral: False to atom atomic num: 7, name: , idx: 4, aromatic: False, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 6, aromatic: False, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 16, name: , idx: 13, aromatic: False, chiral: False\\n')\n", + "\n", + "[H][O][P](=[O])([O][H])[N]([H])[C]1=[N][C](/[C](=[N]/[O][C]([H])([H])[C]([H])([H])[H])[C](=[O])[N]([H])[C@]2([H])[C](=[O])[N]3[C]([C](=[O])[OH])=[C]([S][C]4=[N][C]([C]5=[C]([H])[CH]([H])[N]([C]([H])([H])[H])[C]([H])=[C]5[H])=[C]([H])[S]4)[C]([H])([H])[S][C@@]32[H])=[N][S]1\n", + "(UndefinedStereochemistryError(...), 'Unable to make OFFMol from OEMol: OEMol has unspecified stereochemistry. oemol.GetTitle(): \\nProblematic atoms are:\\nAtom atomic num: 7, name: , idx: 44, aromatic: False, chiral: True with bonds:\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 42, aromatic: False, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 45, aromatic: False, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 49, aromatic: False, chiral: False\\n')\n", + "\n", + "[H][O][P](=[O])([O][H])[N]1[C](=[O])[N]=[C]([C]([H])([H])[N]2[C]([H])([H])[C]([H])([H])[O][C@]([H])([O][C@@]([H])([C]3=[C]([H])[C]([C]([F])([F])[F])=[C]([H])[C]([C]([F])([F])[F])=[C]3[H])[C]([H])([H])[H])[C@]2([H])[C]2=[C]([H])[C]([H])=[C]([F])[C]([H])=[C]2[H])[N]1[H]\n", + "(UndefinedStereochemistryError(...), 'Unable to make OFFMol from OEMol: OEMol has unspecified stereochemistry. oemol.GetTitle(): \\nProblematic atoms are:\\nAtom atomic num: 7, name: , idx: 14, aromatic: False, chiral: True with bonds:\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 11, aromatic: False, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 48, aromatic: False, chiral: True\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 15, aromatic: False, chiral: False\\n')\n", + "\n", + "[H][O][N]([H])[C](=[O])[C@]1([H])[N]([S](=[O])(=[O])[C]2=[C]([H])[C]([H])=[C]([O][C]([H])([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[H])[C]([H])=[C]2[H])[C]([H])([H])[C@@]([H])([N]([H])[S](=[O])(=[O])[C]([H])([H])[H])[C]1([H])[H]\n", + "(UndefinedStereochemistryError(...), 'Unable to make OFFMol from OEMol: OEMol has unspecified stereochemistry. oemol.GetTitle(): \\nProblematic atoms are:\\nAtom atomic num: 7, name: , idx: 8, aromatic: False, chiral: True with bonds:\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 6, aromatic: False, chiral: True\\nbond order: 1, chiral: False to atom atomic num: 16, name: , idx: 9, aromatic: False, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 36, aromatic: False, chiral: False\\n')\n", + "\n", + "[H][O][C]([H])([H])[C@]1([H])[O][C@@]([H])([N]2[C]3=[C]([C]([N]([H])[H])=[N][C]([H])=[N]3)[C@]([H])([I])[N]2[H])[C@]([H])([O][H])[C@@]1([H])[O][H]\n", + "(UndefinedStereochemistryError(...), 'Unable to make OFFMol from OEMol: OEMol has unspecified stereochemistry. oemol.GetTitle(): \\nProblematic atoms are:\\nAtom atomic num: 7, name: , idx: 10, aromatic: False, chiral: True with bonds:\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 8, aromatic: False, chiral: True\\nbond order: 1, chiral: False to atom atomic num: 7, name: , idx: 24, aromatic: False, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 11, aromatic: True, chiral: False\\n')\n", + "\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[H][O][C](=[O])[C]([H])([H])[N]([C]([H])([H])[H])[C]([H])([N]([H])[H])[N]([H])[H]\n", + "(UndefinedStereochemistryError(...), 'Unable to make OFFMol from OEMol: OEMol has unspecified stereochemistry. oemol.GetTitle(): \\nProblematic atoms are:\\nAtom atomic num: 7, name: , idx: 7, aromatic: False, chiral: True with bonds:\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 4, aromatic: False, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 8, aromatic: False, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 12, aromatic: False, chiral: False\\n')\n", + "\n", + "[H][O][C]([H])([H])[C@]([H])([O][S]([OH])([OH])[OH])[C@@]([H])([O][H])[C]([H])([H])[N]1[C]([H])([H])[C@@]([H])([O][H])[C@]([H])([O][H])[C@@]1([H])[C]([H])([H])[O][H]\n", + "(UndefinedStereochemistryError(...), 'Unable to make OFFMol from OEMol: OEMol has unspecified stereochemistry. oemol.GetTitle(): \\nProblematic atoms are:\\nAtom atomic num: 7, name: , idx: 19, aromatic: False, chiral: True with bonds:\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 16, aromatic: False, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 31, aromatic: False, chiral: True\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 20, aromatic: False, chiral: False\\n')\n", + "\n", + "[H][N]([H])[C@]1([H])[N]([H])[C@@]2([H])[C]([H])([H])[C]([H])([H])[C@]([H])([C]([H])([H])[N]3[C]([H])([H])[C]([H])([H])[C@@]4([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[C@]34[H])[C]([H])([H])[C@@]2([H])[C@]([H])([N]([H])[H])[N]1[H]\n", + "(UndefinedStereochemistryError(...), 'Unable to make OFFMol from OEMol: OEMol has unspecified stereochemistry. oemol.GetTitle(): \\nProblematic atoms are:\\nAtom atomic num: 7, name: , idx: 20, aromatic: False, chiral: True with bonds:\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 17, aromatic: False, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 41, aromatic: False, chiral: True\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 21, aromatic: False, chiral: False\\n')\n", + "\n", + "[H][C]1=[C]([H])[C]2=[C]([H])[C](=[C]1[H])[C]([H])([H])[C@]([N]([H])[H])([C]([H])([H])[H])[C](=[O])[O][C]([H])([H])[C]1=[C]([H])[C](=[N][C]([N]([C]([H])([H])[H])[S](=[O])(=[O])[C]([H])([H])[H])=[C]1[H])[C]([H])([H])[C]([H])([H])[C@]([H])([C]([H])([H])[H])[C]([H])([H])[C]2([H])[H]\n", + "(UndefinedStereochemistryError(...), 'Unable to make OFFMol from OEMol: OEMol has unspecified stereochemistry. oemol.GetTitle(): \\nProblematic atoms are:\\nAtom atomic num: 7, name: , idx: 33, aromatic: False, chiral: True with bonds:\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 32, aromatic: True, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 34, aromatic: False, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 16, name: , idx: 38, aromatic: False, chiral: False\\n')\n", + "\n", + "[H][O][C]1=[C]([C]2=[C]([H])[C]([O][H])=[C]([O][H])[C]([H])=[C]2[H])[O][C]2=[C]([N]3[C]([H])([H])[C]([H])([H])[C]([H])([H])[S]3(=[O])=[O])[C]([H])=[C]([C]([H])([H])[H])[C]([H])=[C]2[C]1=[O]\n", + "(UndefinedStereochemistryError(...), 'Unable to make OFFMol from OEMol: OEMol has unspecified stereochemistry. oemol.GetTitle(): \\nProblematic atoms are:\\nAtom atomic num: 7, name: , idx: 20, aromatic: False, chiral: True with bonds:\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 19, aromatic: True, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 16, name: , idx: 30, aromatic: False, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 21, aromatic: False, chiral: False\\n')\n", + "\n", + "[H][O]/[N]=[C](\\[N]([H])[H])[N]1[C]([H])([H])[C]([H])([H])[C]([H])([C]([H])([H])[N]([H])[C](=[O])[C@@]2([H])[N]3[C](=[O])[C]([H])([H])[N]([S](=[O])(=[O])[C]([H])([H])[C]4=[C]([H])[C]([H])=[C]([H])[C]([H])=[C]4[H])[C]([H])([H])[C@]3([H])[C]([H])([H])[C]2([H])[H])[C]([H])([H])[C]1([H])[H]\n", + "(UndefinedStereochemistryError(...), 'Unable to make OFFMol from OEMol: OEMol has unspecified stereochemistry. oemol.GetTitle(): \\nProblematic atoms are:\\nAtom atomic num: 7, name: , idx: 31, aromatic: False, chiral: True with bonds:\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 28, aromatic: False, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 16, name: , idx: 32, aromatic: False, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 49, aromatic: False, chiral: False\\n')\n", + "\n", + "[H][C]1=[C]([H])[C]([N]2[C]([H])([H])[C]([H])([H])[C]([H])([H])[S]2(=[O])=[O])=[C]([H])[C]2=[C]1[N]([H])[N]=[C]2[N]([H])[C](=[O])[C]([H])([H])[C]1=[C]([H])[C]([H])=[C]([N]2[C]([H])([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[C]2([H])[H])[C]([H])=[C]1[H]\n", + "(UndefinedStereochemistryError(...), 'Unable to make OFFMol from OEMol: OEMol has unspecified stereochemistry. oemol.GetTitle(): \\nProblematic atoms are:\\nAtom atomic num: 7, name: , idx: 5, aromatic: False, chiral: True with bonds:\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 4, aromatic: True, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 16, name: , idx: 15, aromatic: False, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 6, aromatic: False, chiral: False\\n')\n", + "\n", + "[H][O][C]([H])([H])[C]([H])([H])[N]([C]1=[C]([C]2([H])[C]([H])([H])[C]2([H])[H])[C]([H])=[C]2[C](=[C]1[H])[O][C]([C]1=[C]([H])[C]([H])=[C]([F])[C]([H])=[C]1[H])=[C]2[C](=[O])[N]([H])[C]([H])([H])[H])[S](=[O])(=[O])[C]([H])([H])[H]\n", + "(UndefinedStereochemistryError(...), 'Unable to make OFFMol from OEMol: OEMol has unspecified stereochemistry. oemol.GetTitle(): \\nProblematic atoms are:\\nAtom atomic num: 7, name: , idx: 8, aromatic: False, chiral: True with bonds:\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 5, aromatic: False, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 6, name: , idx: 9, aromatic: True, chiral: False\\nbond order: 1, chiral: False to atom atomic num: 16, name: , idx: 47, aromatic: False, chiral: False\\n')\n", + "\n" + ] + } + ], + "source": [ + "oe_mols_from_smiles_from_rdk_mols_from_3d = []\n", + "for rdk_mol in rdk_mols_from_3d:\n", + " try:\n", + " smiles = rdk_mol.to_smiles(toolkit_registry=RDKTKW)\n", + " new_mol = Molecule.from_smiles(smiles,\n", + " toolkit_registry=OETKW,\n", + " hydrogens_are_explicit=True\n", + " )\n", + " new_mol.name = rdk_mol.name\n", + " oe_mols_from_smiles_from_rdk_mols_from_3d.append(new_mol)\n", + " except UndefinedStereochemistryError as e:\n", + " print(smiles)\n", + " print(e)\n", + " print()\n", + " pass" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Define a few helper functions for molecule comparison" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [], + "source": [ + "def print_smi_difference(mol_name, \n", + " smi_1, smi_2, \n", + " smi_1_label='OE: ',\n", + " smi_2_label='RDK:'):\n", + " print(mol_name)\n", + " print(smi_1_label, smi_1)\n", + " print(smi_2_label, smi_2)\n", + " differences = list(difflib.ndiff(smi_1, smi_2))\n", + " msg = ''\n", + " for i,s in enumerate(differences):\n", + " if s[0]==' ': \n", + " continue\n", + " elif s[0]=='-':\n", + " msg += u'Delete \"{}\" from position {}\\n'.format(s[-1],i)\n", + " elif s[0]=='+':\n", + " msg += u'Add \"{}\" to position {}\\n'.format(s[-1],i) \n", + " # Sometimes the diffs get really big. Skip printing in those cases\n", + " if msg.count('\\n') < 5:\n", + " print(msg)\n", + " print()\n", + " \n", + " \n", + "def compare_mols_using_smiles(mol_1, mol_2, \n", + " toolkit_wrapper, \n", + " mol_1_label, \n", + " mol_2_label, \n", + " verbose=False):\n", + " mol_1_smi = mol_1.to_smiles(toolkit_registry=toolkit_wrapper)\n", + " mol_2_smi = mol_2.to_smiles(toolkit_registry=toolkit_wrapper)\n", + " if mol_1_smi == mol_2_smi:\n", + " return True\n", + " else:\n", + " if verbose:\n", + " print_smi_difference(mol_1.name,\n", + " mol_1_smi, mol_2_smi, \n", + " smi_1_label=mol_1_label, \n", + " smi_2_label=mol_2_label)\n", + " return False\n", + "\n", + " \n", + "def compare_mols_using_nx(mol_1, mol_2):\n", + " return mol_1 == mol_2\n", + " " + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### And perform the actual comparisons" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\n", + "\n", + "\n", + "There are 371 molecules in the oe_mols_from_3d set\n", + "There are 352 molecules in the rdk_mols_from_3d set\n", + "These sets have 346 molecules in common\n", + "'_CIPCode'\n", + "'_CIPCode'\n", + "'_CIPCode'\n", + "'_CIPCode'\n", + "'_CIPCode'\n", + "'_CIPCode'\n", + "'_CIPCode'\n", + "'_CIPCode'\n", + "'_CIPCode'\n", + "'_CIPCode'\n", + "'_CIPCode'\n", + "'_CIPCode'\n", + "'_CIPCode'\n", + "'_CIPCode'\n", + "'_CIPCode'\n", + "'_CIPCode'\n", + "'_CIPCode'\n", + "'_CIPCode'\n", + "'_CIPCode'\n", + "'_CIPCode'\n", + "'_CIPCode'\n", + "'_CIPCode'\n", + "'_CIPCode'\n", + "'_CIPCode'\n", + "'_CIPCode'\n", + "'_CIPCode'\n", + "In comparing oe_mols_from_3d to rdk_mols_from_3d, I found 284 graph matches, 293 OE SMILES matches (26 comparisons errored), and 293 RDKit SMILES matches (7 comparisons errored) out of 346 molecules\n", + "\n", + "\n", + "\n", + "There are 371 molecules in the oe_mols_from_3d set\n", + "There are 365 molecules in the rdk_mols_from_smiles_from_oe_mols_from_3d set\n", + "These sets have 365 molecules in common\n", + "'_CIPCode'\n", + "'_CIPCode'\n", + "'_CIPCode'\n", + "'_CIPCode'\n", + "'_CIPCode'\n", + "'_CIPCode'\n", + "'_CIPCode'\n", + "'_CIPCode'\n", + "'_CIPCode'\n", + "'_CIPCode'\n", + "'_CIPCode'\n", + "'_CIPCode'\n", + "'_CIPCode'\n", + "'_CIPCode'\n", + "'_CIPCode'\n", + "'_CIPCode'\n", + "'_CIPCode'\n", + "'_CIPCode'\n", + "'_CIPCode'\n", + "'_CIPCode'\n", + "'_CIPCode'\n", + "'_CIPCode'\n", + "'_CIPCode'\n", + "'_CIPCode'\n", + "'_CIPCode'\n", + "'_CIPCode'\n", + "In comparing oe_mols_from_3d to rdk_mols_from_smiles_from_oe_mols_from_3d, I found 293 graph matches, 293 OE SMILES matches (26 comparisons errored), and 332 RDKit SMILES matches (0 comparisons errored) out of 365 molecules\n", + "\n", + "\n", + "\n", + "There are 319 molecules in the oe_mols_from_smiles_from_rdk_mols_from_3d set\n", + "There are 352 molecules in the rdk_mols_from_3d set\n", + "These sets have 319 molecules in common\n", + "In comparing oe_mols_from_smiles_from_rdk_mols_from_3d to rdk_mols_from_3d, I found 310 graph matches, 219 OE SMILES matches (0 comparisons errored), and 304 RDKit SMILES matches (7 comparisons errored) out of 319 molecules\n" + ] + } + ], + "source": [ + "# NBVAL_SKIP\n", + "mol_sets_to_compare = ((('oe_mols_from_3d', oe_mols_from_3d), \n", + " ('rdk_mols_from_3d', rdk_mols_from_3d)),\n", + " #(('oe_mols_from_smiles', oe_mols_from_smiles), \n", + " # ('rdk_mols_from_smiles', rdk_mols_from_smiles)),\n", + " (('oe_mols_from_3d', oe_mols_from_3d), \n", + " ('rdk_mols_from_smiles_from_oe_mols_from_3d', rdk_mols_from_smiles_from_oe_mols_from_3d)),\n", + " (('oe_mols_from_smiles_from_rdk_mols_from_3d', oe_mols_from_smiles_from_rdk_mols_from_3d),\n", + " ('rdk_mols_from_3d', rdk_mols_from_3d)),\n", + " )\n", + "\n", + "\n", + "for (set_1_name, mol_set_1), (set_2_name, mol_set_2) in mol_sets_to_compare:\n", + " set_1_name_to_mol = {mol.name:mol for mol in mol_set_1 if not(mol is None)}\n", + " set_2_name_to_mol = {mol.name:mol for mol in mol_set_2 if not(mol is None)}\n", + " names_in_common = set(set_1_name_to_mol.keys()) & set(set_2_name_to_mol.keys())\n", + " print()\n", + " print()\n", + " print()\n", + " print('There are {} molecules in the {} set'.format(len(mol_set_1), set_1_name))\n", + " print('There are {} molecules in the {} set'.format(len(mol_set_2), set_2_name))\n", + " print('These sets have {} molecules in common'.format(len(names_in_common)))\n", + " \n", + " graph_matches = 0\n", + " rdk_smiles_matches = 0\n", + " oe_smiles_matches = 0\n", + " \n", + " errored_graph_comparisons = 0\n", + " errored_rdk_smiles_comparisons = 0\n", + " errored_oe_smiles_comparisons = 0\n", + " \n", + " for name in names_in_common:\n", + " set_1_mol = set_1_name_to_mol[name]\n", + " set_2_mol = set_2_name_to_mol[name]\n", + " nx_match = compare_mols_using_nx(set_1_mol, set_2_mol)\n", + " if nx_match:\n", + " graph_matches += 1\n", + " \n", + " try:\n", + " rdk_smi_match = compare_mols_using_smiles(set_1_mol, set_2_mol, \n", + " RDKTKW, \n", + " 'OE--(RDKTKW)-->SMILES: ','RDK--(RDKTKW)-->SMILES:',\n", + " verbose = False)\n", + " if rdk_smi_match:\n", + " rdk_smiles_matches += 1\n", + " except Exception as e:\n", + " errored_rdk_smiles_comparisons += 1\n", + " print(e)\n", + " try:\n", + " #if 1:\n", + " oe_smi_match = compare_mols_using_smiles(set_1_mol, set_2_mol, \n", + " OETKW, \n", + " 'OE--(OETKW)-->SMILES: ','RDK--(OETKW)-->SMILES:',\n", + " verbose = False)\n", + " if oe_smi_match:\n", + " oe_smiles_matches += 1\n", + " except:\n", + " errored_oe_smiles_comparisons += 1\n", + " \n", + " print(\"In comparing {} to {}, I found {} graph matches, {} OE SMILES matches ({} comparisons errored), and \" \\\n", + " \"{} RDKit SMILES matches ({} comparisons errored) out of {} molecules\".format(set_1_name, \n", + " set_2_name, \n", + " graph_matches, \n", + " rdk_smiles_matches, \n", + " errored_rdk_smiles_comparisons,\n", + " oe_smiles_matches, \n", + " errored_oe_smiles_comparisons,\n", + " len(names_in_common)))\n" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.6.8" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/examples/testing/OE_bondorder_testing.ipynb b/examples/deprecated/testing/OE_bondorder_testing.ipynb similarity index 95% rename from examples/testing/OE_bondorder_testing.ipynb rename to examples/deprecated/testing/OE_bondorder_testing.ipynb index 4fa1bef37..69f7010e0 100644 --- a/examples/testing/OE_bondorder_testing.ipynb +++ b/examples/deprecated/testing/OE_bondorder_testing.ipynb @@ -27,11 +27,10 @@ { "cell_type": "code", "execution_count": 33, - "metadata": { - "collapsed": false - }, + "metadata": {}, "outputs": [], "source": [ + "# NBVAL_SKIP\n", "from openeye.oechem import *\n", "mol = OEMol()\n", "#smiles = 'CC(c1ccccc1)C(=O)[O-]'\n", @@ -52,9 +51,7 @@ { "cell_type": "code", "execution_count": 34, - "metadata": { - "collapsed": false - }, + "metadata": {}, "outputs": [], "source": [ "def get_atom_properties(mol):\n", @@ -147,9 +144,7 @@ { "cell_type": "code", "execution_count": 36, - "metadata": { - "collapsed": false - }, + "metadata": {}, "outputs": [ { "name": "stdout", @@ -160,6 +155,7 @@ } ], "source": [ + "# NBVAL_SKIP\n", "atomic_numbers, names, bonds, bond_orders = get_atom_properties(mol)\n", "mol = make_mol_from_properties( atomic_numbers, names, bonds, bond_orders)\n", "smiles = OECreateIsoSmiString(mol)\n", @@ -178,23 +174,23 @@ ], "metadata": { "kernelspec": { - "display_name": "Python 2", + "display_name": "Python 3", "language": "python", - "name": "python2" + "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", - "version": 2 + "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", - "pygments_lexer": "ipython2", - "version": "2.7.11" + "pygments_lexer": "ipython3", + "version": "3.6.8" } }, "nbformat": 4, - "nbformat_minor": 0 + "nbformat_minor": 1 } diff --git a/examples/testing/README.md b/examples/deprecated/testing/README.md similarity index 100% rename from examples/testing/README.md rename to examples/deprecated/testing/README.md diff --git a/examples/testing/test_impropers/1,2-ditert-butylbenzene.crd b/examples/deprecated/testing/test_impropers/1,2-ditert-butylbenzene.crd similarity index 100% rename from examples/testing/test_impropers/1,2-ditert-butylbenzene.crd rename to examples/deprecated/testing/test_impropers/1,2-ditert-butylbenzene.crd diff --git a/examples/testing/test_impropers/1,2-ditert-butylbenzene.mol2 b/examples/deprecated/testing/test_impropers/1,2-ditert-butylbenzene.mol2 similarity index 100% rename from examples/testing/test_impropers/1,2-ditert-butylbenzene.mol2 rename to examples/deprecated/testing/test_impropers/1,2-ditert-butylbenzene.mol2 diff --git a/examples/testing/test_impropers/1,2-ditert-butylbenzene.prmtop b/examples/deprecated/testing/test_impropers/1,2-ditert-butylbenzene.prmtop similarity index 100% rename from examples/testing/test_impropers/1,2-ditert-butylbenzene.prmtop rename to examples/deprecated/testing/test_impropers/1,2-ditert-butylbenzene.prmtop diff --git a/examples/testing/test_impropers/README.md b/examples/deprecated/testing/test_impropers/README.md similarity index 100% rename from examples/testing/test_impropers/README.md rename to examples/deprecated/testing/test_impropers/README.md diff --git a/examples/testing/test_impropers/benzene.crd b/examples/deprecated/testing/test_impropers/benzene.crd similarity index 100% rename from examples/testing/test_impropers/benzene.crd rename to examples/deprecated/testing/test_impropers/benzene.crd diff --git a/examples/testing/test_impropers/benzene.mol2 b/examples/deprecated/testing/test_impropers/benzene.mol2 similarity index 100% rename from examples/testing/test_impropers/benzene.mol2 rename to examples/deprecated/testing/test_impropers/benzene.mol2 diff --git a/examples/testing/test_impropers/benzene.prmtop b/examples/deprecated/testing/test_impropers/benzene.prmtop similarity index 100% rename from examples/testing/test_impropers/benzene.prmtop rename to examples/deprecated/testing/test_impropers/benzene.prmtop diff --git a/examples/testing/test_impropers/o-xylene.crd b/examples/deprecated/testing/test_impropers/o-xylene.crd similarity index 100% rename from examples/testing/test_impropers/o-xylene.crd rename to examples/deprecated/testing/test_impropers/o-xylene.crd diff --git a/examples/testing/test_impropers/o-xylene.mol2 b/examples/deprecated/testing/test_impropers/o-xylene.mol2 similarity index 100% rename from examples/testing/test_impropers/o-xylene.mol2 rename to examples/deprecated/testing/test_impropers/o-xylene.mol2 diff --git a/examples/testing/test_impropers/o-xylene.prmtop b/examples/deprecated/testing/test_impropers/o-xylene.prmtop similarity index 100% rename from examples/testing/test_impropers/o-xylene.prmtop rename to examples/deprecated/testing/test_impropers/o-xylene.prmtop diff --git a/examples/testing/test_impropers/parm_Frosst.frcmod b/examples/deprecated/testing/test_impropers/parm_Frosst.frcmod similarity index 100% rename from examples/testing/test_impropers/parm_Frosst.frcmod rename to examples/deprecated/testing/test_impropers/parm_Frosst.frcmod diff --git a/examples/testing/test_impropers/smirnoff99Frosst_modified.ffxml b/examples/deprecated/testing/test_impropers/smirnoff99Frosst_modified.ffxml similarity index 100% rename from examples/testing/test_impropers/smirnoff99Frosst_modified.ffxml rename to examples/deprecated/testing/test_impropers/smirnoff99Frosst_modified.ffxml diff --git a/examples/testing/test_impropers/test_impropers.ipynb b/examples/deprecated/testing/test_impropers/test_impropers.ipynb similarity index 97% rename from examples/testing/test_impropers/test_impropers.ipynb rename to examples/deprecated/testing/test_impropers/test_impropers.ipynb index 920da955e..55abf1dcb 100644 --- a/examples/testing/test_impropers/test_impropers.ipynb +++ b/examples/deprecated/testing/test_impropers/test_impropers.ipynb @@ -15,11 +15,10 @@ { "cell_type": "code", "execution_count": 1, - "metadata": { - "collapsed": false - }, + "metadata": {}, "outputs": [], "source": [ + "# NBVAL_SKIP\n", "# Import stuff we need\n", "from openforcefield.typing.engines.smirnoff import forcefield, generateTopologyFromOEMol\n", "import openeye.oechem as oechem\n", @@ -37,11 +36,10 @@ { "cell_type": "code", "execution_count": 2, - "metadata": { - "collapsed": false - }, + "metadata": {}, "outputs": [], "source": [ + "# NBVAL_SKIP\n", "# Load our forcefield \n", "#ffxml = 'forcefield/smirnoff99Frosst.offxml'\n", "ffxml = 'smirnoff99Frosst_modified.offxml'\n", @@ -51,9 +49,7 @@ { "cell_type": "code", "execution_count": 3, - "metadata": { - "collapsed": false - }, + "metadata": {}, "outputs": [ { "name": "stdout", @@ -75,6 +71,7 @@ } ], "source": [ + "# NBVAL_SKIP\n", "# Initialize o-xylene and benzene as a test molecules\n", "molnames = ['benzene', 'o-xylene','1,2-ditert-butylbenzene'] \n", "oemols = []\n", @@ -151,11 +148,10 @@ { "cell_type": "code", "execution_count": null, - "metadata": { - "collapsed": false - }, + "metadata": {}, "outputs": [], "source": [ + "# NBVAL_SKIP\n", "# Next step -- need AMBER prmtop/crd files for o-xylene and/or benzene for comparison\n", "# I should be able to get these by hand-typing them with parm@frosst types and then generating from the frcmod, etc.\n", "\n", @@ -205,11 +201,10 @@ { "cell_type": "code", "execution_count": null, - "metadata": { - "collapsed": false - }, + "metadata": {}, "outputs": [], "source": [ + "# NBVAL_SKIP\n", "frcmod = 'parm_Frosst.frcmod'\n", "for (idx, molname) in enumerate(molnames):\n", " prmtop = molname+'.prmtop'\n", @@ -228,11 +223,10 @@ { "cell_type": "code", "execution_count": null, - "metadata": { - "collapsed": false - }, + "metadata": {}, "outputs": [], "source": [ + "# NBVAL_SKIP\n", "from openforcefield.typing.engines.smirnoff import forcefield_utils as ff_utils\n", "import numpy as np\n", "import simtk.unit as unit\n", @@ -272,11 +266,10 @@ { "cell_type": "code", "execution_count": null, - "metadata": { - "collapsed": false - }, + "metadata": {}, "outputs": [], "source": [ + "# NBVAL_SKIP\n", "# We can use the same code as the above but just switch the assertion about checking terms to on\n", "for idx, molname in enumerate(molnames):\n", " print(\"Examining %s...\" % molname)\n", @@ -315,9 +308,9 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.6.0" + "version": "3.6.8" } }, "nbformat": 4, - "nbformat_minor": 0 + "nbformat_minor": 1 } diff --git a/examples/testing/test_impropers/tleap_tools.py b/examples/deprecated/testing/test_impropers/tleap_tools.py similarity index 100% rename from examples/testing/test_impropers/tleap_tools.py rename to examples/deprecated/testing/test_impropers/tleap_tools.py diff --git a/examples/testing/test_system_conversion/README.md b/examples/deprecated/testing/test_system_conversion/README.md similarity index 100% rename from examples/testing/test_system_conversion/README.md rename to examples/deprecated/testing/test_system_conversion/README.md diff --git a/examples/testing/test_system_conversion/amber_system.xml b/examples/deprecated/testing/test_system_conversion/amber_system.xml similarity index 100% rename from examples/testing/test_system_conversion/amber_system.xml rename to examples/deprecated/testing/test_system_conversion/amber_system.xml diff --git a/examples/testing/test_system_conversion/convert_to_amber.ipynb b/examples/deprecated/testing/test_system_conversion/convert_to_amber.ipynb similarity index 99% rename from examples/testing/test_system_conversion/convert_to_amber.ipynb rename to examples/deprecated/testing/test_system_conversion/convert_to_amber.ipynb index ee39a941b..62785db3a 100644 --- a/examples/testing/test_system_conversion/convert_to_amber.ipynb +++ b/examples/deprecated/testing/test_system_conversion/convert_to_amber.ipynb @@ -6,6 +6,7 @@ "metadata": {}, "outputs": [], "source": [ + "# NBVAL_SKIP\n", "from openforcefield.typing.engines.smirnoff import forcefield\n", "from openforcefield.typing.engines.smirnoff import forcefield_utils as ff_utils\n", "from simtk import openmm\n", @@ -24,6 +25,7 @@ "metadata": {}, "outputs": [], "source": [ + "# NBVAL_SKIP\n", "pdbfile = PDBFile('cyclohexane_ethanol_0.4_0.6.pdb')\n", "ff = forcefield.ForceField('forcefield/Frosst_AlkEthOH.offxml')\n", "\n", @@ -17336,6 +17338,7 @@ } ], "source": [ + "# NBVAL_SKIP\n", "# Evaluate energy of OpenMM system and AMBER system to check that they are still the same\n", "parm = parmed.load_file('system.prmtop', 'system.crd')\n", "ambersys = parm.createSystem(nonbondedMethod= app.NoCutoff, constraints = None, implicitSolvent = None)\n", @@ -17348,6 +17351,7 @@ "metadata": {}, "outputs": [], "source": [ + "# NBVAL_SKIP\n", "# Dump OpenMM systems out\n", "\n", "# Do openforcefield system\n", @@ -17368,6 +17372,7 @@ "metadata": {}, "outputs": [], "source": [ + "# NBVAL_SKIP\n", "# deserialize systems and confirm energies still different without using external tools\n", "smirff_system = XmlSerializer.deserialize(serialized_system_smirff)\n", "amber_system = XmlSerializer.deserialize(serialized_system_amber)\n", @@ -51929,6 +51934,7 @@ } ], "source": [ + "# NBVAL_SKIP\n", "# One more test - use new openforcefield functions to take system, save to AMBER/GROMACS, re-load and check energy\n", "\n", "pdbfile = PDBFile('cyclohexane_ethanol_0.4_0.6.pdb')\n", @@ -69226,6 +69232,7 @@ } ], "source": [ + "# NBVAL_SKIP\n", "# Let's round trip the AMBER system to double check the issue one more time\n", "ff_utils.save_system_to_gromacs( pdbfile.topology, ambersys, pdbfile.positions, 'out2.top', 'out2.gro')\n", "top = parmed.load_file('out2.top')\n", @@ -69249,6 +69256,7 @@ } ], "source": [ + "# NBVAL_SKIP\n", "# Amber system\n", "parm = parmed.load_file('out.prmtop', 'out.crd')\n", "print(parmed.openmm.energy_decomposition_system(parm, parm.createSystem()))\n", @@ -69285,7 +69293,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.5.3" + "version": "3.6.8" } }, "nbformat": 4, diff --git a/examples/testing/test_system_conversion/cyclohexane.frcmod b/examples/deprecated/testing/test_system_conversion/cyclohexane.frcmod similarity index 100% rename from examples/testing/test_system_conversion/cyclohexane.frcmod rename to examples/deprecated/testing/test_system_conversion/cyclohexane.frcmod diff --git a/examples/testing/test_system_conversion/cyclohexane.inpcrd b/examples/deprecated/testing/test_system_conversion/cyclohexane.inpcrd similarity index 100% rename from examples/testing/test_system_conversion/cyclohexane.inpcrd rename to examples/deprecated/testing/test_system_conversion/cyclohexane.inpcrd diff --git a/examples/testing/test_system_conversion/cyclohexane.mol2 b/examples/deprecated/testing/test_system_conversion/cyclohexane.mol2 similarity index 100% rename from examples/testing/test_system_conversion/cyclohexane.mol2 rename to examples/deprecated/testing/test_system_conversion/cyclohexane.mol2 diff --git a/examples/testing/test_system_conversion/cyclohexane.prmtop b/examples/deprecated/testing/test_system_conversion/cyclohexane.prmtop similarity index 100% rename from examples/testing/test_system_conversion/cyclohexane.prmtop rename to examples/deprecated/testing/test_system_conversion/cyclohexane.prmtop diff --git a/examples/testing/test_system_conversion/cyclohexane.sdf b/examples/deprecated/testing/test_system_conversion/cyclohexane.sdf similarity index 100% rename from examples/testing/test_system_conversion/cyclohexane.sdf rename to examples/deprecated/testing/test_system_conversion/cyclohexane.sdf diff --git a/examples/testing/test_system_conversion/cyclohexane_ethanol_0.4_0.6.pdb b/examples/deprecated/testing/test_system_conversion/cyclohexane_ethanol_0.4_0.6.pdb similarity index 100% rename from examples/testing/test_system_conversion/cyclohexane_ethanol_0.4_0.6.pdb rename to examples/deprecated/testing/test_system_conversion/cyclohexane_ethanol_0.4_0.6.pdb diff --git a/examples/testing/test_system_conversion/ethanol.frcmod b/examples/deprecated/testing/test_system_conversion/ethanol.frcmod similarity index 100% rename from examples/testing/test_system_conversion/ethanol.frcmod rename to examples/deprecated/testing/test_system_conversion/ethanol.frcmod diff --git a/examples/testing/test_system_conversion/ethanol.inpcrd b/examples/deprecated/testing/test_system_conversion/ethanol.inpcrd similarity index 100% rename from examples/testing/test_system_conversion/ethanol.inpcrd rename to examples/deprecated/testing/test_system_conversion/ethanol.inpcrd diff --git a/examples/testing/test_system_conversion/ethanol.mol2 b/examples/deprecated/testing/test_system_conversion/ethanol.mol2 similarity index 100% rename from examples/testing/test_system_conversion/ethanol.mol2 rename to examples/deprecated/testing/test_system_conversion/ethanol.mol2 diff --git a/examples/testing/test_system_conversion/ethanol.prmtop b/examples/deprecated/testing/test_system_conversion/ethanol.prmtop similarity index 100% rename from examples/testing/test_system_conversion/ethanol.prmtop rename to examples/deprecated/testing/test_system_conversion/ethanol.prmtop diff --git a/examples/testing/test_system_conversion/ethanol.sdf b/examples/deprecated/testing/test_system_conversion/ethanol.sdf similarity index 100% rename from examples/testing/test_system_conversion/ethanol.sdf rename to examples/deprecated/testing/test_system_conversion/ethanol.sdf diff --git a/examples/testing/test_system_conversion/openforcefield_system.xml b/examples/deprecated/testing/test_system_conversion/openforcefield_system.xml similarity index 100% rename from examples/testing/test_system_conversion/openforcefield_system.xml rename to examples/deprecated/testing/test_system_conversion/openforcefield_system.xml diff --git a/examples/testing/test_system_conversion/smarty_system.xml b/examples/deprecated/testing/test_system_conversion/smarty_system.xml similarity index 100% rename from examples/testing/test_system_conversion/smarty_system.xml rename to examples/deprecated/testing/test_system_conversion/smarty_system.xml diff --git a/examples/forcefield_modification/ManipulateParameters.ipynb b/examples/forcefield_modification/ManipulateParameters.ipynb index fa590bdd8..1a41bcb37 100644 --- a/examples/forcefield_modification/ManipulateParameters.ipynb +++ b/examples/forcefield_modification/ManipulateParameters.ipynb @@ -13,29 +13,30 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 1, "metadata": {}, "outputs": [], "source": [ - "# Imports needed\n", - "from openforcefield.typing.engines.smirnoff.forcefield import ForceField, generateTopologyFromOEMol\n", - "import openeye\n", - "from openeye import oechem\n", + "from openforcefield.topology import Molecule, Topology\n", + "from openforcefield.typing.engines.smirnoff.forcefield import ForceField\n", "from openforcefield.utils import get_data_filename\n", - "from simtk import openmm\n", - "from simtk import unit\n", + "from simtk import openmm, unit\n", "import numpy as np" ] }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Define utility function we'll use to get energy of an OpenMM system" + ] + }, { "cell_type": "code", - "execution_count": 6, - "metadata": { - "collapsed": true - }, + "execution_count": 2, + "metadata": {}, "outputs": [], "source": [ - "# Define utility function we'll use to get energy of an OpenMM system\n", "def get_energy(system, positions):\n", " \"\"\"\n", " Return the potential energy.\n", @@ -55,7 +56,7 @@ " context = openmm.Context(system, integrator)\n", " context.setPositions(positions)\n", " state = context.getState(getEnergy=True)\n", - " energy = state.getPotentialEnergy() / unit.kilocalories_per_mole\n", + " energy = state.getPotentialEnergy().in_units_of(unit.kilocalories_per_mole)\n", " return energy" ] }, @@ -63,116 +64,399 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "## Load an OEMol, evaluate energy before and after a parameter modification" + "## Example 1: Load a molecule and evaluate its energy before and after a parameter modification\n", + "\n", + "In this example, we load a single ethanol molecule with geometry information, parameterize it using the smirnoff99Frosst forcefield, and evaluate its energy. We then modify the parameter that is applied to the C-O-H angle and re-evaluate the energy.\n", + "\n" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Load a molecule" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [], + "source": [ + "molecule = Molecule.from_file(get_data_filename('molecules/ethanol.mol2'))" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Get positions for use below" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [], + "source": [ + "positions = molecule.conformers[0]" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Load the smirnoff99Frosst forcefield file" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [], + "source": [ + "ff = ForceField('smirnoff99Frosst.offxml')" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Generate an openforcefield Topology containing only this molecule" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [], + "source": [ + "topology = molecule.to_topology()" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Parameterize the molecule, creating an OpenMM system" ] }, { "cell_type": "code", "execution_count": 7, "metadata": {}, + "outputs": [], + "source": [ + "orig_system = ff.create_openmm_system(topology)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Calculate energy before parameter modification" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "Original energy: -20.9. New energy: -22.1\n" + "Original energy: -0.27712854782892227 kcal/mol\n" ] } ], "source": [ - "# Load simple OEMol\n", - "verbose = False\n", - "# Load one of the provided files\n", - "ifs = oechem.oemolistream(get_data_filename('molecules/AlkEthOH_c100.mol2'))\n", - "mol = oechem.OEMol()\n", - "# This uses parm@frosst atom types, so make sure to use the forcefield-flavor reader\n", - "flavor = oechem.OEIFlavor_Generic_Default | oechem.OEIFlavor_MOL2_Default | oechem.OEIFlavor_MOL2_Forcefield\n", - "ifs.SetFlavor( oechem.OEFormat_MOL2, flavor)\n", - "oechem.OEReadMolecule(ifs, mol )\n", - "# Perceive tripos types\n", - "oechem.OETriposAtomNames(mol)\n", + "orig_energy = get_energy(orig_system, positions)\n", + "print(f\"Original energy: {orig_energy}\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Get parameters for the C-O-H angle" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": {}, + "outputs": [], + "source": [ + "smirks = '[*:1]-[#8:2]-[*:3]' # SMIRKS for the parameter to retrieve\n", + "parameter = ff.get_handler('Angles').parameters[smirks]" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Modify the parameters" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "metadata": {}, + "outputs": [], + "source": [ + "parameter.k *= 0.9\n", + "parameter.angle *= 1.1" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Evaluate energy after parameter modification" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "metadata": {}, + "outputs": [], + "source": [ + "new_system = ff.create_openmm_system(topology)\n", + "new_energy = get_energy(new_system, positions)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Print out energy" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Original energy: -0.27712854782892227 kcal/mol. New energy: 3.318374972954307 kcal/mol\n" + ] + } + ], + "source": [ + "print(f\"Original energy: {orig_energy}. New energy: {new_energy}\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Example 2: Inspect and manipulate nonbonded treatment\n", "\n", - "#Get positions for use below\n", - "coordinates = mol.GetCoords()\n", - "natoms=len(coordinates)\n", - "positions = np.zeros([natoms,3], np.float32)\n", - "for index in range(natoms):\n", - " (x,y,z) = coordinates[index]\n", - " positions[index,0] = x\n", - " positions[index,1] = y\n", - " positions[index,2] = z\n", - "positions = unit.Quantity(positions, unit.angstroms)\n", + "The SMIRNOFF spec aims to specify _all aspects of a system that contribute to the energy_ within the `ForceField` object. This includes the treatment of long-range electrostatics and van der Waals interactions. This may be different for some users, as other packages set these parameters at runtime, for example in an AMBER `mdin` file or GROMACS `MDP` file. \n", "\n", - "# Load forcefield file\n", - "ffxml = get_data_filename('forcefield/Frosst_AlkEthOH.offxml')\n", - "ff = ForceField(ffxml)\n", + "This example evaluates the energy of a periodic box of solvent molecules using the \"standard\" `smirnoff99Frosst` settings (PME for electrostatics, 9 Angstrom cutoff for vdW interactions). It then changes the `ForceField`'s vdW treatment method to \"PME\" and re-evaluates the energy.\n", "\n", - "# Generate a topology\n", - "topology = generateTopologyFromOEMol(mol)\n", + "
\n", + " Note: The Open Force Field toolkit ensures that its `create_openmm_system` function produces a system that employs the `ForceField`-specified nonbonded treatment. However, operations which convert this system to AMBER or GROMACS-format topologies/structures are likely to lose these details, as there is no equivalent data field in those objects. In the future we will work on developing robust ways to create other system formats which preserve all details of a `ForceField` object.\n", + "
" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "The vdW method is currently set to: cutoff\n" + ] + } + ], + "source": [ + "# Create a new ForceField containing the smirnoff99Frosst parameter set:\n", + "forcefield = ForceField('smirnoff99Frosst.offxml')\n", + "# Inspect the long-range van der Waals method:\n", + "vdw_handler = forcefield.get_handler('vdW')\n", + "print(f\"The vdW method is currently set to: {vdw_handler.method}\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Select a solvent box to parameterize. \n", "\n", - "# Create initial system\n", - "system = ff.createSystem(topology, [mol], verbose=verbose)\n", + "
\n", + " Note: This process will parameterize water using smirnoff99Frosst parameters. We do not recommend this, and instead suggest parameterizing water externally with a model like TIP3P and merging systems using ParmEd.\n", + "
" + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "metadata": {}, + "outputs": [], + "source": [ + "from simtk.openmm import app\n", "\n", - "# Get initial energy before parameter modification\n", - "old_energy=get_energy(system, positions)\n", + "# A 239-molecule mixture of cyclohexane and ethanol\n", + "pdbfile = app.PDBFile(get_data_filename('systems/packmol_boxes/cyclohexane_ethanol_0.4_0.6.pdb'))\n", "\n", - "# Get params for an angle\n", - "params = ff.getParameter(smirks='[a,A:1]-[#6X4:2]-[a,A:3]')\n", - "# Modify params\n", - "params['k']='0.0'\n", - "ff.setParameter(params, smirks='[a,A:1]-[#6X4:2]-[a,A:3]')\n", + "# A 340-molecule mixture of propane, methane, and butanol.\n", + "#pdbfile = app.PDBFile(get_data_filename('systems/packmol_boxes/propane_methane_butanol_0.2_0.3_0.5.pdb'))\n", "\n", - "# Evaluate energy after parameter modification\n", - "system=ff.createSystem(topology, [mol], verbose=verbose)\n", - "energy=get_energy(system, positions)\n", + "# One cyclohexane in a box of roughly 1400 waters\n", + "#pdbfile = app.PDBFile(get_data_filename('systems/packmol_boxes/cyclohexane_water.pdb'))\n", "\n", - "# Print out energy\n", - "print(\"Original energy: %.3g. New energy: %.3g\" % (old_energy, energy))" + "# One ethanol in a box of roughly 1300 waters\n", + "#pdbfile = app.PDBFile(get_data_filename('systems/packmol_boxes/ethanol_water.pdb'))\n", + "\n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "## Take a look at what other info is provided on parameters and how to access it" + "Provide a \"complete\" (including bond orders, charges, and stereochemistry) representation of each molecule that might be in the PDB. This is necessary because a PDB representation of a molecule does not contain sufficient information for parameterization." ] }, { "cell_type": "code", - "execution_count": 8, + "execution_count": 15, + "metadata": {}, + "outputs": [], + "source": [ + "molecules = [Molecule.from_smiles('C'), # methane\n", + " Molecule.from_smiles('CCC'),# propane\n", + " Molecule.from_smiles('CCCCO'), # butanol\n", + " Molecule.from_smiles('O'), # water\n", + " Molecule.from_smiles('CCO'), #ethanol\n", + " Molecule.from_smiles('C1CCCCC1'), #cyclohexane\n", + " ]" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Create an Open Force Field Topology object by matching the Open Force Field molecules defined above to those in the PDB\n", + "\n", + "
\n", + " Note: This function is currently unoptimized and may take a minute to run.\n", + "
" + ] + }, + { + "cell_type": "code", + "execution_count": 16, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "{'smirks': '[#6X4:1]-[#6X4:2]', 'length': '1.526', 'k': '620.0', 'id': 'b0001', 'parent_id': 'b0001'}\n", - "None\n" + "Original energy: 6304.242805926919 kcal/mol\n" ] } ], "source": [ - "# Load forcefield file\n", - "ffxml = get_data_filename('forcefield/Frosst_AlkEthOH.offxml')\n", - "ff = ForceField(ffxml)\n", - "\n", - "# Get a parameter by parameter id\n", - "param = ff.getParameter(paramID='b0001')\n", - "print(param)\n", - "\n", - "# Get a parameter with a search restricted to a particular section, by smirks\n", - "param = ff.getParameter(smirks='[$([#1]-C):1]', force_type='NonbondedForce')\n", - "print(param)" + "top = Topology.from_openmm(pdbfile.topology, unique_molecules=molecules)\n", + "orig_system = forcefield.create_openmm_system(top)\n", + "orig_energy = get_energy(orig_system, pdbfile.getPositions())\n", + "print(f\"Original energy: {orig_energy}\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Change the long-range van der Waals method to be PME" + ] + }, + { + "cell_type": "code", + "execution_count": 17, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "The vdW method is currently set to: PME\n" + ] + } + ], + "source": [ + "vdw_handler.method = 'PME'\n", + "print(f\"The vdW method is currently set to: {vdw_handler.method}\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "The Open Force Field toolkit applies vdW parameters using a SMIRKS-based typing scheme. Inspect the first few vdW parameters. These can be changed programmatically, as shown in example 1." ] }, { "cell_type": "code", - "execution_count": null, + "execution_count": 18, "metadata": { - "collapsed": true + "scrolled": true }, - "outputs": [], - "source": [] + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\n", + "\n", + "\n" + ] + } + ], + "source": [ + "for vdw_param in forcefield.get_handler('vdW').parameters[0:3]:\n", + " print(vdw_param)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Now recompute the energy of the system using PME for long-range vdW interactions\n", + "
\n", + " Note: This function is currently unoptimized and may take a minute to run.\n", + "
" + ] + }, + { + "cell_type": "code", + "execution_count": 19, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Original energy (with LJ cutoff): 6304.242805926919 kcal/mol\n", + "New energy (using LJ PME): 4155.516177700764 kcal/mol\n" + ] + } + ], + "source": [ + "new_system = forcefield.create_openmm_system(top)\n", + "new_energy = get_energy(new_system, pdbfile.getPositions())\n", + "\n", + "print(f\"Original energy (with LJ cutoff): {orig_energy}\")\n", + "print(f\"New energy (using LJ PME): {new_energy}\")" + ] } ], "metadata": { @@ -191,7 +475,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.5.3" + "version": "3.6.8" } }, "nbformat": 4, diff --git a/examples/forcefield_modification/README.md b/examples/forcefield_modification/README.md new file mode 100644 index 000000000..ce4a98c1e --- /dev/null +++ b/examples/forcefield_modification/README.md @@ -0,0 +1,3 @@ +## Manipulating SMIRNOFF parameters after loading into a `ForceField` object + +In this example, we illustrate how to use the API for manipulating SMIRNOFF parameters after they are loaded into a `ForceField` object. diff --git a/examples/host_guest_simulation/README.md b/examples/host_guest_simulation/README.md deleted file mode 100644 index 1453f1793..000000000 --- a/examples/host_guest_simulation/README.md +++ /dev/null @@ -1,17 +0,0 @@ -# Setting up a host-guest simulation using SMIRNOFF parameters - -This attempts to provide an example of how easy it is to set up rather nontrivial simulations with SMIRNOFF force fields. -In this case we will begin with a guest SMILES string and a 3D structure of a host, dock the host into the guest, solvate, and proceed to simulations. - -## Authorship - -Example provided by David Mobley (UCI) - -## Source materials -- Based in part on a host-guest [docking Jupyter notebook](https://github.com/MobleyLab/SAMPL6/blob/master/host_guest/GenerateInputs.ipynb) I constructed for SAMPL6 - - -## Manifest -- smirnoff_host_guest.ipynb -- hbonds.offxml: Force field XML file for constraining hbonds (from https://github.com/MobleyLab/SMIRNOFF_paper_code/blob/master/scripts/hbonds.offxml, courtesy Andrea Rizzi ) -- OA.mol2: mol2 file of Octa Acid with AM1-BCC charges, as distributed with SAMPL5 (where it was labeled OAH.mol2). Atom types converted from GAFF to SYBYL via Antechember. diff --git a/examples/inspect_assigned_parameters/README.md b/examples/inspect_assigned_parameters/README.md new file mode 100644 index 000000000..06aa7ad14 --- /dev/null +++ b/examples/inspect_assigned_parameters/README.md @@ -0,0 +1,3 @@ +## Inspecting which SMIRNOFF parameters are assigned to specific molecules + +These examples illustrate how to inspect which SMIRNOFF parameters are assigned to specific atoms for a test molecule, and to sets of molecules. diff --git a/examples/inspect_assigned_parameters/inspect_assigned_parameters.ipynb b/examples/inspect_assigned_parameters/inspect_assigned_parameters.ipynb new file mode 100644 index 000000000..693367eea --- /dev/null +++ b/examples/inspect_assigned_parameters/inspect_assigned_parameters.ipynb @@ -0,0 +1,492 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Usage example showing how to determine which parameters are used for specific molecules\n", + "\n", + "The Open Force Field toolkit applies parameters based on the [SMARTS/SMIRKS language](http://www.daylight.com/dayhtml_tutorials/languages/smarts/). These examples are intended to expose how `ForceField` assigns SMIRKS-based parameters to test molecules.\n", + "\n", + "
\n", + " Note: This API is not final, and we will be implementing a better way to visualize assigned parameters in the future.\n", + "
" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Example 1: Create an example molecule and label the force terms applied to it.\n", + "\n", + "This example shows the parameters applied to a single molecule that is created from a SMILES string. \n", + "\n", + "The first output section consists of `Bond` parameters that would be assigned to the molecule. Each bond is described by the indices of the two atoms it connects, its \"parameter ID\", and the SMIRKS that caused it to match the target bond. \n", + "\n", + "The other `ParameterHandler`s print in order after that. \n", + "\n", + "Note that the `ToolkitAM1BCC` and `Electrostatics` handlers do not assign SMIRKS-based parameters, therefore they do not print any match information." + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "metadata": { + "scrolled": false + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Forces for molecule 0\n", + "\n", + "Bonds:\n", + "atoms: 0 1 parameter_id: b6 smirks [#6X3:1]=[#6X3:2]\n", + "atoms: 0 4 parameter_id: b84 smirks [#6X3:1]-[#1:2]\n", + "atoms: 0 5 parameter_id: b84 smirks [#6X3:1]-[#1:2]\n", + "atoms: 1 2 parameter_id: b8 smirks [#6X3:1]-[#7X3:2]\n", + "atoms: 1 3 parameter_id: b2 smirks [#6X4:1]-[#6X3:2]\n", + "atoms: 2 6 parameter_id: b86 smirks [#7:1]-[#1:2]\n", + "atoms: 2 7 parameter_id: b86 smirks [#7:1]-[#1:2]\n", + "atoms: 3 8 parameter_id: b83 smirks [#6X4:1]-[#1:2]\n", + "atoms: 3 9 parameter_id: b83 smirks [#6X4:1]-[#1:2]\n", + "atoms: 3 10 parameter_id: b83 smirks [#6X4:1]-[#1:2]\n", + "\n", + "Angles:\n", + "atoms: 0 1 2 parameter_id: a10 smirks [*:1]~[#6X3:2]~[*:3]\n", + "atoms: 0 1 3 parameter_id: a10 smirks [*:1]~[#6X3:2]~[*:3]\n", + "atoms: 1 0 4 parameter_id: a11 smirks [#1:1]-[#6X3:2]~[*:3]\n", + "atoms: 1 0 5 parameter_id: a11 smirks [#1:1]-[#6X3:2]~[*:3]\n", + "atoms: 1 2 6 parameter_id: a20 smirks [#1:1]-[#7X3$(*~[#6X3,#6X2,#7X2+0]):2]-[*:3]\n", + "atoms: 1 2 7 parameter_id: a20 smirks [#1:1]-[#7X3$(*~[#6X3,#6X2,#7X2+0]):2]-[*:3]\n", + "atoms: 1 3 8 parameter_id: a1 smirks [*:1]~[#6X4:2]-[*:3]\n", + "atoms: 1 3 9 parameter_id: a1 smirks [*:1]~[#6X4:2]-[*:3]\n", + "atoms: 1 3 10 parameter_id: a1 smirks [*:1]~[#6X4:2]-[*:3]\n", + "atoms: 2 1 3 parameter_id: a10 smirks [*:1]~[#6X3:2]~[*:3]\n", + "atoms: 4 0 5 parameter_id: a12 smirks [#1:1]-[#6X3:2]-[#1:3]\n", + "atoms: 6 2 7 parameter_id: a20 smirks [#1:1]-[#7X3$(*~[#6X3,#6X2,#7X2+0]):2]-[*:3]\n", + "atoms: 8 3 9 parameter_id: a2 smirks [#1:1]-[#6X4:2]-[#1:3]\n", + "atoms: 8 3 10 parameter_id: a2 smirks [#1:1]-[#6X4:2]-[#1:3]\n", + "atoms: 9 3 10 parameter_id: a2 smirks [#1:1]-[#6X4:2]-[#1:3]\n", + "\n", + "ProperTorsions:\n", + "atoms: 0 1 2 6 parameter_id: t69 smirks [*:1]~[#7X3,#7X2-1:2]-!@[#6X3:3]~[*:4]\n", + "atoms: 0 1 2 7 parameter_id: t69 smirks [*:1]~[#7X3,#7X2-1:2]-!@[#6X3:3]~[*:4]\n", + "atoms: 0 1 3 8 parameter_id: t20 smirks [*:1]-[#6X4:2]-[#6X3:3]=[*:4]\n", + "atoms: 0 1 3 9 parameter_id: t20 smirks [*:1]-[#6X4:2]-[#6X3:3]=[*:4]\n", + "atoms: 0 1 3 10 parameter_id: t20 smirks [*:1]-[#6X4:2]-[#6X3:3]=[*:4]\n", + "atoms: 2 1 0 4 parameter_id: t45 smirks [*:1]-,:[#6X3:2]=[#6X3:3]-,:[*:4]\n", + "atoms: 2 1 0 5 parameter_id: t45 smirks [*:1]-,:[#6X3:2]=[#6X3:3]-,:[*:4]\n", + "atoms: 2 1 3 8 parameter_id: t17 smirks [*:1]~[#6X3:2]-[#6X4:3]-[*:4]\n", + "atoms: 2 1 3 9 parameter_id: t17 smirks [*:1]~[#6X3:2]-[#6X4:3]-[*:4]\n", + "atoms: 2 1 3 10 parameter_id: t17 smirks [*:1]~[#6X3:2]-[#6X4:3]-[*:4]\n", + "atoms: 3 1 0 4 parameter_id: t45 smirks [*:1]-,:[#6X3:2]=[#6X3:3]-,:[*:4]\n", + "atoms: 3 1 0 5 parameter_id: t45 smirks [*:1]-,:[#6X3:2]=[#6X3:3]-,:[*:4]\n", + "atoms: 3 1 2 6 parameter_id: t69 smirks [*:1]~[#7X3,#7X2-1:2]-!@[#6X3:3]~[*:4]\n", + "atoms: 3 1 2 7 parameter_id: t69 smirks [*:1]~[#7X3,#7X2-1:2]-!@[#6X3:3]~[*:4]\n", + "\n", + "ImproperTorsions:\n", + "atoms: 0 1 2 3 parameter_id: i1 smirks [*:1]~[#6X3:2](~[*:3])~[*:4]\n", + "atoms: 1 0 4 5 parameter_id: i1 smirks [*:1]~[#6X3:2](~[*:3])~[*:4]\n", + "atoms: 1 2 6 7 parameter_id: i3 smirks [*:1]~[#7X3$(*~[#6X3]):2](~[*:3])~[*:4]\n", + "\n", + "vdW:\n", + "atoms: 0 parameter_id: n14 smirks [#6:1]\n", + "atoms: 1 parameter_id: n14 smirks [#6:1]\n", + "atoms: 2 parameter_id: n20 smirks [#7:1]\n", + "atoms: 3 parameter_id: n16 smirks [#6X4:1]\n", + "atoms: 4 parameter_id: n7 smirks [#1:1]-[#6X3]\n", + "atoms: 5 parameter_id: n7 smirks [#1:1]-[#6X3]\n", + "atoms: 6 parameter_id: n11 smirks [#1:1]-[#7]\n", + "atoms: 7 parameter_id: n11 smirks [#1:1]-[#7]\n", + "atoms: 8 parameter_id: n2 smirks [#1:1]-[#6X4]\n", + "atoms: 9 parameter_id: n2 smirks [#1:1]-[#6X4]\n", + "atoms: 10 parameter_id: n2 smirks [#1:1]-[#6X4]\n", + "\n", + "Electrostatics:\n", + "\n", + "ToolkitAM1BCC:\n" + ] + } + ], + "source": [ + "from openforcefield.topology import Molecule, Topology\n", + "from openforcefield.typing.engines.smirnoff import ForceField\n", + "\n", + "# Create a simple molecule from SMILES and turn it into a topology.\n", + "molecule = Molecule.from_smiles('C=C(N)(C)')\n", + "topology = Topology.from_molecules([molecule])\n", + "\n", + "# Let's label using the smirnoff99Frosst force field\n", + "forcefield = ForceField('smirnoff99Frosst.offxml')\n", + "\n", + "# Run the molecule labeling\n", + "molecule_force_list = forcefield.label_molecules(topology)\n", + "\n", + "# Print out a formatted description of the parameters applied to this molecule\n", + "for mol_idx, mol_forces in enumerate(molecule_force_list):\n", + " print(f'Forces for molecule {mol_idx}')\n", + " for force_tag, force_dict in mol_forces.items():\n", + " print(f\"\\n{force_tag}:\")\n", + " for (atom_indices, parameter) in force_dict.items():\n", + " atomstr=''\n", + " for idx in atom_indices:\n", + " atomstr += '%3s' % idx\n", + " print(\"atoms: %s parameter_id: %s smirks %s\" % (atomstr, parameter.id, parameter.smirks) )\n" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Example 2: Analyze the parameters assigned to groups of molecules\n", + "\n", + "Here we analyze which parameters are applied to a group of molecules. \n", + "\n", + "This example uses `get_molecule_parameterIDs`, a simple utility function similar to `label_molecules`, but intended for use on large datasets. `get_molecule_parameterIDs` processes a list of molecules using a specified `ForceField` and returns the parameters that would be assigned to each molecule, grouping the results both by molecule and by parameter.\n", + "\n", + "This example may be useful when adding new parameters, to ensure that they are applied to molecules in a given data set. \n", + "\n", + "This example also highlights the difference between \"specific\" and \"generic\" parameters. In the SMIRNOFF format, more than one SMIRKS-based parameter may match a motif in a molecule. Therefore, some parameters have precedence over others. Parameters which are \"generic\" are listed near the top of a parameter section, while more \"specific\" parameters occur near the end of the section. During parameter assignment, the furthest-down parameter that matches a motif in the molecule is assigned. \n", + "\n", + "During actual parameter assignment, if the toolkit is unable to assign SMIRKS-based parameters to any part of a molecule, an `UnassignedValenceParameterException` will be raised." + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": { + "scrolled": false + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Molecules with parameter IDs:\n", + "a1\n", + "\t [H][C@]1(C(OC(O1)([H])[H])([H])[H])O[H]\n", + "\t [H][C@@]1([C@](OC1([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1([C@](OC(C(C1([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1(C(O[C@](O1)([H])O[H])([H])[H])O[H]\n", + "\t [H]C1(C(C(O1)([H])[H])([H])O[H])[H]\n", + "\t [H][C@@]1([C@](C(C(C1([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1(C([C@@](OC1([H])[H])([H])O[H])([H])[H])O[H]\n", + "\t [H][C@]1(C([C@](O1)([H])O[H])([H])[H])O[H]\n", + "\t [H][C@]1([C@@](C(OC(C(C1([H])[H])([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "a2\n", + "\t [H][C@]1(C(OC(O1)([H])[H])([H])[H])O[H]\n", + "\t [H]C1(C(C(C1([H])O[H])([H])[H])([H])O[H])[H]\n", + "\t [H][C@@]1([C@](OC1([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1([C@](OC(C(C1([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1(C(O[C@](O1)([H])O[H])([H])[H])O[H]\n", + "\t [H]C1(C(C(O1)([H])[H])([H])O[H])[H]\n", + "\t [H][C@@]1([C@](C(C(C1([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1(C([C@@](OC1([H])[H])([H])O[H])([H])[H])O[H]\n", + "\t [H][C@]1(C([C@](O1)([H])O[H])([H])[H])O[H]\n", + "\t [H][C@]1([C@@](C(OC(C(C1([H])[H])([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "a27\n", + "\t [H][C@]1(C(OC(O1)([H])[H])([H])[H])O[H]\n", + "\t [H]C1(C(C(C1([H])O[H])([H])[H])([H])O[H])[H]\n", + "\t [H][C@@]1([C@](OC1([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1([C@](OC(C(C1([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1(C(O[C@](O1)([H])O[H])([H])[H])O[H]\n", + "\t [H]C1(C(C(O1)([H])[H])([H])O[H])[H]\n", + "\t [H][C@@]1([C@](C(C(C1([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1(C([C@@](OC1([H])[H])([H])O[H])([H])[H])O[H]\n", + "\t [H][C@]1(C([C@](O1)([H])O[H])([H])[H])O[H]\n", + "\t [H][C@]1([C@@](C(OC(C(C1([H])[H])([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "a7\n", + "\t [H][C@]1(C([C@](O1)([H])O[H])([H])[H])O[H]\n", + "\t [H]C1(C(C(C1([H])O[H])([H])[H])([H])O[H])[H]\n", + "\t [H]C1(C(C(O1)([H])[H])([H])O[H])[H]\n", + "\t [H][C@@]1([C@](OC1([H])[H])([H])O[H])O[H]\n", + "a8\n", + "\t [H][C@]1(C([C@](O1)([H])O[H])([H])[H])O[H]\n", + "\t [H]C1(C(C(C1([H])O[H])([H])[H])([H])O[H])[H]\n", + "\t [H]C1(C(C(O1)([H])[H])([H])O[H])[H]\n", + "\t [H][C@@]1([C@](OC1([H])[H])([H])O[H])O[H]\n", + "a9\n", + "\t [H][C@]1(C([C@](O1)([H])O[H])([H])[H])O[H]\n", + "\t [H]C1(C(C(C1([H])O[H])([H])[H])([H])O[H])[H]\n", + "\t [H]C1(C(C(O1)([H])[H])([H])O[H])[H]\n", + "\t [H][C@@]1([C@](OC1([H])[H])([H])O[H])O[H]\n", + "b1\n", + "\t [H][C@]1(C(OC(O1)([H])[H])([H])[H])O[H]\n", + "\t [H]C1(C(C(C1([H])O[H])([H])[H])([H])O[H])[H]\n", + "\t [H][C@@]1([C@](OC1([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1([C@](OC(C(C1([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1(C(O[C@](O1)([H])O[H])([H])[H])O[H]\n", + "\t [H]C1(C(C(O1)([H])[H])([H])O[H])[H]\n", + "\t [H][C@@]1([C@](C(C(C1([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1(C([C@@](OC1([H])[H])([H])O[H])([H])[H])O[H]\n", + "\t [H][C@]1(C([C@](O1)([H])O[H])([H])[H])O[H]\n", + "\t [H][C@]1([C@@](C(OC(C(C1([H])[H])([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "b14\n", + "\t [H][C@]1(C(OC(O1)([H])[H])([H])[H])O[H]\n", + "\t [H]C1(C(C(C1([H])O[H])([H])[H])([H])O[H])[H]\n", + "\t [H][C@@]1([C@](OC1([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1([C@](OC(C(C1([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1(C(O[C@](O1)([H])O[H])([H])[H])O[H]\n", + "\t [H]C1(C(C(O1)([H])[H])([H])O[H])[H]\n", + "\t [H][C@@]1([C@](C(C(C1([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1(C([C@@](OC1([H])[H])([H])O[H])([H])[H])O[H]\n", + "\t [H][C@]1(C([C@](O1)([H])O[H])([H])[H])O[H]\n", + "\t [H][C@]1([C@@](C(OC(C(C1([H])[H])([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "b15\n", + "\t [H][C@]1(C(OC(O1)([H])[H])([H])[H])O[H]\n", + "\t [H][C@@]1([C@](OC1([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1([C@](OC(C(C1([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1(C(O[C@](O1)([H])O[H])([H])[H])O[H]\n", + "\t [H]C1(C(C(O1)([H])[H])([H])O[H])[H]\n", + "\t [H][C@@]1(C([C@@](OC1([H])[H])([H])O[H])([H])[H])O[H]\n", + "\t [H][C@]1(C([C@](O1)([H])O[H])([H])[H])O[H]\n", + "\t [H][C@]1([C@@](C(OC(C(C1([H])[H])([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "b83\n", + "\t [H][C@]1(C(OC(O1)([H])[H])([H])[H])O[H]\n", + "\t [H]C1(C(C(C1([H])O[H])([H])[H])([H])O[H])[H]\n", + "\t [H][C@@]1([C@](OC1([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1([C@](OC(C(C1([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1(C(O[C@](O1)([H])O[H])([H])[H])O[H]\n", + "\t [H]C1(C(C(O1)([H])[H])([H])O[H])[H]\n", + "\t [H][C@@]1([C@](C(C(C1([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1(C([C@@](OC1([H])[H])([H])O[H])([H])[H])O[H]\n", + "\t [H][C@]1(C([C@](O1)([H])O[H])([H])[H])O[H]\n", + "\t [H][C@]1([C@@](C(OC(C(C1([H])[H])([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "b87\n", + "\t [H][C@]1(C(OC(O1)([H])[H])([H])[H])O[H]\n", + "\t [H]C1(C(C(C1([H])O[H])([H])[H])([H])O[H])[H]\n", + "\t [H][C@@]1([C@](OC1([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1([C@](OC(C(C1([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1(C(O[C@](O1)([H])O[H])([H])[H])O[H]\n", + "\t [H]C1(C(C(O1)([H])[H])([H])O[H])[H]\n", + "\t [H][C@@]1([C@](C(C(C1([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1(C([C@@](OC1([H])[H])([H])O[H])([H])[H])O[H]\n", + "\t [H][C@]1(C([C@](O1)([H])O[H])([H])[H])O[H]\n", + "\t [H][C@]1([C@@](C(OC(C(C1([H])[H])([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "n12\n", + "\t [H][C@]1(C(OC(O1)([H])[H])([H])[H])O[H]\n", + "\t [H]C1(C(C(C1([H])O[H])([H])[H])([H])O[H])[H]\n", + "\t [H][C@@]1([C@](OC1([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1([C@](OC(C(C1([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1(C(O[C@](O1)([H])O[H])([H])[H])O[H]\n", + "\t [H]C1(C(C(O1)([H])[H])([H])O[H])[H]\n", + "\t [H][C@@]1([C@](C(C(C1([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1(C([C@@](OC1([H])[H])([H])O[H])([H])[H])O[H]\n", + "\t [H][C@]1(C([C@](O1)([H])O[H])([H])[H])O[H]\n", + "\t [H][C@]1([C@@](C(OC(C(C1([H])[H])([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "n16\n", + "\t [H][C@]1(C(OC(O1)([H])[H])([H])[H])O[H]\n", + "\t [H]C1(C(C(C1([H])O[H])([H])[H])([H])O[H])[H]\n", + "\t [H][C@@]1([C@](OC1([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1([C@](OC(C(C1([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1(C(O[C@](O1)([H])O[H])([H])[H])O[H]\n", + "\t [H]C1(C(C(O1)([H])[H])([H])O[H])[H]\n", + "\t [H][C@@]1([C@](C(C(C1([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1(C([C@@](OC1([H])[H])([H])O[H])([H])[H])O[H]\n", + "\t [H][C@]1(C([C@](O1)([H])O[H])([H])[H])O[H]\n", + "\t [H][C@]1([C@@](C(OC(C(C1([H])[H])([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "n18\n", + "\t [H][C@]1(C(OC(O1)([H])[H])([H])[H])O[H]\n", + "\t [H][C@@]1([C@](OC1([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1([C@](OC(C(C1([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1(C(O[C@](O1)([H])O[H])([H])[H])O[H]\n", + "\t [H]C1(C(C(O1)([H])[H])([H])O[H])[H]\n", + "\t [H][C@@]1(C([C@@](OC1([H])[H])([H])O[H])([H])[H])O[H]\n", + "\t [H][C@]1(C([C@](O1)([H])O[H])([H])[H])O[H]\n", + "\t [H][C@]1([C@@](C(OC(C(C1([H])[H])([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "n19\n", + "\t [H][C@]1(C(OC(O1)([H])[H])([H])[H])O[H]\n", + "\t [H]C1(C(C(C1([H])O[H])([H])[H])([H])O[H])[H]\n", + "\t [H][C@@]1([C@](OC1([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1([C@](OC(C(C1([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1(C(O[C@](O1)([H])O[H])([H])[H])O[H]\n", + "\t [H]C1(C(C(O1)([H])[H])([H])O[H])[H]\n", + "\t [H][C@@]1([C@](C(C(C1([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1(C([C@@](OC1([H])[H])([H])O[H])([H])[H])O[H]\n", + "\t [H][C@]1(C([C@](O1)([H])O[H])([H])[H])O[H]\n", + "\t [H][C@]1([C@@](C(OC(C(C1([H])[H])([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "n2\n", + "\t [H]C1(C(C(C1([H])O[H])([H])[H])([H])O[H])[H]\n", + "\t [H][C@@]1([C@](OC(C(C1([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1([C@](C(C(C1([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1(C([C@@](OC1([H])[H])([H])O[H])([H])[H])O[H]\n", + "\t [H][C@]1(C([C@](O1)([H])O[H])([H])[H])O[H]\n", + "\t [H][C@]1([C@@](C(OC(C(C1([H])[H])([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "n3\n", + "\t [H][C@]1(C(OC(O1)([H])[H])([H])[H])O[H]\n", + "\t [H]C1(C(C(C1([H])O[H])([H])[H])([H])O[H])[H]\n", + "\t [H][C@@]1([C@](OC1([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1([C@](OC(C(C1([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1(C(O[C@](O1)([H])O[H])([H])[H])O[H]\n", + "\t [H]C1(C(C(O1)([H])[H])([H])O[H])[H]\n", + "\t [H][C@@]1([C@](C(C(C1([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1(C([C@@](OC1([H])[H])([H])O[H])([H])[H])O[H]\n", + "\t [H][C@]1([C@@](C(OC(C(C1([H])[H])([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "n4\n", + "\t [H][C@]1(C(OC(O1)([H])[H])([H])[H])O[H]\n", + "\t [H][C@@]1([C@](OC1([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1([C@](OC(C(C1([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1(C(O[C@](O1)([H])O[H])([H])[H])O[H]\n", + "\t [H][C@@]1(C([C@@](OC1([H])[H])([H])O[H])([H])[H])O[H]\n", + "\t [H][C@]1(C([C@](O1)([H])O[H])([H])[H])O[H]\n", + "n5\n", + "\t [H][C@@]1(C(O[C@](O1)([H])O[H])([H])[H])O[H]\n", + "t1\n", + "\t [H]C1(C(C(C1([H])O[H])([H])[H])([H])O[H])[H]\n", + "\t [H][C@@]1([C@](OC1([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1([C@](OC(C(C1([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "\t [H]C1(C(C(O1)([H])[H])([H])O[H])[H]\n", + "\t [H][C@@]1([C@](C(C(C1([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1(C([C@@](OC1([H])[H])([H])O[H])([H])[H])O[H]\n", + "\t [H][C@]1(C([C@](O1)([H])O[H])([H])[H])O[H]\n", + "\t [H][C@]1([C@@](C(OC(C(C1([H])[H])([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "t2\n", + "\t [H]C1(C(C(C1([H])O[H])([H])[H])([H])O[H])[H]\n", + "\t [H][C@@]1([C@](OC(C(C1([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1([C@](C(C(C1([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1(C([C@@](OC1([H])[H])([H])O[H])([H])[H])O[H]\n", + "\t [H][C@]1([C@@](C(OC(C(C1([H])[H])([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "t3\n", + "\t [H][C@]1(C(OC(O1)([H])[H])([H])[H])O[H]\n", + "\t [H]C1(C(C(C1([H])O[H])([H])[H])([H])O[H])[H]\n", + "\t [H][C@@]1([C@](OC1([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1([C@](OC(C(C1([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1(C(O[C@](O1)([H])O[H])([H])[H])O[H]\n", + "\t [H]C1(C(C(O1)([H])[H])([H])O[H])[H]\n", + "\t [H][C@@]1([C@](C(C(C1([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1(C([C@@](OC1([H])[H])([H])O[H])([H])[H])O[H]\n", + "\t [H][C@]1(C([C@](O1)([H])O[H])([H])[H])O[H]\n", + "\t [H][C@]1([C@@](C(OC(C(C1([H])[H])([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "t4\n", + "\t [H]C1(C(C(C1([H])O[H])([H])[H])([H])O[H])[H]\n", + "\t [H][C@@]1([C@](OC1([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1([C@](OC(C(C1([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "\t [H]C1(C(C(O1)([H])[H])([H])O[H])[H]\n", + "\t [H][C@@]1([C@](C(C(C1([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1(C([C@@](OC1([H])[H])([H])O[H])([H])[H])O[H]\n", + "\t [H][C@]1(C([C@](O1)([H])O[H])([H])[H])O[H]\n", + "\t [H][C@]1([C@@](C(OC(C(C1([H])[H])([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "t5\n", + "\t [H][C@]1(C(OC(O1)([H])[H])([H])[H])O[H]\n", + "\t [H][C@@]1([C@](OC1([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1([C@](OC(C(C1([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1(C(O[C@](O1)([H])O[H])([H])[H])O[H]\n", + "\t [H]C1(C(C(O1)([H])[H])([H])O[H])[H]\n", + "\t [H][C@@]1([C@](C(C(C1([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1(C([C@@](OC1([H])[H])([H])O[H])([H])[H])O[H]\n", + "\t [H][C@]1([C@@](C(OC(C(C1([H])[H])([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "t84\n", + "\t [H][C@]1(C(OC(O1)([H])[H])([H])[H])O[H]\n", + "\t [H]C1(C(C(C1([H])O[H])([H])[H])([H])O[H])[H]\n", + "\t [H][C@@]1([C@](OC1([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1([C@](OC(C(C1([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1(C(O[C@](O1)([H])O[H])([H])[H])O[H]\n", + "\t [H]C1(C(C(O1)([H])[H])([H])O[H])[H]\n", + "\t [H][C@@]1([C@](C(C(C1([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1(C([C@@](OC1([H])[H])([H])O[H])([H])[H])O[H]\n", + "\t [H][C@]1(C([C@](O1)([H])O[H])([H])[H])O[H]\n", + "\t [H][C@]1([C@@](C(OC(C(C1([H])[H])([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "t85\n", + "\t [H][C@]1(C(OC(O1)([H])[H])([H])[H])O[H]\n", + "\t [H]C1(C(C(C1([H])O[H])([H])[H])([H])O[H])[H]\n", + "\t [H][C@@]1([C@](OC1([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1([C@](OC(C(C1([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1(C(O[C@](O1)([H])O[H])([H])[H])O[H]\n", + "\t [H]C1(C(C(O1)([H])[H])([H])O[H])[H]\n", + "\t [H][C@@]1([C@](C(C(C1([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1(C([C@@](OC1([H])[H])([H])O[H])([H])[H])O[H]\n", + "\t [H][C@]1(C([C@](O1)([H])O[H])([H])[H])O[H]\n", + "\t [H][C@]1([C@@](C(OC(C(C1([H])[H])([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "t86\n", + "\t [H][C@]1(C(OC(O1)([H])[H])([H])[H])O[H]\n", + "\t [H][C@@]1([C@](OC1([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1([C@](OC(C(C1([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1(C(O[C@](O1)([H])O[H])([H])[H])O[H]\n", + "\t [H]C1(C(C(O1)([H])[H])([H])O[H])[H]\n", + "\t [H][C@@]1(C([C@@](OC1([H])[H])([H])O[H])([H])[H])O[H]\n", + "\t [H][C@]1(C([C@](O1)([H])O[H])([H])[H])O[H]\n", + "\t [H][C@]1([C@@](C(OC(C(C1([H])[H])([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "t87\n", + "\t [H][C@]1(C(OC(O1)([H])[H])([H])[H])O[H]\n", + "\t [H][C@@]1([C@](OC1([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1([C@](OC(C(C1([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1(C(O[C@](O1)([H])O[H])([H])[H])O[H]\n", + "\t [H]C1(C(C(O1)([H])[H])([H])O[H])[H]\n", + "\t [H][C@@]1(C([C@@](OC1([H])[H])([H])O[H])([H])[H])O[H]\n", + "\t [H][C@]1(C([C@](O1)([H])O[H])([H])[H])O[H]\n", + "\t [H][C@]1([C@@](C(OC(C(C1([H])[H])([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "t89\n", + "\t [H][C@]1(C(OC(O1)([H])[H])([H])[H])O[H]\n", + "\t [H][C@@]1([C@](OC1([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1([C@](OC(C(C1([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1(C(O[C@](O1)([H])O[H])([H])[H])O[H]\n", + "\t [H][C@@]1(C([C@@](OC1([H])[H])([H])O[H])([H])[H])O[H]\n", + "\t [H][C@]1(C([C@](O1)([H])O[H])([H])[H])O[H]\n", + "t9\n", + "\t [H][C@]1(C(OC(O1)([H])[H])([H])[H])O[H]\n", + "\t [H]C1(C(C(C1([H])O[H])([H])[H])([H])O[H])[H]\n", + "\t [H][C@@]1([C@](OC1([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1([C@](OC(C(C1([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1(C(O[C@](O1)([H])O[H])([H])[H])O[H]\n", + "\t [H]C1(C(C(O1)([H])[H])([H])O[H])[H]\n", + "\t [H][C@@]1([C@](C(C(C1([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n", + "\t [H][C@@]1(C([C@@](OC1([H])[H])([H])O[H])([H])[H])O[H]\n", + "\t [H][C@]1(C([C@](O1)([H])O[H])([H])[H])O[H]\n", + "\t [H][C@]1([C@@](C(OC(C(C1([H])[H])([H])[H])([H])[H])([H])[H])([H])O[H])O[H]\n" + ] + } + ], + "source": [ + "from openforcefield.utils import get_data_filename\n", + "from openforcefield.topology import Molecule\n", + "from openforcefield.typing.engines.smirnoff import ForceField\n", + "from openforcefield.utils.structure import get_molecule_parameterIDs\n", + "\n", + "# Retrieve molecules from the AlkEthOH test set\n", + "mols = Molecule.from_file(get_data_filename('molecules/AlkEthOH_test_filt1_tripos.mol2'))\n", + "# The test set is quite large, so to limit the size of the output we only \n", + "# analyze the first 10 molecules\n", + "mols = mols[:10]\n", + "\n", + "# Let's label using the smirnoff99Frosst force field\n", + "forcefield = ForceField('smirnoff99Frosst.offxml')\n", + "\n", + "# This utility function creates dictionaries describing parameter assignment, \n", + "# grouped both by molecule and by parameter\n", + "parameters_by_molecule, parameters_by_ID = get_molecule_parameterIDs(mols, forcefield)\n", + "\n", + "print(\"Molecules with parameter IDs:\")\n", + "# parameters_by_ID is a dictionary where keys are parameter IDs and values\n", + "# are molecules in which each parameter ID occurs.\n", + "pids_ordered = sorted(list(parameters_by_ID.keys()))\n", + "for pid in pids_ordered:\n", + " print(pid)\n", + " for ids in parameters_by_ID[pid]:\n", + " print('\\t', ids)\n" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.6.8" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/examples/label_molecule/README.md b/examples/label_molecule/README.md deleted file mode 100644 index 5d59cb081..000000000 --- a/examples/label_molecule/README.md +++ /dev/null @@ -1,7 +0,0 @@ -# Usage example showing how to determine which parameters are used for specific molecules - -Shows how to use forcefield to see what SMIRNOFF parameter numbers are assigned to specific atoms for a test molecule (which must be covered by the AlkEthOH parameter set). - -## Manifest -* label_molecule.py: Creates a simple example molecule and uses the labeler to indicate what force terms are applied to which atoms. -* get_parameter_statistics.py: Pulls details on which parameters are used in each molecule, and which molecules each parameter occurs in. diff --git a/examples/label_molecule/get_parameter_statistics.py b/examples/label_molecule/get_parameter_statistics.py deleted file mode 100644 index 36f9674a1..000000000 --- a/examples/label_molecule/get_parameter_statistics.py +++ /dev/null @@ -1,19 +0,0 @@ -#!/bin/env python - -from openforcefield.utils import * -from openforcefield.typing.engines.smirnoff import get_molecule_parameterIDs - -oemols = read_molecules(get_data_filename('molecules/AlkEthOH-tripos.mol2.gz')) -ffxml = get_data_filename('forcefield/Frosst_AlkEthOH.offxml') - -parameters_by_molecule, parameters_by_ID = get_molecule_parameterIDs( oemols, ffxml) - -# Print some info -print "Parameters by molecule:" -for smi in parameters_by_molecule.keys(): - print smi, parameters_by_molecule[smi] - - -print "Molecules with parameter IDs:" -for pid in parameters_by_ID.keys(): - print pid, parameters_by_ID[pid] diff --git a/examples/label_molecule/label_molecule.py b/examples/label_molecule/label_molecule.py deleted file mode 100644 index d8378f10d..000000000 --- a/examples/label_molecule/label_molecule.py +++ /dev/null @@ -1,24 +0,0 @@ -#!/bin/env python - - -from openforcefield.utils import * -from openforcefield.typing.engines.smirnoff import get_molecule_parameterIDs, ForceField - -# Create an oemol -mol = OEMol() -OEParseSmiles(mol, 'CCC') -OEAddExplicitHydrogens(mol) - - -ff = ForceField( get_data_filename('forcefield/Frosst_AlkEthOH.offxml') ) - -labels= ff.labelMolecules( [mol], verbose = True ) -print labels -for mol_entry in range(len(labels)): - for force in labels[mol_entry].keys(): - print("\n%s:" % force) - for (atom_indices, pid, smirks) in labels[mol_entry][force]: - atomstr='' - for idx in atom_indices: - atomstr += '%6s' % idx - print("%s : %s \t smirks %s" % (atomstr, pid, smirks) ) diff --git a/examples/mixedFF_structure/generate_mixedFF_complex.py b/examples/mixedFF_structure/generate_mixedFF_complex.py deleted file mode 100644 index 955f86cc9..000000000 --- a/examples/mixedFF_structure/generate_mixedFF_complex.py +++ /dev/null @@ -1,21 +0,0 @@ -#!/bin/env python - -from simtk.openmm import app -import openforcefield.utils as utils -from openeye import oechem - -molecule = oechem.OEMol() -molpdb = utils.get_data_filename('molecules/toluene.pdb') -with oechem.oemolistream(molpdb) as ifs: - oechem.OEReadMolecule(ifs, molecule) - -molecule_structure = utils.generateSMIRNOFFStructure(molecule) -print('Molecule:', molecule_structure) - -pdbfile = utils.get_data_filename('proteins/T4-protein.pdb') -proteinpdb = app.PDBFile(pdbfile) -protein_structure = utils.generateProteinStructure(proteinpdb) -print('Protein:', protein_structure) - -structure = utils.mergeStructure(protein_structure, molecule_structure) -print('Complex:', structure) diff --git a/examples/partial_bondorder/README.md b/examples/partial_bondorder/README.md deleted file mode 100644 index 6a1cd29f7..000000000 --- a/examples/partial_bondorder/README.md +++ /dev/null @@ -1,6 +0,0 @@ -# Example/test showing how a SMIRNOFF file with partial bond order information can be used to have a single line give bond parameters relevant for benzene but also singly and doubly-bonded trivalent carbon. - - -## Manifest -* `Frosst_AlkEthOH_extracarbons.offxml`: SMIRNOFF FFXML file adding extra carbon parameters to cover benzene (adapted from work by Christopher Bayly, and using partial bond orders to compress the [#6X3]-[#6X3], [#6X3]:[#6X3] and [#6X3]=[#6X3] bond parameters to a single line. -* `test_partialbondorder.ipynb`: Apply these parameters to benzene and print info about the bonded parameters which are assigned. diff --git a/examples/using_smirnoff_in_amber_or_gromacs/1_cyclohexane_1_ethanol.pdb b/examples/using_smirnoff_in_amber_or_gromacs/1_cyclohexane_1_ethanol.pdb new file mode 100644 index 000000000..6c44bc5ca --- /dev/null +++ b/examples/using_smirnoff_in_amber_or_gromacs/1_cyclohexane_1_ethanol.pdb @@ -0,0 +1,61 @@ +REMARK 1 CREATED WITH MDTraj 1.7.2, 2016-06-27 +CRYST1 31.885 31.885 31.885 90.00 90.00 90.00 P 1 1 +MODEL 0 +ATOM 1 C1 ZBE A 1 12.532 10.813 10.386 1.00 0.00 C +ATOM 2 C2 ZBE A 1 12.348 10.339 11.825 1.00 0.00 C +ATOM 3 C3 ZBE A 1 10.880 10.365 12.244 1.00 0.00 C +ATOM 4 C4 ZBE A 1 10.256 11.739 12.020 1.00 0.00 C +ATOM 5 C5 ZBE A 1 10.439 12.213 10.581 1.00 0.00 C +ATOM 6 C6 ZBE A 1 11.907 12.187 10.162 1.00 0.00 C +ATOM 7 H1 ZBE A 1 12.072 10.088 9.703 1.00 0.00 H +ATOM 8 H2 ZBE A 1 13.600 10.849 10.143 1.00 0.00 H +ATOM 9 H3 ZBE A 1 12.745 9.324 11.932 1.00 0.00 H +ATOM 10 H4 ZBE A 1 12.930 10.982 12.497 1.00 0.00 H +ATOM 11 H5 ZBE A 1 10.324 9.614 11.669 1.00 0.00 H +ATOM 12 H6 ZBE A 1 10.793 10.088 13.300 1.00 0.00 H +ATOM 13 H7 ZBE A 1 9.188 11.703 12.264 1.00 0.00 H +ATOM 14 H8 ZBE A 1 10.716 12.464 12.704 1.00 0.00 H +ATOM 15 H9 ZBE A 1 9.858 11.571 9.909 1.00 0.00 H +ATOM 16 H10 ZBE A 1 10.043 13.230 10.474 1.00 0.00 H +ATOM 17 H11 ZBE A 1 11.994 12.465 9.105 1.00 0.00 H +ATOM 18 H12 ZBE A 1 12.463 12.938 10.737 1.00 0.00 H +TER 19 ZBE A 1 +ATOM 20 C1 ZXQ S 1 10.172 31.276 27.866 1.00 0.00 C +ATOM 21 C2 ZXQ S 1 8.746 30.961 27.471 1.00 0.00 C +ATOM 22 O1 ZXQ S 1 8.752 30.264 26.234 1.00 0.00 O +ATOM 23 H1 ZXQ S 1 10.204 31.815 28.818 1.00 0.00 H +ATOM 24 H2 ZXQ S 1 10.758 30.356 27.962 1.00 0.00 H +ATOM 25 H3 ZXQ S 1 10.661 31.886 27.099 1.00 0.00 H +ATOM 26 H4 ZXQ S 1 8.169 31.883 27.352 1.00 0.00 H +ATOM 27 H5 ZXQ S 1 8.267 30.333 28.228 1.00 0.00 H +ATOM 28 H6 ZXQ S 1 7.826 30.079 26.011 1.00 0.00 H +TER 29 ZXQ S 1 +ENDMDL +CONECT 1 6 2 7 8 +CONECT 2 1 3 9 10 +CONECT 3 2 4 11 12 +CONECT 4 3 5 13 14 +CONECT 5 4 6 15 16 +CONECT 6 1 5 17 18 +CONECT 7 1 +CONECT 8 1 +CONECT 9 2 +CONECT 10 2 +CONECT 11 3 +CONECT 12 3 +CONECT 13 4 +CONECT 14 4 +CONECT 15 5 +CONECT 16 5 +CONECT 17 6 +CONECT 18 6 +CONECT 20 21 23 24 25 +CONECT 21 20 22 26 27 +CONECT 22 21 28 +CONECT 23 20 +CONECT 24 20 +CONECT 25 20 +CONECT 26 21 +CONECT 27 21 +CONECT 28 22 +END diff --git a/examples/using_smirnoff_in_amber_or_gromacs/README.md b/examples/using_smirnoff_in_amber_or_gromacs/README.md new file mode 100644 index 000000000..3a84c0d76 --- /dev/null +++ b/examples/using_smirnoff_in_amber_or_gromacs/README.md @@ -0,0 +1,8 @@ +## Export OpenFF-generated System to AMBER and GROMACS files + +This example shows how you can convert a `System` generated with the Open Forcefield Toolkit, which can be simulated natively with OpenMM, into AMBER prmtop/inpcrd and GROMACS top/gro input files through the ParmEd library. + +#### Manifest: + +- `convert_to_amber_gromacs.ipynb`: IPython notebook showing how to generate AMBER and GROMACS topology and coordinates files starting from a PDB. +- `1_cyclohexane_1_ethanol.pdb`: PDB file containing one molecule of cyclohexane and one of ethanol in vacuum. diff --git a/examples/using_smirnoff_in_amber_or_gromacs/convert_to_amber_gromacs.ipynb b/examples/using_smirnoff_in_amber_or_gromacs/convert_to_amber_gromacs.ipynb new file mode 100644 index 000000000..b37d93fbe --- /dev/null +++ b/examples/using_smirnoff_in_amber_or_gromacs/convert_to_amber_gromacs.ipynb @@ -0,0 +1,251 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Convert Open Forcefield System to AMBER and GROMACS input files\n", + "\n", + "The Open Forcefield Toolkit can create parametrized `System` objects that can be natively simulated with OpenMM. This example shows how you can convert a `System` into AMBER prmtop/inpcrd and GROMACS top/gro input files through the ParmEd library." + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Create an OpenMM System\n", + "\n", + "We start by loading a PDB file containing one copy of ethanol and cyclohexane. Our goal is to create an OFF `Topology` object describing this system that we can parametrize with the smirnoff99Frosst force field.\n", + "\n", + "The two `Molecule` objects created from the SMILES strings can contain information such as partial charges and stereochemistry that is not included in an OpenMM topology. In this example, partial charges are not explicitly given, and `ForceField` will assign AM1/BCC charges as specified by the smirnoff99Frosst force field." + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [], + "source": [ + "from simtk.openmm.app import PDBFile\n", + "from openforcefield.topology import Molecule, Topology\n", + "from openforcefield.typing.engines.smirnoff import ForceField" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [], + "source": [ + "ethanol = Molecule.from_smiles(\"CCO\")\n", + "cyclohexane = Molecule.from_smiles(\"C1CCCCC1\")\n", + "\n", + "# Obtain the OpenMM Topology object from the PDB file.\n", + "pdbfile = PDBFile('1_cyclohexane_1_ethanol.pdb')\n", + "omm_topology = pdbfile.topology\n", + "\n", + "# Create the Open Forcefield Topology.\n", + "off_topology = Topology.from_openmm(omm_topology, unique_molecules=[ethanol, cyclohexane])" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Now we parametrize the OFF `Topology` to create an OpenMM `System`." + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [], + "source": [ + "# Load the smirnoff99Frosst force field.\n", + "forcefield = ForceField('smirnoff99Frosst.offxml')\n", + "omm_system = forcefield.create_openmm_system(off_topology)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Convert OpenMM System to AMBER and GROMACS files\n", + "\n", + "\n", + "First, we convert the OpenMM `System` into a ParmEd `Structure`. We'll use the atom positions in the PDB to create the coordinate files.\n", + "\n", + "
\n", + " Warning: ParmEd's Structure model is inspired by AMBER, and some information in an OpenMM System are not directly translatable into a Structure. In particular, as of today (4/2/2019), long-range interaction treatment method (e.g., PME, CutoffPeriodic) and parameters (e.g., cutoff and cutoff switching distance, PME error tolerance) are known to be lost during the conversion.\n", + "
" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [], + "source": [ + "import parmed\n", + "\n", + "# Convert OpenMM System to a ParmEd structure.\n", + "parmed_structure = parmed.openmm.load_topology(omm_topology, omm_system, pdbfile.positions)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "We can then use ParmEd to convert an OpenMM `System` to prmtop/inpcrd or top/gro files that can be read by AMBER and GROMACS respectively. ParmEd is capable of converting parametrized files to other formats as well. For further information, see ParmEd's documentation: https://parmed.github.io/ParmEd/html/readwrite.html ." + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [], + "source": [ + "# Export AMBER files.\n", + "parmed_structure.save('system.prmtop', overwrite=True)\n", + "parmed_structure.save('system.inpcrd', overwrite=True)\n", + "\n", + "# Export GROMACS files.\n", + "parmed_structure.save('system.top', overwrite=True)\n", + "parmed_structure.save('system.gro', overwrite=True)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Validate the conversion\n", + "\n", + "ParmEd is generally a reliable and robust library, but we can easily check that everything went as expected during the conversion by loading the exported files into an OpenMM `System` and comparing it with the original. Note that you'll have to specify the correct nonbonded method and cutoff settings for the energy comparison to make sense since they are not included in the AMBER prmtop (or GROMACS top/gro) files." + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "0.9 nm\n", + "False\n", + "True\n" + ] + } + ], + "source": [ + "from simtk import openmm\n", + "for force in omm_system.getForces():\n", + " if isinstance(force, openmm.NonbondedForce):\n", + " break\n", + "print(force.getCutoffDistance())\n", + "print(force.getUseSwitchingFunction())\n", + "print(force.getNonbondedMethod() == openmm.NonbondedForce.PME)" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": {}, + "outputs": [], + "source": [ + "from simtk import unit\n", + "from simtk.openmm.app import PME, HBonds\n", + "from openforcefield.tests.utils import compare_system_parameters, compare_system_energies\n", + "\n", + "# Load the prmtop/inpcrd files into a ParmEd Structure.as an OpenMM System object.\n", + "amber_structure = parmed.load_file('system.prmtop', 'system.inpcrd')\n", + "\n", + "# Convert the Structure to an OpenMM System. Note that by\n", + "# default ParmEd will add a CMMotionRemover force to the\n", + "# System, and won't constrain the hydrogen bonds.\n", + "amber_system = amber_structure.createSystem(nonbondedMethod=PME,\n", + " nonbondedCutoff=9.0*unit.angstrom,\n", + " switchDistance=0.0*unit.angstrom,\n", + " constraints=HBonds,\n", + " removeCMMotion=False)\n", + "\n", + "# Compare the parameters of the original and converted Systems.\n", + "# This raises FailedParameterComparisonError if the comparison fails.\n", + "compare_system_parameters(omm_system, amber_system)\n", + "\n", + "# Compare the energies by force.\n", + "# This raises FailedEnergyComparisonError if the comparison fails.\n", + "amber_energies, omm_energies = compare_system_energies(\n", + " amber_system, omm_system, amber_structure.positions, amber_structure.box_vectors,\n", + " rtol=1e-3)" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "System loaded from AMBER files:\n", + "-------------------------------\n", + "{'HarmonicAngleForce': Quantity(value=6.823125839233398, unit=kilojoule/mole),\n", + " 'HarmonicBondForce': Quantity(value=1.4782228469848633, unit=kilojoule/mole),\n", + " 'NonbondedForce': Quantity(value=4.263674188305515, unit=kilojoule/mole),\n", + " 'PeriodicTorsionForce': Quantity(value=15.065959930419922, unit=kilojoule/mole)}\n", + "\n", + "Original OpenMM System:\n", + "-----------------------\n", + "{'HarmonicAngleForce': Quantity(value=6.823125839233398, unit=kilojoule/mole),\n", + " 'HarmonicBondForce': Quantity(value=1.4782228469848633, unit=kilojoule/mole),\n", + " 'NonbondedForce': Quantity(value=4.26299796164875, unit=kilojoule/mole),\n", + " 'PeriodicTorsionForce': Quantity(value=15.065959930419922, unit=kilojoule/mole)}\n" + ] + } + ], + "source": [ + "# Pretty-print the energies by component.\n", + "from pprint import pprint\n", + "\n", + "print('System loaded from AMBER files:')\n", + "print('-------------------------------')\n", + "pprint(amber_energies)\n", + "\n", + "print('\\nOriginal OpenMM System:')\n", + "print('-----------------------')\n", + "pprint(omm_energies)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.6.8" + } + }, + "nbformat": 4, + "nbformat_minor": 1 +} diff --git a/examples/using_smirnoff_with_amber_protein_forcefield/README.md b/examples/using_smirnoff_with_amber_protein_forcefield/README.md new file mode 100644 index 000000000..e1e5aad44 --- /dev/null +++ b/examples/using_smirnoff_with_amber_protein_forcefield/README.md @@ -0,0 +1,3 @@ +## Combining a SMIRNOFF parameterized small molecule with an AMBER parameterized protein using ParmEd + +This example illustrates how the [ParmEd](http://parmed.github.io/ParmEd/html/index.html) utility can be used to merge a small molecule parameterized by SMIRNOFF with a traditionally parameterized protein (or other biopolymer) to create a fully parameterized protein-ligand system. diff --git a/examples/using_smirnoff_with_amber_protein_forcefield/toluene_in_T4_lysozyme.ipynb b/examples/using_smirnoff_with_amber_protein_forcefield/toluene_in_T4_lysozyme.ipynb new file mode 100644 index 000000000..ed1d65233 --- /dev/null +++ b/examples/using_smirnoff_with_amber_protein_forcefield/toluene_in_T4_lysozyme.ipynb @@ -0,0 +1,209 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Create a system mixing SMIRNOFF and non-SMIRNOFF-formatted force fields\n", + "\n", + "This example shows how to create a receptor-ligand `System` where the ligand (toluene) is parametrized with a SMIRNOFF force field and the protein (T4 Lysozyme) is assigned AMBER parameters through the ParmEd library." + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Parametrize a molecule with smirnoff99Frosst\n", + "\n", + "First, we parametrize the ligand (toluene) with the smirnoff99Frosst force field through the usual route" + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [], + "source": [ + "from simtk.openmm.app import PDBFile\n", + "\n", + "from openforcefield.utils import get_data_filename\n", + "from openforcefield.topology import Molecule, Topology\n", + "from openforcefield.typing.engines.smirnoff import ForceField" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [], + "source": [ + "# Create an OpenFF Topology of toluene from a pdb file.\n", + "toluene_pdb_file_path = get_data_filename('molecules/toluene.pdb')\n", + "toluene_pdbfile = PDBFile(toluene_pdb_file_path)\n", + "toluene = Molecule.from_smiles('Cc1ccccc1')\n", + "off_topology = Topology.from_openmm(openmm_topology=toluene_pdbfile.topology,\n", + " unique_molecules=[toluene])\n", + "\n", + "# Load the smirnoff99Frosst system from disk.\n", + "force_field = ForceField('smirnoff99Frosst.offxml')\n", + "\n", + "# Parametrize the toluene molecule.\n", + "toluene_system = force_field.create_openmm_system(off_topology)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "and we convert the OpenMM `System` to a ParmEd `Structure` that we'll be able to mix with the protein\n", + "\n", + "
\n", + " Warning: ParmEd's Structure model is inspired by AMBER. Some information in an OpenMM System are not directly translatable into a Structure. In particular, long-range interaction treatment method (e.g., PME, CutoffPeriodic) and parameters (e.g., cutoff and cutoff switching distance, PME error tolerance) are known to be lost during the conversion.\n", + "
" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [], + "source": [ + "import parmed\n", + "\n", + "# Convert OpenMM System into a ParmEd Structure.\n", + "toluene_structure = parmed.openmm.load_topology(toluene_pdbfile.topology,\n", + " toluene_system,\n", + " xyz=toluene_pdbfile.positions)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Create a ParmEd `Structure` of an AMBER-parametrized receptor\n", + "\n", + "We have to create a ParmEd `Structure` of the receptor (T4 Lysozyme) to combine to the toluene `Structure`. Here we assign `amber99sbildn` parameters using OpenMM.\n", + "\n", + "
\n", + " Note: If you already have AMBER (prmtop/inpcrd), GROMACS (top/gro), or any other file specifying the protein parameters supported by ParmEd, you can simply load the files directly into a Structure using ParmEd's functionalities. See https://parmed.github.io/ParmEd/html/readwrite.html .\n", + "
" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [], + "source": [ + "t4_pdb_file_path = get_data_filename('proteins/T4-protein.pdb')\n", + "t4_pdbfile = PDBFile(t4_pdb_file_path)\n", + "\n", + "# Load the AMBER protein force field through OpenMM.\n", + "from simtk.openmm import app\n", + "omm_forcefield = app.ForceField('amber99sbildn.xml')\n", + "\n", + "# Parameterize the protein.\n", + "t4_system = omm_forcefield.createSystem(t4_pdbfile.topology)\n", + "\n", + "# Convert the protein System into a ParmEd Structure.\n", + "t4_structure = parmed.openmm.load_topology(t4_pdbfile.topology,\n", + " t4_system,\n", + " xyz=t4_pdbfile.positions)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Combine receptor and ligand structures\n", + "\n", + "We can then merge the receptor and ligand `Structure` objects into a single one." + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [], + "source": [ + "complex_structure = t4_structure + toluene_structure" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Convert back the structure into an OpenMM System or export to AMBER/GROMACS/CHARMM/OpenMM files\n", + "\n", + "Once we have the `Structure` of the complex, we can chose to create a `System` object that we can simulate with OpenMM" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [], + "source": [ + "from simtk.openmm.app import NoCutoff, HBonds\n", + "from simtk import unit\n", + "\n", + "# Convert the Structure to an OpenMM System in vacuum.\n", + "complex_system = complex_structure.createSystem(nonbondedMethod=NoCutoff,\n", + " nonbondedCutoff=9.0*unit.angstrom,\n", + " constraints=HBonds,\n", + " removeCMMotion=False)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "or export it in some file format to be run later or by a different simulation engine" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": {}, + "outputs": [], + "source": [ + "# Export the System to an OpenMM XML file.\n", + "from simtk.openmm import XmlSerializer\n", + "with open('complex.xml', 'w') as f:\n", + " f.write(XmlSerializer.serialize(complex_system))\n", + "\n", + "# Export the Structure to AMBER files.\n", + "complex_structure.save('complex.prmtop', overwrite=True)\n", + "complex_structure.save('complex.inpcrd', overwrite=True)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.6.8" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/openforcefield/__init__.py b/openforcefield/__init__.py index 4a620fb2b..242cd2a01 100644 --- a/openforcefield/__init__.py +++ b/openforcefield/__init__.py @@ -1,6 +1,5 @@ try: import openeye - except Exception as e: print(e) print('Warning: Cannot import openeye toolkit; not all functionality will be available.') @@ -9,4 +8,6 @@ __version__ = get_versions()['version'] del get_versions -from . import typing +#from . import typing +#from . import topology +#from . import utils diff --git a/openforcefield/data/forcefield/Frosst_AlkEthOH.offxml b/openforcefield/data/forcefield/Frosst_AlkEthOH.offxml index 4154ec661..5417308c4 100644 --- a/openforcefield/data/forcefield/Frosst_AlkEthOH.offxml +++ b/openforcefield/data/forcefield/Frosst_AlkEthOH.offxml @@ -1,32 +1,32 @@ - + - + -Date: Tue May 3 2016 +2018-07-14 C. I. Bayly, OpenEye Scientific Software - + - + - + - - + + @@ -39,10 +39,12 @@ + + - + - + @@ -55,6 +57,5 @@ - - + diff --git a/openforcefield/data/forcefield/Frosst_AlkEthOH_GBSA.offxml b/openforcefield/data/forcefield/Frosst_AlkEthOH_GBSA.offxml index 986b7ea9a..5984deeb0 100644 --- a/openforcefield/data/forcefield/Frosst_AlkEthOH_GBSA.offxml +++ b/openforcefield/data/forcefield/Frosst_AlkEthOH_GBSA.offxml @@ -1,9 +1,9 @@ - + - + -Date: Tue May 3 2016 +2018-07-14 C. I. Bayly, OpenEye Scientific Software @@ -11,24 +11,24 @@ - + - + - + - - + + @@ -41,10 +41,12 @@ + + - + - + @@ -57,9 +59,9 @@ - + - + @@ -72,5 +74,5 @@ - + diff --git a/openforcefield/data/forcefield/Frosst_AlkEthOH_MDL.offxml b/openforcefield/data/forcefield/Frosst_AlkEthOH_MDL.offxml index 1dd424e3e..18b14c67c 100644 --- a/openforcefield/data/forcefield/Frosst_AlkEthOH_MDL.offxml +++ b/openforcefield/data/forcefield/Frosst_AlkEthOH_MDL.offxml @@ -1,32 +1,32 @@ - + - + -Date: Tue May 3 2016 +2018-07-14 C. I. Bayly, OpenEye Scientific Software - + - + - + - - + + @@ -39,10 +39,12 @@ + + - + - + @@ -55,6 +57,6 @@ - + diff --git a/openforcefield/data/forcefield/Frosst_AlkEthOH_parmAtFrosst.offxml b/openforcefield/data/forcefield/Frosst_AlkEthOH_parmAtFrosst.offxml index 1fc83c08e..52c23211e 100644 --- a/openforcefield/data/forcefield/Frosst_AlkEthOH_parmAtFrosst.offxml +++ b/openforcefield/data/forcefield/Frosst_AlkEthOH_parmAtFrosst.offxml @@ -1,32 +1,32 @@ - + - + - -Date: Tue May 3 2016 + +2018-07-14 C. I. Bayly, OpenEye Scientific Software - + - + - + - - + + @@ -40,13 +40,15 @@ - - + + + + - + - - + + @@ -58,6 +60,5 @@ - - + diff --git a/openforcefield/data/forcefield/ammonia_minimal.offxml b/openforcefield/data/forcefield/ammonia_minimal.offxml index 82bfc1d42..80af78d94 100644 --- a/openforcefield/data/forcefield/ammonia_minimal.offxml +++ b/openforcefield/data/forcefield/ammonia_minimal.offxml @@ -1,26 +1,27 @@ - + + - Date: Apr. 05, 2018 + 2018-04-05 V. T. Lim, UC Irvine - + - + - + - - + + - + - + - + diff --git a/openforcefield/data/forcefield/benzene_minimal.offxml b/openforcefield/data/forcefield/benzene_minimal.offxml index 6743d4dd4..71381ea43 100644 --- a/openforcefield/data/forcefield/benzene_minimal.offxml +++ b/openforcefield/data/forcefield/benzene_minimal.offxml @@ -1,26 +1,29 @@ - + + - Date: Sept. 22, 2016 + 2016-09-22 D. L. Mobley, UC Irvine - + - + - - + + - - - + + - + + + + - + - + diff --git a/openforcefield/data/forcefield/chargeincrement-test.offxml b/openforcefield/data/forcefield/chargeincrement-test.offxml new file mode 100644 index 000000000..3fd120ae7 --- /dev/null +++ b/openforcefield/data/forcefield/chargeincrement-test.offxml @@ -0,0 +1,16 @@ + + + + + 2016-05-25 + J. D. Chodera (MSKCC) charge increment tests + + + + + + + + + + diff --git a/openforcefield/data/forcefield/old/README.md b/openforcefield/data/forcefield/old/README.md new file mode 100644 index 000000000..b864119d8 --- /dev/null +++ b/openforcefield/data/forcefield/old/README.md @@ -0,0 +1,9 @@ +# Previously released SMIRNOFF force field + +These files are mostly used for regression tests. + +## Manifest +- `smirnoff99Frosst_0_0_2.offxml`: smirnof99Frosst force field released with `openforcefield 0.0.2`. +- `smirnoff99Frosst_0_0_4.offxml`: smirnof99Frosst force field released with `openforcefield 0.0.4`. +- `smirnoff99Frosst_0_0_4_fixed.offxml`: smirnof99Frosst force field released with `openforcefield 0.0.4` with a bugfix correction for the issue described in #179. +- `hbonds.offxml`: Separate file adding only hydrogen bond constraints to the parameterization. diff --git a/openforcefield/data/forcefield/old/hbonds.offxml b/openforcefield/data/forcefield/old/hbonds.offxml new file mode 100644 index 000000000..422ccfc27 --- /dev/null +++ b/openforcefield/data/forcefield/old/hbonds.offxml @@ -0,0 +1,11 @@ + + + + 2017-05-01 + J. D. Chodera, MSKCC; A. Rizzi, Weill Cornell; + + + + + + diff --git a/openforcefield/data/forcefield/old/smirnoff99Frosst_0_0_2.offxml b/openforcefield/data/forcefield/old/smirnoff99Frosst_0_0_2.offxml new file mode 100644 index 000000000..159d07a0e --- /dev/null +++ b/openforcefield/data/forcefield/old/smirnoff99Frosst_0_0_2.offxml @@ -0,0 +1,338 @@ + + + + Date: April 26, 2017 + C. I. Bayly, OpenEye/UC Irvine; C. C. Bannan, UC Irvine; D. L. Mobley, UC Irvine + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/openforcefield/data/forcefield/old/smirnoff99Frosst_0_0_4.offxml b/openforcefield/data/forcefield/old/smirnoff99Frosst_0_0_4.offxml new file mode 100644 index 000000000..ead8f5333 --- /dev/null +++ b/openforcefield/data/forcefield/old/smirnoff99Frosst_0_0_4.offxml @@ -0,0 +1,346 @@ + + + + Date: Feb. 27, 2018 + C. I. Bayly, OpenEye/UC Irvine; C. C. Bannan, UC Irvine; D. L. Mobley, UC Irvine + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/openforcefield/data/forcefield/old/smirnoff99Frosst_0_0_4_fixed.offxml b/openforcefield/data/forcefield/old/smirnoff99Frosst_0_0_4_fixed.offxml new file mode 100644 index 000000000..8901aef58 --- /dev/null +++ b/openforcefield/data/forcefield/old/smirnoff99Frosst_0_0_4_fixed.offxml @@ -0,0 +1,348 @@ + + + + + Date: Feb. 27, 2018 + C. I. Bayly, OpenEye/UC Irvine; C. C. Bannan, UC Irvine; D. L. Mobley, UC Irvine + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/openforcefield/data/forcefield/smirnoff99Frosst.offxml b/openforcefield/data/forcefield/smirnoff99Frosst.offxml index 2c44c46d6..830fe4f27 100755 --- a/openforcefield/data/forcefield/smirnoff99Frosst.offxml +++ b/openforcefield/data/forcefield/smirnoff99Frosst.offxml @@ -1,11 +1,13 @@ - + + + - Date: Feb. 14, 2019 + 2019-02-14 C. I. Bayly, OpenEye/UC Irvine; C. C. Bannan, UC Irvine; D. L. Mobley, UC Irvine - + @@ -93,9 +95,9 @@ - + - + @@ -134,12 +136,8 @@ - - - - - - + + @@ -298,9 +296,15 @@ - + + + + + + + - + @@ -336,5 +340,8 @@ - + + + + diff --git a/openforcefield/data/forcefield/tip3p.offxml b/openforcefield/data/forcefield/tip3p.offxml index 8afa2f873..be77a50a9 100644 --- a/openforcefield/data/forcefield/tip3p.offxml +++ b/openforcefield/data/forcefield/tip3p.offxml @@ -1,21 +1,26 @@ - - + + + + - 2017-04-29 + 2019-04-04 J. D. Chodera, MSKCC; A. Rizzi, Weill Cornell; C. C. Bannan, UC Irvine + - + - + + + diff --git a/openforcefield/data/molecules/AlkEthOH-tripos.mol2.gz b/openforcefield/data/molecules/AlkEthOH-tripos.mol2.gz deleted file mode 100644 index 2f83cb4ea..000000000 Binary files a/openforcefield/data/molecules/AlkEthOH-tripos.mol2.gz and /dev/null differ diff --git a/openforcefield/data/molecules/AlkEthOH_c100.crd b/openforcefield/data/molecules/AlkEthOH_c100.crd deleted file mode 100644 index 2ba44da7f..000000000 --- a/openforcefield/data/molecules/AlkEthOH_c100.crd +++ /dev/null @@ -1,15 +0,0 @@ -AlkEthOH_c100 - 26 - -0.9553000 0.4818000 -0.2077000 -0.3490000 1.5118000 -3.9233000 - 2.2817000 2.6277000 -0.7960000 1.2497000 4.6992000 -1.7325000 - -1.2082000 0.6003000 -1.7062000 -0.0897000 1.3641000 -2.4285000 - 1.3968000 3.1877000 -1.9119000 -2.4504000 1.2717000 -1.9070000 - 2.0195000 2.9930000 -3.1820000 0.0656000 2.6662000 -1.8674000 - -0.8584000 1.4672000 0.2604000 -0.0508000 -0.0987000 -0.0023000 - -1.8018000 -0.0117000 0.2823000 -1.2912000 2.0347000 -4.1123000 - 0.4621000 2.0550000 -4.4201000 -0.3970000 0.5255000 -4.3979000 - 2.4059000 1.5440000 -0.8979000 3.2673000 3.1044000 -0.7929000 - 1.8318000 2.7934000 0.1888000 0.6177000 5.1189000 -2.5244000 - 2.2188000 5.2065000 -1.7918000 0.7741000 4.9438000 -0.7766000 - -1.2996000 -0.4020000 -2.1404000 0.8600000 0.8372000 -2.2840000 - -3.1291000 0.7293000 -1.4768000 2.8732000 3.4574000 -3.1770000 diff --git a/openforcefield/data/molecules/AlkEthOH_c100.mol2 b/openforcefield/data/molecules/AlkEthOH_c100.mol2 deleted file mode 100644 index 2ebf0d15d..000000000 --- a/openforcefield/data/molecules/AlkEthOH_c100.mol2 +++ /dev/null @@ -1,61 +0,0 @@ -@MOLECULE -AlkEthOH_c100 - 26 25 1 0 0 -SMALL -USER_CHARGES - -@ATOM - 1 C1 -0.9553 0.4818 -0.2077 CT 1 <0> -0.12819 - 2 C2 -0.3490 1.5118 -3.9233 CT 1 <0> -0.11278 - 3 C3 2.2817 2.6277 -0.7960 CT 1 <0> -0.13028 - 4 C4 1.2497 4.6992 -1.7325 CT 1 <0> -0.13028 - 5 C5 -1.2082 0.6003 -1.7062 CT 1 <0> 0.13828 - 6 C6 -0.0897 1.3641 -2.4285 CT 1 <0> 0.17039 - 7 C7 1.3968 3.1877 -1.9119 CT 1 <0> 0.34809 - 8 O1 -2.4504 1.2717 -1.9070 OH 1 <0> -0.58269 - 9 O2 2.0195 2.9930 -3.1820 OH 1 <0> -0.62548 - 10 O3 0.0656 2.6662 -1.8674 OS 1 <0> -0.40486 - 11 H1 -0.8584 1.4672 0.2604 HC 1 <0> 0.04431 - 12 H2 -0.0508 -0.0987 -0.0023 HC 1 <0> 0.04431 - 13 H3 -1.8018 -0.0117 0.2823 HC 1 <0> 0.04431 - 14 H4 -1.2912 2.0347 -4.1123 HC 1 <0> 0.04980 - 15 H5 0.4621 2.0550 -4.4201 HC 1 <0> 0.04980 - 16 H6 -0.3970 0.5255 -4.3979 HC 1 <0> 0.04980 - 17 H7 2.4059 1.5440 -0.8979 HC 1 <0> 0.05049 - 18 H8 3.2673 3.1044 -0.7929 HC 1 <0> 0.05049 - 19 H9 1.8318 2.7934 0.1888 HC 1 <0> 0.05049 - 20 H10 0.6177 5.1189 -2.5244 HC 1 <0> 0.05049 - 21 H11 2.2188 5.2065 -1.7918 HC 1 <0> 0.05049 - 22 H12 0.7741 4.9438 -0.7766 HC 1 <0> 0.05049 - 23 H13 -1.2996 -0.4020 -2.1404 H1 1 <0> 0.02625 - 24 H14 0.8600 0.8372 -2.2840 H1 1 <0> 0.04199 - 25 H15 -3.1291 0.7293 -1.4768 HO 1 <0> 0.39414 - 26 H16 2.8732 3.4574 -3.1770 HO 1 <0> 0.41015 -@BOND - 1 1 5 1 - 2 2 6 1 - 3 3 7 1 - 4 4 7 1 - 5 5 6 1 - 6 5 8 1 - 7 6 10 1 - 8 7 9 1 - 9 7 10 1 - 10 1 11 1 - 11 1 12 1 - 12 1 13 1 - 13 2 14 1 - 14 2 15 1 - 15 2 16 1 - 16 3 17 1 - 17 3 18 1 - 18 3 19 1 - 19 4 20 1 - 20 4 21 1 - 21 4 22 1 - 22 5 23 1 - 23 6 24 1 - 24 8 25 1 - 25 9 26 1 -@SUBSTRUCTURE - 1 <0> 1 GROUP 0 A **** diff --git a/openforcefield/data/molecules/AlkEthOH_c100.top b/openforcefield/data/molecules/AlkEthOH_c100.top deleted file mode 100644 index f3efc07a7..000000000 --- a/openforcefield/data/molecules/AlkEthOH_c100.top +++ /dev/null @@ -1,266 +0,0 @@ -%VERSION VERSION_STAMP = V0001.000 DATE = 06/24/16 11:20:35 -%FLAG TITLE -%FORMAT(20a4) -AlkEthOH_c100 -%FLAG POINTERS -%FORMAT(10I8) - 26 6 16 9 32 13 72 16 0 0 - 132 1 9 13 16 6 11 13 6 0 - 0 0 0 0 0 0 0 0 26 0 - 0 -%FLAG ATOM_NAME -%FORMAT(20a4) -C1 C2 C3 C4 C5 C6 C7 O1 O2 O3 H1 H2 H3 H4 H5 H6 H7 H8 H9 H10 -H11 H12 H13 H14 H15 H16 -%FLAG CHARGE -%FORMAT(5E16.8) - -2.33591664E+00 -2.05511099E+00 -2.37400124E+00 -2.37400124E+00 2.51977964E+00 - 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HC HC HC HC HC HC HC HC -HC HC H1 H1 HO HO -%FLAG TREE_CHAIN_CLASSIFICATION -%FORMAT(20a4) -BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA -BLA BLA BLA BLA BLA BLA -%FLAG JOIN_ARRAY -%FORMAT(10I8) - 0 0 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 -%FLAG IROTAT -%FORMAT(10I8) - 0 0 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 -%FLAG RADIUS_SET -%FORMAT(1a80) -modified Bondi radii (mbondi) -%FLAG RADII -%FORMAT(5E16.8) - 1.70000000E+00 1.70000000E+00 1.70000000E+00 1.70000000E+00 1.70000000E+00 - 1.70000000E+00 1.70000000E+00 1.50000000E+00 1.50000000E+00 1.50000000E+00 - 1.30000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00 - 1.30000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00 - 1.30000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00 8.00000000E-01 - 8.00000000E-01 -%FLAG SCREEN -%FORMAT(5E16.8) - 7.20000000E-01 7.20000000E-01 7.20000000E-01 7.20000000E-01 7.20000000E-01 - 7.20000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 - 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 - 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 - 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 - 8.50000000E-01 -%FLAG IPOL -%FORMAT(1I8) - 0 diff --git a/openforcefield/data/molecules/AlkEthOH_c1161.crd b/openforcefield/data/molecules/AlkEthOH_c1161.crd deleted file mode 100644 index ac0b3664c..000000000 --- a/openforcefield/data/molecules/AlkEthOH_c1161.crd +++ /dev/null @@ -1,12 +0,0 @@ -AlkEthOH_c1161 - 19 - 4.7510000 3.6140000 -3.2542000 3.5394000 -1.7658000 -1.0787000 - 4.7737000 2.8514000 -1.9417000 3.6022000 1.8883000 -1.8264000 - 2.6065000 0.2954000 -0.3894000 2.5751000 -0.7579000 -1.3523000 - 3.6773000 1.2212000 -0.5734000 4.7693000 2.9275000 -4.1067000 - 3.8423000 4.2198000 -3.3257000 5.6129000 4.2840000 -3.3335000 - 3.4770000 -2.5471000 -1.8401000 3.3530000 -2.1907000 -0.0892000 - 4.5362000 -1.3190000 -1.0993000 4.7549000 3.5560000 -1.1015000 - 5.7157000 2.2977000 -1.8490000 2.6490000 2.4241000 -1.8793000 - 3.6334000 1.1380000 -2.6230000 1.6496000 0.8277000 -0.4333000 - 2.6909000 -0.1298000 0.6171000 diff --git a/openforcefield/data/molecules/AlkEthOH_c1161.mol2 b/openforcefield/data/molecules/AlkEthOH_c1161.mol2 deleted file mode 100644 index 4808034f5..000000000 --- a/openforcefield/data/molecules/AlkEthOH_c1161.mol2 +++ /dev/null @@ -1,47 +0,0 @@ -@MOLECULE -AlkEthOH_c1161 - 19 18 1 0 0 -SMALL -USER_CHARGES - -@ATOM - 1 C1 4.7510 3.6140 -3.2542 CT 1 <0> -0.09365 - 2 C2 3.5394 -1.7658 -1.0787 CT 1 <0> 0.12002 - 3 C3 4.7737 2.8514 -1.9417 CT 1 <0> -0.08428 - 4 C4 3.6022 1.8883 -1.8264 CT 1 <0> 0.13349 - 5 C5 2.6065 0.2954 -0.3894 CT 1 <0> 0.31731 - 6 O1 2.5751 -0.7579 -1.3523 OS 1 <0> -0.44981 - 7 O2 3.6773 1.2212 -0.5734 OS 1 <0> -0.45061 - 8 H1 4.7693 2.9275 -4.1067 HC 1 <0> 0.03488 - 9 H2 3.8423 4.2198 -3.3257 HC 1 <0> 0.03488 - 10 H3 5.6129 4.2840 -3.3335 HC 1 <0> 0.03488 - 11 H4 3.4770 -2.5471 -1.8401 H1 1 <0> 0.03589 - 12 H5 3.3530 -2.1907 -0.0892 H1 1 <0> 0.03589 - 13 H6 4.5362 -1.3190 -1.0993 H1 1 <0> 0.03589 - 14 H7 4.7549 3.5560 -1.1015 HC 1 <0> 0.05196 - 15 H8 5.7157 2.2977 -1.8490 HC 1 <0> 0.05196 - 16 H9 2.6490 2.4241 -1.8793 H1 1 <0> 0.03353 - 17 H10 3.6334 1.1380 -2.6230 H1 1 <0> 0.03353 - 18 H11 1.6496 0.8277 -0.4333 H2 1 <0> 0.06212 - 19 H12 2.6909 -0.1298 0.6171 H2 1 <0> 0.06212 -@BOND - 1 1 3 1 - 2 2 6 1 - 3 3 4 1 - 4 4 7 1 - 5 5 6 1 - 6 5 7 1 - 7 1 8 1 - 8 1 9 1 - 9 1 10 1 - 10 2 11 1 - 11 2 12 1 - 12 2 13 1 - 13 3 14 1 - 14 3 15 1 - 15 4 16 1 - 16 4 17 1 - 17 5 18 1 - 18 5 19 1 -@SUBSTRUCTURE - 1 <0> 1 GROUP 0 A **** diff --git a/openforcefield/data/molecules/AlkEthOH_c1161.top b/openforcefield/data/molecules/AlkEthOH_c1161.top deleted file mode 100644 index adf129691..000000000 --- a/openforcefield/data/molecules/AlkEthOH_c1161.top +++ /dev/null @@ -1,204 +0,0 @@ -%VERSION VERSION_STAMP = V0001.000 DATE = 06/24/16 11:20:58 -%FLAG TITLE -%FORMAT(20a4) -AlkEthOH_c1161 -%FLAG POINTERS -%FORMAT(10I8) - 19 5 12 6 27 5 28 9 0 0 - 83 1 6 5 9 5 11 11 5 0 - 0 0 0 0 0 0 0 0 19 0 - 0 -%FLAG ATOM_NAME -%FORMAT(20a4) -C1 C2 C3 C4 C5 O1 O2 H1 H2 H3 H4 H5 H6 H7 H8 H9 H10 H11 H12 -%FLAG CHARGE -%FORMAT(5E16.8) - -1.70651840E+00 2.18704045E+00 -1.53577544E+00 2.43249483E+00 5.78211801E+00 - -8.19657276E+00 -8.21115060E+00 6.35593824E-01 6.35593824E-01 6.35593824E-01 - 6.53998347E-01 6.53998347E-01 6.53998347E-01 9.46830708E-01 9.46830708E-01 - 6.10993719E-01 6.10993719E-01 1.13196928E+00 1.13196928E+00 -%FLAG ATOMIC_NUMBER -%FORMAT(10I8) - 6 6 6 6 6 8 8 1 1 1 - 1 1 1 1 1 1 1 1 1 -%FLAG MASS -%FORMAT(5E16.8) - 1.20100000E+01 1.20100000E+01 1.20100000E+01 1.20100000E+01 1.20100000E+01 - 1.60000000E+01 1.60000000E+01 1.00800000E+00 1.00800000E+00 1.00800000E+00 - 1.00800000E+00 1.00800000E+00 1.00800000E+00 1.00800000E+00 1.00800000E+00 - 1.00800000E+00 1.00800000E+00 1.00800000E+00 1.00800000E+00 -%FLAG ATOM_TYPE_INDEX -%FORMAT(10I8) - 1 1 1 1 1 2 2 3 3 3 - 4 4 4 3 3 4 4 5 5 -%FLAG NUMBER_EXCLUDED_ATOMS -%FORMAT(10I8) - 10 8 10 12 9 6 6 4 3 2 - 2 1 1 3 2 1 1 1 1 -%FLAG NONBONDED_PARM_INDEX -%FORMAT(10I8) - 1 2 4 7 11 2 3 5 8 12 - 4 5 6 9 13 7 8 9 10 14 - 11 12 13 14 15 -%FLAG RESIDUE_LABEL -%FORMAT(20a4) -<0> -%FLAG RESIDUE_POINTER -%FORMAT(10I8) - 1 -%FLAG BOND_FORCE_CONSTANT -%FORMAT(5E16.8) - 3.10000000E+02 3.40000000E+02 3.20000000E+02 3.40000000E+02 3.40000000E+02 -%FLAG BOND_EQUIL_VALUE -%FORMAT(5E16.8) - 1.52600000E+00 1.09000000E+00 1.37000000E+00 1.09000000E+00 1.09000000E+00 -%FLAG ANGLE_FORCE_CONSTANT -%FORMAT(5E16.8) - 4.00000000E+01 5.00000000E+01 6.00000000E+01 5.00000000E+01 5.00000000E+01 - 5.00000000E+01 7.00000000E+01 5.00000000E+01 3.50000000E+01 3.50000000E+01 - 3.50000000E+01 -%FLAG ANGLE_EQUIL_VALUE -%FORMAT(5E16.8) - 1.91113635E+00 1.91113635E+00 1.91113635E+00 1.91113635E+00 1.91113635E+00 - 1.91113635E+00 1.91113635E+00 1.91113635E+00 1.91113635E+00 1.91113635E+00 - 1.91113635E+00 -%FLAG DIHEDRAL_FORCE_CONSTANT -%FORMAT(5E16.8) - 1.55555556E-01 1.35000000E+00 8.50000000E-01 1.00000000E-01 3.83333333E-01 - 1.00000000E-01 3.83000000E-01 1.60000000E-01 2.50000000E-01 0.00000000E+00 - 1.50000000E-01 -%FLAG DIHEDRAL_PERIODICITY -%FORMAT(5E16.8) - 3.00000000E+00 1.00000000E+00 2.00000000E+00 3.00000000E+00 3.00000000E+00 - 2.00000000E+00 3.00000000E+00 3.00000000E+00 1.00000000E+00 3.00000000E+00 - 3.00000000E+00 -%FLAG DIHEDRAL_PHASE -%FORMAT(5E16.8) - 0.00000000E+00 3.14159400E+00 3.14159400E+00 0.00000000E+00 0.00000000E+00 - 3.14159400E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 - 0.00000000E+00 -%FLAG SCEE_SCALE_FACTOR -%FORMAT(5E16.8) - 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 - 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 - 1.20000000E+00 -%FLAG SCNB_SCALE_FACTOR -%FORMAT(5E16.8) - 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 - 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 - 2.00000000E+00 -%FLAG SOLTY -%FORMAT(5E16.8) - 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 -%FLAG LENNARD_JONES_ACOEF -%FORMAT(5E16.8) - 1.04308023E+06 6.28541240E+05 3.61397723E+05 9.71708117E+04 5.33379252E+04 - 7.51607703E+03 6.78771368E+04 3.63097246E+04 4.98586848E+03 3.25969625E+03 - 4.68930885E+04 2.44050579E+04 3.25969625E+03 2.09814978E+03 1.32801250E+03 -%FLAG LENNARD_JONES_BCOEF -%FORMAT(5E16.8) - 6.75612247E+02 5.85549272E+02 4.95732238E+02 1.26919150E+02 1.04986921E+02 - 2.17257828E+01 1.06076943E+02 8.66220817E+01 1.76949863E+01 1.43076527E+01 - 8.81685417E+01 7.10161395E+01 1.43076527E+01 1.14788417E+01 9.13231543E+00 -%FLAG BONDS_INC_HYDROGEN -%FORMAT(10I8) - 0 21 2 0 24 2 0 27 2 3 - 30 4 3 33 4 3 36 4 6 39 - 2 6 42 2 9 45 4 9 48 4 - 12 51 5 12 54 5 -%FLAG BONDS_WITHOUT_HYDROGEN -%FORMAT(10I8) - 0 6 1 3 15 3 6 9 1 9 - 18 3 12 15 3 12 18 3 -%FLAG ANGLES_INC_HYDROGEN -%FORMAT(10I8) - 0 6 39 2 0 6 42 2 6 0 - 21 2 6 0 24 2 6 0 27 2 - 6 9 45 5 6 9 48 5 9 6 - 39 2 9 6 42 2 15 3 30 6 - 15 3 33 6 15 3 36 6 15 12 - 51 8 15 12 54 8 18 9 45 6 - 18 9 48 6 18 12 51 8 18 12 - 54 8 21 0 24 9 21 0 27 9 - 24 0 27 9 30 3 33 10 30 3 - 36 10 33 3 36 10 39 6 42 9 - 45 9 48 10 51 12 54 11 -%FLAG ANGLES_WITHOUT_HYDROGEN -%FORMAT(10I8) - 0 6 9 1 3 15 12 3 6 9 - 18 4 9 18 12 3 15 12 18 7 -%FLAG DIHEDRALS_INC_HYDROGEN -%FORMAT(10I8) - 0 6 9 45 1 0 6 9 48 1 - 3 15 12 51 5 3 15 12 54 5 - 21 0 6 9 8 24 0 6 9 8 - 27 0 6 9 8 9 18 12 51 5 - 9 18 12 54 5 12 15 3 30 5 - 12 15 3 33 5 12 15 3 36 5 - 12 18 9 45 5 12 18 9 48 5 - 18 9 6 39 9 18 9 -6 39 10 - 18 9 6 42 9 18 9 -6 42 10 - 21 0 6 39 11 21 0 6 42 11 - 24 0 6 39 11 24 0 6 42 11 - 27 0 6 39 11 27 0 6 42 11 - 39 6 9 45 1 39 6 9 48 1 - 42 6 9 45 1 42 6 9 48 1 -%FLAG DIHEDRALS_WITHOUT_HYDROGEN -%FORMAT(10I8) - 0 6 9 18 1 3 15 12 18 2 - 3 15 -12 18 3 3 15 -12 18 4 - 6 9 18 12 6 6 9 -18 12 7 - 9 18 12 15 2 9 18 -12 15 3 - 9 18 -12 15 4 -%FLAG EXCLUDED_ATOMS_LIST -%FORMAT(10I8) - 3 4 7 8 9 10 14 15 16 17 - 5 6 7 11 12 13 18 19 4 5 - 7 8 9 10 14 15 16 17 5 6 - 7 8 9 10 14 15 16 17 18 19 - 6 7 11 12 13 16 17 18 19 7 - 11 12 13 18 19 14 15 16 17 18 - 19 9 10 14 15 10 14 15 14 15 - 12 13 13 0 15 16 17 16 17 17 - 0 19 0 -%FLAG HBOND_ACOEF -%FORMAT(5E16.8) - -%FLAG HBOND_BCOEF -%FORMAT(5E16.8) - -%FLAG HBCUT -%FORMAT(5E16.8) - -%FLAG AMBER_ATOM_TYPE -%FORMAT(20a4) -CT CT CT CT CT OS OS HC HC HC H1 H1 H1 HC HC H1 H1 H2 H2 -%FLAG TREE_CHAIN_CLASSIFICATION -%FORMAT(20a4) -BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA -%FLAG JOIN_ARRAY -%FORMAT(10I8) - 0 0 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 0 -%FLAG IROTAT -%FORMAT(10I8) - 0 0 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 0 -%FLAG RADIUS_SET -%FORMAT(1a80) -modified Bondi radii (mbondi) -%FLAG RADII -%FORMAT(5E16.8) - 1.70000000E+00 1.70000000E+00 1.70000000E+00 1.70000000E+00 1.70000000E+00 - 1.50000000E+00 1.50000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00 - 1.30000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00 - 1.30000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00 -%FLAG SCREEN -%FORMAT(5E16.8) - 7.20000000E-01 7.20000000E-01 7.20000000E-01 7.20000000E-01 7.20000000E-01 - 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 - 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 - 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 -%FLAG IPOL -%FORMAT(1I8) - 0 diff --git a/openforcefield/data/molecules/AlkEthOH_c1266.crd b/openforcefield/data/molecules/AlkEthOH_c1266.crd deleted file mode 100644 index 9752e8bc1..000000000 --- a/openforcefield/data/molecules/AlkEthOH_c1266.crd +++ /dev/null @@ -1,10 +0,0 @@ -AlkEthOH_c1266 - 15 - 0.9167000 1.4498000 0.5861000 1.9430000 1.3174000 -4.0752000 - 1.9101000 0.9126000 -0.4220000 2.4157000 0.8471000 -2.7161000 - 1.5170000 1.3236000 -1.7228000 0.8863000 2.5427000 0.5597000 - -0.0873000 1.0632000 0.3824000 1.1823000 1.1282000 1.5986000 - 0.9435000 0.9324000 -4.2954000 1.9180000 2.4112000 -4.1179000 - 2.6307000 0.9839000 -4.8595000 1.9355000 -0.1807000 -0.3905000 - 2.9125000 1.3005000 -0.2176000 3.4159000 1.2356000 -2.5021000 - 2.4394000 -0.2460000 -2.6749000 diff --git a/openforcefield/data/molecules/AlkEthOH_c1266.mol2 b/openforcefield/data/molecules/AlkEthOH_c1266.mol2 deleted file mode 100644 index 39024189f..000000000 --- a/openforcefield/data/molecules/AlkEthOH_c1266.mol2 +++ /dev/null @@ -1,39 +0,0 @@ -@MOLECULE -AlkEthOH_c1266 - 15 14 1 0 0 -SMALL -USER_CHARGES - -@ATOM - 1 C1 0.9167 1.4498 0.5861 CT 1 <0> -0.09697 - 2 C2 1.9430 1.3174 -4.0752 CT 1 <0> -0.09694 - 3 C3 1.9101 0.9126 -0.4220 CT 1 <0> 0.12965 - 4 C4 2.4157 0.8471 -2.7161 CT 1 <0> 0.12965 - 5 O1 1.5170 1.3236 -1.7228 OS 1 <0> -0.42433 - 6 H1 0.8863 2.5427 0.5597 HC 1 <0> 0.04459 - 7 H2 -0.0873 1.0632 0.3824 HC 1 <0> 0.04459 - 8 H3 1.1823 1.1282 1.5986 HC 1 <0> 0.04459 - 9 H4 0.9435 0.9324 -4.2954 HC 1 <0> 0.04459 - 10 H5 1.9180 2.4112 -4.1179 HC 1 <0> 0.04459 - 11 H6 2.6307 0.9839 -4.8595 HC 1 <0> 0.04459 - 12 H7 1.9355 -0.1807 -0.3905 H1 1 <0> 0.02285 - 13 H8 2.9125 1.3005 -0.2176 H1 1 <0> 0.02285 - 14 H9 3.4159 1.2356 -2.5021 H1 1 <0> 0.02285 - 15 H10 2.4394 -0.2460 -2.6749 H1 1 <0> 0.02285 -@BOND - 1 1 3 1 - 2 2 4 1 - 3 3 5 1 - 4 4 5 1 - 5 1 6 1 - 6 1 7 1 - 7 1 8 1 - 8 2 9 1 - 9 2 10 1 - 10 2 11 1 - 11 3 12 1 - 12 3 13 1 - 13 4 14 1 - 14 4 15 1 -@SUBSTRUCTURE - 1 <0> 1 GROUP 0 A **** diff --git a/openforcefield/data/molecules/AlkEthOH_c1266.top b/openforcefield/data/molecules/AlkEthOH_c1266.top deleted file mode 100644 index 4c8bc6512..000000000 --- a/openforcefield/data/molecules/AlkEthOH_c1266.top +++ /dev/null @@ -1,182 +0,0 @@ -%VERSION VERSION_STAMP = V0001.000 DATE = 06/24/16 11:21:00 -%FLAG TITLE -%FORMAT(20a4) -AlkEthOH_c1266 -%FLAG POINTERS -%FORMAT(10I8) - 15 4 10 4 22 3 28 4 0 0 - 65 1 4 3 4 4 7 6 4 0 - 0 0 0 0 0 0 0 0 15 0 - 0 -%FLAG ATOM_NAME -%FORMAT(20a4) -C1 C2 C3 C4 O1 H1 H2 H3 H4 H5 H6 H7 H8 H9 H10 -%FLAG CHARGE -%FORMAT(5E16.8) - -1.76701643E+00 -1.76646976E+00 2.36252119E+00 2.36252119E+00 -7.73226856E+00 - 8.12532357E-01 8.12532357E-01 8.12532357E-01 8.12532357E-01 8.12532357E-01 - 8.12532357E-01 4.16379555E-01 4.16379555E-01 4.16379555E-01 4.16379555E-01 -%FLAG ATOMIC_NUMBER -%FORMAT(10I8) - 6 6 6 6 8 1 1 1 1 1 - 1 1 1 1 1 -%FLAG MASS -%FORMAT(5E16.8) - 1.20100000E+01 1.20100000E+01 1.20100000E+01 1.20100000E+01 1.60000000E+01 - 1.00800000E+00 1.00800000E+00 1.00800000E+00 1.00800000E+00 1.00800000E+00 - 1.00800000E+00 1.00800000E+00 1.00800000E+00 1.00800000E+00 1.00800000E+00 -%FLAG ATOM_TYPE_INDEX -%FORMAT(10I8) - 1 1 1 1 2 3 3 3 3 3 - 3 4 4 4 4 -%FLAG NUMBER_EXCLUDED_ATOMS -%FORMAT(10I8) - 8 8 9 8 10 4 3 2 4 3 - 2 1 1 1 1 -%FLAG NONBONDED_PARM_INDEX -%FORMAT(10I8) - 1 2 4 7 2 3 5 8 4 5 - 6 9 7 8 9 10 -%FLAG RESIDUE_LABEL -%FORMAT(20a4) -<0> -%FLAG RESIDUE_POINTER -%FORMAT(10I8) - 1 -%FLAG BOND_FORCE_CONSTANT -%FORMAT(5E16.8) - 3.10000000E+02 3.40000000E+02 3.20000000E+02 3.40000000E+02 -%FLAG BOND_EQUIL_VALUE -%FORMAT(5E16.8) - 1.52600000E+00 1.09000000E+00 1.37000000E+00 1.09000000E+00 -%FLAG ANGLE_FORCE_CONSTANT -%FORMAT(5E16.8) - 5.00000000E+01 5.00000000E+01 5.00000000E+01 6.00000000E+01 5.00000000E+01 - 3.50000000E+01 3.50000000E+01 -%FLAG ANGLE_EQUIL_VALUE -%FORMAT(5E16.8) - 1.91113635E+00 1.91113635E+00 1.91113635E+00 1.91113635E+00 1.91113635E+00 - 1.91113635E+00 1.91113635E+00 -%FLAG DIHEDRAL_FORCE_CONSTANT -%FORMAT(5E16.8) - 1.00000000E-01 3.83000000E-01 3.83333333E-01 2.50000000E-01 0.00000000E+00 - 1.55555556E-01 -%FLAG DIHEDRAL_PERIODICITY -%FORMAT(5E16.8) - 2.00000000E+00 3.00000000E+00 3.00000000E+00 1.00000000E+00 3.00000000E+00 - 3.00000000E+00 -%FLAG DIHEDRAL_PHASE -%FORMAT(5E16.8) - 3.14159400E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 - 0.00000000E+00 -%FLAG SCEE_SCALE_FACTOR -%FORMAT(5E16.8) - 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 - 1.20000000E+00 -%FLAG SCNB_SCALE_FACTOR -%FORMAT(5E16.8) - 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 - 2.00000000E+00 -%FLAG SOLTY -%FORMAT(5E16.8) - 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 -%FLAG LENNARD_JONES_ACOEF -%FORMAT(5E16.8) - 1.04308023E+06 6.28541240E+05 3.61397723E+05 9.71708117E+04 5.33379252E+04 - 7.51607703E+03 6.78771368E+04 3.63097246E+04 4.98586848E+03 3.25969625E+03 -%FLAG LENNARD_JONES_BCOEF -%FORMAT(5E16.8) - 6.75612247E+02 5.85549272E+02 4.95732238E+02 1.26919150E+02 1.04986921E+02 - 2.17257828E+01 1.06076943E+02 8.66220817E+01 1.76949863E+01 1.43076527E+01 -%FLAG BONDS_INC_HYDROGEN -%FORMAT(10I8) - 0 15 2 0 18 2 0 21 2 3 - 24 2 3 27 2 3 30 2 6 33 - 4 6 36 4 9 39 4 9 42 4 -%FLAG BONDS_WITHOUT_HYDROGEN -%FORMAT(10I8) - 0 6 1 3 9 1 6 12 3 9 - 12 3 -%FLAG ANGLES_INC_HYDROGEN -%FORMAT(10I8) - 0 6 33 2 0 6 36 2 3 9 - 39 2 3 9 42 2 6 0 15 3 - 6 0 18 3 6 0 21 3 9 3 - 24 3 9 3 27 3 9 3 30 3 - 12 6 33 5 12 6 36 5 12 9 - 39 5 12 9 42 5 15 0 18 6 - 15 0 21 6 18 0 21 6 24 3 - 27 6 24 3 30 6 27 3 30 6 - 33 6 36 7 39 9 42 7 -%FLAG ANGLES_WITHOUT_HYDROGEN -%FORMAT(10I8) - 0 6 12 1 3 9 12 1 6 12 - 9 4 -%FLAG DIHEDRALS_INC_HYDROGEN -%FORMAT(10I8) - 6 12 9 39 3 6 12 9 42 3 - 9 12 6 33 3 9 12 6 36 3 - 15 0 6 12 4 15 0 -6 12 5 - 18 0 6 12 4 18 0 -6 12 5 - 21 0 6 12 4 21 0 -6 12 5 - 12 9 3 24 4 12 9 -3 24 5 - 12 9 3 27 4 12 9 -3 27 5 - 12 9 3 30 4 12 9 -3 30 5 - 15 0 6 33 6 15 0 6 36 6 - 18 0 6 33 6 18 0 6 36 6 - 21 0 6 33 6 21 0 6 36 6 - 24 3 9 39 6 24 3 9 42 6 - 27 3 9 39 6 27 3 9 42 6 - 30 3 9 39 6 30 3 9 42 6 -%FLAG DIHEDRALS_WITHOUT_HYDROGEN -%FORMAT(10I8) - 0 6 12 9 1 0 6 -12 9 2 - 3 9 12 6 1 3 9 -12 6 2 -%FLAG EXCLUDED_ATOMS_LIST -%FORMAT(10I8) - 3 4 5 6 7 8 12 13 3 4 - 5 9 10 11 14 15 4 5 6 7 - 8 12 13 14 15 5 9 10 11 12 - 13 14 15 6 7 8 9 10 11 12 - 13 14 15 7 8 12 13 8 12 13 - 12 13 10 11 14 15 11 14 15 14 - 15 13 0 15 0 -%FLAG HBOND_ACOEF -%FORMAT(5E16.8) - -%FLAG HBOND_BCOEF -%FORMAT(5E16.8) - -%FLAG HBCUT -%FORMAT(5E16.8) - -%FLAG AMBER_ATOM_TYPE -%FORMAT(20a4) -CT CT CT CT OS HC HC HC HC HC HC H1 H1 H1 H1 -%FLAG TREE_CHAIN_CLASSIFICATION -%FORMAT(20a4) -BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA -%FLAG JOIN_ARRAY -%FORMAT(10I8) - 0 0 0 0 0 0 0 0 0 0 - 0 0 0 0 0 -%FLAG IROTAT -%FORMAT(10I8) - 0 0 0 0 0 0 0 0 0 0 - 0 0 0 0 0 -%FLAG RADIUS_SET -%FORMAT(1a80) -modified Bondi radii (mbondi) -%FLAG RADII -%FORMAT(5E16.8) - 1.70000000E+00 1.70000000E+00 1.70000000E+00 1.70000000E+00 1.50000000E+00 - 1.30000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00 - 1.30000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00 -%FLAG SCREEN -%FORMAT(5E16.8) - 7.20000000E-01 7.20000000E-01 7.20000000E-01 7.20000000E-01 8.50000000E-01 - 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 - 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 -%FLAG IPOL -%FORMAT(1I8) - 0 diff --git a/openforcefield/data/molecules/AlkEthOH_c38.crd b/openforcefield/data/molecules/AlkEthOH_c38.crd deleted file mode 100644 index caa6fc0ac..000000000 --- a/openforcefield/data/molecules/AlkEthOH_c38.crd +++ /dev/null @@ -1,6 +0,0 @@ -AlkEthOH_c38 - 8 - 0.8151000 -0.5383000 0.4928000 2.1548000 -0.0516000 -0.0117000 - 0.0001000 0.0007000 0.0006000 0.6931000 -1.6067000 0.2906000 - 0.7303000 -0.3800000 1.5721000 2.9698000 -0.5906000 0.4805000 - 2.2767000 1.0166000 0.1908000 2.2396000 -0.2097000 -1.0909000 diff --git a/openforcefield/data/molecules/AlkEthOH_c38.mol2 b/openforcefield/data/molecules/AlkEthOH_c38.mol2 deleted file mode 100644 index 315ecb4a6..000000000 --- a/openforcefield/data/molecules/AlkEthOH_c38.mol2 +++ /dev/null @@ -1,25 +0,0 @@ -@MOLECULE -AlkEthOH_c38 - 8 7 1 0 0 -SMALL -USER_CHARGES - -@ATOM - 1 C1 0.8151 -0.5383 0.4928 CT 1 <0> -0.09384 - 2 C2 2.1548 -0.0516 -0.0117 CT 1 <0> -0.09384 - 3 H1 0.0001 0.0007 0.0006 HC 1 <0> 0.03128 - 4 H2 0.6931 -1.6067 0.2906 HC 1 <0> 0.03128 - 5 H3 0.7303 -0.3800 1.5721 HC 1 <0> 0.03128 - 6 H4 2.9698 -0.5906 0.4805 HC 1 <0> 0.03128 - 7 H5 2.2767 1.0166 0.1908 HC 1 <0> 0.03128 - 8 H6 2.2396 -0.2097 -1.0909 HC 1 <0> 0.03128 -@BOND - 1 1 2 1 - 2 1 3 1 - 3 1 4 1 - 4 1 5 1 - 5 2 6 1 - 6 2 7 1 - 7 2 8 1 -@SUBSTRUCTURE - 1 <0> 1 GROUP 0 A **** diff --git a/openforcefield/data/molecules/AlkEthOH_c38.top b/openforcefield/data/molecules/AlkEthOH_c38.top deleted file mode 100644 index a3e362819..000000000 --- a/openforcefield/data/molecules/AlkEthOH_c38.top +++ /dev/null @@ -1,142 +0,0 @@ -%VERSION VERSION_STAMP = V0001.000 DATE = 06/24/16 11:20:34 -%FLAG TITLE -%FORMAT(20a4) -AlkEthOH_c38 -%FLAG POINTERS -%FORMAT(10I8) - 8 2 6 1 12 0 9 0 0 0 - 29 1 1 0 0 2 2 1 2 0 - 0 0 0 0 0 0 0 0 8 0 - 0 -%FLAG ATOM_NAME -%FORMAT(20a4) -C1 C2 H1 H2 H3 H4 H5 H6 -%FLAG CHARGE -%FORMAT(5E16.8) - -1.70998063E+00 -1.70998063E+00 5.69993544E-01 5.69993544E-01 5.69993544E-01 - 5.69993544E-01 5.69993544E-01 5.69993544E-01 -%FLAG ATOMIC_NUMBER -%FORMAT(10I8) - 6 6 1 1 1 1 1 1 -%FLAG MASS -%FORMAT(5E16.8) - 1.20100000E+01 1.20100000E+01 1.00800000E+00 1.00800000E+00 1.00800000E+00 - 1.00800000E+00 1.00800000E+00 1.00800000E+00 -%FLAG ATOM_TYPE_INDEX -%FORMAT(10I8) - 1 1 2 2 2 2 2 2 -%FLAG NUMBER_EXCLUDED_ATOMS -%FORMAT(10I8) - 7 6 5 4 3 2 1 1 -%FLAG NONBONDED_PARM_INDEX -%FORMAT(10I8) - 1 2 2 3 -%FLAG RESIDUE_LABEL -%FORMAT(20a4) -<0> -%FLAG RESIDUE_POINTER -%FORMAT(10I8) - 1 -%FLAG BOND_FORCE_CONSTANT -%FORMAT(5E16.8) - 3.10000000E+02 3.40000000E+02 -%FLAG BOND_EQUIL_VALUE -%FORMAT(5E16.8) - 1.52600000E+00 1.09000000E+00 -%FLAG ANGLE_FORCE_CONSTANT -%FORMAT(5E16.8) - 5.00000000E+01 3.50000000E+01 -%FLAG ANGLE_EQUIL_VALUE -%FORMAT(5E16.8) - 1.91113635E+00 1.91113635E+00 -%FLAG DIHEDRAL_FORCE_CONSTANT -%FORMAT(5E16.8) - 1.50000000E-01 -%FLAG DIHEDRAL_PERIODICITY -%FORMAT(5E16.8) - 3.00000000E+00 -%FLAG DIHEDRAL_PHASE -%FORMAT(5E16.8) - 0.00000000E+00 -%FLAG SCEE_SCALE_FACTOR -%FORMAT(5E16.8) - 1.20000000E+00 -%FLAG SCNB_SCALE_FACTOR -%FORMAT(5E16.8) - 2.00000000E+00 -%FLAG SOLTY -%FORMAT(5E16.8) - 0.00000000E+00 0.00000000E+00 -%FLAG LENNARD_JONES_ACOEF -%FORMAT(5E16.8) - 1.04308023E+06 9.71708117E+04 7.51607703E+03 -%FLAG LENNARD_JONES_BCOEF -%FORMAT(5E16.8) - 6.75612247E+02 1.26919150E+02 2.17257828E+01 -%FLAG BONDS_INC_HYDROGEN -%FORMAT(10I8) - 0 6 2 0 9 2 0 12 2 3 - 15 2 3 18 2 3 21 2 -%FLAG BONDS_WITHOUT_HYDROGEN -%FORMAT(10I8) - 0 3 1 -%FLAG ANGLES_INC_HYDROGEN -%FORMAT(10I8) - 0 3 15 1 0 3 18 1 0 3 - 21 1 3 0 6 1 3 0 9 1 - 3 0 12 1 6 0 9 2 6 0 - 12 2 9 0 12 2 15 3 18 2 - 15 3 21 2 18 3 21 2 -%FLAG ANGLES_WITHOUT_HYDROGEN -%FORMAT(10I8) - -%FLAG DIHEDRALS_INC_HYDROGEN -%FORMAT(10I8) - 6 0 3 15 1 6 0 3 18 1 - 6 0 3 21 1 9 0 3 15 1 - 9 0 3 18 1 9 0 3 21 1 - 12 0 3 15 1 12 0 3 18 1 - 12 0 3 21 1 -%FLAG DIHEDRALS_WITHOUT_HYDROGEN -%FORMAT(10I8) - -%FLAG EXCLUDED_ATOMS_LIST -%FORMAT(10I8) - 2 3 4 5 6 7 8 3 4 5 - 6 7 8 4 5 6 7 8 5 6 - 7 8 6 7 8 7 8 8 0 -%FLAG HBOND_ACOEF -%FORMAT(5E16.8) - -%FLAG HBOND_BCOEF -%FORMAT(5E16.8) - -%FLAG HBCUT -%FORMAT(5E16.8) - -%FLAG AMBER_ATOM_TYPE -%FORMAT(20a4) -CT CT HC HC HC HC HC HC -%FLAG TREE_CHAIN_CLASSIFICATION -%FORMAT(20a4) -BLA BLA BLA BLA BLA BLA BLA BLA -%FLAG JOIN_ARRAY -%FORMAT(10I8) - 0 0 0 0 0 0 0 0 -%FLAG IROTAT -%FORMAT(10I8) - 0 0 0 0 0 0 0 0 -%FLAG RADIUS_SET -%FORMAT(1a80) -modified Bondi radii (mbondi) -%FLAG RADII -%FORMAT(5E16.8) - 1.70000000E+00 1.70000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00 - 1.30000000E+00 1.30000000E+00 1.30000000E+00 -%FLAG SCREEN -%FORMAT(5E16.8) - 7.20000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 - 8.50000000E-01 8.50000000E-01 8.50000000E-01 -%FLAG IPOL -%FORMAT(1I8) - 0 diff --git a/openforcefield/data/molecules/AlkEthOH_r0.crd b/openforcefield/data/molecules/AlkEthOH_r0.crd deleted file mode 100644 index ff6dd5456..000000000 --- a/openforcefield/data/molecules/AlkEthOH_r0.crd +++ /dev/null @@ -1,8 +0,0 @@ -AlkEthOH_r0 - 12 - 0.1466000 -0.6972000 -1.2190000 0.1072000 -0.7754000 0.3061000 - -0.1521000 0.7339000 0.2375000 0.0894000 0.7465000 -1.1920000 - 1.3221000 -1.1878000 0.9520000 -1.4710000 1.1671000 0.6094000 - 1.0701000 -1.0576000 -1.6805000 -0.7173000 -1.1199000 -1.7408000 - -0.7451000 -1.3515000 0.6836000 0.6019000 1.3396000 0.7541000 - 1.1323000 -1.1855000 1.8998000 -1.4701000 2.1287000 0.5135000 diff --git a/openforcefield/data/molecules/AlkEthOH_r0.mol2 b/openforcefield/data/molecules/AlkEthOH_r0.mol2 deleted file mode 100644 index ce0d13f20..000000000 --- a/openforcefield/data/molecules/AlkEthOH_r0.mol2 +++ /dev/null @@ -1,34 +0,0 @@ -@MOLECULE -AlkEthOH_r0 - 12 12 1 0 0 -SMALL -USER_CHARGES - -@ATOM - 1 C1 0.1466 -0.6972 -1.2190 CT 1 <0> 0.12422 - 2 C2 0.1072 -0.7754 0.3061 CT 1 <0> 0.09371 - 3 C3 -0.1521 0.7339 0.2375 CT 1 <0> 0.28012 - 4 O1 0.0894 0.7465 -1.1920 OS 1 <0> -0.45191 - 5 O2 1.3221 -1.1878 0.9520 OH 1 <0> -0.57726 - 6 O3 -1.4710 1.1671 0.6094 OH 1 <0> -0.60584 - 7 H1 1.0701 -1.0576 -1.6805 H1 1 <0> 0.07102 - 8 H2 -0.7173 -1.1199 -1.7408 H1 1 <0> 0.07102 - 9 H3 -0.7451 -1.3515 0.6836 H1 1 <0> 0.07642 - 10 H4 0.6019 1.3396 0.7541 H2 1 <0> 0.07902 - 11 H5 1.1323 -1.1855 1.8998 HO 1 <0> 0.41214 - 12 H6 -1.4701 2.1287 0.5135 HO 1 <0> 0.42734 -@BOND - 1 1 2 1 - 2 1 4 1 - 3 2 3 1 - 4 2 5 1 - 5 3 4 1 - 6 3 6 1 - 7 1 7 1 - 8 1 8 1 - 9 2 9 1 - 10 3 10 1 - 11 5 11 1 - 12 6 12 1 -@SUBSTRUCTURE - 1 <0> 1 GROUP 0 A **** diff --git a/openforcefield/data/molecules/AlkEthOH_r0.top b/openforcefield/data/molecules/AlkEthOH_r0.top deleted file mode 100644 index c0757972a..000000000 --- a/openforcefield/data/molecules/AlkEthOH_r0.top +++ /dev/null @@ -1,198 +0,0 @@ -%VERSION VERSION_STAMP = V0001.000 DATE = 06/24/16 11:21:01 -%FLAG TITLE -%FORMAT(20a4) -AlkEthOH_r0 -%FLAG POINTERS -%FORMAT(10I8) - 12 6 6 6 13 8 29 14 0 0 - 53 1 6 8 14 6 13 10 6 0 - 0 0 0 0 0 0 0 0 12 0 - 0 -%FLAG ATOM_NAME -%FORMAT(20a4) -C1 C2 C3 O1 O2 O3 H1 H2 H3 H4 H5 H6 -%FLAG CHARGE -%FORMAT(5E16.8) - 2.26357411E+00 1.70761173E+00 5.10443068E+00 -8.23483959E+00 -1.05190049E+01 - -1.10397982E+01 1.29414775E+00 1.29414775E+00 1.39254817E+00 1.43992615E+00 - 7.51013872E+00 7.78711768E+00 -%FLAG ATOMIC_NUMBER -%FORMAT(10I8) - 6 6 6 8 8 8 1 1 1 1 - 1 1 -%FLAG MASS -%FORMAT(5E16.8) - 1.20100000E+01 1.20100000E+01 1.20100000E+01 1.60000000E+01 1.60000000E+01 - 1.60000000E+01 1.00800000E+00 1.00800000E+00 1.00800000E+00 1.00800000E+00 - 1.00800000E+00 1.00800000E+00 -%FLAG ATOM_TYPE_INDEX -%FORMAT(10I8) - 1 1 1 2 3 3 4 4 4 5 - 6 6 -%FLAG NUMBER_EXCLUDED_ATOMS -%FORMAT(10I8) - 10 10 9 7 6 3 2 1 2 1 - 1 1 -%FLAG NONBONDED_PARM_INDEX -%FORMAT(10I8) - 1 2 4 7 11 16 2 3 5 8 - 12 17 4 5 6 9 13 18 7 8 - 9 10 14 19 11 12 13 14 15 20 - 16 17 18 19 20 21 -%FLAG RESIDUE_LABEL -%FORMAT(20a4) -<0> -%FLAG RESIDUE_POINTER -%FORMAT(10I8) - 1 -%FLAG BOND_FORCE_CONSTANT -%FORMAT(5E16.8) - 3.10000000E+02 3.20000000E+02 3.40000000E+02 3.20000000E+02 3.40000000E+02 - 5.53000000E+02 -%FLAG BOND_EQUIL_VALUE -%FORMAT(5E16.8) - 1.52600000E+00 1.37000000E+00 1.09000000E+00 1.41000000E+00 1.09000000E+00 - 9.60000000E-01 -%FLAG ANGLE_FORCE_CONSTANT -%FORMAT(5E16.8) - 4.00000000E+01 5.00000000E+01 5.00000000E+01 6.00000000E+01 5.00000000E+01 - 5.00000000E+01 5.50000000E+01 5.00000000E+01 7.00000000E+01 5.00000000E+01 - 5.00000000E+01 5.00000000E+01 3.50000000E+01 -%FLAG ANGLE_EQUIL_VALUE -%FORMAT(5E16.8) - 1.91113635E+00 1.91113635E+00 1.91113635E+00 1.91113635E+00 1.91113635E+00 - 1.91113635E+00 1.89368305E+00 1.91113635E+00 1.91113635E+00 1.91113635E+00 - 1.91113635E+00 1.91113635E+00 1.91113635E+00 -%FLAG DIHEDRAL_FORCE_CONSTANT -%FORMAT(5E16.8) - 1.55555556E-01 2.50000000E-01 1.60000000E-01 1.00000000E-01 3.83000000E-01 - 3.83333333E-01 1.17500000E+00 1.44000000E-01 0.00000000E+00 1.66666667E-01 -%FLAG DIHEDRAL_PERIODICITY -%FORMAT(5E16.8) - 3.00000000E+00 1.00000000E+00 3.00000000E+00 2.00000000E+00 3.00000000E+00 - 3.00000000E+00 2.00000000E+00 3.00000000E+00 3.00000000E+00 3.00000000E+00 -%FLAG DIHEDRAL_PHASE -%FORMAT(5E16.8) - 0.00000000E+00 0.00000000E+00 0.00000000E+00 3.14159400E+00 0.00000000E+00 - 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 -%FLAG SCEE_SCALE_FACTOR -%FORMAT(5E16.8) - 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 - 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 -%FLAG SCNB_SCALE_FACTOR -%FORMAT(5E16.8) - 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 - 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 -%FLAG SOLTY -%FORMAT(5E16.8) - 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 - 0.00000000E+00 -%FLAG LENNARD_JONES_ACOEF -%FORMAT(5E16.8) - 1.04308023E+06 6.28541240E+05 3.61397723E+05 7.91544157E+05 4.58874091E+05 - 5.81803229E+05 6.78771368E+04 3.63097246E+04 4.66922514E+04 3.25969625E+03 - 4.68930885E+04 2.44050579E+04 3.15360051E+04 2.09814978E+03 1.32801250E+03 - 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 - 0.00000000E+00 -%FLAG LENNARD_JONES_BCOEF -%FORMAT(5E16.8) - 6.75612247E+02 5.85549272E+02 4.95732238E+02 6.93079947E+02 5.89183300E+02 - 6.99746810E+02 1.06076943E+02 8.66220817E+01 1.03606917E+02 1.43076527E+01 - 8.81685417E+01 7.10161395E+01 8.51470647E+01 1.14788417E+01 9.13231543E+00 - 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 - 0.00000000E+00 -%FLAG BONDS_INC_HYDROGEN -%FORMAT(10I8) - 0 18 3 0 21 3 3 24 3 6 - 27 5 12 30 6 15 33 6 -%FLAG BONDS_WITHOUT_HYDROGEN -%FORMAT(10I8) - 0 3 1 0 9 2 3 6 1 3 - 12 4 6 9 2 6 15 4 -%FLAG ANGLES_INC_HYDROGEN -%FORMAT(10I8) - 0 3 24 3 3 0 18 3 3 0 - 21 3 3 6 27 6 3 12 30 7 - 6 3 24 3 6 15 33 7 9 0 - 18 8 9 0 21 8 9 6 27 10 - 12 3 24 11 15 6 27 12 18 0 - 21 13 -%FLAG ANGLES_WITHOUT_HYDROGEN -%FORMAT(10I8) - 0 3 6 1 0 3 12 2 0 9 - 6 4 3 0 9 5 3 6 9 5 - 3 6 15 2 6 3 12 2 9 6 - 15 9 -%FLAG DIHEDRALS_INC_HYDROGEN -%FORMAT(10I8) - 0 3 6 27 1 0 3 12 30 2 - 0 3 -12 30 3 0 9 -6 27 6 - 3 6 15 33 2 3 6 -15 33 3 - 18 0 3 6 1 21 0 3 6 1 - 6 3 12 30 2 6 3 -12 30 3 - 18 0 -9 6 6 21 0 -9 6 6 - 9 0 3 24 2 9 0 -3 24 9 - 9 6 -3 24 2 9 6 -3 24 9 - 9 6 15 33 10 18 0 3 12 2 - 18 0 -3 12 9 21 0 3 12 2 - 21 0 -3 12 9 12 3 6 27 1 - 15 6 3 24 2 15 6 -3 24 9 - 18 0 3 24 1 21 0 3 24 1 - 24 3 6 27 1 24 3 12 30 10 - 27 6 15 33 10 -%FLAG DIHEDRALS_WITHOUT_HYDROGEN -%FORMAT(10I8) - 0 3 -6 9 1 0 3 6 15 1 - 0 9 -6 3 4 0 9 -6 3 5 - 0 9 -6 15 6 3 0 -9 6 4 - 3 0 -9 6 5 9 0 -3 6 1 - 9 0 3 12 7 9 0 -3 12 8 - 9 6 -3 12 7 9 6 -3 12 8 - 12 3 6 15 7 12 3 -6 15 8 -%FLAG EXCLUDED_ATOMS_LIST -%FORMAT(10I8) - 2 3 4 5 6 7 8 9 10 11 - 3 4 5 6 7 8 9 10 11 12 - 4 5 6 7 8 9 10 11 12 5 - 6 7 8 9 10 12 6 7 8 9 - 10 11 9 10 12 8 9 9 10 11 - 12 0 0 -%FLAG HBOND_ACOEF -%FORMAT(5E16.8) - -%FLAG HBOND_BCOEF -%FORMAT(5E16.8) - -%FLAG HBCUT -%FORMAT(5E16.8) - -%FLAG AMBER_ATOM_TYPE -%FORMAT(20a4) -CT CT CT OS OH OH H1 H1 H1 H2 HO HO -%FLAG TREE_CHAIN_CLASSIFICATION -%FORMAT(20a4) -BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA -%FLAG JOIN_ARRAY -%FORMAT(10I8) - 0 0 0 0 0 0 0 0 0 0 - 0 0 -%FLAG IROTAT -%FORMAT(10I8) - 0 0 0 0 0 0 0 0 0 0 - 0 0 -%FLAG RADIUS_SET -%FORMAT(1a80) -modified Bondi radii (mbondi) -%FLAG RADII -%FORMAT(5E16.8) - 1.70000000E+00 1.70000000E+00 1.70000000E+00 1.50000000E+00 1.50000000E+00 - 1.50000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00 - 8.00000000E-01 8.00000000E-01 -%FLAG SCREEN -%FORMAT(5E16.8) - 7.20000000E-01 7.20000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01 - 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 - 8.50000000E-01 8.50000000E-01 -%FLAG IPOL -%FORMAT(1I8) - 0 diff --git a/openforcefield/data/molecules/AlkEthOH_r118.crd b/openforcefield/data/molecules/AlkEthOH_r118.crd deleted file mode 100644 index b4edd7527..000000000 --- a/openforcefield/data/molecules/AlkEthOH_r118.crd +++ /dev/null @@ -1,10 +0,0 @@ -AlkEthOH_r118 - 15 - -0.4889000 -0.3488000 -1.2837000 -0.4364000 -1.4994000 -0.2985000 - -0.3513000 0.8535000 -0.3791000 0.6046000 0.3458000 0.6876000 - 0.3500000 -1.0623000 0.8180000 -1.6194000 1.1396000 0.1996000 - 1.9415000 0.5717000 0.2562000 0.3701000 -0.4078000 -1.9621000 - -1.4079000 -0.3639000 -1.8764000 -1.4353000 -1.7492000 0.0745000 - 0.0073000 -2.4005000 -0.7314000 0.0029000 1.7405000 -0.9126000 - 0.4509000 0.8287000 1.6582000 -1.4960000 1.9133000 0.7720000 - 2.5211000 0.2368000 0.9587000 diff --git a/openforcefield/data/molecules/AlkEthOH_r118.mol2 b/openforcefield/data/molecules/AlkEthOH_r118.mol2 deleted file mode 100644 index d8d8bc9ab..000000000 --- a/openforcefield/data/molecules/AlkEthOH_r118.mol2 +++ /dev/null @@ -1,40 +0,0 @@ -@MOLECULE -AlkEthOH_r118 - 15 15 1 0 0 -SMALL -USER_CHARGES - -@ATOM - 1 C1 -0.4889 -0.3488 -1.2837 CT 1 <0> -0.11003 - 2 C2 -0.4364 -1.4994 -0.2985 CT 1 <0> 0.13137 - 3 C3 -0.3513 0.8535 -0.3791 CT 1 <0> 0.11345 - 4 C4 0.6046 0.3458 0.6876 CT 1 <0> 0.30025 - 5 O1 0.3500 -1.0623 0.8180 OS 1 <0> -0.45581 - 6 O2 -1.6194 1.1396 0.1996 OH 1 <0> -0.58877 - 7 O3 1.9415 0.5717 0.2562 OH 1 <0> -0.62658 - 8 H1 0.3701 -0.4078 -1.9621 HC 1 <0> 0.07229 - 9 H2 -1.4079 -0.3639 -1.8764 HC 1 <0> 0.07229 - 10 H3 -1.4353 -1.7492 0.0745 H1 1 <0> 0.05724 - 11 H4 0.0073 -2.4005 -0.7314 H1 1 <0> 0.05724 - 12 H5 0.0029 1.7405 -0.9126 H1 1 <0> 0.07131 - 13 H6 0.4509 0.8287 1.6582 H2 1 <0> 0.06726 - 14 H7 -1.4960 1.9133 0.7720 HO 1 <0> 0.40735 - 15 H8 2.5211 0.2368 0.9587 HO 1 <0> 0.43114 -@BOND - 1 1 2 1 - 2 1 3 1 - 3 2 5 1 - 4 3 4 1 - 5 3 6 1 - 6 4 5 1 - 7 4 7 1 - 8 1 8 1 - 9 1 9 1 - 10 2 10 1 - 11 2 11 1 - 12 3 12 1 - 13 4 13 1 - 14 6 14 1 - 15 7 15 1 -@SUBSTRUCTURE - 1 <0> 1 GROUP 0 A **** diff --git a/openforcefield/data/molecules/AlkEthOH_r118.top b/openforcefield/data/molecules/AlkEthOH_r118.top deleted file mode 100644 index 6a4cbae14..000000000 --- a/openforcefield/data/molecules/AlkEthOH_r118.top +++ /dev/null @@ -1,217 +0,0 @@ -%VERSION VERSION_STAMP = V0001.000 DATE = 06/24/16 11:21:05 -%FLAG TITLE -%FORMAT(20a4) -AlkEthOH_r118 -%FLAG POINTERS -%FORMAT(10I8) - 15 7 8 7 18 9 38 16 0 0 - 79 1 7 9 16 7 15 13 7 0 - 0 0 0 0 0 0 0 0 15 0 - 0 -%FLAG ATOM_NAME -%FORMAT(20a4) -C1 C2 C3 C4 O1 O2 O3 H1 H2 H3 H4 H5 H6 H7 H8 -%FLAG CHARGE -%FORMAT(5E16.8) - -2.00499967E+00 2.39386355E+00 2.06731993E+00 5.47124558E+00 -8.30590656E+00 - -1.07287436E+01 -1.14177287E+01 1.31729007E+00 1.31729007E+00 1.04304445E+00 - 1.04304445E+00 1.29943221E+00 1.22563190E+00 7.42285391E+00 7.85636242E+00 -%FLAG ATOMIC_NUMBER -%FORMAT(10I8) - 6 6 6 6 8 8 8 1 1 1 - 1 1 1 1 1 -%FLAG MASS -%FORMAT(5E16.8) - 1.20100000E+01 1.20100000E+01 1.20100000E+01 1.20100000E+01 1.60000000E+01 - 1.60000000E+01 1.60000000E+01 1.00800000E+00 1.00800000E+00 1.00800000E+00 - 1.00800000E+00 1.00800000E+00 1.00800000E+00 1.00800000E+00 1.00800000E+00 -%FLAG ATOM_TYPE_INDEX -%FORMAT(10I8) - 1 1 1 1 2 3 3 4 4 5 - 5 5 6 7 7 -%FLAG NUMBER_EXCLUDED_ATOMS -%FORMAT(10I8) - 13 11 12 11 9 6 3 4 3 1 - 1 2 1 1 1 -%FLAG NONBONDED_PARM_INDEX 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1.91113635E+00 - 1.91113635E+00 1.91113635E+00 1.91113635E+00 1.91113635E+00 1.91113635E+00 -%FLAG DIHEDRAL_FORCE_CONSTANT -%FORMAT(5E16.8) - 1.00000000E-01 3.83000000E-01 1.55555556E-01 2.50000000E-01 1.60000000E-01 - 2.00000000E-01 2.50000000E-01 1.80000000E-01 3.83333333E-01 0.00000000E+00 - 1.17500000E+00 1.44000000E-01 1.66666667E-01 -%FLAG DIHEDRAL_PERIODICITY -%FORMAT(5E16.8) - 2.00000000E+00 3.00000000E+00 3.00000000E+00 1.00000000E+00 3.00000000E+00 - 1.00000000E+00 2.00000000E+00 3.00000000E+00 3.00000000E+00 3.00000000E+00 - 2.00000000E+00 3.00000000E+00 3.00000000E+00 -%FLAG DIHEDRAL_PHASE -%FORMAT(5E16.8) - 3.14159400E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 - 3.14159400E+00 3.14159400E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 - 0.00000000E+00 0.00000000E+00 0.00000000E+00 -%FLAG SCEE_SCALE_FACTOR -%FORMAT(5E16.8) - 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 - 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 - 1.20000000E+00 1.20000000E+00 1.20000000E+00 -%FLAG SCNB_SCALE_FACTOR -%FORMAT(5E16.8) - 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 - 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 - 2.00000000E+00 2.00000000E+00 2.00000000E+00 -%FLAG SOLTY -%FORMAT(5E16.8) - 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 - 0.00000000E+00 0.00000000E+00 -%FLAG LENNARD_JONES_ACOEF -%FORMAT(5E16.8) - 1.04308023E+06 6.28541240E+05 3.61397723E+05 7.91544157E+05 4.58874091E+05 - 5.81803229E+05 9.71708117E+04 5.33379252E+04 6.82786631E+04 7.51607703E+03 - 6.78771368E+04 3.63097246E+04 4.66922514E+04 4.98586848E+03 3.25969625E+03 - 4.68930885E+04 2.44050579E+04 3.15360051E+04 3.25969625E+03 2.09814978E+03 - 1.32801250E+03 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 - 0.00000000E+00 0.00000000E+00 0.00000000E+00 -%FLAG LENNARD_JONES_BCOEF -%FORMAT(5E16.8) - 6.75612247E+02 5.85549272E+02 4.95732238E+02 6.93079947E+02 5.89183300E+02 - 6.99746810E+02 1.26919150E+02 1.04986921E+02 1.25287818E+02 2.17257828E+01 - 1.06076943E+02 8.66220817E+01 1.03606917E+02 1.76949863E+01 1.43076527E+01 - 8.81685417E+01 7.10161395E+01 8.51470647E+01 1.43076527E+01 1.14788417E+01 - 9.13231543E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 - 0.00000000E+00 0.00000000E+00 0.00000000E+00 -%FLAG BONDS_INC_HYDROGEN -%FORMAT(10I8) - 0 21 2 0 24 2 3 27 4 3 - 30 4 6 33 4 9 36 6 15 39 - 7 18 42 7 -%FLAG BONDS_WITHOUT_HYDROGEN -%FORMAT(10I8) - 0 3 1 0 6 1 3 12 3 6 - 9 1 6 15 5 9 12 3 9 18 - 5 -%FLAG ANGLES_INC_HYDROGEN -%FORMAT(10I8) - 0 3 27 2 0 3 30 2 0 6 - 33 2 3 0 21 5 3 0 24 5 - 6 0 21 5 6 0 24 5 6 9 - 36 7 6 15 39 8 9 6 33 2 - 9 18 42 8 12 3 27 9 12 3 - 30 9 12 9 36 11 15 6 33 12 - 18 9 36 13 21 0 24 14 27 3 - 30 15 -%FLAG ANGLES_WITHOUT_HYDROGEN -%FORMAT(10I8) - 0 3 12 1 0 6 9 3 0 6 - 15 4 3 0 6 3 3 12 9 6 - 6 9 12 1 6 9 18 4 9 6 - 15 4 12 9 18 10 -%FLAG DIHEDRALS_INC_HYDROGEN -%FORMAT(10I8) - 0 6 9 36 3 0 6 15 39 4 - 0 6 -15 39 5 3 0 6 33 3 - 3 12 9 36 9 6 0 3 27 3 - 6 0 3 30 3 6 9 18 42 4 - 6 9 -18 42 5 21 0 6 9 5 - 24 0 6 9 5 9 6 15 39 4 - 9 6 -15 39 5 9 12 3 27 9 - 9 12 3 30 9 21 0 3 12 4 - 21 0 -3 12 10 24 0 3 12 4 - 24 0 -3 12 10 12 9 6 33 4 - 12 9 -6 33 10 12 9 18 42 13 - 21 0 6 15 4 21 0 -6 15 10 - 24 0 6 15 4 24 0 -6 15 10 - 15 6 9 36 3 18 9 6 33 4 - 18 9 -6 33 10 21 0 3 27 3 - 21 0 3 30 3 21 0 6 33 3 - 24 0 3 27 3 24 0 3 30 3 - 24 0 6 33 3 33 6 9 36 3 - 33 6 15 39 13 36 9 18 42 13 -%FLAG DIHEDRALS_WITHOUT_HYDROGEN -%FORMAT(10I8) - 0 3 -12 9 1 0 3 -12 9 2 - 0 6 -9 12 3 0 6 9 18 3 - 3 0 -6 9 6 3 0 -6 9 7 - 3 0 -6 9 8 3 0 6 15 3 - 3 12 -9 6 1 3 12 -9 6 2 - 3 12 9 18 9 6 0 -3 12 3 - 12 9 6 15 11 12 9 -6 15 12 - 15 6 9 18 11 15 6 -9 18 12 -%FLAG EXCLUDED_ATOMS_LIST -%FORMAT(10I8) - 2 3 4 5 6 7 8 9 10 11 - 12 13 14 3 4 5 6 7 8 9 - 10 11 12 13 4 5 6 7 8 9 - 10 11 12 13 14 15 5 6 7 8 - 9 10 11 12 13 14 15 6 7 8 - 9 10 11 12 13 15 7 8 9 12 - 13 14 12 13 15 9 10 11 12 10 - 11 12 11 0 13 14 15 0 0 -%FLAG HBOND_ACOEF -%FORMAT(5E16.8) - -%FLAG HBOND_BCOEF -%FORMAT(5E16.8) - -%FLAG HBCUT -%FORMAT(5E16.8) - -%FLAG AMBER_ATOM_TYPE -%FORMAT(20a4) -CT CT CT CT OS OH OH HC HC H1 H1 H1 H2 HO HO -%FLAG TREE_CHAIN_CLASSIFICATION -%FORMAT(20a4) -BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA -%FLAG JOIN_ARRAY -%FORMAT(10I8) - 0 0 0 0 0 0 0 0 0 0 - 0 0 0 0 0 -%FLAG IROTAT -%FORMAT(10I8) - 0 0 0 0 0 0 0 0 0 0 - 0 0 0 0 0 -%FLAG RADIUS_SET -%FORMAT(1a80) -modified Bondi radii (mbondi) -%FLAG RADII -%FORMAT(5E16.8) - 1.70000000E+00 1.70000000E+00 1.70000000E+00 1.70000000E+00 1.50000000E+00 - 1.50000000E+00 1.50000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00 - 1.30000000E+00 1.30000000E+00 1.30000000E+00 8.00000000E-01 8.00000000E-01 -%FLAG SCREEN -%FORMAT(5E16.8) - 7.20000000E-01 7.20000000E-01 7.20000000E-01 7.20000000E-01 8.50000000E-01 - 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 - 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 -%FLAG IPOL -%FORMAT(1I8) - 0 diff --git a/openforcefield/data/molecules/AlkEthOH_r12.crd b/openforcefield/data/molecules/AlkEthOH_r12.crd deleted file mode 100644 index 00671e958..000000000 --- a/openforcefield/data/molecules/AlkEthOH_r12.crd +++ /dev/null @@ -1,11 +0,0 @@ -AlkEthOH_r12 - 18 - 0.6732000 -0.4390000 -0.7436000 0.6660000 -1.9571000 -0.6351000 - 0.2699000 -0.0071000 -2.1462000 1.4748000 -2.5870000 -1.7665000 - 1.0536000 -2.0225000 -3.1247000 1.1312000 -0.5970000 -3.1181000 - 1.2739000 -3.9968000 -1.7632000 1.9372000 -2.5500000 -4.1132000 - -0.0389000 -0.0250000 -0.0204000 1.6636000 -0.0448000 -0.4957000 - 1.0972000 -2.2509000 0.3296000 -0.3696000 -2.3154000 -0.6586000 - -0.7481000 -0.3439000 -2.3578000 0.2858000 1.0820000 -2.2491000 - 2.5429000 -2.3975000 -1.5896000 0.0514000 -2.3023000 -3.3624000 - 1.5781000 -4.3150000 -0.8998000 1.6528000 -2.1802000 -4.9634000 diff --git a/openforcefield/data/molecules/AlkEthOH_r12.mol2 b/openforcefield/data/molecules/AlkEthOH_r12.mol2 deleted file mode 100644 index ed2f7a2ca..000000000 --- a/openforcefield/data/molecules/AlkEthOH_r12.mol2 +++ /dev/null @@ -1,46 +0,0 @@ -@MOLECULE -AlkEthOH_r12 - 18 18 1 0 0 -SMALL -USER_CHARGES - -@ATOM - 1 C1 0.6732 -0.4390 -0.7436 CT 1 <0> -0.11098 - 2 C2 0.6660 -1.9571 -0.6351 CT 1 <0> -0.11751 - 3 C3 0.2699 -0.0071 -2.1462 CT 1 <0> 0.13893 - 4 C4 1.4748 -2.5870 -1.7665 CT 1 <0> 0.11892 - 5 C5 1.0536 -2.0225 -3.1247 CT 1 <0> 0.34658 - 6 O1 1.1312 -0.5970 -3.1181 OS 1 <0> -0.45964 - 7 O2 1.2739 -3.9968 -1.7632 OH 1 <0> -0.58563 - 8 O3 1.9372 -2.5500 -4.1132 OH 1 <0> -0.58545 - 9 H1 -0.0389 -0.0250 -0.0204 HC 1 <0> 0.05546 - 10 H2 1.6636 -0.0448 -0.4957 HC 1 <0> 0.05546 - 11 H3 1.0972 -2.2509 0.3296 HC 1 <0> 0.05199 - 12 H4 -0.3696 -2.3154 -0.6586 HC 1 <0> 0.05199 - 13 H5 -0.7481 -0.3439 -2.3578 H1 1 <0> 0.05025 - 14 H6 0.2858 1.0820 -2.2491 H1 1 <0> 0.05025 - 15 H7 2.5429 -2.3975 -1.5896 H1 1 <0> 0.06304 - 16 H8 0.0514 -2.3023 -3.3624 H2 1 <0> 0.05030 - 17 H9 1.5781 -4.3150 -0.8998 HO 1 <0> 0.40312 - 18 H10 1.6528 -2.1802 -4.9634 HO 1 <0> 0.42292 -@BOND - 1 1 2 1 - 2 1 3 1 - 3 2 4 1 - 4 3 6 1 - 5 4 5 1 - 6 4 7 1 - 7 5 6 1 - 8 5 8 1 - 9 1 9 1 - 10 1 10 1 - 11 2 11 1 - 12 2 12 1 - 13 3 13 1 - 14 3 14 1 - 15 4 15 1 - 16 5 16 1 - 17 7 17 1 - 18 8 18 1 -@SUBSTRUCTURE - 1 <0> 1 GROUP 0 A **** diff --git a/openforcefield/data/molecules/AlkEthOH_r12.top b/openforcefield/data/molecules/AlkEthOH_r12.top deleted file mode 100644 index 20eba19ea..000000000 --- a/openforcefield/data/molecules/AlkEthOH_r12.top +++ /dev/null @@ -1,231 +0,0 @@ -%VERSION VERSION_STAMP = V0001.000 DATE = 06/24/16 11:21:02 -%FLAG TITLE -%FORMAT(20a4) -AlkEthOH_r12 -%FLAG POINTERS -%FORMAT(10I8) - 18 7 10 8 23 10 46 19 0 0 - 99 1 8 10 19 7 15 14 7 0 - 0 0 0 0 0 0 0 0 18 0 - 0 -%FLAG ATOM_NAME -%FORMAT(20a4) -C1 C2 C3 C4 C5 O1 O2 O3 H1 H2 H3 H4 H5 H6 H7 H8 H9 H10 -%FLAG CHARGE -%FORMAT(5E16.8) - -2.02231085E+00 -2.14130247E+00 2.53162414E+00 2.16699592E+00 6.31548473E+00 - -8.37569797E+00 -1.06715255E+01 -1.06682455E+01 1.01060876E+00 1.01060876E+00 - 9.47377377E-01 9.47377377E-01 9.15670575E-01 9.15670575E-01 1.14873379E+00 - 9.16581690E-01 7.34577358E+00 7.70657512E+00 -%FLAG ATOMIC_NUMBER -%FORMAT(10I8) - 6 6 6 6 6 8 8 8 1 1 - 1 1 1 1 1 1 1 1 -%FLAG MASS -%FORMAT(5E16.8) - 1.20100000E+01 1.20100000E+01 1.20100000E+01 1.20100000E+01 1.20100000E+01 - 1.60000000E+01 1.60000000E+01 1.60000000E+01 1.00800000E+00 1.00800000E+00 - 1.00800000E+00 1.00800000E+00 1.00800000E+00 1.00800000E+00 1.00800000E+00 - 1.00800000E+00 1.00800000E+00 1.00800000E+00 -%FLAG ATOM_TYPE_INDEX -%FORMAT(10I8) - 1 1 1 1 1 2 3 3 4 4 - 4 4 5 5 5 6 7 7 -%FLAG NUMBER_EXCLUDED_ATOMS -%FORMAT(10I8) - 13 15 11 12 11 9 6 3 5 4 - 2 1 1 1 2 1 1 1 -%FLAG NONBONDED_PARM_INDEX -%FORMAT(10I8) - 1 2 4 7 11 16 22 2 3 5 - 8 12 17 23 4 5 6 9 13 18 - 24 7 8 9 10 14 19 25 11 12 - 13 14 15 20 26 16 17 18 19 20 - 21 27 22 23 24 25 26 27 28 -%FLAG RESIDUE_LABEL -%FORMAT(20a4) -<0> -%FLAG RESIDUE_POINTER -%FORMAT(10I8) - 1 -%FLAG BOND_FORCE_CONSTANT -%FORMAT(5E16.8) - 3.10000000E+02 3.40000000E+02 3.20000000E+02 3.40000000E+02 3.20000000E+02 - 3.40000000E+02 5.53000000E+02 -%FLAG BOND_EQUIL_VALUE -%FORMAT(5E16.8) - 1.52600000E+00 1.09000000E+00 1.37000000E+00 1.09000000E+00 1.41000000E+00 - 1.09000000E+00 9.60000000E-01 -%FLAG ANGLE_FORCE_CONSTANT -%FORMAT(5E16.8) - 4.00000000E+01 5.00000000E+01 5.00000000E+01 5.00000000E+01 5.00000000E+01 - 6.00000000E+01 5.00000000E+01 5.50000000E+01 5.00000000E+01 7.00000000E+01 - 5.00000000E+01 5.00000000E+01 5.00000000E+01 3.50000000E+01 3.50000000E+01 -%FLAG ANGLE_EQUIL_VALUE -%FORMAT(5E16.8) - 1.91113635E+00 1.91113635E+00 1.91113635E+00 1.91113635E+00 1.91113635E+00 - 1.91113635E+00 1.91113635E+00 1.89368305E+00 1.91113635E+00 1.91113635E+00 - 1.91113635E+00 1.91113635E+00 1.91113635E+00 1.91113635E+00 1.91113635E+00 -%FLAG DIHEDRAL_FORCE_CONSTANT -%FORMAT(5E16.8) - 2.00000000E-01 2.50000000E-01 1.80000000E-01 1.55555556E-01 1.00000000E-01 - 3.83000000E-01 2.50000000E-01 1.60000000E-01 3.83333333E-01 0.00000000E+00 - 1.17500000E+00 1.44000000E-01 1.66666667E-01 1.50000000E-01 -%FLAG DIHEDRAL_PERIODICITY -%FORMAT(5E16.8) - 1.00000000E+00 2.00000000E+00 3.00000000E+00 3.00000000E+00 2.00000000E+00 - 3.00000000E+00 1.00000000E+00 3.00000000E+00 3.00000000E+00 3.00000000E+00 - 2.00000000E+00 3.00000000E+00 3.00000000E+00 3.00000000E+00 -%FLAG DIHEDRAL_PHASE -%FORMAT(5E16.8) - 3.14159400E+00 3.14159400E+00 0.00000000E+00 0.00000000E+00 3.14159400E+00 - 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 - 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 -%FLAG SCEE_SCALE_FACTOR -%FORMAT(5E16.8) - 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 - 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 - 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 -%FLAG SCNB_SCALE_FACTOR -%FORMAT(5E16.8) - 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 - 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 - 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 -%FLAG SOLTY -%FORMAT(5E16.8) - 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 - 0.00000000E+00 0.00000000E+00 -%FLAG LENNARD_JONES_ACOEF -%FORMAT(5E16.8) - 1.04308023E+06 6.28541240E+05 3.61397723E+05 7.91544157E+05 4.58874091E+05 - 5.81803229E+05 9.71708117E+04 5.33379252E+04 6.82786631E+04 7.51607703E+03 - 6.78771368E+04 3.63097246E+04 4.66922514E+04 4.98586848E+03 3.25969625E+03 - 4.68930885E+04 2.44050579E+04 3.15360051E+04 3.25969625E+03 2.09814978E+03 - 1.32801250E+03 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 - 0.00000000E+00 0.00000000E+00 0.00000000E+00 -%FLAG LENNARD_JONES_BCOEF -%FORMAT(5E16.8) - 6.75612247E+02 5.85549272E+02 4.95732238E+02 6.93079947E+02 5.89183300E+02 - 6.99746810E+02 1.26919150E+02 1.04986921E+02 1.25287818E+02 2.17257828E+01 - 1.06076943E+02 8.66220817E+01 1.03606917E+02 1.76949863E+01 1.43076527E+01 - 8.81685417E+01 7.10161395E+01 8.51470647E+01 1.43076527E+01 1.14788417E+01 - 9.13231543E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 - 0.00000000E+00 0.00000000E+00 0.00000000E+00 -%FLAG BONDS_INC_HYDROGEN -%FORMAT(10I8) - 0 24 2 0 27 2 3 30 2 3 - 33 2 6 36 4 6 39 4 9 42 - 4 12 45 6 18 48 7 21 51 7 -%FLAG BONDS_WITHOUT_HYDROGEN -%FORMAT(10I8) - 0 3 1 0 6 1 3 9 1 6 - 15 3 9 12 1 9 18 5 12 15 - 3 12 21 5 -%FLAG ANGLES_INC_HYDROGEN -%FORMAT(10I8) - 0 3 30 2 0 3 33 2 0 6 - 36 4 0 6 39 4 3 0 24 2 - 3 0 27 2 3 9 42 4 6 0 - 24 2 6 0 27 2 9 3 30 2 - 9 3 33 2 9 12 45 7 9 18 - 48 8 12 9 42 4 12 21 51 8 - 15 6 36 9 15 6 39 9 15 12 - 45 11 18 9 42 12 21 12 45 13 - 24 0 27 14 30 3 33 14 36 6 - 39 15 -%FLAG ANGLES_WITHOUT_HYDROGEN -%FORMAT(10I8) - 0 3 9 1 0 6 15 3 3 0 - 6 1 3 9 12 1 3 9 18 5 - 6 15 12 6 9 12 15 3 9 12 - 21 5 12 9 18 5 15 12 21 10 -%FLAG DIHEDRALS_INC_HYDROGEN -%FORMAT(10I8) - 0 3 9 42 4 3 0 6 36 4 - 3 0 6 39 4 3 9 12 45 4 - 3 9 18 48 7 3 9 -18 48 8 - 6 0 3 30 8 6 0 3 33 8 - 6 15 12 45 9 24 0 3 9 8 - 27 0 3 9 8 9 12 21 51 7 - 9 12 -21 51 8 12 9 3 30 8 - 12 9 3 33 8 12 9 18 48 7 - 12 9 -18 48 8 12 15 6 36 9 - 12 15 6 39 9 24 0 6 15 7 - 24 0 -6 15 10 27 0 6 15 7 - 27 0 -6 15 10 15 12 9 42 7 - 15 12 -9 42 10 15 12 21 51 13 - 18 9 3 30 7 18 9 -3 30 10 - 18 9 3 33 7 18 9 -3 33 10 - 18 9 12 45 4 21 12 9 42 7 - 21 12 -9 42 10 24 0 3 30 14 - 24 0 3 33 14 24 0 6 36 4 - 24 0 6 39 4 27 0 3 30 14 - 27 0 3 33 14 27 0 6 36 4 - 27 0 6 39 4 30 3 9 42 4 - 33 3 9 42 4 42 9 12 45 4 - 42 9 18 48 13 45 12 21 51 13 -%FLAG DIHEDRALS_WITHOUT_HYDROGEN -%FORMAT(10I8) - 0 3 9 12 1 0 3 -9 12 2 - 0 3 -9 12 3 0 3 9 18 4 - 0 6 -15 12 5 0 6 -15 12 6 - 3 0 6 15 4 3 9 -12 15 4 - 3 9 12 21 4 6 0 3 9 1 - 6 0 -3 9 2 6 0 -3 9 3 - 6 15 -12 9 5 6 15 -12 9 6 - 6 15 12 21 9 15 12 9 18 11 - 15 12 -9 18 12 18 9 12 21 11 - 18 9 -12 21 12 -%FLAG EXCLUDED_ATOMS_LIST -%FORMAT(10I8) - 2 3 4 5 6 7 9 10 11 12 - 13 14 15 3 4 5 6 7 8 9 - 10 11 12 13 14 15 16 17 4 5 - 6 8 9 10 11 12 13 14 16 5 - 6 7 8 9 10 11 12 15 16 17 - 18 6 7 8 11 12 13 14 15 16 - 17 18 7 8 9 10 13 14 15 16 - 18 8 11 12 15 16 17 15 16 18 - 10 11 12 13 14 11 12 13 14 12 - 15 15 14 0 16 17 18 0 0 -%FLAG HBOND_ACOEF -%FORMAT(5E16.8) - -%FLAG HBOND_BCOEF -%FORMAT(5E16.8) - -%FLAG HBCUT -%FORMAT(5E16.8) - -%FLAG AMBER_ATOM_TYPE -%FORMAT(20a4) -CT CT CT CT CT OS OH OH HC HC HC HC H1 H1 H1 H2 HO HO -%FLAG TREE_CHAIN_CLASSIFICATION -%FORMAT(20a4) -BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA -%FLAG JOIN_ARRAY -%FORMAT(10I8) - 0 0 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 -%FLAG IROTAT -%FORMAT(10I8) - 0 0 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 -%FLAG RADIUS_SET -%FORMAT(1a80) -modified Bondi radii (mbondi) -%FLAG RADII -%FORMAT(5E16.8) - 1.70000000E+00 1.70000000E+00 1.70000000E+00 1.70000000E+00 1.70000000E+00 - 1.50000000E+00 1.50000000E+00 1.50000000E+00 1.30000000E+00 1.30000000E+00 - 1.30000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00 - 1.30000000E+00 8.00000000E-01 8.00000000E-01 -%FLAG SCREEN -%FORMAT(5E16.8) - 7.20000000E-01 7.20000000E-01 7.20000000E-01 7.20000000E-01 7.20000000E-01 - 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 - 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 - 8.50000000E-01 8.50000000E-01 8.50000000E-01 -%FLAG IPOL -%FORMAT(1I8) - 0 diff --git a/openforcefield/data/molecules/AlkEthOH_tripos.tar.gz b/openforcefield/data/molecules/AlkEthOH_tripos.tar.gz new file mode 100644 index 000000000..b7fab106d Binary files /dev/null and b/openforcefield/data/molecules/AlkEthOH_tripos.tar.gz differ diff --git a/openforcefield/data/molecules/FreeSolv.tar.gz b/openforcefield/data/molecules/FreeSolv.tar.gz new file mode 100644 index 000000000..7fbc34ba4 Binary files /dev/null and b/openforcefield/data/molecules/FreeSolv.tar.gz differ diff --git a/openforcefield/data/molecules/MiniDrugBank.sdf b/openforcefield/data/molecules/MiniDrugBank.sdf new file mode 100644 index 000000000..80b0db215 --- /dev/null +++ b/openforcefield/data/molecules/MiniDrugBank.sdf @@ -0,0 +1,33988 @@ +DrugBank_5354 + OpenBabel01151909533D + + 44 45 0 0 1 0 0 0 0 0999 V2000 + 1.8325 -2.6083 6.9051 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.4804 -2.7387 5.6768 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.5879 -1.3407 7.4335 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.5187 1.3150 1.2216 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.2695 0.9300 0.7351 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.8838 -1.6016 4.9768 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.9912 -0.2036 6.7335 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.7779 1.2698 2.5915 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.5384 0.4547 2.9883 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.2793 0.4999 1.6184 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.6392 -0.3340 5.5052 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.7877 0.8397 3.4748 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.0716 0.0841 1.0921 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.1690 -1.4081 0.7460 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.5542 -1.8055 0.2232 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.7220 -3.2936 -0.1137 C 0 0 2 0 0 0 0 0 0 0 0 0 + -0.0324 -4.7546 1.5737 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.6632 -4.0097 -0.9965 O 0 0 0 0 0 0 0 0 0 0 0 0 + -0.9370 -2.9514 -2.6389 O 0 0 0 0 0 0 0 0 0 0 0 0 + -2.3477 -5.7173 0.8129 O 0 0 0 0 0 0 0 0 0 0 0 0 + -2.3166 -3.8139 2.4606 O 0 0 0 0 0 0 0 0 0 0 0 0 + -1.3529 -5.2566 -1.7603 O 0 0 0 0 0 0 0 0 0 0 0 0 + 3.0409 0.7951 4.8115 O 0 0 0 0 0 0 0 0 0 0 0 0 + -1.4584 -4.4334 1.2381 P 0 0 0 0 0 0 0 0 0 0 0 0 + -0.6830 -3.7958 -1.4903 S 0 0 0 0 0 0 0 0 0 0 0 0 + 1.5178 -3.4934 7.4501 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2.6711 -3.7257 5.2653 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.0831 -1.2400 8.3900 H 0 0 0 0 0 0 0 0 0 0 0 0 + 4.2897 1.6494 0.5339 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2.0767 0.9689 -0.3338 H 0 0 0 0 0 0 0 0 0 0 0 0 + 3.3893 -1.7101 4.0212 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.7996 0.7812 7.1508 H 0 0 0 0 0 0 0 0 0 0 0 0 + 4.7529 1.5710 2.9642 H 0 0 0 0 0 0 0 0 0 0 0 0 + 0.7683 0.1201 3.6793 H 0 0 0 0 0 0 0 0 0 0 0 0 + -0.8572 0.3487 1.8110 H 0 0 0 0 0 0 0 0 0 0 0 0 + -0.2822 0.6749 0.1913 H 0 0 0 0 0 0 0 0 0 0 0 0 + 0.5806 -1.6169 -0.0246 H 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0965 -2.0075 1.6225 H 0 0 0 0 0 0 0 0 0 0 0 0 + -1.7582 -1.2235 -0.6842 H 0 0 0 0 0 0 0 0 0 0 0 0 + -2.3201 -1.5196 0.9530 H 0 0 0 0 0 0 0 0 0 0 0 0 + -2.7529 -3.4164 -0.4700 H 0 0 0 0 0 0 0 0 0 0 0 0 + -2.4571 -6.4511 1.4545 H 0 0 0 0 0 0 0 0 0 0 0 0 + -2.4266 -4.3430 3.2791 H 0 0 0 0 0 0 0 0 0 0 0 0 + -2.3282 -5.2572 -1.9053 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 2 0 0 0 0 + 1 3 1 0 0 0 0 + 1 26 1 0 0 0 0 + 2 6 1 0 0 0 0 + 2 27 1 0 0 0 0 + 3 7 2 0 0 0 0 + 3 28 1 0 0 0 0 + 4 5 2 0 0 0 0 + 4 8 1 0 0 0 0 + 4 29 1 0 0 0 0 + 5 10 1 0 0 0 0 + 5 30 1 0 0 0 0 + 6 11 2 0 0 0 0 + 6 31 1 0 0 0 0 + 7 11 1 0 0 0 0 + 7 32 1 0 0 0 0 + 8 12 2 0 0 0 0 + 8 33 1 0 0 0 0 + 9 10 2 0 0 0 0 + 9 12 1 0 0 0 0 + 9 34 1 0 0 0 0 + 10 13 1 0 0 0 0 + 11 23 1 0 0 0 0 + 12 23 1 0 0 0 0 + 13 14 1 0 0 0 0 + 13 35 1 0 0 0 0 + 13 36 1 0 0 0 0 + 14 15 1 0 0 0 0 + 14 37 1 0 0 0 0 + 14 38 1 0 0 0 0 + 15 16 1 0 0 0 0 + 15 39 1 0 0 0 0 + 15 40 1 0 0 0 0 + 16 24 1 0 0 0 0 + 16 25 1 0 0 0 0 + 16 41 1 6 0 0 0 + 17 24 2 0 0 0 0 + 18 25 2 0 0 0 0 + 19 25 2 0 0 0 0 + 20 24 1 0 0 0 0 + 20 42 1 0 0 0 0 + 21 24 1 0 0 0 0 + 21 43 1 0 0 0 0 + 22 25 1 0 0 0 0 + 22 44 1 0 0 0 0 +M END +$$$$ +DrugBank_2791 + OpenBabel01151909533D + + 19 19 0 0 0 0 0 0 0 0999 V2000 + 1.8851 -1.0363 -0.1124 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.8783 -1.6520 2.0022 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.8066 -0.4630 0.5610 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.7997 -1.0786 2.6757 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.9210 -1.6309 0.6081 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.7638 -0.4841 1.9551 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.0740 -2.2446 -0.1116 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.1406 0.5892 4.1386 O 0 0 0 0 0 0 0 0 0 0 0 0 + -1.1494 1.2431 1.9139 O 0 0 0 0 0 0 0 0 0 0 0 0 + -1.6805 -0.9673 2.9614 O 0 0 0 0 0 0 0 0 0 0 0 0 + -0.5850 0.2354 2.7982 S 0 0 0 0 0 0 0 0 0 0 0 0 + 1.9097 -1.0154 -1.1987 H 0 0 0 0 0 0 0 0 0 0 0 0 + 3.6806 -2.1133 2.5719 H 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0045 -0.0029 -0.0100 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.7763 -1.1011 3.7620 H 0 0 0 0 0 0 0 0 0 0 0 0 + 4.8660 -1.5020 -0.2676 H 0 0 0 0 0 0 0 0 0 0 0 0 + 4.4935 -3.0872 0.4532 H 0 0 0 0 0 0 0 0 0 0 0 0 + 3.7689 -2.6386 -1.0899 H 0 0 0 0 0 0 0 0 0 0 0 0 + -1.4031 -1.7124 3.5447 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1 3 2 0 0 0 0 + 1 5 1 0 0 0 0 + 1 12 1 0 0 0 0 + 2 4 1 0 0 0 0 + 2 5 2 0 0 0 0 + 2 13 1 0 0 0 0 + 3 6 1 0 0 0 0 + 3 14 1 0 0 0 0 + 4 6 2 0 0 0 0 + 4 15 1 0 0 0 0 + 5 7 1 0 0 0 0 + 6 11 1 0 0 0 0 + 7 16 1 0 0 0 0 + 7 17 1 0 0 0 0 + 7 18 1 0 0 0 0 + 8 11 2 0 0 0 0 + 9 11 2 0 0 0 0 + 10 11 1 0 0 0 0 + 10 19 1 0 0 0 0 +M END +$$$$ +DrugBank_5373 + OpenBabel01151909533D + + 28 28 0 0 0 0 0 0 0 0999 V2000 + -3.3232 -1.2658 2.1675 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.9077 -1.3132 2.1564 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.3386 -2.2768 3.1284 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.9231 -2.3242 3.1173 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.1077 -0.7840 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1.9431 1.7895 H 1 <0> 0.00000 + 44 H17 0.0036 0.9792 2.5158 H 1 <0> 0.00000 + 45 H18 2.4196 1.3011 1.5791 H 1 <0> 0.00000 + 46 H19 2.7537 2.7418 0.6190 H 1 <0> 0.00000 + 47 H20 0.2983 3.2235 0.4752 H 1 <0> 0.00000 + 48 H21 0.8701 3.1874 2.1424 H 1 <0> 0.00000 +@BOND + 1 1 2 ar + 2 1 3 ar + 3 2 8 ar + 4 3 9 ar + 5 4 6 ar + 6 4 10 ar + 7 5 7 ar + 8 5 11 ar + 9 6 12 ar + 10 7 13 ar + 11 8 14 ar + 12 9 14 ar + 13 10 15 ar + 14 11 16 ar + 15 12 25 ar + 16 13 26 ar + 17 14 27 1 + 18 15 17 1 + 19 15 25 ar + 20 16 18 1 + 21 16 26 ar + 22 17 19 2 + 23 17 27 1 + 24 18 20 2 + 25 18 27 1 + 26 19 20 1 + 27 19 21 1 + 28 20 22 1 + 29 21 23 1 + 30 22 24 1 + 31 23 24 1 + 32 1 28 1 + 33 2 29 1 + 34 3 30 1 + 35 4 31 1 + 36 5 32 1 + 37 6 33 1 + 38 7 34 1 + 39 8 35 1 + 40 9 36 1 + 41 10 37 1 + 42 11 38 1 + 43 12 39 1 + 44 13 40 1 + 45 21 41 1 46 21 42 1 - 47 21 43 1 + 47 22 43 1 48 22 44 1 - 49 22 45 1 - 50 25 46 1 - 51 25 47 1 - 52 29 48 1 - 53 31 49 1 - 54 31 50 1 - 55 32 51 1 - 56 33 52 1 - 57 34 53 1 - 58 34 54 1 - 59 35 55 1 - 60 35 56 1 - 61 36 57 1 - 62 36 58 1 -@SUBSTRUCTURE - 1 <0> 1 GROUP 0 A **** -@MOLECULE -MiniDrugBank_362 - 40 40 1 0 0 -SMALL -NO_CHARGES - -@ATOM - 1 C1 -3.5627 -1.6055 -0.6662 C.3 1 <0> 0.00000 - 2 C2 -2.7936 -1.3798 -1.9703 C.3 1 <0> 0.00000 - 3 C3 -3.7548 -1.4462 -3.1578 C.3 1 <0> 0.00000 - 4 C4 -2.0563 -0.0355 -1.9644 C.3 1 <0> 0.00000 - 5 C5 -1.0770 0.0298 -0.8478 C.2 1 <0> 0.00000 - 6 N1 -1.3303 0.4693 0.3453 N.2 1 <0> 0.00000 - 7 C6 -0.0524 0.3381 1.1046 C.3 1 <0> 0.00000 - 8 O1 -0.1320 -0.5057 2.2543 O.3 1 <0> 0.00000 - 9 C7 0.3398 1.7453 1.5628 C.3 1 <0> 0.00000 - 10 N2 -0.7038 2.2820 2.4040 N.3 1 <0> 0.00000 - 11 C8 0.6595 2.6738 0.3792 C.3 1 <0> 0.00000 - 12 C9 1.0511 4.0776 0.8270 C.3 1 <0> 0.00000 - 13 O2 -0.4549 2.7888 -0.5020 O.3 1 <0> 0.00000 - 14 N3 0.9120 -0.2209 0.1716 N.am 1 <0> 0.00000 - 15 C10 2.2940 -0.5113 0.5038 C.3 1 <0> 0.00000 - 16 C11 2.3565 -1.9180 1.0108 C.2 1 <0> 0.00000 - 17 O3 3.4125 -2.4336 1.3684 O.2 1 <0> 0.00000 - 18 C12 0.3345 -0.4297 -1.0479 C.2 1 <0> 0.00000 - 19 O4 0.7507 -0.8677 -2.0967 O.2 1 <0> 0.00000 - 20 H1 -2.8867 -1.5608 0.1945 H 1 <0> 0.00000 - 21 H2 -4.0539 -2.5846 -0.6587 H 1 <0> 0.00000 - 22 H3 -4.3311 -0.8394 -0.5213 H 1 <0> 0.00000 - 23 H4 -2.0624 -2.1915 -2.0770 H 1 <0> 0.00000 - 24 H5 -3.2204 -1.2865 -4.1003 H 1 <0> 0.00000 - 25 H6 -4.2396 -2.4267 -3.2122 H 1 <0> 0.00000 - 26 H7 -4.5381 -0.6844 -3.0787 H 1 <0> 0.00000 - 27 H8 -1.4910 0.0930 -2.8940 H 1 <0> 0.00000 - 28 H9 -2.7553 0.8017 -1.8666 H 1 <0> 0.00000 - 29 H10 -0.3929 -1.3816 1.9326 H 1 <0> 0.00000 - 30 H11 1.2303 1.6605 2.1949 H 1 <0> 0.00000 - 31 H12 -0.7159 2.0374 3.3785 H 1 <0> 0.00000 - 32 H13 -1.5014 2.7143 1.9719 H 1 <0> 0.00000 - 33 H14 1.4920 2.2553 -0.1994 H 1 <0> 0.00000 - 34 H15 1.2751 4.7243 -0.0281 H 1 <0> 0.00000 - 35 H16 0.2183 4.5495 1.3600 H 1 <0> 0.00000 - 36 H17 1.9197 4.0557 1.4921 H 1 <0> 0.00000 - 37 H18 -0.1811 3.3840 -1.2170 H 1 <0> 0.00000 - 38 H19 2.6123 0.1965 1.2636 H 1 <0> 0.00000 - 39 H20 2.8696 -0.4172 -0.4132 H 1 <0> 0.00000 - 40 H21 1.4293 -2.5158 0.9801 H 1 <0> 0.00000 -@BOND - 1 1 2 1 - 2 2 3 1 - 3 2 4 1 - 4 4 5 1 - 5 5 6 2 - 6 6 7 1 - 7 7 8 1 - 8 7 9 1 - 9 9 10 1 - 10 9 11 1 - 11 11 12 1 - 12 11 13 1 - 13 7 14 1 - 14 14 15 1 - 15 15 16 1 - 16 16 17 2 - 17 14 18 am - 18 5 18 1 - 19 18 19 2 - 20 1 20 1 - 21 1 21 1 - 22 1 22 1 - 23 2 23 1 - 24 3 24 1 - 25 3 25 1 - 26 3 26 1 - 27 4 27 1 - 28 4 28 1 - 29 8 29 1 - 30 9 30 1 - 31 10 31 1 - 32 10 32 1 - 33 11 33 1 - 34 12 34 1 - 35 12 35 1 - 36 12 36 1 - 37 13 37 1 - 38 15 38 1 - 39 15 39 1 - 40 16 40 1 + 49 23 45 1 + 50 23 46 1 + 51 24 47 1 + 52 24 48 1 @SUBSTRUCTURE 1 <0> 1 GROUP 0 A **** diff --git a/openforcefield/data/molecules/README.md b/openforcefield/data/molecules/README.md index 406eecc90..470e80586 100644 --- a/openforcefield/data/molecules/README.md +++ b/openforcefield/data/molecules/README.md @@ -1,19 +1,19 @@ # Molecule Files -This is a list of the molecule files provided here -including a brieg description when possible +This is a list of the molecule files provided here including a brief description when possible -* `AlkEthOH-tripos.mol2.gz`: set of 42 alkanes, ethers, and alcohols -* `*.crd`, `*.mol2`, and `*.top` for the following AlkEthOH molecules - - `AlkEthOH_c100` - - `AlkEthOH_c1161` - - `AlkEthOH_c1266` - - `AlkEthOH_c38` - - `AlkEthOH_r0` - - `AlkEthOH_r118` - - `AlkEthOH_r12` +* `AlkEthOH_tripos.tar.gz`: `*.crd`, `*.top`, and `*.mol2` (with Tripos SYBYL atom types) for all the molecules in +the AlkEthOH dataset. All molecules were taken from +https://github.com/openforcefield/open-forcefield-data/blob/master/Model-Systems/AlkEthOH_distrib/inputfiles.tar.gz. +All the files in the archive can be accessed through `openforcefield.tests.utils:get_alkethoh_filepath()`. The archive +has the following structure: + - `AlkEthOH_rings_filt1`: A collection of cyclic alkanes, alcohols, and ethers. + - `AlkEthOH_chain_filt1`: Acyclic alkanes, alcohols, and ethers. + - `AlkEthOH_test_filt1`: A smaller test set composed of the first 42 molecules in `AlkEthOH_rings_filt1/`. + - `convert_to_sybyl.py`: A script used to convert the original data from GAFF to Tripos SYBYL atom types. +* `AlkEthOH_test_filt1_*.mol2`: A test set of 42 alkanes, ethers, and alcohols from the AlkEthOH set. This is file +contains all the molecules in `AlkEthOH_tripos.tar.gz/AlkEthOH_test_filt1`. * `*.crd`, `*.mol2`, and `*.top` for benzene -* `AlkEthOH_test_filt1_*.mol2`: A different set of 42 alkanes ethers and alcohols * `zinc-subset-*.mol2.gz`: set of 7505 molecules * `PhEthOH_pFrosstTyped.oeb`: 5082 molecules with phenyl groups in addition to alkanes, ethers, and alcohols * `PhEthOH_pFrosstTyped_first200.oeb`: first 200 in PhEthOH set used for testing smarty and smirky diff --git a/openforcefield/data/molecules/cyclohexane.mol2 b/openforcefield/data/molecules/cyclohexane.mol2 new file mode 100644 index 000000000..353bee3da --- /dev/null +++ b/openforcefield/data/molecules/cyclohexane.mol2 @@ -0,0 +1,44 @@ +@MOLECULE +***** + 18 18 0 0 0 +SMALL +NO_CHARGES + +@ATOM + 1 C1 -0.8669 0.5776 -1.0448 C.3 1 <0> 0.0000 + 2 C2 -1.3841 0.3492 0.3729 C.3 1 <0> 0.0000 + 3 C3 -0.2545 0.3955 1.3984 C.3 1 <0> 0.0000 + 4 C4 0.8667 -0.5779 1.0447 C.3 1 <0> 0.0000 + 5 C5 1.3842 -0.3490 -0.3729 C.3 1 <0> 0.0000 + 6 C6 0.2547 -0.3955 -1.3983 C.3 1 <0> 0.0000 + 7 H1 -0.4982 1.6068 -1.1365 H 1 <0> 0.0000 + 8 H2 -1.6896 0.4671 -1.7603 H 1 <0> 0.0000 + 9 H3 -2.1360 1.1077 0.6185 H 1 <0> 0.0000 + 10 H4 -1.8840 -0.6259 0.4256 H 1 <0> 0.0000 + 11 H5 0.1498 1.4141 1.4491 H 1 <0> 0.0000 + 12 H6 -0.6490 0.1579 2.3928 H 1 <0> 0.0000 + 13 H7 1.6899 -0.4683 1.7597 H 1 <0> 0.0000 + 14 H8 0.4982 -1.6071 1.1363 H 1 <0> 0.0000 + 15 H9 1.8840 0.6262 -0.4253 H 1 <0> 0.0000 + 16 H10 2.1365 -1.1075 -0.6173 H 1 <0> 0.0000 + 17 H11 -0.1496 -1.4141 -1.4491 H 1 <0> 0.0000 + 18 H12 0.6489 -0.1579 -2.3928 H 1 <0> 0.0000 +@BOND + 1 1 6 1 + 2 1 2 1 + 3 2 3 1 + 4 3 4 1 + 5 4 5 1 + 6 5 6 1 + 7 1 7 1 + 8 1 8 1 + 9 2 9 1 + 10 2 10 1 + 11 3 11 1 + 12 3 12 1 + 13 4 13 1 + 14 4 14 1 + 15 5 15 1 + 16 5 16 1 + 17 6 17 1 + 18 6 18 1 diff --git a/openforcefield/data/molecules/ethanol.mol2 b/openforcefield/data/molecules/ethanol.mol2 new file mode 100644 index 000000000..4af1ca765 --- /dev/null +++ b/openforcefield/data/molecules/ethanol.mol2 @@ -0,0 +1,25 @@ +@MOLECULE +***** + 9 8 0 0 0 +SMALL +NO_CHARGES + +@ATOM + 1 C1 1.0616 -0.2681 -0.0006 C.3 1 <0> 0.0000 + 2 C2 1.9101 0.9126 -0.4220 C.3 1 <0> 0.0000 + 3 O1 1.5170 1.3236 -1.7228 O.3 1 <0> 0.0000 + 4 H1 2.0787 2.0794 -1.9612 H 1 <0> 0.0000 + 5 H2 1.3393 -0.6108 1.0001 H 1 <0> 0.0000 + 6 H3 -0.0000 -0.0002 -0.0006 H 1 <0> 0.0000 + 7 H4 1.1801 -1.0990 -0.7040 H 1 <0> 0.0000 + 8 H5 2.9684 0.6361 -0.4446 H 1 <0> 0.0000 + 9 H6 1.7730 1.7499 0.2687 H 1 <0> 0.0000 +@BOND + 1 1 2 1 + 2 2 3 1 + 3 3 4 1 + 4 1 5 1 + 5 1 6 1 + 6 1 7 1 + 7 2 8 1 + 8 2 9 1 diff --git a/openforcefield/data/molecules/ethanol.sdf b/openforcefield/data/molecules/ethanol.sdf new file mode 100644 index 000000000..3dc03d29a --- /dev/null +++ b/openforcefield/data/molecules/ethanol.sdf @@ -0,0 +1,23 @@ +***** + OpenBabel02041915453D + + 9 8 0 0 0 0 0 0 0 0999 V2000 + 1.0616 -0.2681 -0.0006 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.9101 0.9126 -0.4220 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.5170 1.3236 -1.7228 O 0 0 0 0 0 0 0 0 0 0 0 0 + 2.0787 2.0794 -1.9612 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.3393 -0.6108 1.0001 H 0 0 0 0 0 0 0 0 0 0 0 0 + -0.0000 -0.0002 -0.0006 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.1801 -1.0990 -0.7040 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2.9684 0.6361 -0.4446 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.7730 1.7499 0.2687 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 1 5 1 0 0 0 0 + 1 6 1 0 0 0 0 + 1 7 1 0 0 0 0 + 2 3 1 0 0 0 0 + 2 8 1 0 0 0 0 + 2 9 1 0 0 0 0 + 3 4 1 0 0 0 0 +M END +$$$$ diff --git a/openforcefield/data/molecules/ethanol_reordered.mol2 b/openforcefield/data/molecules/ethanol_reordered.mol2 new file mode 100644 index 000000000..db6394e49 --- /dev/null +++ b/openforcefield/data/molecules/ethanol_reordered.mol2 @@ -0,0 +1,25 @@ +@MOLECULE +***** + 9 8 0 0 0 +SMALL +NO_CHARGES + +@ATOM + 1 C1 1.0616 -0.2681 -0.0006 C.3 1 <0> 0.0000 + 2 O1 1.5170 1.3236 -1.7228 O.3 1 <0> 0.0000 + 3 C2 1.9101 0.9126 -0.4220 C.3 1 <0> 0.0000 + 4 H1 2.0787 2.0794 -1.9612 H 1 <0> 0.0000 + 5 H2 1.3393 -0.6108 1.0001 H 1 <0> 0.0000 + 6 H3 -0.0000 -0.0002 -0.0006 H 1 <0> 0.0000 + 7 H4 1.1801 -1.0990 -0.7040 H 1 <0> 0.0000 + 8 H5 2.9684 0.6361 -0.4446 H 1 <0> 0.0000 + 9 H6 1.7730 1.7499 0.2687 H 1 <0> 0.0000 +@BOND + 1 1 3 1 + 3 3 2 1 + 2 2 4 1 + 4 1 5 1 + 5 1 6 1 + 6 1 7 1 + 7 3 8 1 + 8 3 9 1 diff --git a/openforcefield/data/molecules/ethanol_reordered.sdf b/openforcefield/data/molecules/ethanol_reordered.sdf new file mode 100644 index 000000000..e67a9bc44 --- /dev/null +++ b/openforcefield/data/molecules/ethanol_reordered.sdf @@ -0,0 +1,23 @@ +***** + OpenBabel02041915453D + + 9 8 0 0 0 0 0 0 0 0999 V2000 + 1.0616 -0.2681 -0.0006 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.5170 1.3236 -1.7228 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1.9101 0.9126 -0.4220 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.0787 2.0794 -1.9612 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.3393 -0.6108 1.0001 H 0 0 0 0 0 0 0 0 0 0 0 0 + -0.0000 -0.0002 -0.0006 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.1801 -1.0990 -0.7040 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2.9684 0.6361 -0.4446 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.7730 1.7499 0.2687 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1 3 1 0 0 0 0 + 1 5 1 0 0 0 0 + 1 6 1 0 0 0 0 + 1 7 1 0 0 0 0 + 2 4 1 0 0 0 0 + 3 2 1 0 0 0 0 + 3 8 1 0 0 0 0 + 3 9 1 0 0 0 0 +M END +$$$$ diff --git a/openforcefield/data/molecules/laromustine_ff.mol2 b/openforcefield/data/molecules/laromustine_ff.mol2 new file mode 100644 index 000000000..f8f069286 --- /dev/null +++ b/openforcefield/data/molecules/laromustine_ff.mol2 @@ -0,0 +1,71 @@ +@MOLECULE +MiniDrugBank_20 + 31 30 1 0 0 +SMALL +NO_CHARGES + +@ATOM + 1 Cl1 4.5080 2.2688 0.0000 CL 1 <0> 0.00000 + 2 S1 4.5080 -0.2063 0.0000 SO 1 <0> 0.00000 + 3 S2 2.3645 0.2063 0.0000 SO 1 <0> 0.00000 + 4 O1 4.9205 0.5082 0.0000 O2 1 <0> 0.00000 + 5 O2 4.0955 -0.9207 0.0000 O2 1 <0> 0.00000 + 6 O3 1.9520 -0.5082 0.0000 O2 1 <0> 0.00000 + 7 O4 2.7770 0.9207 0.0000 O2 1 <0> 0.00000 + 8 O5 3.7935 -1.4438 0.0000 O 1 <0> 0.00000 + 9 N1 3.7935 0.2063 0.0000 N3 1 <0> 0.00000 + 10 N2 3.0791 -0.2063 0.0000 N 1 <0> 0.00000 + 11 N3 2.3645 -1.4438 0.0000 N 1 <0> 0.00000 + 12 C1 3.7935 1.0313 0.0000 CT 1 <0> 0.00000 + 13 C2 5.2224 -0.6188 0.0000 CT 1 <0> 0.00000 + 14 C3 4.5080 1.4438 0.0000 CT 1 <0> 0.00000 + 15 C4 3.0791 -1.0313 0.0000 C 1 <0> 0.00000 + 16 C5 1.6500 0.6188 0.0000 CT 1 <0> 0.00000 + 17 C6 2.3645 -2.2688 0.0000 CT 1 <0> 0.00000 + 18 H1 2.3645 -1.4438 0.0000 H 1 <0> 0.00000 + 19 H2 3.7935 1.0313 0.0000 H1 1 <0> 0.00000 + 20 H3 3.7935 1.0313 0.0000 H1 1 <0> 0.00000 + 21 H4 5.2224 -0.6188 0.0000 H1 1 <0> 0.00000 + 22 H5 5.2224 -0.6188 0.0000 H1 1 <0> 0.00000 + 23 H6 5.2224 -0.6188 0.0000 H1 1 <0> 0.00000 + 24 H7 4.5080 1.4438 0.0000 H1 1 <0> 0.00000 + 25 H8 4.5080 1.4438 0.0000 H1 1 <0> 0.00000 + 26 H9 1.6500 0.6188 0.0000 H1 1 <0> 0.00000 + 27 H10 1.6500 0.6188 0.0000 H1 1 <0> 0.00000 + 28 H11 1.6500 0.6188 0.0000 H1 1 <0> 0.00000 + 29 H12 2.3645 -2.2688 0.0000 H1 1 <0> 0.00000 + 30 H13 2.3645 -2.2688 0.0000 H1 1 <0> 0.00000 + 31 H14 2.3645 -2.2688 0.0000 H1 1 <0> 0.00000 +@BOND + 1 1 14 1 + 2 2 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0.00000 + 7 O4 2.7770 0.9207 0.0000 O.2 1 <0> 0.00000 + 8 O5 3.7935 -1.4438 0.0000 O.2 1 <0> 0.00000 + 9 N1 3.7935 0.2063 0.0000 N.pl3 1 <0> 0.00000 + 10 N2 3.0791 -0.2063 0.0000 N.am 1 <0> 0.00000 + 11 N3 2.3645 -1.4438 0.0000 N.am 1 <0> 0.00000 + 12 C1 3.7935 1.0313 0.0000 C.3 1 <0> 0.00000 + 13 C2 5.2224 -0.6188 0.0000 C.3 1 <0> 0.00000 + 14 C3 4.5080 1.4438 0.0000 C.3 1 <0> 0.00000 + 15 C4 3.0791 -1.0313 0.0000 C.2 1 <0> 0.00000 + 16 C5 1.6500 0.6188 0.0000 C.3 1 <0> 0.00000 + 17 C6 2.3645 -2.2688 0.0000 C.3 1 <0> 0.00000 + 18 H1 2.3645 -1.4438 0.0000 H 1 <0> 0.00000 + 19 H2 3.7935 1.0313 0.0000 H 1 <0> 0.00000 + 20 H3 3.7935 1.0313 0.0000 H 1 <0> 0.00000 + 21 H4 5.2224 -0.6188 0.0000 H 1 <0> 0.00000 + 22 H5 5.2224 -0.6188 0.0000 H 1 <0> 0.00000 + 23 H6 5.2224 -0.6188 0.0000 H 1 <0> 0.00000 + 24 H7 4.5080 1.4438 0.0000 H 1 <0> 0.00000 + 25 H8 4.5080 1.4438 0.0000 H 1 <0> 0.00000 + 26 H9 1.6500 0.6188 0.0000 H 1 <0> 0.00000 + 27 H10 1.6500 0.6188 0.0000 H 1 <0> 0.00000 + 28 H11 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2.3428 H 1 <0> 0.40552 -@BOND - 1 1 2 1 - 2 1 3 1 - 3 2 4 1 - 4 3 5 1 - 5 4 6 1 - 6 5 7 1 - 7 5 8 1 - 8 6 7 1 - 9 6 9 1 - 10 1 10 1 - 11 1 11 1 - 12 2 12 1 - 13 2 13 1 - 14 3 14 1 - 15 3 15 1 - 16 4 16 1 - 17 4 17 1 - 18 5 18 1 - 19 6 19 1 - 20 8 20 1 - 21 9 21 1 -@SUBSTRUCTURE - 1 <0> 1 GROUP 0 A **** -@MOLECULE -AlkEthOH_r47 - 24 24 1 0 0 -SMALL -USER_CHARGES - -@ATOM - 1 C1 2.1442 -0.0312 0.0135 C.3 1 <0> -0.07792 - 2 C2 1.5676 0.2532 1.4035 C.3 1 <0> -0.06843 - 3 C3 1.7315 0.9617 -1.0780 C.3 1 <0> -0.06843 - 4 C4 0.3737 -0.6281 1.7892 C.3 1 <0> -0.12979 - 5 C5 0.2484 1.3147 -1.1871 C.3 1 <0> -0.12979 - 6 C6 -0.8729 -0.4518 0.9234 C.3 1 <0> 0.34079 - 7 C7 -0.6896 0.1246 -1.4070 C.3 1 <0> 0.34079 - 8 O1 -0.5812 -0.8788 -0.4025 O.3 1 <0> -0.39016 - 9 O2 -1.8979 -1.2764 1.4782 O.3 1 <0> -0.60370 - 10 O3 -2.0239 0.6121 -1.5333 O.3 1 <0> -0.60370 - 11 H1 3.2393 0.0156 0.0840 H 1 <0> 0.04913 - 12 H2 1.9221 -1.0576 -0.3003 H 1 <0> 0.04913 - 13 H3 2.3576 0.0529 2.1394 H 1 <0> 0.03845 - 14 H4 1.3135 1.3128 1.5185 H 1 <0> 0.03845 - 15 H5 2.2832 1.8969 -0.9159 H 1 <0> 0.03845 - 16 H6 2.0779 0.5735 -2.0441 H 1 <0> 0.03845 - 17 H7 0.6881 -1.6800 1.7593 H 1 <0> 0.05291 - 18 H8 0.1116 -0.4272 2.8359 H 1 <0> 0.05291 - 19 H9 -0.0563 1.8878 -0.3043 H 1 <0> 0.05291 - 20 H10 0.1177 2.0156 -2.0226 H 1 <0> 0.05291 - 21 H11 -1.2268 0.5835 0.9758 H 1 <0> 0.05837 - 22 H12 -0.4246 -0.3503 -2.3585 H 1 <0> 0.05837 - 23 H13 -2.0398 -0.9641 2.3845 H 1 <0> 0.40495 - 24 H14 -2.0276 1.2092 -2.2970 H 1 <0> 0.40495 -@BOND - 1 1 2 1 - 2 1 3 1 - 3 2 4 1 - 4 3 5 1 - 5 4 6 1 - 6 5 7 1 - 7 6 8 1 - 8 6 9 1 - 9 7 8 1 - 10 7 10 1 - 11 1 11 1 - 12 1 12 1 - 13 2 13 1 - 14 2 14 1 - 15 3 15 1 - 16 3 16 1 - 17 4 17 1 - 18 4 18 1 - 19 5 19 1 - 20 5 20 1 - 21 6 21 1 - 22 7 22 1 - 23 9 23 1 - 24 10 24 1 -@SUBSTRUCTURE - 1 <0> 1 GROUP 0 A **** -@MOLECULE -AlkEthOH_r48 - 25 25 1 0 0 -SMALL -USER_CHARGES - -@ATOM - 1 C1 -1.7143 0.8561 0.7391 C.3 1 <0> -0.07783 - 2 C2 -1.7956 -0.6198 1.1372 C.3 1 <0> -0.06377 - 3 C3 -0.6262 1.6669 1.4527 C.3 1 <0> -0.09876 - 4 C4 -0.5622 -1.4916 0.8792 C.3 1 <0> -0.09750 - 5 C5 0.6276 1.9090 0.6130 C.3 1 <0> 0.14649 - 6 C6 -0.1318 -1.6141 -0.5876 C.3 1 <0> 0.36887 - 7 C7 1.5368 0.1082 -0.6795 C.3 1 <0> 0.53827 - 8 O1 1.4624 0.7565 0.5932 O.3 1 <0> -0.44875 - 9 O2 0.2807 -0.3761 -1.1587 O.3 1 <0> -0.53408 - 10 O3 -1.2318 -2.1421 -1.3293 O.3 1 <0> -0.59157 - 11 O4 2.1543 0.9470 -1.6593 O.3 1 <0> -0.61949 - 12 H1 -1.6467 0.9678 -0.3479 H 1 <0> 0.04665 - 13 H2 -2.6818 1.2997 1.0120 H 1 <0> 0.04665 - 14 H3 -2.0282 -0.6754 2.2088 H 1 <0> 0.04422 - 15 H4 -2.6585 -1.0637 0.6249 H 1 <0> 0.04422 - 16 H5 -1.0506 2.6517 1.6859 H 1 <0> 0.04883 - 17 H6 -0.3629 1.1967 2.4071 H 1 <0> 0.04883 - 18 H7 0.2669 -1.1448 1.5020 H 1 <0> 0.06228 - 19 H8 -0.8098 -2.4993 1.2392 H 1 <0> 0.06228 - 20 H9 0.3734 2.2648 -0.3924 H 1 <0> 0.05177 - 21 H10 1.2130 2.7014 1.0925 H 1 <0> 0.05177 - 22 H11 0.6839 -2.3436 -0.6635 H 1 <0> 0.02168 - 23 H12 2.2128 -0.7445 -0.5449 H 1 <0> 0.09427 - 24 H13 -0.9345 -2.2093 -2.2491 H 1 <0> 0.41949 - 25 H14 2.1655 0.4387 -2.4835 H 1 <0> 0.43518 -@BOND - 1 1 2 1 - 2 1 3 1 - 3 2 4 1 - 4 3 5 1 - 5 4 6 1 - 6 5 8 1 - 7 6 9 1 - 8 6 10 1 - 9 7 8 1 - 10 7 9 1 - 11 7 11 1 - 12 1 12 1 - 13 1 13 1 - 14 2 14 1 - 15 2 15 1 - 16 3 16 1 - 17 3 17 1 - 18 4 18 1 - 19 4 19 1 - 20 5 20 1 - 21 5 21 1 - 22 6 22 1 - 23 7 23 1 - 24 10 24 1 - 25 11 25 1 -@SUBSTRUCTURE - 1 <0> 1 GROUP 0 A **** -@MOLECULE -AlkEthOH_r49 - 20 20 1 0 0 -SMALL -USER_CHARGES - -@ATOM - 1 C1 0.7797 1.7543 -0.0953 C.3 1 <0> -0.07263 - 2 C2 0.6184 0.9908 -1.4108 C.3 1 <0> -0.07451 - 3 C3 1.3381 0.8842 1.0282 C.3 1 <0> -0.11564 - 4 C4 -0.4857 -0.0642 -1.4229 C.3 1 <0> -0.12663 - 5 C5 0.2973 0.0264 1.7440 C.3 1 <0> 0.13279 - 6 C6 -0.4234 -1.0599 -0.2661 C.3 1 <0> 0.33508 - 7 O1 -0.7918 -0.3985 0.9382 O.3 1 <0> -0.39738 - 8 O2 -1.3326 -2.1330 -0.5153 O.3 1 <0> -0.58887 - 9 H1 1.4897 2.5717 -0.2736 H 1 <0> 0.04914 - 10 H2 -0.1668 2.2199 0.2029 H 1 <0> 0.04914 - 11 H3 0.4083 1.7132 -2.2092 H 1 <0> 0.03854 - 12 H4 1.5716 0.5152 -1.6738 H 1 <0> 0.03854 - 13 H5 2.1275 0.2361 0.6273 H 1 <0> 0.04408 - 14 H6 1.8303 1.5181 1.7761 H 1 <0> 0.04408 - 15 H7 -1.4574 0.4471 -1.4012 H 1 <0> 0.05682 - 16 H8 -0.4498 -0.6035 -2.3778 H 1 <0> 0.05682 - 17 H9 0.7733 -0.8492 2.2010 H 1 <0> 0.04906 - 18 H10 -0.1375 0.6082 2.5643 H 1 <0> 0.04906 - 19 H11 0.5885 -1.5064 -0.1809 H 1 <0> 0.02855 - 20 H12 -1.0484 -2.5455 -1.3448 H 1 <0> 0.40396 -@BOND - 1 1 2 1 - 2 1 3 1 - 3 2 4 1 - 4 3 5 1 - 5 4 6 1 - 6 5 7 1 - 7 6 7 1 - 8 6 8 1 - 9 1 9 1 - 10 1 10 1 - 11 2 11 1 - 12 2 12 1 - 13 3 13 1 - 14 3 14 1 - 15 4 15 1 - 16 4 16 1 - 17 5 17 1 - 18 5 18 1 - 19 6 19 1 - 20 8 20 1 -@SUBSTRUCTURE - 1 <0> 1 GROUP 0 A **** diff --git a/openforcefield/data/molecules/toluene.mol2 b/openforcefield/data/molecules/toluene.mol2 new file mode 100644 index 000000000..f335ebb79 --- /dev/null +++ b/openforcefield/data/molecules/toluene.mol2 @@ -0,0 +1,38 @@ +@MOLECULE +***** + 15 15 0 0 0 +SMALL +NO_CHARGES + +@ATOM + 1 C1 22.3700 21.6800 29.7700 C.ar 1 LIG164 0.0000 + 2 C2 22.6000 22.9300 30.4200 C.ar 1 LIG164 0.0000 + 3 C3 23.4000 21.0800 29.0100 C.ar 1 LIG164 0.0000 + 4 C4 23.7600 23.5900 30.2500 C.ar 1 LIG164 0.0000 + 5 C5 24.6200 21.7600 28.9500 C.ar 1 LIG164 0.0000 + 6 C6 24.8300 22.9800 29.5800 C.ar 1 LIG164 0.0000 + 7 C7 26.1000 23.6800 29.4000 C.3 1 LIG164 0.0000 + 8 H1 21.3900 21.2200 29.8600 H 1 LIG164 0.0000 + 9 H2 21.8300 23.4200 31.0200 H 1 LIG164 0.0000 + 10 H3 23.1500 20.1800 28.4600 H 1 LIG164 0.0000 + 11 H4 23.9900 24.5700 30.6800 H 1 LIG164 0.0000 + 12 H5 25.4400 21.2700 28.4100 H 1 LIG164 0.0000 + 13 H6 25.9100 24.7300 29.1500 H 1 LIG164 0.0000 + 14 H7 26.6700 23.6400 30.3400 H 1 LIG164 0.0000 + 15 H8 26.7900 23.1900 28.7200 H 1 LIG164 0.0000 +@BOND + 1 1 8 1 + 2 1 2 ar + 3 1 3 ar + 4 2 9 1 + 5 2 4 ar + 6 3 10 1 + 7 3 5 ar + 8 4 11 1 + 9 4 6 ar + 10 5 12 1 + 11 5 6 ar + 12 6 7 1 + 13 7 13 1 + 14 7 14 1 + 15 7 15 1 diff --git a/openforcefield/data/molecules/toluene.mol2.gz b/openforcefield/data/molecules/toluene.mol2.gz new file mode 100644 index 000000000..94c3d5fde Binary files /dev/null and b/openforcefield/data/molecules/toluene.mol2.gz differ diff --git a/openforcefield/data/molecules/toluene.sdf b/openforcefield/data/molecules/toluene.sdf new file mode 100644 index 000000000..639bdf89f --- /dev/null +++ b/openforcefield/data/molecules/toluene.sdf @@ -0,0 +1,36 @@ + + -OEChem-10231818092D + + 15 15 0 0 0 0 0 0 0999 V2000 + 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.8675 0.4975 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.8675 0.4975 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.8675 1.5027 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.8675 1.5027 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.0000 2.0104 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.0000 3.0104 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 -0.7500 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + -1.5165 0.1216 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.5165 0.1216 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + -1.5181 1.8758 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.5181 1.8758 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + -0.7500 3.0104 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 0.7500 3.0104 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + -0.0000 3.7604 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1 8 1 0 0 0 0 + 1 2 2 0 0 0 0 + 1 3 1 0 0 0 0 + 2 9 1 0 0 0 0 + 2 4 1 0 0 0 0 + 3 10 1 0 0 0 0 + 3 5 2 0 0 0 0 + 4 11 1 0 0 0 0 + 4 6 2 0 0 0 0 + 5 12 1 0 0 0 0 + 5 6 1 0 0 0 0 + 6 7 1 0 0 0 0 + 7 13 1 0 0 0 0 + 7 14 1 0 0 0 0 + 7 15 1 0 0 0 0 +M END +$$$$ diff --git a/openforcefield/data/molecules/toluene_charged.mol2 b/openforcefield/data/molecules/toluene_charged.mol2 new file mode 100644 index 000000000..4db65b4ab --- /dev/null +++ b/openforcefield/data/molecules/toluene_charged.mol2 @@ -0,0 +1,38 @@ +@MOLECULE +***** + 15 15 0 0 0 +SMALL +USER_CHARGES + +@ATOM + 1 C1 22.3700 21.6800 29.7700 C.ar 1 <0> -0.1342 + 2 C2 22.6000 22.9300 30.4200 C.ar 1 <0> -0.1271 + 3 C3 23.4000 21.0800 29.0100 C.ar 1 <0> -0.1271 + 4 C4 23.7600 23.5900 30.2500 C.ar 1 <0> -0.1310 + 5 C5 24.6200 21.7600 28.9500 C.ar 1 <0> -0.1310 + 6 C6 24.8300 22.9800 29.5800 C.ar 1 <0> -0.0765 + 7 C7 26.1000 23.6800 29.4000 C.3 1 <0> -0.0541 + 8 H1 21.3900 21.2200 29.8600 H 1 <0> 0.1314 + 9 H2 21.8300 23.4200 31.0200 H 1 <0> 0.1286 + 10 H3 23.1500 20.1800 28.4600 H 1 <0> 0.1286 + 11 H4 23.9900 24.5700 30.6800 H 1 <0> 0.1303 + 12 H5 25.4400 21.2700 28.4100 H 1 <0> 0.1303 + 13 H6 25.9100 24.7300 29.1500 H 1 <0> 0.0440 + 14 H7 26.6700 23.6400 30.3400 H 1 <0> 0.0440 + 15 H8 26.7900 23.1900 28.7200 H 1 <0> 0.0440 +@BOND + 1 1 8 1 + 2 1 2 ar + 3 1 3 ar + 4 2 9 1 + 5 2 4 ar + 6 3 10 1 + 7 3 5 ar + 8 4 11 1 + 9 4 6 ar + 10 5 12 1 + 11 5 6 ar + 12 6 7 1 + 13 7 13 1 + 14 7 14 1 + 15 7 15 1 diff --git a/openforcefield/data/systems/packmol_boxes/cyclohexane_ethanol_0.4_0.6.pdb b/openforcefield/data/systems/packmol_boxes/cyclohexane_ethanol_0.4_0.6.pdb index fa887d54f..f369b83d4 100644 --- a/openforcefield/data/systems/packmol_boxes/cyclohexane_ethanol_0.4_0.6.pdb +++ b/openforcefield/data/systems/packmol_boxes/cyclohexane_ethanol_0.4_0.6.pdb @@ -1,5 +1,5 @@ REMARK 1 CREATED WITH MDTraj 1.7.2, 2016-06-27 -CRYST1 31.885 31.885 31.885 90.00 90.00 90.00 P 1 1 +CRYST1 32.885 32.885 32.885 90.00 90.00 90.00 P 1 1 MODEL 0 ATOM 1 C1 ZBE A 1 12.532 10.813 10.386 1.00 0.00 C ATOM 2 C2 ZBE A 1 12.348 10.339 11.825 1.00 0.00 C diff --git a/openforcefield/data/systems/packmol_boxes/propane_methane_butanol_0.2_0.3_0.5.pdb b/openforcefield/data/systems/packmol_boxes/propane_methane_butanol_0.2_0.3_0.5.pdb index 6b4a3a7d2..5f5d1fce5 100644 --- a/openforcefield/data/systems/packmol_boxes/propane_methane_butanol_0.2_0.3_0.5.pdb +++ b/openforcefield/data/systems/packmol_boxes/propane_methane_butanol_0.2_0.3_0.5.pdb @@ -1,5 +1,5 @@ REMARK 1 CREATED WITH MDTraj 1.7.2, 2016-06-27 -CRYST1 33.647 33.647 33.647 90.00 90.00 90.00 P 1 1 +CRYST1 34.647 34.647 34.647 90.00 90.00 90.00 P 1 1 MODEL 0 ATOM 1 C1 ZEM A 1 8.221 30.879 2.585 1.00 0.00 C ATOM 2 C2 ZEM A 1 8.638 29.750 1.658 1.00 0.00 C diff --git a/openforcefield/data/systems/test_systems/1_cyclohexane_1_ethanol.pdb b/openforcefield/data/systems/test_systems/1_cyclohexane_1_ethanol.pdb new file mode 100644 index 000000000..6c44bc5ca --- /dev/null +++ b/openforcefield/data/systems/test_systems/1_cyclohexane_1_ethanol.pdb @@ -0,0 +1,61 @@ +REMARK 1 CREATED WITH MDTraj 1.7.2, 2016-06-27 +CRYST1 31.885 31.885 31.885 90.00 90.00 90.00 P 1 1 +MODEL 0 +ATOM 1 C1 ZBE A 1 12.532 10.813 10.386 1.00 0.00 C +ATOM 2 C2 ZBE A 1 12.348 10.339 11.825 1.00 0.00 C +ATOM 3 C3 ZBE A 1 10.880 10.365 12.244 1.00 0.00 C +ATOM 4 C4 ZBE A 1 10.256 11.739 12.020 1.00 0.00 C +ATOM 5 C5 ZBE A 1 10.439 12.213 10.581 1.00 0.00 C +ATOM 6 C6 ZBE A 1 11.907 12.187 10.162 1.00 0.00 C +ATOM 7 H1 ZBE A 1 12.072 10.088 9.703 1.00 0.00 H +ATOM 8 H2 ZBE A 1 13.600 10.849 10.143 1.00 0.00 H +ATOM 9 H3 ZBE A 1 12.745 9.324 11.932 1.00 0.00 H +ATOM 10 H4 ZBE A 1 12.930 10.982 12.497 1.00 0.00 H +ATOM 11 H5 ZBE A 1 10.324 9.614 11.669 1.00 0.00 H +ATOM 12 H6 ZBE A 1 10.793 10.088 13.300 1.00 0.00 H +ATOM 13 H7 ZBE A 1 9.188 11.703 12.264 1.00 0.00 H +ATOM 14 H8 ZBE A 1 10.716 12.464 12.704 1.00 0.00 H +ATOM 15 H9 ZBE A 1 9.858 11.571 9.909 1.00 0.00 H +ATOM 16 H10 ZBE A 1 10.043 13.230 10.474 1.00 0.00 H +ATOM 17 H11 ZBE A 1 11.994 12.465 9.105 1.00 0.00 H +ATOM 18 H12 ZBE A 1 12.463 12.938 10.737 1.00 0.00 H +TER 19 ZBE A 1 +ATOM 20 C1 ZXQ S 1 10.172 31.276 27.866 1.00 0.00 C +ATOM 21 C2 ZXQ S 1 8.746 30.961 27.471 1.00 0.00 C +ATOM 22 O1 ZXQ S 1 8.752 30.264 26.234 1.00 0.00 O +ATOM 23 H1 ZXQ S 1 10.204 31.815 28.818 1.00 0.00 H +ATOM 24 H2 ZXQ S 1 10.758 30.356 27.962 1.00 0.00 H +ATOM 25 H3 ZXQ S 1 10.661 31.886 27.099 1.00 0.00 H +ATOM 26 H4 ZXQ S 1 8.169 31.883 27.352 1.00 0.00 H +ATOM 27 H5 ZXQ S 1 8.267 30.333 28.228 1.00 0.00 H +ATOM 28 H6 ZXQ S 1 7.826 30.079 26.011 1.00 0.00 H +TER 29 ZXQ S 1 +ENDMDL +CONECT 1 6 2 7 8 +CONECT 2 1 3 9 10 +CONECT 3 2 4 11 12 +CONECT 4 3 5 13 14 +CONECT 5 4 6 15 16 +CONECT 6 1 5 17 18 +CONECT 7 1 +CONECT 8 1 +CONECT 9 2 +CONECT 10 2 +CONECT 11 3 +CONECT 12 3 +CONECT 13 4 +CONECT 14 4 +CONECT 15 5 +CONECT 16 5 +CONECT 17 6 +CONECT 18 6 +CONECT 20 21 23 24 25 +CONECT 21 20 22 26 27 +CONECT 22 21 28 +CONECT 23 20 +CONECT 24 20 +CONECT 25 20 +CONECT 26 21 +CONECT 27 21 +CONECT 28 22 +END diff --git a/openforcefield/data/systems/test_systems/1_ethanol.pdb b/openforcefield/data/systems/test_systems/1_ethanol.pdb new file mode 100644 index 000000000..663b8b48b --- /dev/null +++ b/openforcefield/data/systems/test_systems/1_ethanol.pdb @@ -0,0 +1,24 @@ +REMARK 1 CREATED WITH MDTraj 1.7.2, 2016-06-27 +CRYST1 31.885 31.885 31.885 90.00 90.00 90.00 P 1 1 +MODEL 0 +ATOM 20 C1 ZXQ S 1 10.172 31.276 27.866 1.00 0.00 C +ATOM 21 C2 ZXQ S 1 8.746 30.961 27.471 1.00 0.00 C +ATOM 22 O1 ZXQ S 1 8.752 30.264 26.234 1.00 0.00 O +ATOM 23 H1 ZXQ S 1 10.204 31.815 28.818 1.00 0.00 H +ATOM 24 H2 ZXQ S 1 10.758 30.356 27.962 1.00 0.00 H +ATOM 25 H3 ZXQ S 1 10.661 31.886 27.099 1.00 0.00 H +ATOM 26 H4 ZXQ S 1 8.169 31.883 27.352 1.00 0.00 H +ATOM 27 H5 ZXQ S 1 8.267 30.333 28.228 1.00 0.00 H +ATOM 28 H6 ZXQ S 1 7.826 30.079 26.011 1.00 0.00 H +TER 29 ZXQ S 1 +ENDMDL +CONECT 20 21 23 24 25 +CONECT 21 20 22 26 27 +CONECT 22 21 28 +CONECT 23 20 +CONECT 24 20 +CONECT 25 20 +CONECT 26 21 +CONECT 27 21 +CONECT 28 22 +END diff --git a/openforcefield/data/systems/test_systems/1_ethanol_reordered.pdb b/openforcefield/data/systems/test_systems/1_ethanol_reordered.pdb new file mode 100644 index 000000000..3f5d35542 --- /dev/null +++ b/openforcefield/data/systems/test_systems/1_ethanol_reordered.pdb @@ -0,0 +1,24 @@ +REMARK 1 CREATED WITH MDTraj 1.7.2, 2016-06-27 +CRYST1 31.885 31.885 31.885 90.00 90.00 90.00 P 1 1 +MODEL 0 +ATOM 20 O1 ZXQ S 1 8.752 30.264 26.234 1.00 0.00 O +ATOM 21 C1 ZXQ S 1 10.172 31.276 27.866 1.00 0.00 C +ATOM 22 C2 ZXQ S 1 8.746 30.961 27.471 1.00 0.00 C +ATOM 23 H1 ZXQ S 1 10.204 31.815 28.818 1.00 0.00 H +ATOM 24 H2 ZXQ S 1 10.758 30.356 27.962 1.00 0.00 H +ATOM 25 H3 ZXQ S 1 10.661 31.886 27.099 1.00 0.00 H +ATOM 26 H4 ZXQ S 1 8.169 31.883 27.352 1.00 0.00 H +ATOM 27 H5 ZXQ S 1 8.267 30.333 28.228 1.00 0.00 H +ATOM 28 H6 ZXQ S 1 7.826 30.079 26.011 1.00 0.00 H +TER 29 ZXQ S 1 +ENDMDL +CONECT 21 22 23 24 25 +CONECT 22 21 20 26 27 +CONECT 20 22 28 +CONECT 23 21 +CONECT 24 21 +CONECT 25 21 +CONECT 26 22 +CONECT 27 22 +CONECT 28 20 +END diff --git a/openforcefield/tests/conftest.py b/openforcefield/tests/conftest.py new file mode 100644 index 000000000..438a06fcb --- /dev/null +++ b/openforcefield/tests/conftest.py @@ -0,0 +1,89 @@ +#!/usr/bin/env python + +#============================================================================================= +# MODULE DOCSTRING +#============================================================================================= + +""" +Configuration file for pytest. + +This adds the following command line options. +- runslow: Run tests marked as slow (default is False). + +""" + + +#============================================================================================= +# GLOBAL IMPORTS +#============================================================================================= + +import pytest + + +#============================================================================================= +# UTILITY FUNCTIONS +#============================================================================================= + +def untar_full_alkethoh_and_freesolv_set(): + """When running slow tests, we unpack the full AlkEthOH and FreeSolv test + sets in advance to speed things up. + + See + test_forcefield.py::test_alkethoh_parameters_assignment + test_forcefield.py::test_freesolv_parameters_assignment + """ + import os + import tarfile + from openforcefield.utils import get_data_filename + + molecule_dir_path = get_data_filename('molecules') + for tarfile_name in ['AlkEthOH_tripos.tar.gz', 'FreeSolv.tar.gz']: + tarfile_path = os.path.join(molecule_dir_path, tarfile_name) + with tarfile.open(tarfile_path, 'r:gz') as tar: + tar.extractall(path=molecule_dir_path) + + +#============================================================================================= +# CONFIGURATION +#============================================================================================= + +def pytest_addoption(parser): + """Add the pytest command line option --runslow and --failwip. + + If --runslow is not given, tests marked with pytest.mark.slow are + skipped. + + If --failwip is not give, tests marked with pytest.mark.wip are + xfailed. + """ + parser.addoption( + "--runslow", action="store_true", default=False, help="run slow tests" + ) + parser.addoption( + "--failwip", action="store_true", default=False, help="fail work in progress tests" + ) + + +def pytest_collection_modifyitems(config, items): + + if config.getoption("runslow"): + # If --runslow is given, we don't have to mark items for skipping, + # but we need to extract the whole AlkEthOH and FreeSolv sets (see + # test_forcefield::test_alkethoh/freesolv_parameters_assignment). + untar_full_alkethoh_and_freesolv_set() + else: + # Mark for skipping all items marked as slow. + skip_slow = pytest.mark.skip(reason="specify --runslow pytest option to run this test.") + for item in items: + if "slow" in item.keywords: + item.add_marker(skip_slow) + + # Mark work-in-progress tests for xfail. + if not config.getoption("failwip"): + xfail_wip_reason = ("This is a work in progress test. Specify " + "--failwip pytest option to make this test fail.") + for item in items: + if 'wip' in item.keywords: + # Augment original reason. + reason = xfail_wip_reason + item.get_closest_marker('wip').kwargs.get('reason', '') + item.add_marker(pytest.mark.xfail(reason=reason)) diff --git a/openforcefield/tests/test_chemicalenvironment.py b/openforcefield/tests/test_chemicalenvironment.py index 5fafc8abe..01c4cbb26 100644 --- a/openforcefield/tests/test_chemicalenvironment.py +++ b/openforcefield/tests/test_chemicalenvironment.py @@ -2,9 +2,11 @@ from openforcefield.typing.chemistry import * from openforcefield.utils import get_data_filename from unittest import TestCase -import openeye.oechem -from openeye.oechem import * +import pytest +from openforcefield.utils.toolkits import OPENEYE_AVAILABLE +# TODO: Bring these back online once OpenEye dependence is resolved +@pytest.mark.skip class TestChemicalEnvironments(TestCase): def test_createEnvironments(self): """ @@ -19,6 +21,8 @@ def test_createEnvironments(self): torsion = TorsionChemicalEnvironment('[#6X4:1]-[#6X4:2]-[#6X4:3]-[#6X4:4]', 'CT-CT-CT-CT') improper = ImproperChemicalEnvironment('[#6X4:1]-[#6X4:2](-[#6X4:3])-[#6X4:4]', 'CT-CT(-CT)-CT') + # TODO: Can we remove explicit OE dependence from this? + @pytest.mark.skip def test_complicatedTorsion(self): """ Test ChemicalEnvironment objects with complicated torsion @@ -28,6 +32,7 @@ def test_complicatedTorsion(self): This is the SMIRK for the final torsion "[*:1] - [#6:2](=[#8,#7;H0]) - [#6:3](-[#7X3,#8X2;+0]-[#1])(-[#1]) - [*:4]" """ + #from openeye.oechem import * torsion_smirks = "[*:1]-[#6:2]-[#6:3]-[*:4]" torsion = TorsionChemicalEnvironment(torsion_smirks) # save atoms (use selectAtom) diff --git a/openforcefield/tests/test_examples.py b/openforcefield/tests/test_examples.py new file mode 100644 index 000000000..680522f49 --- /dev/null +++ b/openforcefield/tests/test_examples.py @@ -0,0 +1,113 @@ +#!/usr/bin/env python + +#====================================================================== +# MODULE DOCSTRING +#====================================================================== + +""" +Test that the examples in the repo run without errors. +""" + +#====================================================================== +# GLOBAL IMPORTS +#====================================================================== + +import glob +import os +import re +import subprocess +import textwrap + +import pytest + +from openforcefield.utils import temporary_directory + + +#====================================================================== +# TEST UTILITIES +#====================================================================== + +ROOT_DIR_PATH = os.path.join(os.path.dirname(os.path.realpath(__file__)), '..', '..') + + +def run_script_file(file_path): + """Run through the shell a python script.""" + cmd = ['python', file_path] + try: + subprocess.check_call(cmd) + except subprocess.CalledProcessError: + raise Exception('Example {file_path} failed'.format(file_path=file_path)) + + +def run_script_str(script_str): + """Execute a Python string through the shell in a temporary directory. + + With respect to eval, this has the advantage of catching all import errors. + + """ + with temporary_directory() as tmp_dir: + temp_file_path = os.path.join(tmp_dir, 'temp.py') + # Create temporary python script. + with open(temp_file_path, 'w') as f: + f.write(script_str) + # Run the Python script. + try: + run_script_file(temp_file_path) + except: + script_str = textwrap.indent(script_str, ' ') + raise Exception(f'The following script failed:\n{script_str}') + + +def find_examples(): + """Find all examples in the examples folder. + + Returns + ------- + example_file_paths : List[str] + List of python script to execute. + """ + slow_examples = { + os.path.join('SMIRNOFF_comparison', 'compare_set_energies.py') + } + examples_dir_path = os.path.join(ROOT_DIR_PATH, 'examples') + + example_file_paths = [] + for example_file_path in glob.glob(os.path.join(examples_dir_path, '*', '*.py')): + example_file_path = os.path.relpath(example_file_path) + # Check if this is a slow test. + for slow_example in slow_examples: + if slow_example in example_file_path: + # This is a slow example. + example_file_path = pytest.param(example_file_path, marks=pytest.mark.slow) + example_file_paths.append(example_file_path) + return example_file_paths + + +def find_readme_examples(): + """Yield the Python scripts in a readme file. + + Returns + ------- + readme_examples : List[str] + The list of Python scripts included in the README.md files. + """ + readme_file_path = os.path.join(ROOT_DIR_PATH, 'README.md') + with open(readme_file_path, 'r') as f: + readme_content = f.read() + return re.findall('```python(.*?)```', readme_content, flags=re.DOTALL) + + +#====================================================================== +# TESTS +#====================================================================== + +@pytest.mark.parametrize('readme_example_str', find_readme_examples()) +def test_readme(readme_example_str): + """Test the example""" + run_script_str(readme_example_str) + + +@pytest.mark.parametrize('example_file_path', find_examples()) +def test_examples(example_file_path): + """Test that the example run without errors.""" + run_script_file(example_file_path) diff --git a/openforcefield/tests/test_forcefield.py b/openforcefield/tests/test_forcefield.py new file mode 100644 index 000000000..48fef3487 --- /dev/null +++ b/openforcefield/tests/test_forcefield.py @@ -0,0 +1,1011 @@ +#!/usr/bin/env python + +#============================================================================================= +# MODULE DOCSTRING +#============================================================================================= + +""" +Tests for forcefield class + +""" + + +#============================================================================================= +# GLOBAL IMPORTS +#============================================================================================= + +import copy +import os + +from simtk import openmm, unit +import numpy as np + +import pytest +from openforcefield.utils.toolkits import OpenEyeToolkitWrapper, RDKitToolkitWrapper, AmberToolsToolkitWrapper, ToolkitRegistry + +from openforcefield.utils import get_data_filename + +from openforcefield.topology import Molecule, Topology +from openforcefield.typing.engines.smirnoff import ForceField, IncompatibleParameterError + + +#====================================================================== +# GLOBAL CONSTANTS +#====================================================================== + +# File paths. +TIP3P_SDF_FILE_PATH = get_data_filename(os.path.join('systems', 'monomers', 'water.sdf')) + +GENERIC_BOND_LENGTH = 1.09 * unit.angstrom +XML_FF_GENERICS = f""" + + + + + + + + + + + + + + + + + + + +""" + +simple_xml_ff = str.encode(''' + + + + + + + + + + + + + + + + + + + + + + + + +''') + +xml_ff_w_comments = ''' + + + 2018-07-14 + C. I. Bayly, OpenEye/UC Irvine; C. C. Bannan, UC Irvine; D. L. Mobley, UC Irvine + + + + + + + + + + + + + + + + + + + + + + + + + + +''' + +xml_ff_w_cosmetic_elements = ''' + + + 2018-07-14 + C. I. Bayly, OpenEye/UC Irvine; C. C. Bannan, UC Irvine; D. L. Mobley, UC Irvine + + + + + + + + + + + + + + + + + + + + + + + + + + +''' + + +#====================================================================== +# TEST UTILITY FUNCTIONS +#====================================================================== + +def round_charge(xml): + """Round charge fields in a serialized OpenMM system to 2 decimal places""" + # Example Particle line: + xmlsp = xml.split(' q="') + for index, chunk in enumerate(xmlsp): + # Skip file before first q= + if index == 0: + continue + chunksp = chunk.split('" sig') + chunksp[0] = str('%.2d' % (float(chunksp[0]))) + chunk = '" sig'.join(chunksp) + xmlsp[index] = chunk + return ' q="'.join(xmlsp) + +def create_ethanol(): + """ + Creates an openforcefield.topology.Molecule representation of + ethanol without the use of a cheminformatics toolkit + """ + # Create an ethanol molecule without using a toolkit + ethanol = Molecule() + ethanol.add_atom(6, 0, False) # C0 + ethanol.add_atom(6, 0, False) # C1 + ethanol.add_atom(8, 0, False) # O2 + ethanol.add_atom(1, 0, False) # H3 + ethanol.add_atom(1, 0, False) # H4 + ethanol.add_atom(1, 0, False) # H5 + ethanol.add_atom(1, 0, False) # H6 + ethanol.add_atom(1, 0, False) # H7 + ethanol.add_atom(1, 0, False) # H8 + ethanol.add_bond(0, 1, 1, False) # C0 - C1 + ethanol.add_bond(1, 2, 1, False) # C1 - O2 + ethanol.add_bond(0, 3, 1, False) # C0 - H3 + ethanol.add_bond(0, 4, 1, False) # C0 - H4 + ethanol.add_bond(0, 5, 1, False) # C0 - H5 + ethanol.add_bond(1, 6, 1, False) # C1 - H6 + ethanol.add_bond(1, 7, 1, False) # C1 - H7 + ethanol.add_bond(2, 8, 1, False) # O2 - H8 + charges = unit.Quantity(np.array([-0.4, -0.3, -0.2, -0.1, 0.01, 0.1, 0.2, 0.3, 0.4]), unit.elementary_charge) + ethanol.partial_charges = charges + return ethanol + +def create_cyclohexane(): + """ + Creates an openforcefield.topology.Molecule representation of + cyclohexane without the use of a cheminformatics toolkit + """ + cyclohexane = Molecule() + cyclohexane.add_atom(6, 0, False) # C0 + cyclohexane.add_atom(6, 0, False) # C1 + cyclohexane.add_atom(6, 0, False) # C2 + cyclohexane.add_atom(6, 0, False) # C3 + cyclohexane.add_atom(6, 0, False) # C4 + cyclohexane.add_atom(6, 0, False) # C5 + cyclohexane.add_atom(1, 0, False) # H6 + cyclohexane.add_atom(1, 0, False) # H7 + cyclohexane.add_atom(1, 0, False) # H8 + cyclohexane.add_atom(1, 0, False) # H9 + cyclohexane.add_atom(1, 0, False) # H10 + cyclohexane.add_atom(1, 0, False) # H11 + cyclohexane.add_atom(1, 0, False) # H12 + cyclohexane.add_atom(1, 0, False) # H13 + cyclohexane.add_atom(1, 0, False) # H14 + cyclohexane.add_atom(1, 0, False) # H15 + cyclohexane.add_atom(1, 0, False) # H16 + cyclohexane.add_atom(1, 0, False) # H17 + cyclohexane.add_bond(0, 1, 1, False) # C0 - C1 + cyclohexane.add_bond(1, 2, 1, False) # C1 - C2 + cyclohexane.add_bond(2, 3, 1, False) # C2 - C3 + cyclohexane.add_bond(3, 4, 1, False) # C3 - C4 + cyclohexane.add_bond(4, 5, 1, False) # C4 - C5 + cyclohexane.add_bond(5, 0, 1, False) # C5 - C0 + cyclohexane.add_bond(0, 6, 1, False) # C0 - H6 + cyclohexane.add_bond(0, 7, 1, False) # C0 - H7 + cyclohexane.add_bond(1, 8, 1, False) # C1 - H8 + cyclohexane.add_bond(1, 9, 1, False) # C1 - H9 + cyclohexane.add_bond(2, 10, 1, False) # C2 - H10 + cyclohexane.add_bond(2, 11, 1, False) # C2 - H11 + cyclohexane.add_bond(3, 12, 1, False) # C3 - H12 + cyclohexane.add_bond(3, 13, 1, False) # C3 - H13 + cyclohexane.add_bond(4, 14, 1, False) # C4 - H14 + cyclohexane.add_bond(4, 15, 1, False) # C4 - H15 + cyclohexane.add_bond(5, 16, 1, False) # C5 - H16 + cyclohexane.add_bond(5, 17, 1, False) # C5 - H17 + return cyclohexane + + + +nonbonded_resolution_matrix = [ + {'vdw_method': 'cutoff', 'electrostatics_method': 'Coulomb', 'has_periodic_box': True, + 'omm_force': None, 'exception': IncompatibleParameterError, 'exception_match': ''}, + {'vdw_method': 'cutoff', 'electrostatics_method': 'Coulomb', 'has_periodic_box': False, + 'omm_force': openmm.NonbondedForce.NoCutoff, 'exception': None, 'exception_match': ''}, + {'vdw_method': 'cutoff', 'electrostatics_method': 'reaction-field', 'has_periodic_box': True, + 'omm_force': None, 'exception': IncompatibleParameterError, 'exception_match': ''}, + {'vdw_method': 'cutoff', 'electrostatics_method': 'reaction-field', 'has_periodic_box': False, + 'omm_force': None, 'exception': IncompatibleParameterError, 'exception_match': ''}, + {'vdw_method': 'cutoff', 'electrostatics_method': 'PME', 'has_periodic_box': True, + 'omm_force': openmm.NonbondedForce.PME, 'exception': None, 'exception_match': ''}, + {'vdw_method': 'cutoff', 'electrostatics_method': 'PME', 'has_periodic_box': False, + 'omm_force': openmm.NonbondedForce.NoCutoff, 'exception': None, 'exception_match': ''}, + + {'vdw_method': 'PME', 'electrostatics_method': 'Coulomb', 'has_periodic_box': True, + 'omm_force': None, 'exception': IncompatibleParameterError, 'exception_match': ''}, + {'vdw_method': 'PME', 'electrostatics_method': 'Coulomb', 'has_periodic_box': False, + 'omm_force': openmm.NonbondedForce.NoCutoff, 'exception': None, 'exception_match': ''}, + {'vdw_method': 'PME', 'electrostatics_method': 'reaction-field', 'has_periodic_box': True, + 'omm_force': None, 'exception': IncompatibleParameterError, 'exception_match': ''}, + {'vdw_method': 'PME', 'electrostatics_method': 'reaction-field', 'has_periodic_box': False, + 'omm_force': None, 'exception': IncompatibleParameterError, 'exception_match': ''}, + {'vdw_method': 'PME', 'electrostatics_method': 'PME', 'has_periodic_box': True, + 'omm_force': openmm.NonbondedForce.LJPME, 'exception': None, 'exception_match': ''}, + {'vdw_method': 'PME', 'electrostatics_method': 'PME', 'has_periodic_box': False, + 'omm_force': openmm.NonbondedForce.NoCutoff, 'exception': None, 'exception_match': ''}, + ] + + +#============================================================================================= +# TESTS +#============================================================================================= + + +toolkit_registries = [] +if OpenEyeToolkitWrapper.toolkit_is_available(): + + toolkit_registries.append((ToolkitRegistry(toolkit_precedence=[OpenEyeToolkitWrapper]), "OE")) +if RDKitToolkitWrapper.toolkit_is_available() and AmberToolsToolkitWrapper.toolkit_is_available(): + toolkit_registries.append((ToolkitRegistry(toolkit_precedence=[RDKitToolkitWrapper, AmberToolsToolkitWrapper]), + 'RDKit+AmberTools')) + + +class TestForceField(): + """Test the ForceField class""" + + def test_create_forcefield_from_file(self): + """Test empty constructor""" + forcefield = ForceField('smirnoff99Frosst.offxml') + assert len(forcefield._parameter_handlers['Bonds']._parameters) == 87 + assert len(forcefield._parameter_handlers['Angles']._parameters) == 38 + assert len(forcefield._parameter_handlers['ProperTorsions']._parameters) == 158 + assert len(forcefield._parameter_handlers['ImproperTorsions']._parameters) == 4 + assert len(forcefield._parameter_handlers['vdW']._parameters) == 35 + + @pytest.mark.skip(reason='Needs to be updated for 0.2.0 syntax') + def test_create_forcefield_from_file_list(self): + # These offxml files are located in package data path, which is automatically installed and searched + filenames = [smirnoff99Frosst_offxml_filename, tip3p_offxml_filename] + # Create a forcefield from multiple offxml files + forcefield = ForceField(filenames) + + @pytest.mark.skip(reason='Needs to be updated for 0.2.0 syntax') + def test_create_forcefield_from_filename_iterator(self): + # These offxml files are located in package data path, which is automatically installed and searched + filenames = [smirnoff99Frosst_offxml_filename, tip3p_offxml_filename] + # A generator should work as well + forcefield = ForceField(iter(filenames)) + + @pytest.mark.skip(reason='Needs to be updated for 0.2.0 syntax') + def test_create_gbsa(): + """Test reading of ffxml files with GBSA support. + """ + forcefield = ForceField('Frosst_AlkEthOH_GBSA.offxml') + + @pytest.mark.skip(reason='Needs to be updated for 0.2.0 syntax') + def test_create_forcefield_from_url(self): + urls = [ + 'https://raw.githubusercontent.com/openforcefield/openforcefield/master/openforcefield/data/forcefield/smirnoff99Frosst.offxml', + 'https://raw.githubusercontent.com/openforcefield/openforcefield/master/openforcefield/data/forcefield/tip3p.offxml' + ] + # Test creation with smirnoff99frosst URL + forcefield = ForceField(urls[0]) + + @pytest.mark.skip(reason='Needs to be updated for 0.2.0 syntax') + def test_create_forcefield_from_url_list(self): + urls = [ + 'https://raw.githubusercontent.com/openforcefield/openforcefield/master/openforcefield/data/forcefield/smirnoff99Frosst.offxml', + 'https://raw.githubusercontent.com/openforcefield/openforcefield/master/openforcefield/data/forcefield/tip3p.offxml' + ] + # Test creation with multiple URLs + forcefield = ForceField(urls) + + @pytest.mark.skip(reason='Needs to be updated for 0.2.0 syntax') + def test_create_forcefield_from_url_iterator(self): + urls = [ + 'https://raw.githubusercontent.com/openforcefield/openforcefield/master/openforcefield/data/forcefield/smirnoff99Frosst.offxml', + 'https://raw.githubusercontent.com/openforcefield/openforcefield/master/openforcefield/data/forcefield/tip3p.offxml' + ] + # A generator should work as well + forcefield = ForceField(iter(urls)) + + + def test_create_forcefield_from_xml_string(self): + forcefield = ForceField(simple_xml_ff) + assert len(forcefield._parameter_handlers['Bonds']._parameters) == 2 + assert len(forcefield._parameter_handlers['Angles']._parameters) == 2 + assert len(forcefield._parameter_handlers['ProperTorsions']._parameters) == 2 + assert len(forcefield._parameter_handlers['ImproperTorsions']._parameters) == 2 + assert len(forcefield._parameter_handlers['vdW']._parameters) == 2 + + @pytest.mark.skip(reason='Needs to be updated for 0.2.0 syntax') + def test_deep_copy(self): + forcefield = ForceField(smirnoff99Frosst_offxml_filename) + # Deep copy + forcefield2 = copy.deepcopy(cls.forcefield) + assert_forcefields_equal(cls.forcefield, forcefield2, + "ForceField deep copy does not match original ForceField") + + + @pytest.mark.skip(reason='Needs to be updated for 0.2.0 syntax') + # TODO: This should check the output of forcefield.to_dict + def test_serialize(self): + + forcefield = ForceField(smirnoff99Frosst_offxml_filename) + # Serialize/deserialize + serialized_forcefield = cls.forcefield.__getstate__() + forcefield2 = ForceField.__setstate__(serialized_forcefield) + assert_forcefields_equal(cls.forcefield, forcefield2, + "Deserialized serialized ForceField does not match original ForceField") + + def test_xml_string_roundtrip(self): + """ + Test + 1) loading a forcefield from string + 2) writing it to an XML string ("string_1") + 3) Initialize "forcefield_2" using "string_1" + 4) serialize "forcefield_2" to "string_2" + 5) Check that "string_1" is equal to "string_2" + + """ + forcefield_1 = ForceField(simple_xml_ff) + string_1 = forcefield_1._parameter_io_handlers['XML'].to_string(forcefield_1.to_smirnoff_data()) + forcefield_2 = ForceField(string_1) + string_2 = forcefield_2._parameter_io_handlers['XML'].to_string(forcefield_2.to_smirnoff_data()) + assert string_1 == string_2 + + @pytest.mark.parametrize("toolkit_registry,registry_description", toolkit_registries) + def test_parameterize_ethanol(self, toolkit_registry, registry_description): + from simtk.openmm import app + + forcefield = ForceField('smirnoff99Frosst.offxml') + pdbfile = app.PDBFile(get_data_filename('systems/test_systems/1_ethanol.pdb')) + molecules = [] + molecules.append(Molecule.from_smiles('CCO')) + topology = Topology.from_openmm(pdbfile.topology, unique_molecules=molecules) + + omm_system = forcefield.create_openmm_system(topology, toolkit_registry=toolkit_registry) + + @pytest.mark.parametrize("toolkit_registry,registry_description", toolkit_registries) + def test_parameterize_1_cyclohexane_1_ethanol(self, toolkit_registry, registry_description): + from simtk.openmm import app + + forcefield = ForceField('smirnoff99Frosst.offxml') + pdbfile = app.PDBFile(get_data_filename('systems/test_systems/1_cyclohexane_1_ethanol.pdb')) + # toolkit_wrapper = RDKitToolkitWrapper() + molecules = [] + molecules.append(Molecule.from_smiles('CCO')) + molecules.append(Molecule.from_smiles('C1CCCCC1')) + # molecules = [Molecule.from_file(get_data_filename(name)) for name in ('molecules/ethanol.mol2', + # 'molecules/cyclohexane.mol2')] + topology = Topology.from_openmm(pdbfile.topology, unique_molecules=molecules) + + omm_system = forcefield.create_openmm_system(topology) + + @pytest.mark.parametrize("toolkit_registry,registry_description", toolkit_registries) + def test_parameterize_1_cyclohexane_1_ethanol_vacuum(self, toolkit_registry, registry_description): + from simtk.openmm import app + + forcefield = ForceField('smirnoff99Frosst.offxml') + pdbfile = app.PDBFile(get_data_filename('systems/test_systems/1_cyclohexane_1_ethanol.pdb')) + # toolkit_wrapper = RDKitToolkitWrapper() + molecules = [] + molecules.append(Molecule.from_smiles('CCO')) + molecules.append(Molecule.from_smiles('C1CCCCC1')) + # molecules = [Molecule.from_file(get_data_filename(name)) for name in ('molecules/ethanol.mol2', + # 'molecules/cyclohexane.mol2')] + topology = Topology.from_openmm(pdbfile.topology, unique_molecules=molecules) + topology.box_vectors = None + #forcefield.get_handler("Electrostatics", {})._method = "Coulomb" + #forcefield.get_handler("vdW", {})._method = "cutoff" + + omm_system = forcefield.create_openmm_system(topology) + + + + @pytest.mark.parametrize("toolkit_registry,registry_description", toolkit_registries) + def test_parameterize_no_matching_reference(self, toolkit_registry, registry_description): + from simtk.openmm import app + + forcefield = ForceField('smirnoff99Frosst.offxml') + pdbfile = app.PDBFile(get_data_filename('systems/test_systems/1_cyclohexane_1_ethanol.pdb')) + # toolkit_wrapper = RDKitToolkitWrapper() + molecules = [] + molecules.append(Molecule.from_smiles('CC')) + with pytest.raises(ValueError, match='No match found for molecule'): + topology = Topology.from_openmm(pdbfile.topology, unique_molecules=molecules) + + @pytest.mark.slow + @pytest.mark.parametrize("toolkit_registry,registry_description", toolkit_registries) + @pytest.mark.parametrize("box", ['ethanol_water.pdb', + 'cyclohexane_water.pdb', + 'cyclohexane_ethanol_0.4_0.6.pdb', + 'propane_methane_butanol_0.2_0.3_0.5.pdb']) + def test_parameterize_large_system(self, toolkit_registry, registry_description, box): + from simtk.openmm import app + + forcefield = ForceField('smirnoff99Frosst.offxml') + box_filename = get_data_filename(os.path.join('systems', 'packmol_boxes', box)) + pdbfile = app.PDBFile(box_filename) + mol_names = ['water', 'cyclohexane', 'ethanol', 'propane', 'methane', 'butanol'] + sdf_files = [get_data_filename(os.path.join('systems', 'monomers', name+'.sdf')) for name in mol_names] + molecules = [Molecule.from_file(sdf_file) for sdf_file in sdf_files] + topology = Topology.from_openmm(pdbfile.topology, unique_molecules=molecules, ) + + omm_system = forcefield.create_openmm_system(topology, toolkit_registry=toolkit_registry) + # TODO: Add check to ensure system energy is finite + + @pytest.mark.skipif( not(OpenEyeToolkitWrapper.toolkit_is_available()), reason='Test requires OE toolkit') + def test_parameterize_ethanol_different_reference_ordering_openeye(self): + """ + Test parameterizing the same PDB, using reference mol2s that have different atom orderings. + The results of both should be identical. + """ + toolkit_registry = ToolkitRegistry(toolkit_precedence=[OpenEyeToolkitWrapper]) + from simtk.openmm import app + from simtk.openmm import XmlSerializer + + forcefield = ForceField('smirnoff99Frosst.offxml') + pdbfile = app.PDBFile(get_data_filename('systems/test_systems/1_ethanol.pdb')) + # Load the unique molecules with one atom ordering + molecules1 = [Molecule.from_file(get_data_filename('molecules/ethanol.sdf'))] + topology1 = Topology.from_openmm(pdbfile.topology, + unique_molecules=molecules1, + ) + omm_system1 = forcefield.create_openmm_system(topology1, + toolkit_registry=toolkit_registry) + # Load the unique molecules with a different atom ordering + molecules2 = [Molecule.from_file(get_data_filename('molecules/ethanol_reordered.sdf'))] + topology2 = Topology.from_openmm(pdbfile.topology, + unique_molecules=molecules2, + ) + omm_system2 = forcefield.create_openmm_system(topology2, + toolkit_registry=toolkit_registry) + + serialized_1 = XmlSerializer.serialize(omm_system1) + serialized_2 = XmlSerializer.serialize(omm_system2) + + serialized_1 = round_charge(serialized_1) + serialized_2 = round_charge(serialized_2) + + assert serialized_1 == serialized_2 + + + @pytest.mark.skipif(not RDKitToolkitWrapper.toolkit_is_available(), reason='Test requires RDKit toolkit') + def test_parameterize_ethanol_different_reference_ordering_rdkit(self): + """ + Test parameterizing the same PDB, using reference mol2s that have different atom orderings. + The results of both should be identical. + """ + from simtk.openmm import app + from simtk.openmm import XmlSerializer + + toolkit_registry = ToolkitRegistry(toolkit_precedence=[RDKitToolkitWrapper, AmberToolsToolkitWrapper]) + forcefield = ForceField('smirnoff99Frosst.offxml') + pdbfile = app.PDBFile(get_data_filename('systems/test_systems/1_ethanol.pdb')) + + # Load the unique molecules with one atom ordering + molecules1 = [Molecule.from_file(get_data_filename('molecules/ethanol.sdf'))] + topology1 = Topology.from_openmm(pdbfile.topology, + unique_molecules=molecules1, + + ) + omm_system1 = forcefield.create_openmm_system(topology1, + toolkit_registry=toolkit_registry) + + # Load the unique molecules with a different atom ordering + molecules2 = [Molecule.from_file(get_data_filename('molecules/ethanol_reordered.sdf'))] + topology2 = Topology.from_openmm(pdbfile.topology, + unique_molecules=molecules2, + ) + omm_system2 = forcefield.create_openmm_system(topology2, + toolkit_registry=toolkit_registry) + + serialized_1 = XmlSerializer.serialize(omm_system1) + serialized_2 = XmlSerializer.serialize(omm_system2) + + serialized_1 = round_charge(serialized_1) + serialized_2 = round_charge(serialized_2) + + assert serialized_1 == serialized_2 + + + @pytest.mark.skip(reason="We will not support going directly to ParmEd for now." + "We will instead feed OpenMM System objects to ParmEd " + "for further processing.") + def test_parameterize_ethanol_to_parmed(self): + from simtk.openmm import app + + forcefield = ForceField('smirnoff99Frosst.offxml') + pdbfile = app.PDBFile(get_data_filename('systems/test_systems/1_ethanol.pdb')) + #toolkit_wrapper = RDKitToolkitWrapper() + molecules = [ Molecule.from_file(get_data_filename(name)) for name in ('molecules/ethanol.mol2',) ] + topology = Topology.from_openmm(pdbfile.topology, unique_molecules=molecules) + + parmed_system = forcefield.create_parmed_structure(topology, positions=pdbfile.getPositions()) + + @pytest.mark.parametrize("toolkit_registry,registry_description", toolkit_registries) + def test_charges_from_molecule(self, toolkit_registry, registry_description): + """Test skipping charge generation and instead getting charges from the original Molecule""" + # Create an ethanol molecule without using a toolkit + molecules = [create_ethanol()] + + from simtk.openmm import app, NonbondedForce + + filename = get_data_filename('forcefield/smirnoff99Frosst.offxml') + forcefield = ForceField(filename) + pdbfile = app.PDBFile(get_data_filename('systems/test_systems/1_ethanol.pdb')) + topology = Topology.from_openmm(pdbfile.topology, unique_molecules=molecules) + omm_system = forcefield.create_openmm_system(topology, charge_from_molecules=molecules, + toolkit_registry=toolkit_registry) + nonbondedForce = [f for f in omm_system.getForces() if type(f) == NonbondedForce][0] + expected_charges = ((0, -0.4 * unit.elementary_charge), + (1, -0.3 * unit.elementary_charge), + (2, -0.2 * unit.elementary_charge), + ) + for particle_index, expected_charge in expected_charges: + q, sigma, epsilon = nonbondedForce.getParticleParameters(particle_index) + assert q == expected_charge + + # In 1_ethanol_reordered.pdb, the first three atoms go O-C-C instead of C-C-O. This part of the test ensures + # that the charges are correctly mapped according to this PDB in the resulting system. + pdbfile2 = app.PDBFile(get_data_filename('systems/test_systems/1_ethanol_reordered.pdb')) + topology2 = Topology.from_openmm(pdbfile2.topology, unique_molecules=molecules) + + omm_system2 = forcefield.create_openmm_system(topology2, charge_from_molecules=molecules, + toolkit_registry=toolkit_registry) + nonbondedForce2 = [f for f in omm_system2.getForces() if type(f) == NonbondedForce][0] + expected_charges2 = ((0, -0.2*unit.elementary_charge), + (1, -0.4*unit.elementary_charge), + (2, -0.3*unit.elementary_charge), + ) + for particle_index, expected_charge in expected_charges2: + q, sigma, epsilon = nonbondedForce2.getParticleParameters(particle_index) + assert q == expected_charge + + + @pytest.mark.parametrize("toolkit_registry,registry_description", toolkit_registries) + def test_some_charges_from_molecule(self, toolkit_registry, registry_description): + """ + Test creating an OpenMM system where some charges come from a Molecule, but others come from toolkit + calculation + """ + ethanol = create_ethanol() + cyclohexane = create_cyclohexane() + molecules = [ethanol, cyclohexane] + + from simtk.openmm import app, NonbondedForce + + filename = get_data_filename('forcefield/smirnoff99Frosst.offxml') + forcefield = ForceField(filename) + pdbfile = app.PDBFile(get_data_filename('systems/test_systems/1_cyclohexane_1_ethanol.pdb')) + topology = Topology.from_openmm(pdbfile.topology, unique_molecules=molecules, ) + + omm_system = forcefield.create_openmm_system(topology, + charge_from_molecules=[ethanol], + toolkit_registry=toolkit_registry) + nonbondedForce = [f for f in omm_system.getForces() if type(f) == NonbondedForce][0] + expected_charges = ((18, -0.4 * unit.elementary_charge), + (19, -0.3 * unit.elementary_charge), + (20, -0.2 * unit.elementary_charge), + ) + for particle_index, expected_charge in expected_charges: + q, sigma, epsilon = nonbondedForce.getParticleParameters(particle_index) + assert q == expected_charge + for particle_index in range(topology.n_topology_particles): + q, sigma, epsilon = nonbondedForce.getParticleParameters(particle_index) + assert q != (0. * unit.elementary_charge) + #from simtk.openmm import XmlSerializer + #print(XmlSerializer.serialize(omm_system)) + + + + @pytest.mark.parametrize("toolkit_registry,registry_description", toolkit_registries) + def test_pass_invalid_kwarg_to_create_openmm_system(self, toolkit_registry, registry_description): + """Test to ensure an exception is raised when an unrecognized kwarg is passed """ + from simtk.openmm import app + + filename = get_data_filename('forcefield/smirnoff99Frosst.offxml') + forcefield = ForceField(filename) + pdbfile = app.PDBFile(get_data_filename('systems/test_systems/1_ethanol.pdb')) + molecules = [] + molecules.append(Molecule.from_smiles('CCO')) + topology = Topology.from_openmm(pdbfile.topology, unique_molecules=molecules) + + with pytest.raises(ValueError, match=".* not used by any registered force Handler: {'invalid_kwarg'}.*") as e: + omm_system = forcefield.create_openmm_system(topology, invalid_kwarg='aaa', toolkit_registry=toolkit_registry) + + + @pytest.mark.parametrize("inputs", nonbonded_resolution_matrix) + def test_nonbonded_method_resolution(self, + inputs + ): + """Test predefined permutations of input options to ensure nonbonded handling is correctly resolved""" + from simtk.openmm import app + + vdw_method = inputs['vdw_method'] + electrostatics_method = inputs['electrostatics_method'] + has_periodic_box = inputs['has_periodic_box'] + omm_force = inputs['omm_force'] + exception = inputs['exception'] + exception_match= inputs['exception_match'] + + molecules = [create_ethanol()] + forcefield = ForceField('smirnoff99Frosst.offxml') + forcefield.get_handler('vdW', {})._method = vdw_method + forcefield.get_handler('Electrostatics', {})._method = electrostatics_method + + pdbfile = app.PDBFile(get_data_filename('systems/test_systems/1_ethanol.pdb')) + topology = Topology.from_openmm(pdbfile.topology, unique_molecules=molecules) + + if not(has_periodic_box): + topology.box_vectors = None + + if exception is None: + omm_system = forcefield.create_openmm_system(topology) + nonbond_method_matched = False + for f_idx in range(omm_system.getNumForces()): + force = omm_system.getForce(f_idx) + if isinstance(force, openmm.NonbondedForce): + if force.getNonbondedMethod() == omm_force: + nonbond_method_matched = True + assert nonbond_method_matched + else: + with pytest.raises(exception, match=exception_match) as excinfo: + omm_system = forcefield.create_openmm_system(topology) + + +#====================================================================== +# TEST CONSTRAINTS +#====================================================================== + +class TestForceFieldConstraints: + """Tests that constraints are correctly applied and behave correctly.""" + + @classmethod + def check_molecule_constraints(cls, molecule, system, bond_elements, bond_length): + """Check that the bonds in the molecule is correctly constrained.""" + for constraint_idx in range(system.getNumConstraints()): + atom1_idx, atom2_idx, distance = system.getConstraintParameters(constraint_idx) + atom_elements = {molecule.atoms[atom1_idx].element.symbol, + molecule.atoms[atom2_idx].element.symbol} + assert atom_elements == bond_elements + assert np.isclose(distance/unit.angstrom, bond_length/unit.angstrom) + + def test_constraints_hbonds(self): + """Test that hydrogen bonds constraints are applied correctly to a ethane molecule.""" + # Parametrize an ethane molecule. + ethane = Molecule.from_smiles('CC') + topology = Topology.from_molecules([ethane]) + ff = ForceField(XML_FF_GENERICS, 'old/hbonds.offxml') + system = ff.create_openmm_system(topology) + + # Check that all C-H bonds have been constrained to the FF bond length. + self.check_molecule_constraints(ethane, system, + bond_elements={'C', 'H'}, + bond_length=GENERIC_BOND_LENGTH) + + +#====================================================================== +# TEST PARAMETER ASSIGNMENT +#====================================================================== + +def generate_alkethoh_parameters_assignment_cases(): + """Create dynamically all test cases that should be ran for the AlkEthOH set.""" + # These AlkEthOH molecules are always run by test_alkethoh_parameters_assignment. + fast_test_cases = [ + 'r0', + 'r12', + 'r118', + 'c38', + 'c100', + 'c1161', + 'c1266' + ] + + def extract_id(file_path): + """Extract the AlkEthOH molecule ID from the file path.""" + # An example of file path is AlkEthOH_tripos/AlkEthOH_chain_filt1/AlkEthOH_c555.crd + return os.path.splitext(os.path.basename(file_path))[0][9:] + + # Get all the molecules ids from the tarfiles. The tarball is extracted + # in conftest.py if slow tests are activated. + import tarfile + alkethoh_tar_file_path = get_data_filename(os.path.join('molecules', 'AlkEthOH_tripos.tar.gz')) + with tarfile.open(alkethoh_tar_file_path, 'r:gz') as tar: + # Collect all the files discarding the duplicates in the test_filt1 folder. + slow_test_cases = {extract_id(m.name) for m in tar.getmembers() + if 'crd' in m.name and 'test_filt1' not in m.name} + + # Remove fast test cases from slow ones to avoid duplicate tests. + # Remove also water (c1302), which was reparameterized in AlkEthOH + # to be TIP3P (not covered by Frosst_AlkEthOH_parmAtFrosst. + for fast_test_case in fast_test_cases + ['c1302']: + slow_test_cases.remove(fast_test_case) + + # Mark all slow cases as slow. + slow_test_cases = [pytest.param(case, marks=pytest.mark.slow) + for case in sorted(slow_test_cases)] + + # Isolate the AlkEthOH ID. + return fast_test_cases + slow_test_cases + + +def generate_freesolv_parameters_assignment_cases(): + """Create dynamically all test cases that should be ran for the FreeSolv set.""" + import tarfile + + # For these tests, UndefinedStereochemistryError is ignored. + # The chirality was manually checked (see issue #175). + ignore_undefined_stereo = { + '2501588', + '3266352', + '7829570' + } + + # These molecules are always tested by test_freesolv_parameters_assignment(). + # Each test case is (freesolv_id, force_field_version, allow_undefined_stereo). + fast_test_cases = [ + ('1019269', '0_0_4_fixed', False), + ('63712', '0_0_2', False), # The XML was regenerated after fixing the issue described in #179. + ('1723043', '0_0_2', False), + ('2501588', '0_0_2', True), # Test impropers and undefined stereochemistry. + ('3323117', '0_0_2', False), # The XML was regenerated after fixing the issue described in #179. + ] + + def extract_id(file_path): + """Extract the FreeSolv ID and force field version from the file subpath.""" + # An example of file path is FreeSolv/xml_0_0_4_fixed/mobley_7913234_vacuum.xml + freesolv_id = os.path.basename(file_path).split('_')[1] + force_field_version = os.path.basename(os.path.dirname(file_path))[4:] + allow_undefined_stereo = freesolv_id in ignore_undefined_stereo + return (freesolv_id, force_field_version, allow_undefined_stereo) + + # Get all the tarball XML files available. The tarball is extracted + # in conftest.py if slow tests are activated. + freesolv_tar_file_path = get_data_filename(os.path.join('molecules', 'FreeSolv.tar.gz')) + with tarfile.open(freesolv_tar_file_path, 'r:gz') as tar: + slow_test_cases = {extract_id(m.name) for m in tar.getmembers() if '.xml' in m.name} + + # Remove fast test cases from slow ones to avoid duplicate tests. + for fast_test_case in fast_test_cases: + slow_test_cases.remove(fast_test_case) + + # Mark all slow cases as slow. + slow_test_cases = [pytest.param(*case, marks=pytest.mark.slow) + for case in sorted(slow_test_cases)] + + return fast_test_cases + slow_test_cases + + +class TestForceFieldParameterAssignment: + """Regression tests checking that parameters are assigned correctly.""" + + @pytest.mark.skipif(not OpenEyeToolkitWrapper.is_available(), + reason='Test requires OE toolkit to read mol2 files') + @pytest.mark.parametrize('alkethoh_id', generate_alkethoh_parameters_assignment_cases()) + def test_alkethoh_parameters_assignment(self, alkethoh_id): + """Test that ForceField assign parameters correctly in the AlkEthOH set. + The test compares the System parameters of a AlkEthOH molecule + parameterized with AMBER and Frosst_AlkEthOH_parmAtFrosst.offxml. + + The AMBER files were prepared following the pipeline described here: + https://github.com/openforcefield/open-forcefield-data/tree/master/Model-Systems/AlkEthOH_distrib/ + They were built for the SMIRNOFF parametrization to yield exact same + parameters. + + The AlkEthOH set, however, does not have impropers, which should be + tested separately. Currently, test_freesolv_parameters_assignment + does the job. + + """ + from openforcefield.tests.utils import get_alkethoh_filepath, compare_amber_smirnoff + + # Obtain the path to the input files. + alkethoh_name = 'AlkEthOH_' + alkethoh_id + mol2_filepath, top_filepath, crd_filepath = get_alkethoh_filepath(alkethoh_name, get_amber=True) + + # Load molecule. + molecule = Molecule.from_file(mol2_filepath) + + # Load forcefield + forcefield = ForceField('Frosst_AlkEthOH_parmAtFrosst.offxml') + + # Compare parameters. Skip the energy checks as the parameter check should be + # sufficient. We test both energies and parameters in the slow test. + # We ignore the charges for now as they are not included in the force field. + # TODO: Reactivate the charge check when we'll be able to load charges from files. + compare_amber_smirnoff(top_filepath, crd_filepath, forcefield, molecule, + check_energies=False, ignore_charges=True) + + @pytest.mark.skipif(not OpenEyeToolkitWrapper.is_available(), + reason='Test requires OE toolkit to read mol2 files') + def test_multi_alkethoh_parameters_assignment(self): + """Test that systems with multiple reference molecules are parametrized correctly. + + The test relies on the fact that we have already verified we can + parametrize correctly single AlkEthOH molecules in + test_alkethoh_parameters_assignment(). We use ParmEd to merge + the AMBER files to be used as reference parameters. + + """ + import parmed + from openforcefield.tests.utils import (get_alkethoh_filepath, + compare_system_parameters, + compare_system_energies) + + # The AlkEthOH molecule ids to mix in the systems. + alketoh_ids = ['r0', 'c38', 'c1161'] + + # Load molecules and structures. + molecules = [] + structures = [] + for alkethoh_id in alketoh_ids: + mol2_filepath, top_filepath, crd_filepath = get_alkethoh_filepath( + 'AlkEthOH_'+alkethoh_id, get_amber=True) + molecules.append(Molecule.from_file(mol2_filepath)) + amber_parm = parmed.load_file(top_filepath, crd_filepath) + # Convert this into a real structure as mixing AmberParm objects is bugged (see ParmEd#1045). + structures.append(amber_parm.copy(parmed.Structure)) + + # Merge the structures into a single system with two copies of the last molecule. + structure_mixture = structures[0] + structures[1] + structures[2] + structures[-1] + amber_system = structure_mixture.createSystem(nonbondedMethod=openmm.app.NoCutoff) + + # Create the OpenFF System through ForceField. + topology = Topology.from_openmm(structure_mixture.topology, unique_molecules=molecules) + topology.box_vectors = None + ff = ForceField('Frosst_AlkEthOH_parmAtFrosst.offxml') + off_system = ff.create_openmm_system(topology) + + # Translate the molecules a little to avoid overlapping atoms. + positions = copy.deepcopy(structure_mixture.positions) + translate_vectors = [ + np.array([1.0, 0.0, 0.0])*unit.nanometer, + np.array([0.0, 1.0, 0.0])*unit.nanometer, + np.array([0.0, 0.0, 1.0])*unit.nanometer, + # Leave the fourth molecule where it is. + ] + current_atom_idx = 0 + for mol_idx, (translate_vector, mol) in enumerate(zip(translate_vectors, molecules)): + n_mol_atoms = len(mol.atoms) + positions[current_atom_idx:current_atom_idx+n_mol_atoms] += translate_vector + current_atom_idx += n_mol_atoms + + # Compare parameters and systems. + # TODO: Reactivate charges comparison when we'll be able to read them from the file. + compare_system_parameters(amber_system, off_system, + systems_labels=('AMBER', 'SMIRNOFF'), + ignore_charges=True) + compare_system_energies(amber_system, off_system, positions, + ignore_charges=True) + + @pytest.mark.skipif(not OpenEyeToolkitWrapper.is_available(), + reason='Test requires OE toolkit to read mol2 files') + @pytest.mark.parametrize(('freesolv_id', 'forcefield_version', 'allow_undefined_stereo'), + generate_freesolv_parameters_assignment_cases()) + def test_freesolv_parameters_assignment(self, freesolv_id, forcefield_version, allow_undefined_stereo): + """Regression test on parameters assignment based on the FreeSolv set used in the 0.1 paper. + + This, contrarily to the similar AlkEthOH test, checks also constraints + and improper torsions. + + """ + from openforcefield.tests.utils import get_freesolv_filepath, compare_system_parameters + mol2_file_path, xml_file_path = get_freesolv_filepath(freesolv_id, forcefield_version) + + # Load molecules. + molecule = Molecule.from_file(mol2_file_path, allow_undefined_stereo=allow_undefined_stereo) + + # Create OpenFF System with the current toolkit. + forcefield_file_path = 'old/smirnoff99Frosst_' + forcefield_version + '.offxml' + ff = ForceField(forcefield_file_path, 'old/hbonds.offxml') + ff_system = ff.create_openmm_system(molecule.to_topology()) + + # Load OpenMM System created with the 0.1 version of the toolkit. + from simtk import openmm + with open(xml_file_path, 'r') as f: + xml_system = openmm.XmlSerializer.deserialize(f.read()) + + # Compare parameters. We ignore the improper folds as in 0.0.3 we + # used a six-fold implementation while we now use a three-fold way. + # TODO: Reactivate charge comparison once we'll be able to read them from file. + compare_system_parameters(ff_system, xml_system, + systems_labels=('current OpenFF', 'SMIRNOFF 0.0.4'), + ignore_charges=True, ignore_improper_folds=True) + + +@pytest.mark.skip(reason='Needs to be updated for 0.2.0 syntax') +def test_electrostatics_options(self): + """Test parameter assignment using smirnoff99Frosst on laromustine with various long-range electrostatics options. + """ + molecules_filename = get_data_filename('molecules/laromustine_tripos.mol2') + molecule = openforcefield.topology.Molecule.from_file(molecules_filename) + forcefield = ForceField([smirnoff99Frosst_offxml_filename, chargeincrement_offxml_filename]) + for method in ['PME', 'reaction-field', 'Coulomb']: + # Change electrostatics method + forcefield.forces['Electrostatics'].method = method + f = partial(check_system_creation_from_molecule, forcefield, molecule) + f.description = 'Testing {} parameter assignment using molecule {}'.format(offxml_filename, molecule.name) + #yield f + # TODO: Implement a similar test, where we compare OpenMM energy evals from an + # AMBER-parameterized system to OFF-parameterized systems + +@pytest.mark.skip(reason='Needs to be updated for 0.2.0 syntax') +def test_chargeincrement(self): + """Test parameter assignment using smirnoff99Frosst on laromustine with ChargeIncrementModel. + """ + molecules_filename = get_data_filename('molecules/laromustine_tripos.mol2') + molecule = openforcefield.topology.Molecule.from_file(molecules_filename) + forcefield = ForceField(['smirnoff99Frosst.offxml', 'chargeincrement-test']) + check_system_creation_from_molecule(forcefield, molecule) + # TODO: We can't implement a test for chargeincrement yet because we + # haven't settled on a SMIRNOFF spec for chargeincrementmodel + + +@pytest.mark.skip(reason='Needs to be updated for 0.2.0 syntax') +def test_create_system_molecules_parmatfrosst_gbsa(self): + """Test creation of a System object from small molecules to test parm@frosst forcefield with GBSA support. + """ + molecules_filename = get_data_filename('molecules/AlkEthOH_test_filt1_tripos.mol2') + check_parameter_assignment( + offxml_filename='Frosst_AlkEthOH_GBSA.offxml', molecules_filename=molecules_filename) + # TODO: Figure out if we just want to check that energy is finite (this is what the original test did, + # or compare numerically to a reference system. + +# TODO: test_get_new_parameterhandler +# TODO: test_get_existing_parameterhandler +# TODO: test_get_parameter +# TODO: test_add_parameter +# TODO: test_add_parameter_fractional_bondorder +# TODO: test_create_force_fractional_bondorder +# TODO: test_store_cosmetic_attribs +# TODO: test_write_cosmetic_attribs +# TODO: test_store_cosmetic_elements (eg. Author) +# TODO: test_write_cosmetic_elements (eg. Author) +# TODO: add_handler_with_incompatible_kwargs (for example different scale14 vals) +# TODO: test_invalid aromaticity_model +# TODO: test_invalid_file_version +# TODO: test_library_charges +# TODO: test_forcefield_to_dict (ensure that ParameterHandlers serialize without collisions +# and header-level attribs include handler attribs as well as attached units, +# note that header attribs are not ordered) +# TODO: test_create_gbsa \ No newline at end of file diff --git a/openforcefield/tests/test_io.py b/openforcefield/tests/test_io.py new file mode 100644 index 000000000..4b5a10db3 --- /dev/null +++ b/openforcefield/tests/test_io.py @@ -0,0 +1,58 @@ +#!/usr/bin/env python + +#============================================================================================= +# MODULE DOCSTRING +#============================================================================================= + +""" +Test classes and function in module openforcefield.typing.engines.smirnoff.io. + +""" + + +#============================================================================================= +# GLOBAL IMPORTS +#============================================================================================= + +import pytest + + +#============================================================================================= +# QUANTITY PARSING UTILITIES +#============================================================================================= + +class TestXMLParameterIOHandler: + + def test_from_string(self): + pass + + # + # Tests for ForceField writing to XML files + # + + # TODO: Remove ForceField from this whole file. All tests should be for converting between hierarchical SMIRNOFF + # dicts and XML + @pytest.mark.skip(reason='Needs to be updated for 1.0.0 syntax') + def test_save(self): + """Test writing and reading of SMIRNOFF in XML format. + """ + forcefield = ForceField(smirnoff99Frosst_offxml_filename) + # Write XML to a file + with TemporaryDirectory() as tmpdir: + offxml_tmpfile = os.path.join(tmpdir, 'forcefield.offxml') + forcefield.save(offxml_tmpfile) + forcefield2 = ForceField(offxml_tmpfile) + assert_forcefields_equal(cls.forcefield, forcefield2, + "ForceField written to .offxml does not match original ForceField") + + @pytest.mark.skip(reason='Needs to be updated for 1.0.0 syntax') + def test_to_xml(self): + forcefield = ForceField(smirnoff99Frosst_offxml_filename) + # Retrieve XML as a string + xml = forcefield.to_xml() + # Restore ForceField from XML + forcefield2 = ForceField(xml) + assert_forcefields_equal(cls.forcefield, forcefield2, + "ForceField serialized to XML does not match original ForceField") + + diff --git a/openforcefield/tests/test_molecule.py b/openforcefield/tests/test_molecule.py new file mode 100644 index 000000000..360986a83 --- /dev/null +++ b/openforcefield/tests/test_molecule.py @@ -0,0 +1,1034 @@ +#!/usr/bin/env python + +#============================================================================================= +# MODULE DOCSTRING +#============================================================================================= + +""" +Tests for molecular topology representations + +At least one supported cheminformatics toolkit must be installed to run these tests. +Only the tests applicable to that toolkit will be run. + +TODO: +- Add tests comparing RDKit and OpenEye aromaticity perception +- Right now, the test database of TestMolecule is read from mol2, requiring the OE + toolkit. Find a different test set that RDKit can read, or make a database of + serialized OFFMols. + +""" + +#============================================================================================= +# GLOBAL IMPORTS +#============================================================================================= + +import copy +import os +import pickle +from tempfile import NamedTemporaryFile + +import numpy as np +import pytest +from simtk import unit + +from openforcefield.topology.molecule import Molecule, Atom +from openforcefield.utils import get_data_filename +# TODO: Will the ToolkitWrapper allow us to pare that down? +from openforcefield.utils.toolkits import OpenEyeToolkitWrapper, RDKitToolkitWrapper, AmberToolsToolkitWrapper, ToolkitRegistry + + +#============================================================================================= +# TEST UTILITIES +#============================================================================================= + +requires_openeye = pytest.mark.skipif(not OpenEyeToolkitWrapper.toolkit_is_available(), + reason='Test requires OE toolkit') +requires_rdkit = pytest.mark.skipif(not RDKitToolkitWrapper.toolkit_is_available(), + reason='Test requires RDKit') + + +def assert_molecule_is_equal(molecule1, molecule2, msg): + """Compare whether two Molecule objects are equal + + Parameters + ---------- + molecule1, molecule2 : openforcefield.topology.Molecule + Molecules to be compared + msg : str + Message to include if molecules fail to match. + + """ + if not(molecule1.is_isomorphic(molecule2)): + raise AssertionError(msg) + + +def is_four_memebered_ring_torsion(torsion): + """Check that three atoms in the given torsion form a four-membered ring.""" + # Push a copy of the first and second atom in the end to make the code simpler. + torsion = list(torsion) + [torsion[0], torsion[1]] + + is_four_membered_ring = True + for i in range(4): + # The atom is bonded to the next one. + is_four_membered_ring &= torsion[i].is_bonded_to(torsion[i+1]) + # The atom is not bonded to the atom on its diagonal. + is_four_membered_ring &= not torsion[i].is_bonded_to(torsion[i+2]) + + return is_four_membered_ring + + +def is_three_memebered_ring_torsion(torsion): + """Check that three atoms in the given torsion form a three-membered ring. + + In order to be 4 atoms with a three-membered ring, there must be + 1) A central atom connected to all other atoms. + 2) An atom outside the ring connected exclusively to the central atom. + 3) Two atoms in the ring connected to the central atom and to each other. + + """ + # A set of atom indices for the atoms in the torsion. + torsion_atom_indices = set(a.molecule_atom_index for a in torsion) + + # Collect all the bonds involving exclusively atoms in the torsion. + bonds_by_atom_idx = {i: set() for i in torsion_atom_indices} + for atom in torsion: + for bond in atom.bonds: + # Consider the bond only if both atoms are in the torsion. + if (bond.atom1_index in torsion_atom_indices and + bond.atom2_index in torsion_atom_indices): + bonds_by_atom_idx[bond.atom1_index].add(bond.atom2_index) + bonds_by_atom_idx[bond.atom2_index].add(bond.atom1_index) + + # Find the central atom, which is connected to all other atoms. + atom_indices = [i for i in torsion_atom_indices if len(bonds_by_atom_idx[i]) == 3] + if len(atom_indices) != 1: + return False + central_atom_idx = atom_indices[0] + + # Find the atom outside the ring. + atom_indices = [i for i in torsion_atom_indices if len(bonds_by_atom_idx[i]) == 1] + if len(atom_indices) != 1 or central_atom_idx not in bonds_by_atom_idx[atom_indices[0]]: + return False + outside_atom_idx = atom_indices[0] + + # Check that the remaining two atoms are non-central atoms in the membered ring. + atom1, atom2 = [i for i in torsion_atom_indices if i not in [central_atom_idx, outside_atom_idx]] + # The two atoms are bonded to each other. + if atom2 not in bonds_by_atom_idx[atom1] or atom1 not in bonds_by_atom_idx[atom2]: + return False + # Check that they are both bonded to the central atom and none other. + for atom_idx in [atom1, atom2]: + if (central_atom_idx not in bonds_by_atom_idx[atom_idx] or + len(bonds_by_atom_idx[atom_idx]) != 2): + return False + + # This is a torsion including a three-membered ring. + return True + + +#============================================================================================= +# FIXTURES +#============================================================================================= + +def mini_drug_bank(xfail_mols=None, wip_mols=None): + """Load the full MiniDrugBank into Molecule objects. + + Parameters + ---------- + xfail_mols : Dict[str, str or None] + Dictionary mapping the molecule names that are allowed to + failed to the failure reason. + wip_mols : Dict[str, str or None] + Dictionary mapping the molecule names that are work in progress + to the failure reason. + + """ + # If we have already loaded the data set, return the cached one. + if mini_drug_bank.molecules is not None: + molecules = mini_drug_bank.molecules + else: + # Load the dataset. + file_path = get_data_filename('molecules/MiniDrugBank_tripos.mol2') + try: + # We need OpenEye to parse the molecules, but pytest execute this + # whether or not the test class is skipped so if OE is not available + # we just return an empty list of test cases as a workaround. + molecules = Molecule.from_file(file_path, allow_undefined_stereo=True) + except NotImplementedError as e: + assert 'No toolkits in registry can read file' in str(e) + mini_drug_bank.molecules = [] + return [] + else: + mini_drug_bank.molecules = molecules + + # Check if we need to mark anything. + if xfail_mols is None and wip_mols is None: + return molecules + + # Handle mutable default. + if xfail_mols is None: + xfail_mols = {} + if wip_mols is None: + wip_mols = {} + # There should be no molecule in both dictionaries. + assert len(set(xfail_mols).intersection(set(wip_mols))) == 0 + + # Don't modify the cached molecules. + molecules = copy.deepcopy(molecules) + for i, mol in enumerate(molecules): + if mol.name in xfail_mols: + marker = pytest.mark.xfail(reason=xfail_mols[mol.name]) + elif mol.name in wip_mols: + marker = pytest.mark.wip(reason=wip_mols[mol.name]) + else: + marker = None + + if marker is not None: + molecules[i] = pytest.param(mol, marks=marker) + + return molecules + +# Use a "static" variable as a workaround as fixtures cannot be +# used inside pytest.mark.parametrize (see issue #349 in pytest). +mini_drug_bank.molecules = None + + +#============================================================================================= +# TESTS +#============================================================================================= + +class TestAtom: + """Test Atom class.""" + + def test_atom_constructor(self): + """Test Atom creation""" + # Create a non-aromatic carbon atom + atom1 = Atom(6, 0, False) + assert atom1.atomic_number == 6 + assert atom1.formal_charge == 0 + + # Create a chiral carbon atom + atom2 = Atom(6, 0, False, stereochemistry='R', name='CT') + assert atom1.stereochemistry != atom2.stereochemistry + + def test_atom_properties(self): + """Test that atom properties are correctly populated and gettable""" + from simtk.openmm.app import element + formal_charge = 0 + is_aromatic = False + # Attempt to create all elements supported by OpenMM + elements = [getattr(element, name) for name in dir(element) if (type(getattr(element, name)) == element.Element)] + # The above runs into a problem with deuterium (fails name assertion) + elements.remove(element.deuterium) + for this_element in elements: + atom = Atom(this_element.atomic_number, formal_charge, is_aromatic, name=this_element.name) + assert atom.atomic_number == this_element.atomic_number + assert atom.element == this_element + assert atom.mass == this_element.mass + assert atom.formal_charge == formal_charge + assert atom.is_aromatic == is_aromatic + assert atom.name == this_element.name + + +@requires_openeye +class TestMolecule: + """Test Molecule class.""" + + # TODO: Test getstate/setstate + # TODO: Test {to_from}_{dict|yaml|toml|json|bson|messagepack|pickle} + + @pytest.mark.parametrize('molecule', mini_drug_bank()) + def test_pickle_serialization(self, molecule): + """Test pickling of a molecule object.""" + serialized = pickle.dumps(molecule) + molecule_copy = pickle.loads(serialized) + assert molecule == molecule_copy + + # ---------------------------------------------------- + # Test Molecule constructors and conversion utilities. + # ---------------------------------------------------- + + def test_create_empty(self): + """Test empty constructor.""" + molecule = Molecule() + assert len(molecule.atoms) == 0 + assert len(molecule.bonds) == 0 + + @pytest.mark.parametrize('molecule', mini_drug_bank()) + def test_create_copy(self, molecule): + """Test copy constructor.""" + molecule_copy = Molecule(molecule) + assert molecule_copy == molecule + + # TODO: Should there be an equivalent toolkit test and leave this as an integration test? + @pytest.mark.slow + def test_create_from_file(self): + """Test standard constructor taking a filename or file-like object.""" + # TODO: Expand test to both openeye and rdkit toolkits + filename = get_data_filename('molecules/toluene.mol2') + + molecule1 = Molecule(filename, allow_undefined_stereo=True) + with open(filename, 'r') as infile: + molecule2 = Molecule(infile, file_format='MOL2', allow_undefined_stereo=True) + assert molecule1 == molecule2 + + import gzip + with gzip.GzipFile(filename + '.gz', 'r') as infile: + molecule3 = Molecule(infile, file_format='MOL2', allow_undefined_stereo=True) + assert molecule3 == molecule1 + + # Ensure that attempting to initialize a single Molecule from a file + # containing multiple molecules raises a ValueError + with pytest.raises(ValueError) as exc_info: + filename = get_data_filename('molecules/zinc-subset-tripos.mol2.gz') + molecule = Molecule(filename, allow_undefined_stereo=True) + + @pytest.mark.parametrize('molecule', mini_drug_bank()) + def test_create_from_serialized(self, molecule): + """Test standard constructor taking the output of __getstate__().""" + serialized_molecule = molecule.__getstate__() + molecule_copy = Molecule(serialized_molecule) + assert molecule == molecule_copy + + @pytest.mark.parametrize('molecule', mini_drug_bank()) + def test_to_from_dict(self, molecule): + """Test that conversion/creation of a molecule to and from a dict is consistent.""" + serialized = molecule.to_dict() + molecule_copy = Molecule.from_dict(serialized) + assert molecule == molecule_copy + + @pytest.mark.parametrize('molecule', mini_drug_bank()) + def test_to_networkx(self, molecule): + """Test conversion to NetworkX graph.""" + graph = molecule.to_networkx() + + @requires_rdkit + @pytest.mark.parametrize('molecule', mini_drug_bank()) + def test_to_from_rdkit(self, molecule): + """Test that conversion/creation of a molecule to and from an RDKit rdmol is consistent. + + This tests creating an OpenFF Molecule from an RDKit Mol both + through __init__() and from_rdkit(). However, __init__() doesn't + have an allow_undefined_stereo argument yet, so in that case, we + check for equality only for the from_rdkit() molecule. + + """ + import pickle + from openforcefield.utils.toolkits import UndefinedStereochemistryError + + rdmol = molecule.to_rdkit() + + # The constructor should not change the molecule. + rdmol_pickle = pickle.dumps(rdmol) + + # Check if this is a molecule with undefined stereo. + molecule_copies = [] + try: + molecule_copies.append(Molecule(rdmol)) + except UndefinedStereochemistryError: + allow_undefined_stereo = True + else: + allow_undefined_stereo = False + molecule_copies.append(Molecule.from_rdkit( + rdmol, allow_undefined_stereo=allow_undefined_stereo)) + + # Check that the roundtrip did not change anything in the OpenFF Molecule. + for molecule_copy in molecule_copies: + assert molecule == molecule_copy + + # Check that the constructor didn't modify rdmol. + assert rdmol_pickle == pickle.dumps(rdmol) + + # TODO: Should there be an equivalent toolkit test and leave this as an integration test? + @requires_openeye + @pytest.mark.parametrize('molecule', mini_drug_bank( + xfail_mols={ + 'DrugBank_2397': 'OpenEye cannot generate a correct IUPAC name and raises a "Warning: Incorrect name:" or simply return "BLAH".', + 'DrugBank_2543': 'OpenEye cannot generate a correct IUPAC name and raises a "Warning: Incorrect name:" or simply return "BLAH".', + 'DrugBank_2642': 'OpenEye cannot generate a correct IUPAC name and raises a "Warning: Incorrect name:" or simply return "BLAH".', + }, + wip_mols={ + 'DrugBank_1212': 'the roundtrip generates molecules with very different IUPAC/SMILES!', + 'DrugBank_2210': 'the roundtrip generates molecules with very different IUPAC/SMILES!', + 'DrugBank_4584': 'the roundtrip generates molecules with very different IUPAC/SMILES!', + + 'DrugBank_390': 'raises warning "Unable to make OFFMol from OEMol: OEMol has unspecified stereochemistry."', + 'DrugBank_810': 'raises warning "Unable to make OFFMol from OEMol: OEMol has unspecified stereochemistry."', + 'DrugBank_4316': 'raises warning "Unable to make OFFMol from OEMol: OEMol has unspecified stereochemistry."', + 'DrugBank_7124': 'raises warning "Unable to make OFFMol from OEMol: OEMol has unspecified stereochemistry."', + + 'DrugBank_4346': 'raises warning "Failed to parse name:"', + } + )) + def test_to_from_iupac(self, molecule): + """Test that conversion/creation of a molecule to and from a IUPAC name is consistent.""" + from openforcefield.utils.toolkits import UndefinedStereochemistryError + + # All the molecules that raise UndefinedStereochemistryError in Molecule.from_iupac() + undefined_stereo_mols = {'DrugBank_977', 'DrugBank_1634', 'DrugBank_1700', 'DrugBank_1962', + 'DrugBank_2148', 'DrugBank_2178', 'DrugBank_2186', 'DrugBank_2208', + 'DrugBank_2519', 'DrugBank_2538', 'DrugBank_2592', 'DrugBank_2651', + 'DrugBank_2987', 'DrugBank_3332', 'DrugBank_3502', 'DrugBank_3622', + 'DrugBank_3726', 'DrugBank_3844', 'DrugBank_3930', 'DrugBank_4161', + 'DrugBank_4162', 'DrugBank_4778', 'DrugBank_4593', 'DrugBank_4959', + 'DrugBank_5043', 'DrugBank_5076', 'DrugBank_5176', 'DrugBank_5418', + 'DrugBank_5737', 'DrugBank_5902', 'DrugBank_6304', 'DrugBank_6305', + 'DrugBank_6329', 'DrugBank_6355', 'DrugBank_6401', 'DrugBank_6509', + 'DrugBank_6531', 'DrugBank_6647', + + # These test cases are allowed to fail. + 'DrugBank_390', 'DrugBank_810', 'DrugBank_4316', 'DrugBank_4346', + 'DrugBank_7124' + } + undefined_stereo = molecule.name in undefined_stereo_mols + + iupac = molecule.to_iupac() + + if undefined_stereo: + with pytest.raises(UndefinedStereochemistryError): + Molecule.from_iupac(iupac) + + molecule_copy = Molecule.from_iupac(iupac, allow_undefined_stereo=undefined_stereo) + assert molecule.is_isomorphic(molecule_copy, compare_atom_stereochemistry=not undefined_stereo) + + @pytest.mark.parametrize('molecule', mini_drug_bank()) + def test_to_from_topology(self, molecule): + """Test that conversion/creation of a molecule to and from a Topology is consistent.""" + topology = molecule.to_topology() + molecule_copy = Molecule.from_topology(topology) + assert molecule == molecule_copy + + # TODO: Should there be an equivalent toolkit test and leave this as an integration test? + @pytest.mark.parametrize('molecule', mini_drug_bank()) + @pytest.mark.parametrize('format', [ + 'mol2', + 'sdf', + pytest.param('pdb', marks=pytest.mark.wip(reason='Read from pdb has not bee implemented properly yet')) + ]) + def test_to_from_file(self, molecule, format): + """Test that conversion/creation of a molecule to and from a file is consistent.""" + from openforcefield.utils.toolkits import UndefinedStereochemistryError + # TODO: Test all file capabilities; the current test is minimal + + # TODO: This is only for OE. Expand to both OE and RDKit toolkits. + # Molecules that are known to raise UndefinedStereochemistryError. + undefined_stereo_mols = {'DrugBank_1700', 'DrugBank_2987', 'DrugBank_3502', 'DrugBank_4161', + 'DrugBank_4162', 'DrugBank_6531'} + undefined_stereo = molecule.name in undefined_stereo_mols + + # The file is automatically deleted outside the with-clause. + with NamedTemporaryFile(suffix='.' + format) as iofile: + # If this has undefined stereo, check that the exception is raised. + extension = os.path.splitext(iofile.name)[1][1:] + molecule.to_file(iofile.name, extension) + if undefined_stereo: + with pytest.raises(UndefinedStereochemistryError): + Molecule.from_file(iofile.name) + molecule2 = Molecule.from_file(iofile.name, allow_undefined_stereo=undefined_stereo) + assert molecule == molecule2 + # TODO: Test to make sure properties are preserved? + # NOTE: We can't read pdb files and expect chemical information to be preserved + + @requires_openeye + @pytest.mark.parametrize('molecule', mini_drug_bank()) + def test_to_from_oemol(self, molecule): + """Test that conversion/creation of a molecule to and from a OEMol is consistent.""" + from openforcefield.utils.toolkits import UndefinedStereochemistryError + + # Known failures raise an UndefinedStereochemistryError, but + # the round-trip SMILES representation with the OpenEyeToolkit + # doesn't seem to be affected. + + # ZINC test set known failures. + # known_failures = {'ZINC05964684', 'ZINC05885163', 'ZINC05543156', 'ZINC17211981', + # 'ZINC17312986', 'ZINC06424847', 'ZINC04963126'} + + # DrugBank test set known failures. + undefined_stereo_mols = {'DrugBank_1634', 'DrugBank_1700', 'DrugBank_1962', + 'DrugBank_2519', 'DrugBank_2987', 'DrugBank_3502', + 'DrugBank_3930', 'DrugBank_4161', 'DrugBank_4162', + 'DrugBank_5043', 'DrugBank_5418', 'DrugBank_6531'} + undefined_stereo = molecule.name in undefined_stereo_mols + + error_messages = [ + "Molecule(oemol) constructor failed", + "Molecule.to_openeye()/from_openeye() round trip failed" + ] + + toolkit_wrapper = OpenEyeToolkitWrapper() + + oemol = molecule.to_openeye() + molecule_copies = [] + + # If this is a known failure, check that it raises UndefinedStereochemistryError + # and proceed with the test ignoring it. + if undefined_stereo: + with pytest.raises(UndefinedStereochemistryError): + Molecule(oemol) + else: + molecule_copies.append(Molecule(oemol)) + molecule_copies.append(Molecule.from_openeye(oemol, allow_undefined_stereo=undefined_stereo)) + + molecule_smiles = molecule.to_smiles(toolkit_registry=toolkit_wrapper) + for molecule_copy, error_msg in zip(molecule_copies, error_messages): + # Check that the original and the copied molecules have the same SMILES representation. + molecule_copy_smiles = molecule_copy.to_smiles(toolkit_registry=toolkit_wrapper) + assert molecule_smiles == molecule_copy_smiles + + # Check that the two topologies are isomorphic. + assert_molecule_is_equal(molecule, molecule_copy, error_msg) + + # ---------------------------------------------------- + # Test properties. + # ---------------------------------------------------- + + def test_name(self): + """Test Molecule name property""" + molecule1 = Molecule() + molecule1.name = None + + molecule2 = Molecule() + molecule2.name = '' + assert molecule1.name == molecule2.name + + name = 'benzene' + molecule = Molecule() + molecule.name = name + assert molecule.name == name + + @pytest.mark.parametrize('molecule', mini_drug_bank()) + def test_n_particles(self, molecule): + """Test n_particles property""" + n_particles = sum([1 for particle in molecule.particles]) + assert n_particles == molecule.n_particles + + @pytest.mark.parametrize('molecule', mini_drug_bank()) + def test_n_atoms(self, molecule): + """Test n_atoms property""" + n_atoms = sum([1 for atom in molecule.atoms]) + assert n_atoms == molecule.n_atoms + + @pytest.mark.parametrize('molecule', mini_drug_bank()) + def test_n_virtual_sites(self, molecule): + """Test n_virtual_sites property""" + n_virtual_sites = sum([1 for virtual_site in molecule.virtual_sites]) + assert n_virtual_sites == molecule.n_virtual_sites + + @pytest.mark.parametrize('molecule', mini_drug_bank()) + def test_n_bonds(self, molecule): + """Test n_bonds property""" + n_bonds = sum([1 for bond in molecule.bonds]) + assert n_bonds == molecule.n_bonds + + @pytest.mark.parametrize('molecule', mini_drug_bank()) + def test_angles(self, molecule): + """Test angles property""" + for angle in molecule.angles: + assert angle[0].is_bonded_to(angle[1]) + assert angle[1].is_bonded_to(angle[2]) + + @pytest.mark.parametrize('molecule', mini_drug_bank()) + def test_propers(self, molecule): + """Test propers property""" + for proper in molecule.propers: + # The bonds should be in order 0-1-2-3 unless the + # atoms form a three- or four-membered ring. + is_chain = proper[0].is_bonded_to(proper[1]) + is_chain &= proper[1].is_bonded_to(proper[2]) + is_chain &= proper[2].is_bonded_to(proper[3]) + is_chain &= not proper[0].is_bonded_to(proper[2]) + is_chain &= not proper[0].is_bonded_to(proper[3]) + is_chain &= not proper[1].is_bonded_to(proper[3]) + + assert (is_chain or + is_three_memebered_ring_torsion(proper) or + is_four_memebered_ring_torsion(proper)) + + @pytest.mark.parametrize('molecule', mini_drug_bank()) + def test_impropers(self, molecule): + """Test impropers property""" + for improper in molecule.impropers: + assert improper[0].is_bonded_to(improper[1]) + assert improper[1].is_bonded_to(improper[2]) + assert improper[1].is_bonded_to(improper[3]) + + # The non-central atoms can be connected only if + # the improper atoms form a three-membered ring. + is_not_cyclic = not((improper[0].is_bonded_to(improper[2])) or + (improper[0].is_bonded_to(improper[3])) or + (improper[2].is_bonded_to(improper[3]))) + assert is_not_cyclic or is_three_memebered_ring_torsion(improper) + + @pytest.mark.parametrize('molecule', mini_drug_bank()) + def test_torsions(self, molecule): + """Test torsions property""" + # molecule.torsions should be exactly equal to the union of propers and impropers. + assert set(molecule.torsions) == set(molecule.propers) | set(molecule.impropers) + + # The intersection of molecule.propers and molecule.impropers should be largely null. + # The only exception is for molecules containing 3-membered rings (e.g., DrugBank_5514). + common_torsions = molecule.propers & molecule.impropers + if len(common_torsions) > 0: + for torsion in common_torsions: + assert is_three_memebered_ring_torsion(torsion) + + @pytest.mark.parametrize('molecule', mini_drug_bank()) + def test_total_charge(self, molecule): + """Test total charge""" + total_charge = sum([atom.formal_charge for atom in molecule.atoms]) + assert total_charge == molecule.total_charge + + # ---------------------------------------------------- + # Test magic methods. + # ---------------------------------------------------- + + def test_equality(self): + """Test equality operator""" + molecules = mini_drug_bank() + nmolecules = len(molecules) + # TODO: Performance improvements should let us un-restrict this test + for i in range(nmolecules): + for j in range(i, min(i+3, nmolecules)): + assert (molecules[i] == molecules[j]) == (i == j) + + # ---------------------- + # Test Molecule methods. + # ---------------------- + + def test_add_conformers(self): + """Test addition of conformers to a molecule""" + import numpy as np + from simtk import unit + # Define a methane molecule + molecule = Molecule() + molecule.name = 'methane' + C = molecule.add_atom(6, 0, False) + H1 = molecule.add_atom(1, 0, False) + H2 = molecule.add_atom(1, 0, False) + H3 = molecule.add_atom(1, 0, False) + H4 = molecule.add_atom(1, 0, False) + molecule.add_bond(C, H1, 1, False) + molecule.add_bond(C, H2, 1, False) + molecule.add_bond(C, H3, 1, False) + molecule.add_bond(C, H4, 1, False) + + assert molecule.n_conformers == 0 + # Add a conformer that should work + conf1 = unit.Quantity(np.array([[ 1., 2.,3.] ,[4. ,5. ,6.],[7., 8., 9.], + [10.,11.,12.],[13.,14.,15]]), + unit.angstrom) + molecule.add_conformer(conf1) + assert molecule.n_conformers == 1 + + conf2 = unit.Quantity(np.array([[101., 102. ,103.], [104. ,105. ,106.], [107., 108., 109.], + [110.,111.,112.], [113.,114.,115]]), + unit.angstrom) + molecule.add_conformer(conf2) + assert molecule.n_conformers == 2 + + # Add conformers with too few coordinates + conf_missing_z = unit.Quantity(np.array([[101., 102. ,103.], [104. ,105. ,106.], [107., 108., 109.], + [110.,111.,112.], [113.,114.]]), + unit.angstrom) + with pytest.raises(Exception) as excinfo: + molecule.add_conformer(conf_missing_z) + + conf_too_few_atoms = unit.Quantity(np.array([[101., 102. ,103.], [104. ,105. ,106.], [107., 108., 109.], + [110.,111.,112.]]), + unit.angstrom) + with pytest.raises(Exception) as excinfo: + molecule.add_conformer(conf_too_few_atoms) + + + # Add a conformer with too many coordinates + conf_too_many_atoms = unit.Quantity(np.array([[101., 102., 103.], [104., 105., 106.], [107., 108., 109.], + [110., 111., 112.], [113., 114., 115.], [116., 117., 118.]]), + unit.angstrom) + with pytest.raises(Exception) as excinfo: + molecule.add_conformer(conf_too_many_atoms) + + # Add a conformer with no coordinates + conf_no_coordinates = unit.Quantity(np.array([]), + unit.angstrom) + with pytest.raises(Exception) as excinfo: + molecule.add_conformer(conf_no_coordinates) + + # Add a conforer with units of nanometers + conf3 = unit.Quantity(np.array([[ 1., 2.,3.] ,[4. ,5. ,6.],[7., 8., 9.], + [10.,11.,12.],[13.,14.,15]]), + unit.nanometer) + molecule.add_conformer(conf3) + assert molecule.n_conformers == 3 + assert molecule.conformers[2][0][0] == 10. * unit.angstrom + + # Add a conformer with units of nanometers + conf_nonsense_units = unit.Quantity(np.array([[ 1., 2.,3.] ,[4. ,5. ,6.],[7., 8., 9.], + [10.,11.,12.],[13.,14.,15]]), + unit.joule) + with pytest.raises(Exception) as excinfo: + molecule.add_conformer(conf_nonsense_units) + + # Add a conformer with no units + conf_unitless = np.array([[ 1., 2.,3.] ,[4. ,5. ,6.],[7., 8., 9.], + [10.,11.,12.],[13.,14.,15]]) + with pytest.raises(Exception) as excinfo: + molecule.add_conformer(conf_unitless) + + @pytest.mark.parametrize('molecule', mini_drug_bank()) + def test_add_atoms_and_bonds(self, molecule): + """Test the creation of a molecule from the addition of atoms and bonds""" + molecule_copy = Molecule() + for atom in molecule.atoms: + molecule_copy.add_atom(atom.atomic_number, atom.formal_charge, atom.is_aromatic, stereochemistry=atom.stereochemistry) + for bond in molecule.bonds: + molecule_copy.add_bond(bond.atom1_index, bond.atom2_index, bond.bond_order, bond.is_aromatic, + stereochemistry=bond.stereochemistry, + fractional_bond_order=bond.fractional_bond_order) + # Try to add the final bond twice, which should raise an Exception + with pytest.raises(Exception) as excinfo: + molecule_copy.add_bond(bond.atom1_index, bond.atom2_index, bond.bond_order, bond.is_aromatic, + stereochemistry=bond.stereochemistry, + fractional_bond_order=bond.fractional_bond_order) + + assert molecule == molecule_copy + + @pytest.mark.parametrize('molecule', mini_drug_bank()) + def test_add_virtual_site_units(self, molecule): + """ + Tests the unit type checking of the VirtualSite base class + """ + + # TODO: Should these be using BondChargeVirtualSite, or should we just call the base class (which does the unit checks) directly? + + # Prepare values for unit checks + distance_unitless = 0.4 + sigma_unitless = 0.1 + rmin_half_unitless = 0.2 + epsilon_unitless = 0.3 + charge_increments_unitless = [0.1, 0.2, 0.3, 0.4] + distance = distance_unitless * unit.angstrom + sigma = sigma_unitless * unit.angstrom + rmin_half = rmin_half_unitless * unit.angstrom + epsilon = epsilon_unitless * (unit.kilojoule / unit.mole) + charge_increments = charge_increments_unitless * unit.elementary_charge + + # Do not modify the original molecule. + molecule = copy.deepcopy(molecule) + + atom1 = molecule.atoms[0] + atom2 = molecule.atoms[1] + atom3 = molecule.atoms[2] + atom4 = molecule.atoms[3] + + # Try to feed in unitless sigma + with pytest.raises(Exception) as excinfo: + molecule.add_bond_charge_virtual_site([atom1, atom2, atom3], distance, epsilon=epsilon, sigma=sigma_unitless) + + # Try to feed in unitless rmin_half + with pytest.raises(Exception) as excinfo: + molecule.add_bond_charge_virtual_site([atom1, atom2, atom3], distance, epsilon=epsilon, rmin_half=rmin_half_unitless) + + # Try to feed in unitless epsilon + with pytest.raises(Exception) as excinfo: + molecule.add_bond_charge_virtual_site([atom1, atom2, atom3], distance, epsilon=epsilon_unitless, sigma=sigma, rmin_half=rmin_half) + + # Try to feed in unitless charges + with pytest.raises(Exception) as excinfo: + molecule.add_bond_charge_virtual_site([atom1, atom2, atom3, atom4], distance, charge_incrtements=charge_increments_unitless) + + + # We shouldn't be able to give both rmin_half and sigma VdW parameters. + with pytest.raises(Exception) as excinfo: + molecule.add_bond_charge_virtual_site([atom1, atom2, atom3], distance, epsilon=epsilon, sigma=sigma, rmin_half=rmin_half) + + # Try creating virtual site from sigma+epsilon + vsite1_index = molecule.add_bond_charge_virtual_site([atom1, atom2, atom3], distance, epsilon=epsilon, sigma=sigma) + # Try creating virutal site from rmin_half+epsilon + vsite2_index = molecule.add_bond_charge_virtual_site([atom1, atom2, atom3], distance, epsilon=epsilon, rmin_half=rmin_half) + + # TODO: Test the @property getters for sigma, epsilon, and rmin_half + + # We should have to give as many charge increments as atoms (len(charge_increments)) = 4 + with pytest.raises(Exception) as excinfo: + molecule.add_bond_charge_virtual_site([atom1, atom2, atom3], distance, charge_increments=charge_increments) + + vsite3_index = molecule.add_bond_charge_virtual_site([atom1, atom2, atom3, atom4], distance, charge_increments=charge_increments) + + @pytest.mark.parametrize('molecule', mini_drug_bank()) + def test_add_bond_charge_virtual_site(self, molecule): + """Test the addition of a BondChargeVirtualSite to a molecule. + Also tests many of the inputs of the parent VirtualSite class + """ + # Do not modify the original molecule. + molecule = copy.deepcopy(molecule) + + atom1 = molecule.atoms[0] + atom2 = molecule.atoms[1] + atom3 = molecule.atoms[2] + atom4 = molecule.atoms[3] + + # Prepare values for unit checks + distance_unitless = 0.4 + distance = distance_unitless * unit.angstrom + + + # Try to feed in a unitless distance + with pytest.raises(AssertionError) as excinfo: + vsite1_index = molecule.add_bond_charge_virtual_site([atom1, atom2, atom3], distance_unitless) + + + vsite1_index = molecule.add_bond_charge_virtual_site([atom1, atom2, atom3], distance) + vsite1 = molecule.virtual_sites[vsite1_index] + assert atom1 in vsite1.atoms + assert atom2 in vsite1.atoms + assert atom3 in vsite1.atoms + assert vsite1 in atom1.virtual_sites + assert vsite1 in atom2.virtual_sites + assert vsite1 in atom3.virtual_sites + assert vsite1.distance == distance + + # Make an "everything bagel" virtual site + vsite2_index = molecule.add_bond_charge_virtual_site([atom1, atom2, atom3], + distance, + sigma=0.1*unit.angstrom, + epsilon=1.0*unit.kilojoule_per_mole, + charge_increments=unit.Quantity(np.array([0.1, 0.2, 0.3]), + unit.elementary_charge) + ) + vsite2 = molecule.virtual_sites[vsite2_index] + + # test serialization + molecule_dict = molecule.to_dict() + molecule2 = Molecule.from_dict(molecule_dict) + + assert hash(molecule) == hash(molecule2) + + # TODO: Make a test for to_dict and from_dict for VirtualSites (even though they're currently just unloaded using + # (for example) Molecule._add_bond_virtual_site functions + @pytest.mark.parametrize('molecule', mini_drug_bank()) + def test_add_monovalent_lone_pair_virtual_site(self, molecule): + """Test addition of a MonovalentLonePairVirtualSite to the Molecule""" + # Do not modify the original molecule. + molecule = copy.deepcopy(molecule) + + atom1 = molecule.atoms[0] + atom2 = molecule.atoms[1] + atom3 = molecule.atoms[2] + atom4 = molecule.atoms[3] + + # Prepare values for unit checks + distance_unitless = 0.3 + out_of_plane_angle_unitless = 30 + in_plane_angle_unitless = 0.2 + distance = distance_unitless * unit.angstrom + out_of_plane_angle = out_of_plane_angle_unitless * unit.degree + in_plane_angle = in_plane_angle_unitless * unit.radian + + # Try passing in a unitless distance + with pytest.raises(AssertionError) as excinfo: + vsite1_index = molecule.add_monovalent_lone_pair_virtual_site([atom1, atom2], distance_unitless, out_of_plane_angle, in_plane_angle) + + # Try passing in a unitless out_of_plane_angle + with pytest.raises(AssertionError) as excinfo: + vsite1_index = molecule.add_monovalent_lone_pair_virtual_site([atom1, atom2], distance, out_of_plane_angle_unitless, in_plane_angle) + + # Try passing in a unitless in_plane_angle + with pytest.raises(AssertionError) as excinfo: + vsite1_index = molecule.add_monovalent_lone_pair_virtual_site([atom1, atom2], distance, out_of_plane_angle, in_plane_angle_unitless) + + # Try giving two atoms + with pytest.raises(AssertionError) as excinfo: + vsite1_index = molecule.add_monovalent_lone_pair_virtual_site([atom1, atom2], distance, out_of_plane_angle, in_plane_angle) + + # Successfully make a virtual site + vsite1_index = molecule.add_monovalent_lone_pair_virtual_site([atom1, atom2, atom3], distance, out_of_plane_angle, in_plane_angle) + # TODO: Check if we get the same values back out from the @properties + molecule_dict = molecule.to_dict() + molecule2 = Molecule.from_dict(molecule_dict) + assert molecule.to_dict() == molecule2.to_dict() + + @pytest.mark.parametrize('molecule', mini_drug_bank()) + def test_add_divalent_lone_pair_virtual_site(self, molecule): + """Test addition of a DivalentLonePairVirtualSite to the Molecule""" + # Do not modify the original molecule. + molecule = copy.deepcopy(molecule) + + atom1 = molecule.atoms[0] + atom2 = molecule.atoms[1] + atom3 = molecule.atoms[2] + atom4 = molecule.atoms[3] + distance = 0.3 * unit.angstrom + out_of_plane_angle = 30 * unit.degree + in_plane_angle = 0.2 * unit.radian + vsite1_index = molecule.add_divalent_lone_pair_virtual_site([atom1, atom2, atom3], distance, out_of_plane_angle, in_plane_angle) + with pytest.raises(AssertionError) as excinfo: + vsite1_index = molecule.add_divalent_lone_pair_virtual_site([atom1, atom2], distance, out_of_plane_angle, in_plane_angle) + molecule_dict = molecule.to_dict() + molecule2 = Molecule.from_dict(molecule_dict) + assert molecule_dict == molecule2.to_dict() + + @pytest.mark.parametrize('molecule', mini_drug_bank()) + def test_add_trivalent_lone_pair_virtual_site(self, molecule): + """Test addition of a TrivalentLonePairVirtualSite to the Molecule""" + # Do not modify the original molecule. + molecule = copy.deepcopy(molecule) + + atom1 = molecule.atoms[0] + atom2 = molecule.atoms[1] + atom3 = molecule.atoms[2] + atom4 = molecule.atoms[3] + distance = 0.3 * unit.angstrom + out_of_plane_angle = 30 * unit.degree + in_plane_angle = 0.2 * unit.radian + vsite1_index = molecule.add_trivalent_lone_pair_virtual_site([atom1, atom2, atom3, atom4], distance, out_of_plane_angle, in_plane_angle) + # Test for assertion when giving too few atoms + with pytest.raises(AssertionError) as excinfo: + vsite1_index = molecule.add_trivalent_lone_pair_virtual_site([atom1, atom2, atom3], distance, out_of_plane_angle, in_plane_angle) + molecule_dict = molecule.to_dict() + molecule2 = Molecule.from_dict(molecule_dict) + assert molecule.to_dict() == molecule2.to_dict() + + @requires_openeye + def test_chemical_environment_matches_OE(self): + """Test chemical environment matches""" + # TODO: Move this to test_toolkits, test all available toolkits + # Create chiral molecule + from simtk.openmm.app import element + toolkit_wrapper = OpenEyeToolkitWrapper() + molecule = Molecule() + atom_C = molecule.add_atom(element.carbon.atomic_number, 0, False, stereochemistry='R', name='C') + atom_H = molecule.add_atom(element.hydrogen.atomic_number, 0, False, name='H') + atom_Cl = molecule.add_atom(element.chlorine.atomic_number, 0, False, name='Cl') + atom_Br = molecule.add_atom(element.bromine.atomic_number, 0, False, name='Br') + atom_F = molecule.add_atom(element.fluorine.atomic_number, 0, False, name='F') + molecule.add_bond(atom_C, atom_H, 1, False) + molecule.add_bond(atom_C, atom_Cl, 1, False) + molecule.add_bond(atom_C, atom_Br, 1, False) + molecule.add_bond(atom_C, atom_F, 1, False) + # Test known cases + matches = molecule.chemical_environment_matches('[#6:1]', toolkit_registry=toolkit_wrapper) + assert len(matches) == 1 # there should be a unique match, so one atom tuple is returned + assert len(matches[0]) == 1 # it should have one tagged atom + assert set(matches[0]) == set([atom_C]) + matches = molecule.chemical_environment_matches('[#6:1]~[#1:2]', toolkit_registry=toolkit_wrapper) + assert len(matches) == 1 # there should be a unique match, so one atom tuple is returned + assert len(matches[0]) == 2 # it should have two tagged atoms + assert set(matches[0]) == set([atom_C, atom_H]) + matches = molecule.chemical_environment_matches('[Cl:1]-[C:2]-[H:3]', toolkit_registry=toolkit_wrapper) + assert len(matches) == 1 # there should be a unique match, so one atom tuple is returned + assert len(matches[0]) == 3 # it should have three tagged atoms + assert set(matches[0]) == set([atom_Cl, atom_C, atom_H]) + matches = molecule.chemical_environment_matches('[#6:1]~[*:2]', toolkit_registry=toolkit_wrapper) + assert len(matches) == 4 # there should be four matches + for match in matches: + assert len(match) == 2 # each match should have two tagged atoms + + # TODO: Test forgive undef amide enol stereo + # TODO: test forgive undef phospho linker stereo + # TODO: test forgive undef C=NH stereo + # TODO: test forgive undef phospho stereo + # Potentially better OE stereo check: OEFlipper — Toolkits - - Python + # https: // docs.eyesopen.com / toolkits / python / omegatk / OEConfGenFunctions / OEFlipper.html + + @requires_rdkit + def test_chemical_environment_matches_RDKit(self): + """Test chemical environment matches""" + # Create chiral molecule + from simtk.openmm.app import element + toolkit_wrapper = RDKitToolkitWrapper() + molecule = Molecule() + atom_C = molecule.add_atom(element.carbon.atomic_number, 0, False, stereochemistry='R', name='C') + atom_H = molecule.add_atom(element.hydrogen.atomic_number, 0, False, name='H') + atom_Cl = molecule.add_atom(element.chlorine.atomic_number, 0, False, name='Cl') + atom_Br = molecule.add_atom(element.bromine.atomic_number, 0, False, name='Br') + atom_F = molecule.add_atom(element.fluorine.atomic_number, 0, False, name='F') + molecule.add_bond(atom_C, atom_H, 1, False) + molecule.add_bond(atom_C, atom_Cl, 1, False) + molecule.add_bond(atom_C, atom_Br, 1, False) + molecule.add_bond(atom_C, atom_F, 1, False) + # Test known cases + matches = molecule.chemical_environment_matches('[#6:1]', toolkit_registry=toolkit_wrapper) + assert len(matches) == 1 # there should be a unique match, so one atom tuple is returned + assert len(matches[0]) == 1 # it should have one tagged atom + assert set(matches[0]) == set([atom_C]) + matches = molecule.chemical_environment_matches('[#6:1]~[#1:2]', toolkit_registry=toolkit_wrapper) + assert len(matches) == 1 # there should be a unique match, so one atom tuple is returned + assert len(matches[0]) == 2 # it should have two tagged atoms + assert set(matches[0]) == set([atom_C, atom_H]) + matches = molecule.chemical_environment_matches('[Cl:1]-[C:2]-[H:3]', toolkit_registry=toolkit_wrapper) + assert len(matches) == 1 # there should be a unique match, so one atom tuple is returned + assert len(matches[0]) == 3 # it should have three tagged atoms + assert set(matches[0]) == set([atom_Cl, atom_C, atom_H]) + matches = molecule.chemical_environment_matches('[#6:1]~[*:2]', toolkit_registry=toolkit_wrapper) + assert len(matches) == 4 # there should be four matches + for match in matches: + assert len(match) == 2 # each match should have two tagged atoms + + @pytest.mark.slow + def test_compute_partial_charges(self): + """Test computation/retrieval of partial charges""" + # TODO: Test only one molecule for speed? + # TODO: Do we need to deepcopy each molecule, or is setUp called separately for each test method? + from simtk import unit + import numpy as np + + # Do not modify original molecules. + molecules = copy.deepcopy(mini_drug_bank()) + + # Test a single toolkit at a time + # Removed ['amber', 'amberff94'] from OE list, as those won't find the residue types they're expecting + toolkit_to_charge_method = {OpenEyeToolkitWrapper:['mmff', 'mmff94', 'am1bcc', 'am1bccnosymspt', 'am1bccelf10'], + AmberToolsToolkitWrapper:['bcc', 'gas', 'mul']} + + manual_skips = [] + + manual_skips.append('ZINC1564378') # Warning: OEMMFF94Charges: assigning OEMMFFAtomTypes failed on mol . + manual_skips.append('ZINC00265517') # Warning: OEMMFF94Charges: assigning OEMMFFAtomTypes failed on mol . + + for toolkit in list(toolkit_to_charge_method.keys()): + toolkit_registry = ToolkitRegistry(toolkit_precedence=[toolkit]) + for charge_model in toolkit_to_charge_method[toolkit]: + c = 0 + for molecule in molecules[:1]: # Just test first molecule to save time + c += 1 + if molecule.name in manual_skips: # Manual skips, hopefully rare + continue + molecule.compute_partial_charges(charge_model=charge_model, toolkit_registry=toolkit_registry) + charges1 = molecule._partial_charges + # Make sure everything isn't 0s + assert (abs(charges1 / unit.elementary_charge) > 0.01).any() + # Check total charge + charges_sum_unitless = charges1.sum() / unit.elementary_charge + #if abs(charges_sum_unitless - float(molecule.total_charge)) > 0.0001: + # print('c {} molecule {} charge_sum {} molecule.total_charge {}'.format(c, molecule.name, + # charges_sum_unitless, + # molecule.total_charge)) + # assert_almost_equal(charges_sum_unitless, molecule.total_charge, decimal=4) + + # Call should be faster second time due to caching + # TODO: Implement caching + molecule.compute_partial_charges(charge_model=charge_model, toolkit_registry=toolkit_registry) + charges2 = molecule._partial_charges + assert (np.allclose(charges1, charges2, atol=0.002)) + + @requires_openeye + def test_assign_fractional_bond_orders(self): + """Test assignment of fractional bond orders + """ + # TODO: Test only one molecule for speed? + # TODO: Do we need to deepcopy each molecule, or is setUp called separately for each test method? + + # Do not modify the original molecules. + molecules = copy.deepcopy(mini_drug_bank()) + + toolkit_to_bondorder_method = {OpenEyeToolkitWrapper:['am1','pm3']} + for toolkit in list(toolkit_to_bondorder_method.keys()): + toolkit_registry = ToolkitRegistry(toolkit_precedence=[toolkit]) + for charge_model in toolkit_to_bondorder_method[toolkit]: + for molecule in molecules[:5]: # Just test first five molecules for speed + molecule.compute_wiberg_bond_orders(charge_model=charge_model, toolkit_registry=toolkit_registry) + fbo1 = [bond.fractional_bond_order for bond in molecule.bonds] + # Call should be faster the second time due to caching + molecule.compute_wiberg_bond_orders(charge_model=charge_model, toolkit_registry=toolkit_registry) + fbo2 = [bond.fractional_bond_order for bond in molecule.bonds] + assert fbo1 == fbo2 diff --git a/openforcefield/tests/test_parameters.py b/openforcefield/tests/test_parameters.py new file mode 100644 index 000000000..a2425c41b --- /dev/null +++ b/openforcefield/tests/test_parameters.py @@ -0,0 +1,477 @@ +#!/usr/bin/env python + +#============================================================================================= +# MODULE DOCSTRING +#============================================================================================= + +""" +Test classes and function in module openforcefield.typing.engines.smirnoff.parameters. + +""" + + +#============================================================================================= +# GLOBAL IMPORTS +#============================================================================================= + + +from openforcefield.typing.engines.smirnoff.parameters import ParameterList, ParameterType, BondHandler, \ + ParameterHandler, AngleHandler, ConstraintHandler, ProperTorsionHandler, ImproperTorsionHandler, \ + ToolkitAM1BCCHandler, vdWHandler, SMIRNOFFSpecError +from openforcefield.utils import detach_units + +import pytest + + + +class TestParameterHandler: + + def test_different_units_to_dict(self): + """Test ParameterHandler.to_dict() function when some parameters are in + different units (proper behavior is to convert all quantities to the last- + read unit) + """ + from simtk import unit + bh = BondHandler() + bh.add_parameter({'smirks': '[*:1]-[*:2]', + 'length': 1*unit.angstrom, + 'k': 10*unit.kilocalorie_per_mole/unit.angstrom**2}) + bh.add_parameter({'smirks': '[*:1]=[*:2]', + 'length': 0.2*unit.nanometer, + 'k': 0.4*unit.kilojoule_per_mole/unit.nanometer**2}) + bh_dict = bh.to_dict() + assert ('length_unit', 'nanometer') in bh_dict.items() + assert ('k_unit', 'nanometer**-2 * mole**-1 * kilojoule') in bh_dict.items() + assert bh_dict['Bond'][0]['length'] == 0.1 + assert bh_dict['Bond'][1]['length'] == 0.2 + + def test_to_dict_set_output_units(self): + """Test ParameterHandler.to_dict() function when some output units are specified + """ + from simtk import unit + bh = BondHandler() + bh.add_parameter({'smirks': '[*:1]-[*:2]', + 'length': 1*unit.angstrom, + 'k': 10*unit.kilocalorie_per_mole/unit.angstrom**2}) + bh.add_parameter({'smirks': '[*:1]=[*:2]', + 'length': 0.2*unit.nanometer, + 'k': 0.4*unit.kilojoule_per_mole/unit.nanometer**2}) + bh_dict = bh.to_dict(output_units={'length_unit': unit.picometer}) + assert ('length_unit', 'picometer') in bh_dict.items() + assert ('k_unit', 'nanometer**-2 * mole**-1 * kilojoule') in bh_dict.items() + assert abs(bh_dict['Bond'][0]['length'] - 100.) < 1.e-8 + assert abs(bh_dict['Bond'][1]['length'] - 200.) < 1.e-8 + + +class TestParameterList: + """Test capabilities of ParameterList for accessing and manipulating SMIRNOFF parameter definitions. + """ + + def test_create(self): + """Test creation of a parameter list. + """ + p1 = ParameterType(smirks='[*:1]') + p2 = ParameterType(smirks='[#1:1]') + parameters = ParameterList([p1, p2]) + + @pytest.mark.wip(reason="Until ChemicalEnvironment won't be refactored to use the ToolkitRegistry " + "API, the smirks assignment will fail with RDKit.") + def test_getitem(self): + """Test ParameterList __getitem__ overloading. + """ + p1 = ParameterType(smirks='[*:1]') + p2 = ParameterType(smirks='[#1:1]') + parameters = ParameterList([p1, p2]) + assert parameters[0] == p1 + assert parameters[1] == p2 + assert parameters[p1.smirks] == p1 + assert parameters[p2.smirks] == p2 + + # Note that this call access __getitem__, not __setitem__. + parameters['[*:1]'].smirks = '[*X4:1]' + assert parameters[0].smirks == '[*X4:1]' + assert p1.smirks == '[*X4:1]' + + def test_index(self): + """ + Tests the ParameterList.index() function by attempting lookups by SMIRKS and by ParameterType equivalence. + + """ + p1 = ParameterType(smirks='[*:1]') + p2 = ParameterType(smirks='[#1:1]') + p3 = ParameterType(smirks='[#7:1]') + parameters = ParameterList([p1, p2, p3]) + assert parameters.index(p1) == 0 + assert parameters.index(p2) == 1 + assert parameters.index(p3) == 2 + assert parameters.index('[*:1]') == 0 + assert parameters.index('[#1:1]') == 1 + assert parameters.index('[#7:1]') == 2 + with pytest.raises(IndexError, match=r'SMIRKS \[#2:1\] not found in ParameterList') as excinfo: + parameters.index('[#2:1]') + + p4 = ParameterType(smirks='[#2:1]') + with pytest.raises(ValueError, match='is not in list') as excinfo: + parameters.index(p4) + + def test_contains(self): + """Test ParameterList __contains__ overloading. + """ + p1 = ParameterType(smirks='[*:1]') + p2 = ParameterType(smirks='[#1:1]') + p3 = ParameterType(smirks='[#7:1]') + parameters = ParameterList([p1, p2]) + assert p1 in parameters + assert p2 in parameters + assert p3 not in parameters + assert p1.smirks in parameters + assert p2.smirks in parameters + assert p3.smirks not in parameters + + def test_del(self): + """ + Test ParameterList __del__ overloading. + """ + p1 = ParameterType(smirks='[*:1]') + p2 = ParameterType(smirks='[#1:1]') + p3 = ParameterType(smirks='[#7:1]') + parameters = ParameterList([p1, p2, p3]) + + with pytest.raises(IndexError, match='list assignment index out of range'): + del parameters[4] + with pytest.raises(IndexError, match=r'SMIRKS \[#6:1\] not found in ParameterList'): + del parameters['[#6:1]'] + + # Test that original list deletion behavior is preserved. + del parameters[2] + assert len(parameters) == 2 + assert p1 in parameters + assert p2 in parameters + assert p3 not in parameters + + # Test that we can delete elements by their smirks. + del parameters['[#1:1]'] + assert len(parameters) == 1 + assert p1 in parameters + assert p2 not in parameters + + + def test_append(self): + """ + Test ParameterList.append, ensuring that the new parameter was added to the bottom of the list + and that it is properly recorded as the most recently-added. + """ + p1 = ParameterType(smirks='[*:1]-[*:2]') + p2 = ParameterType(smirks='[*:1]=[*:2]') + param_list = ParameterList() + param_list.append(p1) + assert len(param_list) == 1 + assert '[*:1]-[*:2]' in param_list + param_list.append(p2) + assert len(param_list) == 2 + assert '[*:1]=[*:2]' in param_list + assert param_list[-1] == p2 + + def test_insert(self): + """ + Test ParameterList.insert, ensuring that the new parameter was added to the proper spot in + the list and that it is propertly recorded as the most recently added. + """ + p1 = ParameterType(smirks='[*:1]-[*:2]') + p2 = ParameterType(smirks='[*:1]=[*:2]') + p3 = ParameterType(smirks='[*:1]#[*:2]') + param_list = ParameterList([p1, p2]) + param_list.insert(1, p3) + assert param_list[1] == p3 + + def test_extend(self): + """ + Test ParameterList.extend, ensuring that the new parameter was added to the proper spot in + the list and that it is propertly recorded as the most recently added. + """ + p1 = ParameterType(smirks='[*:1]-[*:2]') + p2 = ParameterType(smirks='[*:1]=[*:2]') + param_list1 = ParameterList() + param_list2 = ParameterList([p1, p2]) + + param_list1.extend(param_list2) + assert len(param_list1) == 2 + assert '[*:1]-[*:2]' in param_list1 + assert '[*:1]=[*:2]' in param_list1 + assert param_list1[-1] == p2 + + def test_to_list(self): + """Test basic ParameterList.to_list() function, ensuring units are preserved""" + from simtk import unit + p1 = BondHandler.BondType(smirks='[*:1]-[*:2]', + length=1.01 * unit.angstrom, + k=5 * unit.kilocalorie_per_mole / unit.angstrom ** 2 + ) + p2 = BondHandler.BondType(smirks='[*:1]=[*:2]', + length=1.02 * unit.angstrom, + k=6 * unit.kilocalorie_per_mole / unit.angstrom ** 2 + ) + p3 = BondHandler.BondType(smirks='[*:1]#[*:3]', + length=1.03 * unit.angstrom, + k=7 * unit.kilocalorie_per_mole / unit.angstrom ** 2 + ) + parameter_list = ParameterList([p1, p2, p3]) + ser_param_list = parameter_list.to_list() + assert len(ser_param_list) == 3 + assert ser_param_list[0]['length'] == 1.01 * unit.angstrom + + def test_round_trip(self): + """Test basic ParameterList.to_list() function and constructor""" + from simtk import unit + p1 = BondHandler.BondType(smirks='[*:1]-[*:2]', + length=1.01 * unit.angstrom, + k=5 * unit.kilocalorie_per_mole / unit.angstrom ** 2 + ) + p2 = BondHandler.BondType(smirks='[*:1]=[*:2]', + length=1.02 * unit.angstrom, + k=6 * unit.kilocalorie_per_mole / unit.angstrom ** 2 + ) + p3 = BondHandler.BondType(smirks='[*:1]#[*:3]', + length=1.03 * unit.angstrom, + k=7 * unit.kilocalorie_per_mole / unit.angstrom ** 2 + ) + parameter_list = ParameterList([p1, p2, p3]) + param_dict_list = parameter_list.to_list() + parameter_list_2 = ParameterList() + for param_dict in param_dict_list: + new_parameter = BondHandler.BondType(**param_dict) + parameter_list_2.append(new_parameter) + assert parameter_list.to_list() == parameter_list_2.to_list() + + +class TestParameterType: + + def test_base_parametertype_to_dict(self): + """ + Test ParameterType to_dict. + """ + p1 = ParameterType(smirks='[*:1]') + param_dict = p1.to_dict() + assert param_dict['smirks'] == '[*:1]' + assert len(param_dict.keys()) == 1 + + def test_bondtype_to_dict(self): + """ + Test BondType to_dict. + """ + from simtk import unit + + p1 = BondHandler.BondType(smirks='[*:1]-[*:2]', + length=1.02 * unit.angstrom, + k=5 * unit.kilocalorie_per_mole / unit.angstrom ** 2 + ) + param_dict = p1.to_dict() + param_dict_unitless, attached_units = detach_units(param_dict) + assert param_dict_unitless == {'smirks': '[*:1]-[*:2]', + 'length': 1.02, + 'k': 5,} + assert attached_units == {'length_unit': unit.angstrom, + 'k_unit': (unit.angstrom ** -2) * (unit.mole ** -1) * (unit.kilocalorie ** 1) + } + + + def test_bondtype_to_dict_custom_output_units(self): + """ + Test BondType to_dict with custom output units. + """ + from simtk import unit + p1 = BondHandler.BondType(smirks='[*:1]-[*:2]', + length=1.02*unit.angstrom, + k=5 * unit.kilocalorie_per_mole / unit.angstrom ** 2 + ) + param_dict = p1.to_dict() + param_dict_unitless, attached_units=detach_units(param_dict, output_units={'length_unit': + unit.nanometer}) + assert attached_units['length_unit'] == unit.nanometer + assert abs(param_dict_unitless['length'] - 0.102) < 1e-10 + + + def test_bondtype_to_dict_invalid_output_units(self): + """ + Test ParameterType to_dict with invalid output units. + """ + from simtk import unit + p1 = BondHandler.BondType(smirks='[*:1]-[*:2]', + length=1.02*unit.angstrom, + k=5 * unit.kilocalorie_per_mole / unit.angstrom ** 2 + ) + param_dict = p1.to_dict() + with pytest.raises(ValueError, + match='Requested output unit calorie is not compatible with quantity unit angstrom .' + ) as context: + param_dict_unitless, attached_units = detach_units(param_dict, output_units = {'length_unit': + unit.calorie}) + + + def test_read_write_optional_parameter_attribute(self): + """ + Test ParameterTypes' ability to store and write out optional attributes passed to __init__() + """ + from simtk import unit + + p1 = BondHandler.BondType(smirks='[*:1]-[*:2]', + length=1.02*unit.angstrom, + k=5 * unit.kilocalorie_per_mole / unit.angstrom ** 2, + id='b1' + ) + param_dict= p1.to_dict() + assert ('id', 'b1') in param_dict.items() + + def test_read_write_cosmetic_parameter_attribute(self): + """ + Test ParameterTypes' ability to store and write out cosmetic attributes passed to __init__() + """ + from simtk import unit + + p1 = BondHandler.BondType(smirks='[*:1]-[*:2]', + length=1.02*unit.angstrom, + k=5 * unit.kilocalorie_per_mole / unit.angstrom ** 2, + pilot='alice', + permit_cosmetic_attributes=True + ) + param_dict= p1.to_dict(return_cosmetic_attributes=True) + assert ('pilot', 'alice') in param_dict.items() + + def test_read_but_dont_write_cosmetic_parameter_attribute(self): + """ + Test ParameterTypes' ability to ignore cosmetic attributes passed to __init__() if instructed + """ + from simtk import unit + + p1 = BondHandler.BondType(smirks='[*:1]-[*:2]', + length=1.02*unit.angstrom, + k=5 * unit.kilocalorie_per_mole / unit.angstrom ** 2, + pilot='alice', + permit_cosmetic_attributes=True + ) + param_dict = p1.to_dict(return_cosmetic_attributes=False) + assert ('pilot', 'alice') not in param_dict.items() + + def test_error_cosmetic_parameter_attribute(self): + """ + Test that ParameterTypes raise an error on receiving unexpected attributes passed to __init__() + """ + from simtk import unit + + with pytest.raises(SMIRNOFFSpecError, match="Incompatible kwarg {'pilot': 'alice'}") as context: + p1 = BondHandler.BondType(smirks='[*:1]-[*:2]', + length=1.02*unit.angstrom, + k=5 * unit.kilocalorie_per_mole / unit.angstrom ** 2, + pilot='alice', + permit_cosmetic_attributes=False + ) + + def test_single_term_proper_torsion(self): + """ + Test creation and serialization of a single-term proper torsion + """ + from simtk import unit + + p1 = ProperTorsionHandler.ProperTorsionType(smirks='[*:1]-[*:2]-[*:3]-[*:4]', + phase1=30 * unit.degree, + periodicity1=2, + k1=5 * unit.kilocalorie_per_mole + ) + param_dict = p1.to_dict() + assert ('k1', 5 * unit.kilocalorie_per_mole) in param_dict.items() + assert ('phase1', 30 * unit.degree) in param_dict.items() + assert ('periodicity1', 2) in param_dict.items() + assert 'idivf' not in param_dict + + def test_single_term_proper_torsion_w_idivf(self): + """ + Test creation and serialization of a single-term proper torsion + """ + from simtk import unit + + p1 = ProperTorsionHandler.ProperTorsionType(smirks='[*:1]-[*:2]-[*:3]-[*:4]', + phase1=30 * unit.degree, + periodicity1=2, + k1=5 * unit.kilocalorie_per_mole, + idivf1=4 + ) + + param_dict = p1.to_dict() + assert ('k1', 5 * unit.kilocalorie_per_mole) in param_dict.items() + assert ('phase1', 30 * unit.degree) in param_dict.items() + assert ('periodicity1', 2) in param_dict.items() + assert ('idivf1', 4) in param_dict.items() + + + def test_multi_term_proper_torsion(self): + """ + Test creation and serialization of a multi-term proper torsion + """ + from simtk import unit + + p1 = ProperTorsionHandler.ProperTorsionType(smirks='[*:1]-[*:2]-[*:3]-[*:4]', + phase1=30 * unit.degree, + periodicity1=2, + k1=5 * unit.kilocalorie_per_mole, + phase2=31 * unit.degree, + periodicity2=3, + k2=6 * unit.kilocalorie_per_mole, + ) + param_dict = p1.to_dict() + assert ('k1', 5 * unit.kilocalorie_per_mole) in param_dict.items() + assert ('phase1', 30 * unit.degree) in param_dict.items() + assert ('periodicity1', 2) in param_dict.items() + assert ('k2', 6 * unit.kilocalorie_per_mole) in param_dict.items() + assert ('phase2', 31 * unit.degree) in param_dict.items() + assert ('periodicity2', 3) in param_dict.items() + + def test_multi_term_proper_torsion_skip_index(self): + """ + Test creation and serialization of a multi-term proper torsion where + the indices are not consecutive and a SMIRNOFFSpecError is raised + """ + from simtk import unit + + with pytest.raises(SMIRNOFFSpecError, match="Incompatible kwarg {'phase3': ") as context: + p1 = ProperTorsionHandler.ProperTorsionType(smirks='[*:1]-[*:2]-[*:3]-[*:4]', + phase1=30 * unit.degree, + periodicity1=2, + k1=5 * unit.kilocalorie_per_mole, + phase3=31 * unit.degree, + periodicity3=3, + k3=6 * unit.kilocalorie_per_mole, + ) + + def test_multi_term_proper_torsion_bad_units(self): + """ + Test creation and serialization of a multi-term proper torsion where + one of the terms has incorrect units + """ + from simtk import unit + + with pytest.raises(SMIRNOFFSpecError, match="constructor received kwarg phase2 with value 31 A,") as context: + p1 = ProperTorsionHandler.ProperTorsionType(smirks='[*:1]-[*:2]-[*:3]-[*:4]', + phase1=30 * unit.degree, + periodicity1=2, + k1=5 * unit.kilocalorie_per_mole, + phase2=31 * unit.angstrom, # This should be caught + periodicity2=3, + k2=6 * unit.kilocalorie_per_mole, + ) + + + +# TODO: test_nonbonded_settings (ensure that choices in Electrostatics and vdW tags resolve +# to correct openmm.NonbondedForce subtypes, that setting different cutoffs raises +# exceptions, etc) +# TODO: test_(all attributes of all ParameterTypes) +# TODO: test_add_parameter_fractional_bondorder +# TODO: test_get_indexed_attrib +# TODO: test_set_unitbearing_attrib (requires implementing __getattr__ and __setattr__) +# TODO: test_parametertype_unit_getattr +# TODO: test_parametertype_unit_setattr +# TODO: test_optional_attribs +# TODO: test_optional_indexed_attribs +# TODO: test_attach_units +# TODO: test_detach_units +# TODO: test_(X)handler_compatibility, where X is all handlers \ No newline at end of file diff --git a/openforcefield/tests/test_smirnoff.py b/openforcefield/tests/test_smirnoff.py index f0b4d57e0..83ecac003 100644 --- a/openforcefield/tests/test_smirnoff.py +++ b/openforcefield/tests/test_smirnoff.py @@ -1,14 +1,62 @@ +#!/usr/bin/env python + +#============================================================================================= +# MODULE DOCSTRING +#============================================================================================= +""" +Tests for the SMIRNOFF ForceField class + +""" + +#============================================================================================= +# GLOBAL IMPORTS +#============================================================================================= + +# TODO: Split this file into many test files, potentially distributing tests within each subpackage next to the classes they test + from functools import partial -from openforcefield.typing.engines.smirnoff import * -from openforcefield.utils import get_data_filename, generateTopologyFromOEMol, read_molecules -from openeye import oechem -from simtk.openmm import app -from simtk import unit, openmm -import numpy as np from io import StringIO import tempfile +from tempfile import TemporaryDirectory + +from numpy.testing import assert_equal import parmed -import os +from simtk import unit, openmm +from simtk.openmm import app + +# from openforcefield.utils import get_data_filename #, generateTopologyFromOEMol, read_molecules +# from openforcefield.utils import check_energy_is_finite, get_energy +# from openforcefield.tests.utils import get_packmol_pdbfile, get_monomer_mol2file, compare_system_energies +from openforcefield.tests.utils import * +from openforcefield.typing.engines.smirnoff import * + +# TODO: Fix these imports and unskip these tests +import pytest +pytestmark = pytest.mark.skip('tests in test_smirnoff are outdated and should be integrated with test_forcefield.py') + +#============================================================================================= +# CONSTANTS +#============================================================================================= + +# TODO: Move these to setup? +# These paths should only be found in the test data directories, so we need to use get_data_filename() +AlkEthOH_offxml_filename = 'Frosst_AlkEthOH.offxml' +AlkEthOH_molecules_filename = get_data_filename('molecules/AlkEthOH_test_filt1_tripos.mol2') +MiniDrugBank_molecules_filename = get_data_filename('molecules/MiniDrugBank_tripos.mol2') +#chargeincrement_offxml_filename = get_data_filename('chargeincrement-test.offxml') +# TODO: Swtich all paths to use os.path.join +tip3p_molecule_filename = get_data_filename(os.path.join('systems', 'monomers', 'tip3p_water.mol2')) + +# This is the production form of smirnoff99Frosst that should be found in the data directories +smirnoff99Frosst_offxml_filename = 'smirnoff99Frosst.offxml' +tip3p_offxml_filename = 'tip3p.offxml' + +# TODO: Add tests to compare RDKit and OpenEye derived forcefields to make sure they are the same + +# TODO: Move forcefields for testing only to a special test data directory, separate from the data/ paths that are automatically searched and populated with production force fields +# +# SMIRNOFF ForceField XML definitions for testing purposes +# # This is a test forcefield that is not meant for actual use. # It just tests various capabilities. @@ -17,7 +65,7 @@ Date: May-September 2016 C. I. Bayly, OpenEye Scientific Software and David Mobley, UCI - + @@ -26,9 +74,9 @@ - + - + @@ -39,9 +87,9 @@ - + - + @@ -54,15 +102,18 @@ - - - + + + - + + + + - + - + @@ -75,13 +126,18 @@ - + +""" - - - - - +ffxml_chargeincrement = u"""\ + + + + + + + + """ ffxml_constraints = u"""\ @@ -92,7 +148,7 @@ """ ffxml_gbsa = u"""\ - + @@ -102,7 +158,7 @@ - + """ ffxml_contents_gbsa = u"""\ @@ -117,6 +173,16 @@ """ % globals() +ffxml_contents_chargeincrement = u"""\ + + +%(ffxml_standard)s +%(ffxml_constraints)s +%(ffxml_chargeincrement)s + + +""" % globals() + ffxml_contents_noconstraints = u"""\ @@ -148,388 +214,203 @@ !-- SMIRKS (SMIRKS Force Field) minimal file, not intended for use --> Date: Sept. 7, 2016 D. L. Mobley, UC Irvine - + - - + + - - - + + - - + + + + + - + + """ -def positions_from_oemol(mol): - """ - Extract OpenMM positions from OEMol. - - Parameters - ---------- - mol : oechem.openeye.OEMol - OpenEye molecule from which to extract coordinates. - - Returns - ------- - positions : simtk.unit.Quantity of dimension (nparticles,3) - - """ - from openeye import oeomega - if mol.GetDimension() != 3: - # Assign coordinates - omega = oeomega.OEOmega() - omega.SetMaxConfs(1) - omega.SetIncludeInput(False) - omega.SetCanonOrder(False) - omega.SetSampleHydrogens(True) # Word to the wise: skipping this step can lead to significantly different charges! - status = omega(mol) # generate conformation - - coordinates = mol.GetCoords() - natoms = len(coordinates) - positions = np.zeros([natoms,3], np.float32) - for index in range(natoms): - (x,y,z) = coordinates[index] - positions[index,0] = x - positions[index,1] = y - positions[index,2] = z - positions = unit.Quantity(positions, unit.angstroms) - return positions - -def check_energy_is_finite(system, positions): - """ - Check the potential energy is not NaN. - - Parameters - ---------- - system : simtk.openmm.System - The system to check - positions : simtk.unit.Quantity of dimension (natoms,3) with units of length - The positions to use - - """ - integrator = openmm.VerletIntegrator(1.0 * unit.femtoseconds) - context = openmm.Context(system, integrator) - context.setPositions(positions) - state = context.getState(getEnergy=True) - energy = state.getPotentialEnergy() / unit.kilocalories_per_mole - if np.isnan(energy): - raise Exception('Potential energy is NaN') +#============================================================================================= +# TESTS +#============================================================================================= -def get_energy(system, positions): - """ - Return the potential energy. - - Parameters - ---------- - system : simtk.openmm.System - The system to check - positions : simtk.unit.Quantity of dimension (natoms,3) with units of length - The positions to use - Returns - --------- - energy - """ +# +# Test various components +# - integrator = openmm.VerletIntegrator(1.0 * unit.femtoseconds) - context = openmm.Context(system, integrator) - context.setPositions(positions) - state = context.getState(getEnergy=True) - energy = state.getPotentialEnergy() / unit.kilocalories_per_mole - return energy -def test_read_ffxml(): - """Test reading of ffxml files. +class TestApplyForceField: + """Test the use of ForceField to parameterize Topology objects. """ - forcefield = ForceField(get_data_filename('forcefield/Frosst_AlkEthOH.offxml')) -def test_read_ffxml_gbsa(): - """Test reading of ffxml files with GBSA support. - """ - forcefield = ForceField(get_data_filename('forcefield/Frosst_AlkEthOH_GBSA.offxml')) + def check_system_creation_from_molecule(self, forcefield, molecule): + """ + Generate a System from the given OEMol and SMIRNOFF forcefield and check that its energy is finite. -def check_system_creation_from_molecule(forcefield, mol, chargeMethod=None, verbose=False): - """ - Generate a System from the given OEMol and SMIRNOFF forcefield and check that its energy is finite. + Parameters + ---------- + forcefield : openforcefield.typing.engines.smirnoff.ForceField + SMIRNOFF forcefield object + molecule : openforcefield.topology.Molecule + Molecule to test (which must have coordinates) - Parameters - ---------- - forcefield : ForceField - SMIRNOFF forcefield - mol : oechem.OEMol - Molecule to test (need not have coordinates) - chargeMethod : str, optional, default=None - Charge method to use in creating system + """ + topology = Topology.from_molecules(molecule) + system = forcefield.create_system(topology) + check_energy_is_finite(system, molecule.positions) + # TODO: Add check_energy_is_finite to test_FF.test_paramerize_ethanol - """ + def check_system_creation_from_topology(forcefield, topology, positions): + """ + Generate a System from the given topology, OEMols matching the contents of the topology, and SMIRNOFF forcefield and check that its energy is finite. - topology = generateTopologyFromOEMol(mol) - system = forcefield.createSystem(topology, [mol], chargeMethod=chargeMethod, verbose=verbose) - # Test energy computation. - positions = positions_from_oemol(mol) - check_energy_is_finite(system, positions) + Parameters + ---------- + forcefield : ForceField + SMIRNOFF forcefield + topology : openforcefield.topology.Topology + Topology for which System should be constructed + positions : simtk.unit.Quantity with dimension (natoms,3) with units of length + Positions of all particles -def check_system_creation_from_topology(forcefield, topology, mols, positions, chargeMethod=None, verbose=False): - """ - Generate a System from the given topology, OEMols matching the contents of the topology, and SMIRNOFF forcefield and check that its energy is finite. - - Parameters - ---------- - forcefield : ForceField - SMIRNOFF forcefield - topology : simtk.openmm.app.Topology - Topology to construct system from - mols : list of oechem.OEMol - Reference molecules - positions : simtk.unit.Quantity with dimension (natoms,3) with units of length - chargeMethod : str, optional, default=None - Charge method to use in creating system + """ + system = forcefield.create_system(topology) + check_energy_is_finite(system, positions) + + def check_parameter_assignment(self, + offxml_filename=smirnoff99Frosst_offxml_filename, + molecules_filename=AlkEthOH_molecules_filename): + """Test parameter assignment using specified forcefield on all molecules from specified source. + + Parameters + ---------- + offxml_filename : str, optional, default='smirnoff99Frosst.offxml' + Filename from which SMIRNOFF .offxml XML file is to be loaded. + molecules_filename : str, optional, default='molecules/AlkEthOH_test_filt1_tripos.mol2 + Filename from which molecule identities and positions are to be loaded. + """ + forcefield = ForceField(offxml_filename) + for molecule in openforcefield.topology.Molecule.from_file(molecules_filename): + f = partial(check_system_creation_from_molecule, forcefield, molecule) + f.description = 'Testing {} parameter assignment using molecule {}'.format(offxml_filename, molecule.name) + yield f - """ - from openforcefield.typing.engines.smirnoff import CutoffPeriodic - system = forcefield.createSystem(topology, mols, verbose=verbose, chargeMethod=chargeMethod, nonbondedMethod=CutoffPeriodic) - # Test energy computation. - check_energy_is_finite(system, positions) -def check_AlkEthOH(forcefield, description="", chargeMethod=None, verbose=False): - """Test creation of System from AlkEthOH small molecules. + def test_partial_bondorder(verbose=False): + """Test energies of a molecule which activates partial bond order code.""" + # Create benzene molecule + molecule = Molecule.from_iupac('benzene') + topology = molecule.to_topology() + + # Load forcefield + ff = ForceField(ffxml_contents_noconstraints) + + # Set up once using AM1BCC charges + # TODO: Use OECharges_AM1BCCSym charges + system = ff.create_system(topology) + + # Check that energy is what it ought to be -- the partial bond order + # for benzene makes the energy a bit higher than it would be without it + energy = get_energy(system, positions) + if energy < 7.50 or energy > 7.60: + raise Exception( + "Partial bond order code seems to have issues, as energy for benzene is outside of tolerance in tests." + ) + + # Set up once also without asking for charges + # TODO: Don't create charges + system = ff.create_system(topology) + energy = get_energy(system, positions) + # Energy is lower with user supplied charges (which in this case are zero) + if energy < 4.00 or energy > 6.0: + raise Exception( + "Partial bond order code seems to have issues when run with user-provided charges, as energy for benzene is out of tolerance in tests." + ) + + def test_improper(verbose=False): + """Test implement of impropers on benzene.""" + # Create benzene molecule + molecule = Molecule.from_iupac('benzene') + topology = molecule.to_topology() + + # Load forcefield + ff = ForceField('benzene_minimal.offxml') + + # Load AMBER files and compare + inpcrd = get_data_filename('molecules/benzene.crd') + prmtop = get_data_filename('molecules/benzene.top') + g0, g1, e0, e1 = compare_amber_smirnoff(prmtop, inpcrd, ff, mol, skip_assert=True) + + # Check that torsional energies the same to 1 in 10^6 + rel_error = np.abs((g0['torsion'] - g1['torsion']) / g0['torsion']) + if rel_error > 6e-3: #Note that this will not be tiny because we use three-fold impropers and they use a single improper + raise Exception( + "Improper torsion energy for benzene differs too much (relative error %.4g) between AMBER and SMIRNOFF." + % rel_error) + + +class TestForceFieldLabeling: + """Tests for labeling parameter types in molecules """ - from openeye import oechem - ifs = oechem.oemolistream(get_data_filename('molecules/AlkEthOH-tripos.mol2.gz')) - mol = oechem.OEGraphMol() - while oechem.OEReadMolecule(ifs, mol): - args = { 'verbose' : verbose, 'chargeMethod' : chargeMethod } - f = partial(check_system_creation_from_molecule, forcefield, mol, **args) - f.description ='Testing creation of system object from small molecules (%s) %s' % (mol.GetTitle(), description) - yield f - -def test_create_system_molecules_features(verbose=False): - """Test creation of a System object from small molecules to test various ffxml features - """ - ffxml = StringIO(ffxml_contents_gbsa) - forcefield = ForceField(ffxml) - for chargeMethod in [None, 'BCC', 'OECharges_AM1BCCSym']: - for f in check_AlkEthOH(forcefield, description="to test ffxml features with charge method %s" % str(chargeMethod), chargeMethod=chargeMethod, verbose=verbose): - yield f + def test_label_molecules(self): + """Test labeling/getting stats on labeling molecules""" + molecules = read_molecules(get_data_filename('molecules/AlkEthOH_test_filt1_tripos.mol2'), verbose=verbose) + ffxml = get_data_filename('forcefield/Frosst_AlkEthOH.offxml') + get_molecule_parameterIDs(molecules, ffxml) -def test_create_system_molecules_parmatfrosst(verbose=False): - """Test creation of a System object from small molecules to test parm@frosst forcefield. - """ - forcefield = ForceField(get_data_filename('forcefield/Frosst_AlkEthOH.offxml')) - for f in check_AlkEthOH(forcefield, "to test Parm@Frosst parameters", verbose=verbose): - yield f + def test_molecule_labeling(self): + """Test using labelMolecules to see which parameters applied to a molecule + """ + from openforcefield.topology.testsystems import SMILESTopology + topology = SMILESTopology('CCC') + forcefield = ForceField('Frosst_AlkEthOH.offxml') + labels = forcefield.label_molecules(topology)[0] -def test_create_system_molecules_parmatfrosst_gbsa(verbose=False): - """Test creation of a System object from small molecules to test parm@frosst forcefield with GBSA support. - """ - forcefield = ForceField(get_data_filename('forcefield/Frosst_AlkEthOH_GBSA.offxml')) - for f in check_AlkEthOH(forcefield, "to test Parm@Frosst parameters", verbose=verbose): - yield f + # Check that force terms aren't empty + for forcename in ['Bonds', 'Angles', 'ProperTorsions', 'ImproperTorsions', 'vdW', 'Electrostatics']: + if not forcename in labels: + raise Exception("No force term assigned for {}.".format(forcename)) -def check_boxes(forcefield, description="", chargeMethod=None, verbose=False): - """Test creation of System from boxes of mixed solvents. - """ - # Read monomers - mols = list() - monomers = ['water', 'cyclohexane', 'ethanol', 'propane', 'methane', 'butanol'] - from openeye import oechem - mol = oechem.OEGraphMol() - for monomer in monomers: - filename = get_data_filename(os.path.join('systems', 'monomers', monomer + '.sdf')) - ifs = oechem.oemolistream(filename) - while oechem.OEReadMolecule(ifs, mol): - oechem.OETriposAtomNames(mol) - mols.append( oechem.OEGraphMol(mol) ) - if verbose: print('%d reference molecules loaded' % len(mols)) - - # Read systems. - boxes = ['ethanol_water.pdb', 'cyclohexane_water.pdb', - 'cyclohexane_ethanol_0.4_0.6.pdb', 'propane_methane_butanol_0.2_0.3_0.5.pdb'] - from simtk.openmm.app import PDBFile - for box in boxes: - filename = get_data_filename(os.path.join('systems', 'packmol_boxes', box)) - pdbfile = PDBFile(filename) - f = partial(check_system_creation_from_topology, forcefield, pdbfile.topology, mols, pdbfile.positions, chargeMethod=chargeMethod, verbose=verbose) - f.description = 'Test creation of System object from %s %s' % (box, description) - yield f - -def test_create_system_boxes_features(verbose=False): - """Test creation of a System object from some boxes of mixed solvents to test ffxml features. - """ - ffxml = StringIO(ffxml_contents) - forcefield = ForceField(ffxml) - for chargeMethod in [None, 'BCC', 'OECharges_AM1BCCSym']: - for f in check_boxes(forcefield, description="to test Parm@frosst parameters with charge method %s" % str(chargeMethod), chargeMethod=chargeMethod, verbose=verbose): - yield f -def test_create_system_boxes_smirnoff99Frosst(verbose=False): - """Test creation of a System object from some boxes of mixed solvents to test parm@frosst forcefield. +class TestExceptionHandling: + """Tests for exception handling for incomplete parameterization """ - forcefield = ForceField(get_data_filename('forcefield/smirnoff99Frosst.offxml')) - for f in check_boxes(forcefield, description="to test Parm@frosst parameters", verbose=verbose): - yield f - -def test_smirnoff_energies_vs_parmatfrosst(verbose=False): - """Test evaluation of energies from parm@frosst ffxml files versus energies of equivalent systems.""" - from openeye import oechem - prefix = 'AlkEthOH_' - molecules = [ 'r118', 'r12', 'c1161', 'r0', 'c100', 'c38', 'c1266' ] - - # Loop over molecules, load OEMols and prep for comparison/do comparison - for molnm in molecules: - f_prefix = os.path.join('molecules', prefix+molnm ) - mol2file = get_data_filename( f_prefix+'.mol2') - prmtop = get_data_filename( f_prefix+'.top') - crd = get_data_filename( f_prefix+'.crd') - # Load special parm@frosst with parm99/parm@frosst bugs re-added for testing - forcefield = ForceField( get_data_filename('forcefield/Frosst_AlkEthOH_parmAtFrosst.offxml') ) - - # Load OEMol - mol = oechem.OEGraphMol() - ifs = oechem.oemolistream(mol2file) - flavor = oechem.OEIFlavor_Generic_Default | oechem.OEIFlavor_MOL2_Default | oechem.OEIFlavor_MOL2_Forcefield - ifs.SetFlavor( oechem.OEFormat_MOL2, flavor) - oechem.OEReadMolecule(ifs, mol ) - oechem.OETriposAtomNames(mol) - - # Do comparison - results = compare_molecule_energies( prmtop, crd, forcefield, mol, verbose = verbose ) - -def test_label_molecules(verbose=False): - """Test labeling/getting stats on labeling molecules""" - molecules = read_molecules(get_data_filename('molecules/AlkEthOH-tripos.mol2.gz'), verbose=verbose) - ffxml = get_data_filename('forcefield/Frosst_AlkEthOH.offxml') - get_molecule_parameterIDs( molecules, ffxml) - -def test_molecule_labeling(verbose = False): - """Test using labelMolecules to see which parameters applied to an oemol.""" - from openeye import oechem - mol = oechem.OEMol() - oechem.OEParseSmiles(mol, 'CCC') - oechem.OEAddExplicitHydrogens(mol) - ff = ForceField(get_data_filename('forcefield/Frosst_AlkEthOH.offxml')) - labels = ff.labelMolecules( [mol], verbose = verbose) - - # Check that force terms aren't empty - print(labels[0].keys()) - if not 'HarmonicBondGenerator' in labels[0].keys(): - raise Exception("No force term assigned for harmonic bonds.") - if not 'HarmonicAngleGenerator' in labels[0].keys(): - raise Exception("No force term assigned for harmonic angles.") - if not 'PeriodicTorsionGenerator' in labels[0].keys(): - raise Exception("No force term assigned for periodic torsions.") - if not 'NonbondedGenerator' in labels[0].keys(): - raise Exception("No nonbonded force term assigned.") - -import unittest -class TestExceptionHandling(unittest.TestCase): def test_parameter_completeness_check(self): - """Test that proper exceptions are raised if a force field fails to assign parameters to valence terms in a molecule.""" - from openeye import oechem - mol = oechem.OEMol() - oechem.OEParseSmiles(mol, 'CCC') - oechem.OEAddExplicitHydrogens(mol) - oechem.OETriposAtomNames(mol) - ff = ForceField(get_data_filename('forcefield/Frosst_AlkEthOH.offxml')) - topology = generateTopologyFromOEMol(mol) - - # Test nonbonded error checking by wiping out required LJ parameter - params = ff.getParameter(paramID='n0001') - params['smirks']='[#136:1]' - ff.setParameter(paramID='n0001', params=params) - ff.setParameter(paramID='n0002', params=params) - with self.assertRaises(Exception): - system = ff.createSystem( topology, [mol]) - ff = ForceField(get_data_filename('forcefield/Frosst_AlkEthOH.offxml')) - - # Test bond error checking by wiping out a required bond parameter - params = ff.getParameter(paramID='b0001') - params['smirks'] = '[#136:1]~[*:2]' - ff.setParameter( paramID='b0001', params=params) - with self.assertRaises(Exception): - system = ff.createSystem( topology, [mol]) - ff = ForceField(get_data_filename('forcefield/Frosst_AlkEthOH.offxml')) - - # Test angle error checking by wiping out a required angle parameter - params = ff.getParameter(paramID='a0001') - params['smirks'] = '[#136:1]~[*:2]~[*:3]' - ff.setParameter( paramID='a0001', params=params) - with self.assertRaises(Exception): - system = ff.createSystem( topology, [mol]) - ff = ForceField(get_data_filename('forcefield/Frosst_AlkEthOH.offxml')) - - # Test torsion error checking by wiping out a required torsion parameter - params = ff.getParameter(paramID='t0001') - params['smirks'] = '[#136:1]~[*:2]~[*:3]~[*:4]' - ff.setParameter( paramID='t0001', params=params) - ff.setParameter( paramID='t0004', params=params) - with self.assertRaises(Exception): - system = ff.createSystem( topology, [mol]) - ff = ForceField(get_data_filename('forcefield/Frosst_AlkEthOH.offxml')) - - - -def test_partial_bondorder(verbose = False): - """Test setup of a molecule which activates partial bond order code.""" - from openeye import oechem - mol = oechem.OEMol() - from openeye import oeiupac - oeiupac.OEParseIUPACName(mol, 'benzene') - positions = positions_from_oemol(mol) - oechem.OETriposAtomNames(mol) - topology = generateTopologyFromOEMol(mol) - # Load forcefield from above - ffxml = StringIO(ffxml_contents_noconstraints) - ff = ForceField(ffxml) - - # Set up once using AM1BCC charges - system = ff.createSystem(topology, [mol], chargeMethod = 'OECharges_AM1BCCSym', verbose = verbose) - - # Check that energy is what it ought to be -- the partial bond order - # for benzene makes the energy a bit higher than it would be without it - energy = get_energy(system, positions) - if energy < 7.50 or energy > 7.60: - raise Exception("Partial bond order code seems to have issues, as energy for benzene is outside of tolerance in tests.") - - # Set up once also without asking for charges - system = ff.createSystem(topology, [mol], verbose = verbose) - energy = get_energy(system, positions) - # Energy is lower with user supplied charges (which in this case are zero) - if energy < 4.00 or energy > 6.0: - raise Exception("Partial bond order code seems to have issues when run with user-provided charges, as energy for benzene is out of tolerance in tests.") - -def test_improper(verbose = False): - """Test implement of impropers on benzene.""" - from openeye import oechem - # Load benzene - ifs = oechem.oemolistream(get_data_filename('molecules/benzene.mol2')) - mol = oechem.OEMol() - flavor = oechem.OEIFlavor_Generic_Default | oechem.OEIFlavor_MOL2_Default | oechem.OEIFlavor_MOL2_Forcefield - ifs.SetFlavor( oechem.OEFormat_MOL2, flavor) - oechem.OEReadMolecule(ifs, mol ) - ifs.close() - # Load forcefield - ffxml = get_data_filename('forcefield/benzene_minimal.offxml') - ff = ForceField(ffxml) - - # Load AMBER files and compare - crd = get_data_filename('molecules/benzene.crd') - top = get_data_filename('molecules/benzene.top') - g0, g1, e0, e1 = compare_molecule_energies( top, crd, ff, mol, skip_assert = True) - - # Check that torsional energies the same to 1 in 10^6 - rel_error = np.abs(( g0['torsion']-g1['torsion'])/ g0['torsion']) - if rel_error > 6e-3: #Note that this will not be tiny because we use three-fold impropers and they use a single improper - raise Exception("Improper torsion energy for benzene differs too much (relative error %.4g) between AMBER and SMIRNOFF." % rel_error ) - -def test_improper_pyramidal(verbose = False): + """Test that proper exceptions are raised if a force field fails to assign parameters to valence terms in a molecule. + """ + from openforcefield.topology.testsystems import SMILESTopology + topology = SMILESTopology('CCC') + + # Test vdW error checking by wiping out required parameter + parameter_edits = [ + ('vdW', '[#136:1]'), + ('Bonds', '[#136:1]~[*:2]'), + ('Angles', '[#136:1]~[*:2]~[*:3]'), + ('ProperTorsions', '[#136:1]~[*:2]~[*:3]~[*:4]'), + ] + for (tag, smirks) in parameter_edits: + forcefield = ForceField('Frosst_AlkEthOH.offxml') + forcefield.forces[tag].parameters[0].smirks = smirks + with self.assertRaises(Exception): + system = forcefield.create_system(topology) + + +# +# TODO: Finish updating the tests below this line +# + + +# TODO: Is there any way to make this test not depend on OpenEye? +@pytest.mark.skip +#@requires_openeye_licenses +def test_improper_pyramidal(verbose=False): """Test implement of impropers on ammonia.""" from openeye import oeomega from openeye import oequacpac @@ -551,11 +432,11 @@ def test_improper_pyramidal(verbose = False): oechem.OETriposAtomTypes(mol) oechem.OETriposAtomNames(mol) # Set up minimization - ff = ForceField(get_data_filename('forcefield/ammonia_minimal.offxml')) + ff = ForceField('ammonia_minimal.offxml') topology, positions = oemol_to_openmmTop(mol) system = ff.createSystem(topology, [mol], verbose=verbose) positions = extractPositionsFromOEMol(mol) - integrator = openmm.VerletIntegrator(2.0*unit.femtoseconds) + integrator = openmm.VerletIntegrator(2.0 * unit.femtoseconds) simulation = app.Simulation(topology, system, integrator) simulation.context.setPositions(positions) # Minimize energy @@ -568,14 +449,17 @@ def test_improper_pyramidal(verbose = False): for atom in outmol.GetAtoms(oechem.OEIsInvertibleNitrogen()): aidx = atom.GetIdx() nbors = list(atom.GetAtoms()) - ang1 = math.degrees(oechem.OEGetAngle(outmol, nbors[0],atom,nbors[1])) - ang2 = math.degrees(oechem.OEGetAngle(outmol, nbors[1],atom,nbors[2])) - ang3 = math.degrees(oechem.OEGetAngle(outmol, nbors[2],atom,nbors[0])) - ang_sum = math.fsum([ang1,ang2,ang3]) + ang1 = math.degrees(oechem.OEGetAngle(outmol, nbors[0], atom, nbors[1])) + ang2 = math.degrees(oechem.OEGetAngle(outmol, nbors[1], atom, nbors[2])) + ang3 = math.degrees(oechem.OEGetAngle(outmol, nbors[2], atom, nbors[0])) + ang_sum = math.fsum([ang1, ang2, ang3]) # Check that sum of angles around N is within 1 degree of 353.5 - if abs(ang_sum-353.5) > 1.0: - raise Exception("Improper torsion for ammonia differs too much from reference partly pyramidal geometry." - "The reference case has a sum of H-N-H angles (3x) at 353.5 degrees; the test case has a sum of {}.".format(ang_sum)) + if abs(ang_sum - 353.5) > 1.0: + raise Exception( + "Improper torsion for ammonia differs too much from reference partly pyramidal geometry." + "The reference case has a sum of H-N-H angles (3x) at 353.5 degrees; the test case has a sum of {}.". + format(ang_sum)) + def test_MDL_aromaticity(verbose=False): """Test support for alternate aromaticity models.""" @@ -586,12 +470,12 @@ def test_MDL_aromaticity(verbose=False): oechem.OEParseSmiles(mol, 'c12c(cccc1)occ2') oechem.OEAddExplicitHydrogens(mol) - labels=ff.labelMolecules( [mol], verbose = True) + labels = ff.labelMolecules([mol], verbose=True) # The bond 6-7 should get the b16 parameter iff the MDL model is working, otherwise it will pick up just the generic details = labels[0]['HarmonicBondGenerator'] found = False for (atom_indices, pid, smirks) in details: - if pid == 'b16' and atom_indices==[6,7]: + if pid == 'b16' and atom_indices == [6, 7]: found = True if not found: raise Exception("Didn't find right param.") @@ -603,316 +487,220 @@ def test_change_parameters(verbose=False): ifs = oechem.oemolistream(get_data_filename('molecules/AlkEthOH_c100.mol2')) mol = oechem.OEMol() flavor = oechem.OEIFlavor_Generic_Default | oechem.OEIFlavor_MOL2_Default | oechem.OEIFlavor_MOL2_Forcefield - ifs.SetFlavor( oechem.OEFormat_MOL2, flavor) - oechem.OEReadMolecule(ifs, mol ) + ifs.SetFlavor(oechem.OEFormat_MOL2, flavor) + oechem.OEReadMolecule(ifs, mol) oechem.OETriposAtomNames(mol) # Load forcefield file - ffxml = get_data_filename('forcefield/Frosst_AlkEthOH.offxml') - ff = ForceField(ffxml) + ff = ForceField('Frosst_AlkEthOH.offxml') topology = generateTopologyFromOEMol(mol) # Create initial system system = ff.createSystem(topology, [mol], verbose=verbose) # Get initial energy before parameter modification positions = positions_from_oemol(mol) - old_energy=get_energy(system, positions) + old_energy = get_energy(system, positions) # Get params for an angle params = ff.getParameter(smirks='[a,A:1]-[#6X4:2]-[a,A:3]') # Modify params - params['k']='0.0' + params['k'] = '0.0' ff.setParameter(params, smirks='[a,A:1]-[#6X4:2]-[a,A:3]') # Write params - ff.writeFile( tempfile.TemporaryFile(suffix='.offxml') ) + ff.writeFile(tempfile.TemporaryFile(suffix='.offxml')) # Make sure params changed energy! (Test whether they get rebuilt on system creation) - system=ff.createSystem(topology, [mol], verbose=verbose) - energy=get_energy(system, positions) + system = ff.createSystem(topology, [mol], verbose=verbose) + energy = get_energy(system, positions) if verbose: print("New energy/old energy:", energy, old_energy) - if np.abs(energy-old_energy)<0.1: + if np.abs(energy - old_energy) < 0.1: raise Exception("Error: Parameter modification did not change energy.") -def test_amber_roundtrip(): - """Save a System (a mixture) to AMBER, read back in, verify yields same energy and force terms.""" - - forcefield = ForceField(get_data_filename('forcefield/Frosst_AlkEthOH.offxml')) - filename = get_data_filename(os.path.join('systems', 'packmol_boxes', 'cyclohexane_ethanol_0.4_0.6.pdb')) - from simtk.openmm.app import PDBFile - pdbfile = PDBFile(filename) - mol2files = [get_data_filename(os.path.join('systems', 'monomers', 'ethanol.mol2')), get_data_filename(os.path.join('systems', 'monomers', 'cyclohexane.mol2'))] - flavor = oechem.OEIFlavor_Generic_Default | oechem.OEIFlavor_MOL2_Default | oechem.OEIFlavor_MOL2_Forcefield - mols = [] - mol = oechem.OEMol() - for mol2file in mol2files: - ifs = oechem.oemolistream(mol2file) - ifs.SetFlavor( oechem.OEFormat_MOL2, flavor) - mol = oechem.OEGraphMol() - while oechem.OEReadMolecule(ifs, mol): - oechem.OETriposAtomNames(mol) - mols.append(oechem.OEGraphMol(mol)) - - # setup system - system = forcefield.createSystem( pdbfile.topology, mols) +class TestForceFieldExport: + """Test the ability to export ForceField-parameterized systems to other major simulation packages. + """ - # Create ParmEd structure, save to AMBER - a, prmtop = tempfile.mkstemp(suffix='.prmtop') - a, crd = tempfile.mkstemp(suffix='.crd') - save_system_to_amber( pdbfile.topology, system, pdbfile.positions, prmtop, crd) + @staticmethod + def get_mixture_tesystem(packmol_boxname, monomers): + """Retrieve test system information for specified packmol mixed-component box and monomers. + + Parameters + ---------- + packmol_boxname : str + Prefix of PDB file to be retrieved from systems/packmolboxes in test data directory + monomers : list of str + List of monomer names within packmol box + + Returns + ------- + topology : openforcefield.topology.Topology + Topology for the packmol box + positions : simtk.unit.Quantity with dimension (nparticles,3) with units compatible with angstroms + Positions corresponding to particles in ``topology`` + """ + pdbfile = app.PDBFile(get_packmol_pdbfile(packmol_boxname)) + molecules = [Molecule.from_file(get_monomer_mol2file(name)) for name in monomers] + topology = Topology.from_openmm(pdbfile.topology, unique_molecules=molecules) + positions = pdbfile.positions + return topology, positions + + def test_amber_roundtrip(self): + """Save a System (a mixture) to AMBER, read back in, verify yields same energy and force terms.""" + forcefield = ForceField(AlkEthOH_offxml_filename) + topology, positions = get_mixture_testsystem('cyclohexane_ethanol_0.4_0.6', ['ethanol', 'cyclohexane']) + system = forcefield.create_system(pdbfile.topology, mols) + openmm_topology = topology.to_openmm() + + # TODO: Can we provide a way to more directly export to AMBER? + from openforcefield.utils import save_system_to_amber + with TemporaryDirectory() as tmpdir: + # Write AMBER prmtop, inpcrd + prmtop_filename = os.path.join(tmpdir, 'output.prmtop') + inpcrd_filename = os.path.join(tmpdir, 'output.inpcrd') + save_system_to_amber(openmm_topology, system, positions, prmtop_filename, inpcrd_filename) + + # Read back in and cross-check energies + structure = parmed.load_file(prmtop, inpcrd) # TODO: Is this a structure or prmtop object in ParmEd? + # TODO: Make sure the SMIRNOFF systems is also created with no cutoff, no constraints, and no implicit solvent + amber_system = structure.createSystem(nonbondedMethod=app.NoCutoff, constraints=None, implicitSolvent=None) + groups0, groups1, energy0, energy1 = compare_system_energies( + openmm_topology, openmm_topology, amber_system, system, positions, verbose=False) + + def test_gromacs_roundtrip(self): + """Save a System (a mixture) to gromacs, read back in, verify yields same energy and force terms.""" + forcefield = ForceField(AlkEthOH_offxml_filename) + topology, positions = get_mixture_testsystem('cyclohexane_ethanol_0.4_0.6', ['ethanol', 'cyclohexane']) + system = forcefield.create_system(pdbfile.topology, mols) + openmm_topology = topology.to_openmm() + + # TODO: Can we provide a way to more directly export to gromacs? + from openforcefield.utils import save_system_to_amber + with TemporaryDirectory() as tmpdir: + # Write gromacs .gro and .top files + gro_filename = os.path.join(tmpdir, 'output.gro') + top_filename = os.path.join(tmpdir, 'output.top') + save_system_to_gromacs(openmm_topology, system, positions, top_filename, gro_filename) + + # Read back in and cross-check energies + top = parmed.load_file(top_filename) + gro = parmed.load_file(gro_filename) + # TODO: Make sure the SMIRNOFF systems is also created with no cutoff, no constraints, and no implicit solvent + gromacs_system = top.createSystem(nonbondedMethod=app.NoCutoff, constraints=None, implicitSolvent=None) + groups0, groups1, energy0, energy1 = compare_system_energies( + openmm_topology, openmm_topology, gromacs_system, system, positions, verbose=False) + + +class TestSolventSupport: + """Test support for rigid solvents like TIP3P. + """ - # Read back in and cross-check energies - parm = parmed.load_file(prmtop, crd) - ambersys = parm.createSystem(nonbondedMethod= app.NoCutoff, constraints = None, implicitSolvent = None) - groups0, groups1, energy0, energy1 = compare_system_energies( pdbfile.topology, pdbfile.topology, ambersys, system, pdbfile.positions, verbose = False) + # TODO: Move this to test_forcefield::TestForceFieldConstraints when it will be possible to specify TIP3P electrostatics. + def test_tip3p_constraints(self): + """Test that TIP3P distance costraints are correctly applied.""" + # Specify TIP3P constraint distances + tip3p_oh_distance = 0.9572 # angstrom + tip3p_hoh_angle = 104.52 # angle + tip3p_hh_distance = tip3p_oh_distance * np.sin(np.radians(tip3p_hoh_angle / 2)) * 2 + expected_distances = [tip3p_oh_distance, tip3p_oh_distance, tip3p_hh_distance] + + # Load TIP3P molecule + molecule = Molecule.from_file(tip3p_molecule_filename) + + # Extract topology and positions + topology = Topology.from_molecules(molecule) + positions = molecule.positions + + # Create OpenMM System + ff = ForceField(tip3p_offxml_filename) + system = ff.create_system(topology) + + # TODO: This is probably unnecessary and we can simply check that the System has all the Constraints in their position. + # Run dynamics. + integrator = openmm.VerletIntegrator(2.0 * unit.femtoseconds) + context = openmm.Context(system, integrator) + context.setPositions(positions) + integrator.step(50) + + # Ensure constrained distances are correct + state = context.getState(getPositions=True) + new_positions = state.getPositions(asNumpy=True) / unit.angstroms + distances = [] + for atom_1, atom_2 in [(0, 1), (0, 2), (1, 2)]: # pair of atoms O-H1, O-H2, H1-H2 + distances.append(np.linalg.norm(new_positions[atom_1] - new_positions[atom_2])) + err_msg = 'expected distances [O-H1, O-H2, H1-H2]: {} A, new distances: {} A' + assert np.allclose(expected_distances, distances), err_msg.format(expected_distances, distances) + + # TODO: Move this to test_forcefield::TestForceFieldParameterAssignment when it will be possible to specify TIP3P electrostatics. + def test_tip3p_solvated_molecule_energy(): + """Check the energy of a TIP3P solvated molecule is the same with SMIRNOFF and OpenMM. + + This test makes also use of defining the force field with multiple FFXML files, + and test the energy of mixture systems (i.e. molecule plus water). - # Remove temp files - os.remove(prmtop) - os.remove(crd) + """ + # TODO remove this function when ParmEd#868 is fixed + def add_water_bonds(system): + """Hack to make tip3p waters work with ParmEd Structure.createSystem. -def test_gromacs_roundtrip(): - """Save a System (a mixture) to GROMACS, read back in, verify yields same energy and force terms.""" + Bond parameters need to be specified even when constrained. + """ + k_tip3p = 462750.4 * unit.kilojoule_per_mole / unit.nanometers**2 + length_tip3p = 0.09572 * unit.nanometers + for force in system.getForces(): + if isinstance(force, openmm.HarmonicBondForce): + force.addBond(particle1=0, particle2=1, length=length_tip3p, k=k_tip3p) + force.addBond(particle1=0, particle2=2, length=length_tip3p, k=k_tip3p) - forcefield = ForceField(get_data_filename('forcefield/Frosst_AlkEthOH.offxml')) - filename = get_data_filename(os.path.join('systems', 'packmol_boxes', 'cyclohexane_ethanol_0.4_0.6.pdb')) - from simtk.openmm.app import PDBFile - pdbfile = PDBFile(filename) - mol2files = [get_data_filename(os.path.join('systems', 'monomers', 'ethanol.mol2')), get_data_filename(os.path.join('systems', 'monomers', 'cyclohexane.mol2'))] + monomers_dir = get_data_filename(os.path.join('systems', 'monomers')) - flavor = oechem.OEIFlavor_Generic_Default | oechem.OEIFlavor_MOL2_Default | oechem.OEIFlavor_MOL2_Forcefield - mols = [] - mol = oechem.OEMol() - for mol2file in mol2files: - ifs = oechem.oemolistream(mol2file) - ifs.SetFlavor( oechem.OEFormat_MOL2, flavor) - mol = oechem.OEGraphMol() - while oechem.OEReadMolecule(ifs, mol): - oechem.OETriposAtomNames(mol) - mols.append(oechem.OEGraphMol(mol)) - - # setup system - system = forcefield.createSystem( pdbfile.topology, mols) - - # Create ParmEd structure, save to AMBER - a, topfile = tempfile.mkstemp(suffix='.top') - a, grofile = tempfile.mkstemp(suffix='.gro') - save_system_to_gromacs( pdbfile.topology, system, pdbfile.positions, topfile, grofile) - - # Read back in and cross-check energies - top = parmed.load_file(topfile) - gro = parmed.load_file(grofile) - gromacssys = top.createSystem(nonbondedMethod= app.NoCutoff, constraints = None, implicitSolvent = None) - - groups0, groups1, energy0, energy1 = compare_system_energies( pdbfile.topology, pdbfile.topology, gromacssys, system, pdbfile.positions, verbose = False) - - # Remove temp files - os.remove(topfile) - os.remove(grofile) - - -def test_tip3p_constraints(): - """Test that TIP3P distance costraints are correctly applied.""" - # TIP3P constrained distances. - tip3p_oh_distance = 0.9572 # angstrom - tip3p_hoh_angle = 104.52 # angle - tip3p_hh_distance = tip3p_oh_distance * np.sin(np.radians(tip3p_hoh_angle/2)) * 2 - expected_distances = [tip3p_oh_distance, tip3p_oh_distance, tip3p_hh_distance] - - # Load tip3p molecule as OEMol. - tip3p_mol2_filepath = get_data_filename(os.path.join('systems', 'monomers', 'tip3p_water.mol2')) - tip3p_oemol = read_molecules(tip3p_mol2_filepath, verbose=False)[0] - - # Extract topology and positions. - tip3p_topology = generateTopologyFromOEMol(tip3p_oemol) - tip3p_positions = positions_from_oemol(tip3p_oemol) - - # Create tip3p water system. - ff = ForceField('forcefield/tip3p.offxml') - system = ff.createSystem(tip3p_topology, [tip3p_oemol]) - - # Run dynamics. - integrator = openmm.VerletIntegrator(2.0*unit.femtoseconds) - context = openmm.Context(system, integrator) - context.setPositions(tip3p_positions) - integrator.step(50) - - # Constrained distances are correct. - state = context.getState(getPositions=True) - new_positions = state.getPositions(asNumpy=True) / unit.angstroms - distances = [] - for atom_1, atom_2 in [(0, 1), (0, 2), (1, 2)]: # pair of atoms O-H1, O-H2, H1-H2 - distances.append(np.linalg.norm(new_positions[atom_1] - new_positions[atom_2])) - err_msg = 'expected distances [O-H1, O-H2, H1-H2]: {} A, new distances: {} A' - assert np.allclose(expected_distances, distances), err_msg.format(expected_distances, distances) - - -def test_tip3p_solvated_molecule_energy(): - """Check the energy of a TIP3P solvated molecule is the same with SMIRNOFF and OpenMM. - - This test makes also use of defining the force field with multiple FFXML files, - and test the energy of mixture systems (i.e. molecule plus water). + # Load TIP3P molecule + tip3p_molecule = Molecule.from_file(tip3p_molecule_filename) + tip3p_positions = tip3p_molecule.positions - """ - # TODO remove this function when ParmEd#868 is fixed - def add_water_bonds(system): - """Hack to make tip3p waters work with ParmEd Structure.createSystem. + # Extract topology and positions + top3p_topology = Topology.from_molecules(molecule) - Bond parameters need to be specified even when constrained. - """ - k_tip3p = 462750.4*unit.kilojoule_per_mole/unit.nanometers**2 - length_tip3p = 0.09572*unit.nanometers - for force in system.getForces(): - if isinstance(force, openmm.HarmonicBondForce): - force.addBond(particle1=0, particle2=1, length=length_tip3p, k=k_tip3p) - force.addBond(particle1=0, particle2=2, length=length_tip3p, k=k_tip3p) - - - monomers_dir = get_data_filename(os.path.join('systems', 'monomers')) - - # Load tip3p molecule as OEMol. - tip3p_mol2_filepath = os.path.join(monomers_dir, 'tip3p_water.mol2') - tip3p_oemol = read_molecules(tip3p_mol2_filepath, verbose=False)[0] - - # Create OpenMM-parametrized water ParmEd Structure. - tip3p_openmm_ff = openmm.app.ForceField('tip3p.xml') - tip3p_topology = generateTopologyFromOEMol(tip3p_oemol) - tip3p_positions = positions_from_oemol(tip3p_oemol) - tip3p_openmm_system = tip3p_openmm_ff.createSystem(tip3p_topology) - - # TODO remove this line when ParmEd#868 is fixed - # Hack to make tip3p waters work with ParmEd Structure.createSystem. - add_water_bonds(tip3p_openmm_system) - - tip3p_openmm_structure = parmed.openmm.topsystem.load_topology( - tip3p_topology, tip3p_openmm_system, tip3p_positions) - - # Test case: monomer_filename - test_cases = [('smirnoff99Frosst.offxml', 'ethanol.mol2'), - ('smirnoff99Frosst.offxml', 'methane.mol2')] - - for ff_name, molecule_filename in test_cases: - # Load molecule as OEMol. - molecule_filepath = os.path.join(monomers_dir, molecule_filename) - molecule_oemol = read_molecules(molecule_filepath, verbose=False)[0] - - # Create molecule parametrized ParmEd args. - molecule_ff = ForceField('forcefield/' + ff_name) - molecule_args = forcefield_utils.create_system_from_molecule(molecule_ff, molecule_oemol) - molecule_structure = parmed.openmm.topsystem.load_topology(*molecule_args) - _, _, molecule_positions = molecule_args - - # Merge molecule and OpenMM TIP3P water. - structure = tip3p_openmm_structure + molecule_structure - structure.positions = np.append(tip3p_positions, molecule_positions, axis=0) - system = structure.createSystem() - energy_openmm = get_energy(system, structure.positions) - - # Test the creation of system with multiple force field files. - ff = ForceField('forcefield/' + ff_name, 'forcefield/tip3p.offxml') - system = ff.createSystem(structure.topology, [tip3p_oemol, molecule_oemol]) + # Create OpenMM System + tip3p_forcefield = ForceField(tip3p_offxml_filename) + tip3p_openmm_system = tip3p_forcefield.create_system(tip3p_topology) # TODO remove this line when ParmEd#868 is fixed - # Add bonds to match ParmEd hack above. - add_water_bonds(system) - - energy_smirnoff = get_energy(system, structure.positions) - - # The energies of the systems must be the same. - assert np.isclose(energy_openmm, energy_smirnoff), 'OpenMM: {}, SMIRNOFF: {}'.format( - energy_openmm, energy_smirnoff) + # Hack to make tip3p waters work with ParmEd Structure.createSystem. + add_water_bonds(tip3p_openmm_system) + tip3p_openmm_structure = parmed.openmm.topsystem.load_topology(topology.to_openmm(), tip3p_openmm_system, + tip3p_positions) -def test_component_combination(): - """Test that a system still yields the same energy after building it again out of its components.""" + smirnoff_forcefield = ForceField(smirnoff99Frosst_offxml_filename) - # We've had issues where subsequent instances of a molecule might have zero charges - # Here we'll try to catch this (and also explicitly check the charges) by re-building - # a system out of its components + for monomer in ['ethanol', 'methane']: + # Load molecule + other_molecule_filepath = os.path.join(monomers_dir, monomer + '.mol2') + other_molecule = Molecule.from_file(other_molecule_filepath) - forcefield = ForceField(get_data_filename('forcefield/Frosst_AlkEthOH.offxml')) - filename = get_data_filename(os.path.join('systems', 'packmol_boxes', 'cyclohexane_ethanol_0.4_0.6.pdb')) - from simtk.openmm.app import PDBFile - pdbfile = PDBFile(filename) - mol2files = [get_data_filename(os.path.join('systems', 'monomers', 'ethanol.mol2')), get_data_filename(os.path.join('systems', 'monomers', 'cyclohexane.mol2'))] + # Create ParmEd Structure + other_molecule_structure = smirnoff_forcefield.create_structure(other_molecule.to_topology(), + other_molecule.positions) - flavor = oechem.OEIFlavor_Generic_Default | oechem.OEIFlavor_MOL2_Default | oechem.OEIFlavor_MOL2_Forcefield - mols = [] - mol = oechem.OEMol() - for mol2file in mol2files: - ifs = oechem.oemolistream(mol2file) - ifs.SetFlavor( oechem.OEFormat_MOL2, flavor) - mol = oechem.OEGraphMol() - while oechem.OEReadMolecule(ifs, mol): - oechem.OETriposAtomNames(mol) - mols.append(oechem.OEGraphMol(mol)) - - # setup system - system = forcefield.createSystem( pdbfile.topology, mols, chargeMethod = 'OECharges_AM1BCCSym') - - # Make parmed structure - structure = parmed.openmm.topsystem.load_topology( pdbfile.topology, system, pdbfile.positions) - - # Split the system, then re-compose it out of its components - tmp = structure.split() - strs, nums = [], [] - for s, n in tmp: - strs.append(s) - nums.append(n) - nums = [ len(n) for n in nums] - - # Re-compose system from components - new_structure = strs[0]*nums[0] - for idx in range(1,len(nums)): - new_structure += strs[idx]*nums[idx] - # Swap in coordinates again - new_structure.positions = structure.positions - - # Create System - newsys = new_structure.createSystem(nonbondedMethod= app.NoCutoff, constraints = None, implicitSolvent = None) - - # Cross check energies - groups0, groups1, energy0, energy1 = compare_system_energies( pdbfile.topology, pdbfile.topology, system, newsys, pdbfile.positions, verbose = False) - - # Also check that that the number of components is equal to the number I expect - if not len(nums)==2: - print("Error: Test system has incorrect number of components.") - raise Exception('Incorrect number of components in cyclohexane/ethanol test system.') - - # Also check that none of residues have zero charge - for resnr in range(len(structure.residues)): - abscharges = [ abs(structure.residues[resnr].atoms[idx].charge) for idx in range(len(structure.residues[resnr].atoms))] - if sum(abscharges)==0: - raise Exception('Error: Residue %s in cyclohexane-ethanol test system has a charge of zero, which is incorrect.' % resnr) - -def test_merge_system(): - """Test merging of a system created from AMBER and another created from SMIRNOFF.""" - - #Create System from AMBER - prefix = os.path.join('systems', 'amber', 'cyclohexane_ethanol_0.4_0.6') - prmtop = get_data_filename( prefix+'.prmtop') - incrd = get_data_filename( prefix+'.inpcrd') - - from openforcefield.typing.engines.smirnoff import create_system_from_amber - topology0, system0, positions0 = create_system_from_amber( prmtop, incrd ) - - from openeye import oechem - # Load simple OEMol - ifs = oechem.oemolistream(get_data_filename('molecules/AlkEthOH_c100.mol2')) - mol = oechem.OEMol() - flavor = oechem.OEIFlavor_Generic_Default | oechem.OEIFlavor_MOL2_Default | oechem.OEIFlavor_MOL2_Forcefield - ifs.SetFlavor( oechem.OEFormat_MOL2, flavor) - oechem.OEReadMolecule(ifs, mol ) - oechem.OETriposAtomNames(mol) - - # Load forcefield file - forcefield = ForceField(get_data_filename('forcefield/Frosst_AlkEthOH.offxml')) - topology1, system1, positions1 = create_system_from_molecule(forcefield, mol) + # Merge molecule and OpenMM TIP3P water + combined_structure = tip3p_openmm_structure + other_molecule_structure + #structure.positions = np.append(tip3p_molecule.positions, molecule.positions, axis=0) # TODO: This doesn't seem necessary since positions are correctly concatenated already + system = combined_structure.createSystem() + energy_openmm = get_energy(system, combined_structure.positions) - merge_system( topology0, topology1, system0, system1, positions0, positions1, verbose=True ) + # Test the creation of system with multiple force field files. + ff = ForceField(smirnoff_offxml_filename, tip3p_offxml_filename) + combined_topology = Topology.from_molecules([tip3p_molecule, molecule]) + system = ff.create_system(topology) + # TODO remove this line when ParmEd#868 is fixed + # Add bonds to match ParmEd hack above. + add_water_bonds(system) + energy_smirnoff = get_energy(system, structure.positions) -if __name__ == '__main__': - #test_smirks() - test_merge_system() + # The energies of the systems must be the same. + assert np.isclose(energy_openmm, energy_smirnoff), 'OpenMM: {}, SMIRNOFF: {}'.format( + energy_openmm, energy_smirnoff) diff --git a/openforcefield/tests/test_toolkits.py b/openforcefield/tests/test_toolkits.py new file mode 100644 index 000000000..1980105c1 --- /dev/null +++ b/openforcefield/tests/test_toolkits.py @@ -0,0 +1,791 @@ +#!/usr/bin/env python + +#============================================================================================= +# MODULE DOCSTRING +#============================================================================================= + +""" +Tests for cheminformatics toolkit wrappers + +""" + +#============================================================================================= +# GLOBAL IMPORTS +#============================================================================================= + +from simtk import unit +import numpy as np +from numpy.testing import assert_almost_equal + +import pytest +from openforcefield.utils.toolkits import (OpenEyeToolkitWrapper, RDKitToolkitWrapper, + AmberToolsToolkitWrapper, ToolkitRegistry, + GAFFAtomTypeWarning, UndefinedStereochemistryError) +from openforcefield.utils import get_data_filename +from openforcefield.topology.molecule import Molecule + + +#============================================================================================= +# TESTS +#============================================================================================= + +class TestOpenEyeToolkitWrapper: + """Test the OpenEyeToolkitWrapper""" + + # TODO: Make separate smiles_add_H and smiles_explicit_H tests + + @pytest.mark.skipif(not OpenEyeToolkitWrapper.toolkit_is_available(), reason='OpenEye Toolkit not available') + def test_smiles(self): + """Test OpenEyeToolkitWrapper to_smiles() and from_smiles()""" + toolkit_wrapper = OpenEyeToolkitWrapper() + + # This differs from RDKit's SMILES due to different canonicalization schemes + + smiles = '[H]C([H])([H])C([H])([H])[H]' + molecule = Molecule.from_smiles(smiles, + toolkit_registry=toolkit_wrapper) + smiles2 = molecule.to_smiles(toolkit_registry=toolkit_wrapper) + assert smiles == smiles2 + + @pytest.mark.skipif(not OpenEyeToolkitWrapper.toolkit_is_available(), reason='OpenEye Toolkit not available') + def test_smiles_missing_stereochemistry(self): + """Test OpenEyeToolkitWrapper to_smiles() and from_smiles()""" + toolkit_wrapper = OpenEyeToolkitWrapper() + + unspec_chiral_smiles = r"C\C(F)=C(/F)CC(C)(Cl)Br" + spec_chiral_smiles = r"C\C(F)=C(/F)C[C@@](C)(Cl)Br" + unspec_db_smiles = r"CC(F)=C(F)C[C@@](C)(Cl)Br" + spec_db_smiles = r"C\C(F)=C(/F)C[C@@](C)(Cl)Br" + + for title, smiles, raises_exception in [("unspec_chiral_smiles", unspec_chiral_smiles, True), + ("spec_chiral_smiles", spec_chiral_smiles, False), + ("unspec_db_smiles", unspec_db_smiles, True), + ("spec_db_smiles", spec_db_smiles, False), + ]: + if raises_exception: + with pytest.raises(UndefinedStereochemistryError) as context: + molecule = Molecule.from_smiles(smiles, toolkit_registry=toolkit_wrapper) + else: + molecule = Molecule.from_smiles(smiles, toolkit_registry=toolkit_wrapper) + + # TODO: test_smiles_round_trip + + + @pytest.mark.skipif(not OpenEyeToolkitWrapper.toolkit_is_available(), reason='OpenEye Toolkit not available') + def test_smiles_add_H(self): + """Test OpenEyeToolkitWrapper for adding explicit hydrogens""" + toolkit_wrapper = OpenEyeToolkitWrapper() + # This differs from RDKit's SMILES due to different canonicalization schemes + input_smiles = 'CC' + expected_output_smiles = '[H]C([H])([H])C([H])([H])[H]' + molecule = Molecule.from_smiles(input_smiles, + toolkit_registry=toolkit_wrapper) + smiles2 = molecule.to_smiles(toolkit_registry=toolkit_wrapper) + assert expected_output_smiles == smiles2 + + @pytest.mark.skipif(not OpenEyeToolkitWrapper.toolkit_is_available(), reason='OpenEye Toolkit not available') + def test_smiles_charged(self): + """Test OpenEyeToolkitWrapper functions for reading/writing charged SMILES""" + toolkit_wrapper = OpenEyeToolkitWrapper() + # This differs from RDKit's expected output due to different canonicalization schemes + smiles = '[H]C([H])([H])[N+]([H])([H])[H]' + molecule = Molecule.from_smiles(smiles, + toolkit_registry=toolkit_wrapper) + smiles2 = molecule.to_smiles(toolkit_registry=toolkit_wrapper) + assert smiles == smiles2 + + + @pytest.mark.skipif(not OpenEyeToolkitWrapper.toolkit_is_available(), reason='OpenEye Toolkit not available') + def test_to_from_openeye_core_props_filled(self): + """Test OpenEyeToolkitWrapper to_openeye() and from_openeye()""" + toolkit_wrapper = OpenEyeToolkitWrapper() + + # Replacing with a simple molecule with stereochemistry + input_smiles = r'C\C(F)=C(/F)C[C@@](C)(Cl)Br' + expected_output_smiles = r'[H]C([H])([H])/C(=C(/C([H])([H])[C@@](C([H])([H])[H])(Cl)Br)\F)/F' + molecule = Molecule.from_smiles(input_smiles, toolkit_registry=toolkit_wrapper) + assert molecule.to_smiles(toolkit_registry=toolkit_wrapper) == expected_output_smiles + + # Populate core molecule property fields + molecule.name = 'Alice' + partial_charges = unit.Quantity(np.array([-.9, -.8, -.7, -.6, + -.5, -.4, -.3, -.2, + -.1, 0., .1, .2, + .3, .4, .5, .6, + .7, .8]), unit.elementary_charge) + molecule.partial_charges = partial_charges + coords = unit.Quantity(np.array([['0.0', '1.0', '2.0'], ['3.0', '4.0', '5.0'], ['6.0', '7.0', '8.0'], + ['9.0', '10.0', '11.0'], ['12.0', '13.0', '14.0'], + ['15.0', '16.0', '17.0'], + ['18.0', '19.0', '20.0'], ['21.0', '22.0', '23.0'], + ['24.0', '25.0', '26.0'], + ['27.0', '28.0', '29.0'], ['30.0', '31.0', '32.0'], + ['33.0', '34.0', '35.0'], + ['36.0', '37.0', '38.0'], ['39.0', '40.0', '41.0'], + ['42.0', '43.0', '44.0'], + ['45.0', '46.0', '47.0'], ['48.0', '49.0', '50.0'], + ['51.0', '52.0', '53.0']]), + unit.angstrom) + molecule.add_conformer(coords) + # Populate core atom property fields + molecule.atoms[2].name = 'Bob' + # Ensure one atom has its stereochemistry specified + central_carbon_stereo_specified = False + for atom in molecule.atoms: + if (atom.atomic_number == 6) and atom.stereochemistry == "S": + central_carbon_stereo_specified = True + assert central_carbon_stereo_specified + + # Populate bond core property fields + fractional_bond_orders = [float(val) for val in range(1, 19)] + for fbo, bond in zip(fractional_bond_orders, molecule.bonds): + bond.fractional_bond_order = fbo + + # Do a first conversion to/from oemol + oemol = molecule.to_openeye() + molecule2 = Molecule.from_openeye(oemol) + + # Test that properties survived first conversion + # assert molecule.to_dict() == molecule2.to_dict() + assert molecule.name == molecule2.name + # NOTE: This expects the same indexing scheme in the original and new molecule + + central_carbon_stereo_specified = False + for atom in molecule2.atoms: + if (atom.atomic_number == 6) and atom.stereochemistry == "S": + central_carbon_stereo_specified = True + assert central_carbon_stereo_specified + for atom1, atom2 in zip(molecule.atoms, molecule2.atoms): + assert atom1.to_dict() == atom2.to_dict() + for bond1, bond2 in zip(molecule.bonds, molecule2.bonds): + assert bond1.to_dict() == bond2.to_dict() + assert (molecule._conformers[0] == molecule2._conformers[0]).all() + for pc1, pc2 in zip(molecule._partial_charges, molecule2._partial_charges): + pc1_ul = pc1 / unit.elementary_charge + pc2_ul = pc2 / unit.elementary_charge + assert_almost_equal(pc1_ul, pc2_ul, decimal=6) + assert molecule2.to_smiles(toolkit_registry=toolkit_wrapper) == expected_output_smiles + + + @pytest.mark.skipif(not OpenEyeToolkitWrapper.toolkit_is_available(), reason='OpenEye Toolkit not available') + def test_to_from_openeye_core_props_unset(self): + """Test OpenEyeToolkitWrapper to_openeye() and from_openeye() when given empty core property fields""" + toolkit_wrapper = OpenEyeToolkitWrapper() + + # Using a simple molecule with tetrahedral and bond stereochemistry + input_smiles = r'C\C(F)=C(/F)C[C@](C)(Cl)Br' + + expected_output_smiles = r'[H]C([H])([H])/C(=C(/C([H])([H])[C@](C([H])([H])[H])(Cl)Br)\F)/F' + molecule = Molecule.from_smiles(input_smiles, toolkit_registry=toolkit_wrapper) + assert molecule.to_smiles(toolkit_registry=toolkit_wrapper) == expected_output_smiles + + # Ensure one atom has its stereochemistry specified + central_carbon_stereo_specified = False + for atom in molecule.atoms: + if (atom.atomic_number == 6) and atom.stereochemistry == "R": + central_carbon_stereo_specified = True + assert central_carbon_stereo_specified + + # Do a first conversion to/from oemol + rdmol = molecule.to_openeye() + molecule2 = Molecule.from_openeye(rdmol) + + # Test that properties survived first conversion + assert molecule.name == molecule2.name + # NOTE: This expects the same indexing scheme in the original and new molecule + + central_carbon_stereo_specified = False + for atom in molecule2.atoms: + if (atom.atomic_number == 6) and atom.stereochemistry == "R": + central_carbon_stereo_specified = True + assert central_carbon_stereo_specified + for atom1, atom2 in zip(molecule.atoms, molecule2.atoms): + assert atom1.to_dict() == atom2.to_dict() + for bond1, bond2 in zip(molecule.bonds, molecule2.bonds): + assert bond1.to_dict() == bond2.to_dict() + assert (molecule._conformers == None) + assert (molecule2._conformers == None) + for pc1, pc2 in zip(molecule._partial_charges, molecule2._partial_charges): + pc1_ul = pc1 / unit.elementary_charge + pc2_ul = pc2 / unit.elementary_charge + assert_almost_equal(pc1_ul, pc2_ul, decimal=6) + assert molecule2.to_smiles(toolkit_registry=toolkit_wrapper) == expected_output_smiles + + @pytest.mark.skipif(not OpenEyeToolkitWrapper.toolkit_is_available(), reason='OpenEye Toolkit not available') + def test_get_sdf_coordinates(self): + """Test OpenEyeToolkitWrapper for importing a single set of coordinates from a sdf file""" + toolkit_wrapper = OpenEyeToolkitWrapper() + filename = get_data_filename('molecules/toluene.sdf') + molecule = Molecule.from_file(filename, toolkit_registry=toolkit_wrapper) + assert len(molecule._conformers) == 1 + assert molecule._conformers[0].shape == (15,3) + + @pytest.mark.skipif(not OpenEyeToolkitWrapper.toolkit_is_available(), reason='OpenEye Toolkit not available') + @pytest.mark.skip + def test_get_multiconformer_sdf_coordinates(self): + """Test OpenEyeToolkitWrapper for importing multiple sets of coordinates from a sdf file""" + raise NotImplementedError + toolkit_wrapper = OpenEyeToolkitWrapper() + filename = get_data_filename('molecules/toluene.sdf') + molecule = Molecule.from_file(filename, toolkit_registry=toolkit_wrapper) + assert len(molecule._conformers) == 1 + assert molecule._conformers[0].shape == (15,3) + + @pytest.mark.skipif(not OpenEyeToolkitWrapper.toolkit_is_available(), reason='OpenEye Toolkit not available') + def test_get_mol2_coordinates(self): + """Test OpenEyeToolkitWrapper for importing a single set of molecule coordinates""" + toolkit_wrapper = OpenEyeToolkitWrapper() + filename = get_data_filename('molecules/toluene.mol2') + molecule1 = Molecule.from_file(filename, toolkit_registry=toolkit_wrapper) + assert len(molecule1._conformers) == 1 + assert molecule1._conformers[0].shape == (15, 3) + assert_almost_equal(molecule1.conformers[0][5][1] / unit.angstrom, 22.98, decimal=2) + + # Test loading from file-like object + with open(filename, 'r') as infile: + molecule2 = Molecule(infile, file_format='MOL2', toolkit_registry=toolkit_wrapper) + assert molecule1.is_isomorphic(molecule2) + assert len(molecule2._conformers) == 1 + assert molecule2._conformers[0].shape == (15, 3) + assert_almost_equal(molecule2.conformers[0][5][1] / unit.angstrom, 22.98, decimal=2) + + # Test loading from gzipped mol2 + import gzip + with gzip.GzipFile(filename + '.gz', 'r') as infile: + molecule3 = Molecule(infile, file_format='MOL2', toolkit_registry=toolkit_wrapper) + assert molecule1.is_isomorphic(molecule3) + assert len(molecule3._conformers) == 1 + assert molecule3._conformers[0].shape == (15, 3) + assert_almost_equal(molecule3.conformers[0][5][1] / unit.angstrom, 22.98, decimal=2) + + @pytest.mark.skipif(not OpenEyeToolkitWrapper.toolkit_is_available(), reason='OpenEye Toolkit not available') + def test_get_mol2_charges(self): + """Test OpenEyeToolkitWrapper for importing a mol2 file specifying partial charges""" + toolkit_wrapper = OpenEyeToolkitWrapper() + filename = get_data_filename('molecules/toluene_charged.mol2') + molecule = Molecule.from_file(filename, toolkit_registry=toolkit_wrapper) + assert len(molecule._conformers) == 1 + assert molecule._conformers[0].shape == (15,3) + target_charges = unit.Quantity(np.array([-0.1342,-0.1271,-0.1271,-0.1310, + -0.1310,-0.0765,-0.0541, 0.1314, + 0.1286, 0.1286, 0.1303, 0.1303, + 0.0440, 0.0440, 0.0440]), + unit.elementary_charge) + for pc1, pc2 in zip(molecule._partial_charges, target_charges): + pc1_ul = pc1 / unit.elementary_charge + pc2_ul = pc2 / unit.elementary_charge + assert_almost_equal(pc1_ul, pc2_ul, decimal=4) + + @pytest.mark.skipif(not OpenEyeToolkitWrapper.toolkit_is_available(), reason='OpenEye Toolkit not available') + def test_get_mol2_gaff_atom_types(self): + """Test that a warning is raised OpenEyeToolkitWrapper when it detects GAFF atom types in a mol2 file.""" + toolkit_wrapper = OpenEyeToolkitWrapper() + mol2_file_path = get_data_filename('molecules/AlkEthOH_test_filt1_ff.mol2') + with pytest.warns(GAFFAtomTypeWarning, match='SYBYL'): + Molecule.from_file(mol2_file_path, toolkit_registry=toolkit_wrapper) + + @pytest.mark.skipif(not OpenEyeToolkitWrapper.toolkit_is_available(), reason='OpenEye Toolkit not available') + def test_generate_conformers(self): + """Test OpenEyeToolkitWrapper generate_conformers()""" + toolkit_wrapper = OpenEyeToolkitWrapper() + smiles = '[H]C([H])([H])C([H])([H])[H]' + molecule = toolkit_wrapper.from_smiles(smiles) + molecule.generate_conformers() + assert molecule.n_conformers != 0 + assert not(molecule.conformers[0] == (0.*unit.angstrom)).all() + + # TODO: Make this test more robust + + @pytest.mark.skipif(not OpenEyeToolkitWrapper.toolkit_is_available(), reason='OpenEye Toolkit not available') + def test_compute_partial_charges(self): + """Test OpenEyeToolkitWrapper compute_partial_charges()""" + toolkit_wrapper = OpenEyeToolkitWrapper() + smiles = '[H]C([H])([H])C([H])([H])[H]' + molecule = toolkit_wrapper.from_smiles(smiles) + # Ensure that an exception is raised if no conformers are provided + with pytest.raises(Exception) as excinfo: + molecule.compute_partial_charges(toolkit_registry=toolkit_wrapper) + molecule.generate_conformers(toolkit_registry=toolkit_wrapper) + # Ensure that an exception is raised if an invalid charge model is passed in + with pytest.raises(Exception) as excinfo: + charge_model = 'notARealChargeModel' + molecule.compute_partial_charges(toolkit_registry=toolkit_wrapper, charge_model=charge_model) + + # TODO: Test all supported charge models + # Note: "amber" and "amberff94" only work for a subset of residue types, so we'll need to find testing data for + # those + # charge_model = [,'amber','amberff94'] + # TODO: 'mmff' and 'mmff94' often assign charges of 0, presumably if the molecule is unrecognized. + # charge_model = ['mmff', 'mmff94'] + for charge_model in ['noop', 'am1bcc', 'am1bccnosymspt', 'am1bccelf10']: + with pytest.raises(NotImplementedError) as excinfo: + molecule.compute_partial_charges(toolkit_registry=toolkit_wrapper) # , charge_model=charge_model) + charge_sum = 0 * unit.elementary_charge + for pc in molecule._partial_charges: + charge_sum += pc + assert charge_sum < 0.001 * unit.elementary_charge + + # For now, just test AM1-BCC while the SMIRNOFF spec for other charge models gets worked out + molecule.compute_partial_charges_am1bcc(toolkit_registry=toolkit_wrapper) # , charge_model=charge_model) + charge_sum = 0 * unit.elementary_charge + for pc in molecule._partial_charges: + charge_sum += pc + assert charge_sum < 0.001 * unit.elementary_charge + + @pytest.mark.skipif(not OpenEyeToolkitWrapper.toolkit_is_available(), reason='OpenEye Toolkit not available') + def test_compute_partial_charges_net_charge(self): + """Test OpenEyeToolkitWrapper compute_partial_charges() on a molecule with a net +1 charge""" + + toolkit_wrapper = OpenEyeToolkitWrapper() + smiles = '[H]C([H])([H])[N+]([H])([H])[H]' + molecule = toolkit_wrapper.from_smiles(smiles) + molecule.generate_conformers(toolkit_registry=toolkit_wrapper) + + + with pytest.raises(NotImplementedError) as excinfo: + charge_model = 'notARealChargeModel' + molecule.compute_partial_charges(toolkit_registry=toolkit_wrapper)#, charge_model=charge_model) + + # TODO: Test all supported charge models + # TODO: "amber" and "amberff94" only work for a subset of residue types, so we'll need to find testing data for + # those + # charge_model = [,'amber','amberff94'] + # The 'noop' charge model doesn't add up to the formal charge, so we shouldn't test it + # charge_model = ['noop'] + for charge_model in ['mmff', 'mmff94', 'am1bcc', 'am1bccnosymspt', 'am1bccelf10']: + with pytest.raises(NotImplementedError) as excinfo: + molecule.compute_partial_charges(toolkit_registry=toolkit_wrapper) #, charge_model=charge_model) + charge_sum = 0 * unit.elementary_charge + for pc in molecule._partial_charges: + charge_sum += pc + assert 0.999 * unit.elementary_charge < charge_sum < 1.001 * unit.elementary_charge + # For now, I'm just testing AM1-BCC (will test more when the SMIRNOFF spec for other charges is finalized) + molecule.compute_partial_charges_am1bcc(toolkit_registry=toolkit_wrapper) + charge_sum = 0 * unit.elementary_charge + for pc in molecule._partial_charges: + charge_sum += pc + assert 0.999 * unit.elementary_charge < charge_sum < 1.001 * unit.elementary_charge + + @pytest.mark.skipif(not OpenEyeToolkitWrapper.toolkit_is_available(), reason='OpenEye Toolkit not available') + def test_compute_wiberg_bond_orders(self): + """Test OpenEyeToolkitWrapper compute_wiberg_bond_orders()""" + + toolkit_wrapper = OpenEyeToolkitWrapper() + smiles = '[H]C([H])([H])C([H])([H])[H]' + molecule = toolkit_wrapper.from_smiles(smiles) + molecule.generate_conformers(toolkit_registry=toolkit_wrapper) + for charge_model in ['am1','pm3']: + molecule.compute_wiberg_bond_orders(toolkit_registry=toolkit_wrapper, charge_model=charge_model) + print([bond.fractional_bond_order for bond in molecule.bonds]) + # TODO: Add test for equivalent Wiberg orders for equivalent bonds + + @pytest.mark.skipif(not OpenEyeToolkitWrapper.toolkit_is_available(), reason='OpenEye Toolkit not available') + def test_compute_wiberg_bond_orders_charged(self): + """Test OpenEyeToolkitWrapper compute_wiberg_bond_orders() on a molecule with net charge +1""" + + toolkit_wrapper = OpenEyeToolkitWrapper() + smiles = '[H]C([H])([H])[N+]([H])([H])[H]' + molecule = toolkit_wrapper.from_smiles(smiles) + molecule.generate_conformers(toolkit_registry=toolkit_wrapper) + for charge_model in ['am1', 'pm3']: + molecule.compute_wiberg_bond_orders(toolkit_registry=toolkit_wrapper, charge_model=charge_model) + # TODO: Add test for equivalent Wiberg orders for equivalent bonds + + @pytest.mark.skipif(not OpenEyeToolkitWrapper.toolkit_is_available(), + reason='OpenEye Toolkit not available') + def test_compute_wiberg_bond_orders_double_bond(self): + """Test OpenEyeToolkitWrapper compute_wiberg_bond_orders() on a molecule with a double bond""" + + toolkit_wrapper = OpenEyeToolkitWrapper() + smiles = r'C\C(F)=C(/F)C[C@@](C)(Cl)Br' + molecule = toolkit_wrapper.from_smiles(smiles) + molecule.generate_conformers(toolkit_registry=toolkit_wrapper) + for charge_model in ['am1', 'pm3']: + molecule.compute_wiberg_bond_orders(toolkit_registry=toolkit_wrapper, charge_model=charge_model) + # TODO: Add test for equivalent Wiberg orders for equivalent bonds + + double_bond_has_wbo_near_2 = False + for bond in molecule.bonds: + if bond.bond_order == 2: + if 1.75 < bond.fractional_bond_order < 2.25: + double_bond_has_wbo_near_2 = True + assert double_bond_has_wbo_near_2 + + + + + + # TODO: Check partial charge invariants (total charge, charge equivalence) + + # TODO: Add test for aromaticity + # TODO: Add test and molecule functionality for isotopes + + + +class TestRDKitToolkitWrapper: + """Test the RDKitToolkitWrapper""" + + @pytest.mark.skipif(not RDKitToolkitWrapper.toolkit_is_available(), reason='RDKit Toolkit not available') + def test_smiles(self): + """Test RDKitToolkitWrapper to_smiles() and from_smiles()""" + toolkit_wrapper = RDKitToolkitWrapper() + # This differs from OE's expected output due to different canonicalization schemes + smiles = '[H][C]([H])([H])[C]([H])([H])[H]' + molecule = Molecule.from_smiles(smiles, + toolkit_registry=toolkit_wrapper) + smiles2 = molecule.to_smiles(toolkit_registry=toolkit_wrapper) + #print(smiles, smiles2) + assert smiles == smiles2 + + @pytest.mark.skipif(not RDKitToolkitWrapper.toolkit_is_available(), reason='RDKit Toolkit not available') + @pytest.mark.parametrize("smiles,exception_regex", [ + (r"C\C(F)=C(/F)CC(C)(Cl)Br", "Undefined chiral centers"), + (r"C\C(F)=C(/F)C[C@@](C)(Cl)Br", None), + (r"CC(F)=C(F)C[C@@](C)(Cl)Br", "Bonds with undefined stereochemistry") + ]) + def test_smiles_missing_stereochemistry(self, smiles, exception_regex): + """Test RDKitToolkitWrapper to_smiles() and from_smiles() when given ambiguous stereochemistry""" + toolkit_wrapper = RDKitToolkitWrapper() + + if exception_regex is not None: + with pytest.raises(UndefinedStereochemistryError, match=exception_regex): + Molecule.from_smiles(smiles, toolkit_registry=toolkit_wrapper) + else: + Molecule.from_smiles(smiles, toolkit_registry=toolkit_wrapper) + + # TODO: test_smiles_round_trip + + @pytest.mark.skipif(not RDKitToolkitWrapper.toolkit_is_available(), reason='RDKit Toolkit not available') + def test_smiles_add_H(self): + """Test RDKitToolkitWrapper to_smiles() and from_smiles()""" + toolkit_wrapper = RDKitToolkitWrapper() + input_smiles = 'CC' + # This differs from OE's expected output due to different canonicalization schemes + expected_output_smiles = '[H][C]([H])([H])[C]([H])([H])[H]' + molecule = Molecule.from_smiles(input_smiles, + toolkit_registry=toolkit_wrapper) + smiles2 = molecule.to_smiles(toolkit_registry=toolkit_wrapper) + assert smiles2 == expected_output_smiles + + + @pytest.mark.skipif(not RDKitToolkitWrapper.toolkit_is_available(), reason='RDKit Toolkit not available') + def test_smiles_charged(self): + """Test RDKitWrapper functions for reading/writing charged SMILES""" + toolkit_wrapper = RDKitToolkitWrapper() + # This differs from OE's expected output due to different canonicalization schemes + smiles = '[H][C]([H])([H])[N+]([H])([H])[H]' + molecule = Molecule.from_smiles(smiles, + toolkit_registry=toolkit_wrapper) + smiles2 = molecule.to_smiles(toolkit_registry=toolkit_wrapper) + assert smiles == smiles2 + + @pytest.mark.skipif(not RDKitToolkitWrapper.toolkit_is_available(), reason='RDKit Toolkit not available') + def test_to_from_rdkit_core_props_filled(self): + """Test RDKitToolkitWrapper to_rdkit() and from_rdkit() when given populated core property fields""" + toolkit_wrapper = RDKitToolkitWrapper() + + # Replacing with a simple molecule with stereochemistry + input_smiles = r'C\C(F)=C(/F)C[C@@](C)(Cl)Br' + expected_output_smiles = r'[H][C]([H])([H])/[C]([F])=[C](\[F])[C]([H])([H])[C@@]([Cl])([Br])[C]([H])([H])[H]' + molecule = Molecule.from_smiles(input_smiles, toolkit_registry=toolkit_wrapper) + assert molecule.to_smiles(toolkit_registry=toolkit_wrapper) == expected_output_smiles + + # Populate core molecule property fields + molecule.name = 'Alice' + partial_charges = unit.Quantity(np.array([-.9, -.8, -.7, -.6, + -.5, -.4, -.3, -.2, + -.1, 0., .1, .2, + .3, .4, .5, .6, + .7, .8]), unit.elementary_charge) + molecule.partial_charges = partial_charges + coords = unit.Quantity(np.array([['0.0', '1.0', '2.0'], ['3.0', '4.0', '5.0'], ['6.0', '7.0', '8.0'], + ['9.0', '10.0', '11.0'] , ['12.0', '13.0', '14.0'], ['15.0', '16.0', '17.0'], + ['18.0', '19.0', '20.0'], ['21.0', '22.0', '23.0'], ['24.0', '25.0', '26.0'], + ['27.0', '28.0', '29.0'], ['30.0', '31.0', '32.0'], ['33.0', '34.0', '35.0'], + ['36.0', '37.0', '38.0'], ['39.0', '40.0', '41.0'], ['42.0', '43.0', '44.0'], + ['45.0', '46.0', '47.0'], ['48.0', '49.0', '50.0'], ['51.0', '52.0', '53.0']]), + unit.angstrom) + molecule.add_conformer(coords) + # Populate core atom property fields + molecule.atoms[2].name = 'Bob' + # Ensure one atom has its stereochemistry specified + central_carbon_stereo_specified = False + for atom in molecule.atoms: + if (atom.atomic_number == 6) and atom.stereochemistry == "S": + central_carbon_stereo_specified = True + assert central_carbon_stereo_specified + + # Populate bond core property fields + fractional_bond_orders = [float(val) for val in range(18)] + for fbo, bond in zip(fractional_bond_orders, molecule.bonds): + bond.fractional_bond_order = fbo + + # Do a first conversion to/from oemol + rdmol = molecule.to_rdkit() + molecule2 = Molecule.from_rdkit(rdmol) + + # Test that properties survived first conversion + #assert molecule.to_dict() == molecule2.to_dict() + assert molecule.name == molecule2.name + # NOTE: This expects the same indexing scheme in the original and new molecule + + central_carbon_stereo_specified = False + for atom in molecule2.atoms: + if (atom.atomic_number == 6) and atom.stereochemistry == "S": + central_carbon_stereo_specified = True + assert central_carbon_stereo_specified + for atom1, atom2 in zip(molecule.atoms, molecule2.atoms): + assert atom1.to_dict() == atom2.to_dict() + for bond1, bond2 in zip(molecule.bonds, molecule2.bonds): + assert bond1.to_dict() == bond2.to_dict() + assert (molecule._conformers[0] == molecule2._conformers[0]).all() + for pc1, pc2 in zip(molecule._partial_charges, molecule2._partial_charges): + pc1_ul = pc1 / unit.elementary_charge + pc2_ul = pc2 / unit.elementary_charge + assert_almost_equal(pc1_ul, pc2_ul, decimal=6) + assert molecule2.to_smiles(toolkit_registry=toolkit_wrapper) == expected_output_smiles + # TODO: This should be its own test + + @pytest.mark.skipif(not RDKitToolkitWrapper.toolkit_is_available(), reason='RDKit Toolkit not available') + def test_to_from_rdkit_core_props_unset(self): + """Test RDKitToolkitWrapper to_rdkit() and from_rdkit() when given empty core property fields""" + toolkit_wrapper = RDKitToolkitWrapper() + + # Replacing with a simple molecule with stereochemistry + input_smiles = r'C\C(F)=C(/F)C[C@](C)(Cl)Br' + expected_output_smiles = r'[H][C]([H])([H])/[C]([F])=[C](\[F])[C]([H])([H])[C@]([Cl])([Br])[C]([H])([H])[H]' + molecule = Molecule.from_smiles(input_smiles, toolkit_registry=toolkit_wrapper) + assert molecule.to_smiles(toolkit_registry=toolkit_wrapper) == expected_output_smiles + + # Ensure one atom has its stereochemistry specified + central_carbon_stereo_specified = False + for atom in molecule.atoms: + if (atom.atomic_number == 6) and atom.stereochemistry == "R": + central_carbon_stereo_specified = True + assert central_carbon_stereo_specified + + # Do a first conversion to/from oemol + rdmol = molecule.to_rdkit() + molecule2 = Molecule.from_rdkit(rdmol) + + # Test that properties survived first conversion + assert molecule.name == molecule2.name + # NOTE: This expects the same indexing scheme in the original and new molecule + + central_carbon_stereo_specified = False + for atom in molecule2.atoms: + if (atom.atomic_number == 6) and atom.stereochemistry == "R": + central_carbon_stereo_specified = True + assert central_carbon_stereo_specified + for atom1, atom2 in zip(molecule.atoms, molecule2.atoms): + assert atom1.to_dict() == atom2.to_dict() + for bond1, bond2 in zip(molecule.bonds, molecule2.bonds): + assert bond1.to_dict() == bond2.to_dict() + assert (molecule._conformers == None) + assert (molecule2._conformers == None) + for pc1, pc2 in zip(molecule._partial_charges, molecule2._partial_charges): + pc1_ul = pc1 / unit.elementary_charge + pc2_ul = pc2 / unit.elementary_charge + assert_almost_equal(pc1_ul, pc2_ul, decimal=6) + assert molecule2.to_smiles(toolkit_registry=toolkit_wrapper) == expected_output_smiles + + @pytest.mark.skipif(not RDKitToolkitWrapper.toolkit_is_available(), reason='RDKit Toolkit not available') + def test_get_sdf_coordinates(self): + """Test RDKitToolkitWrapper for importing a single set of coordinates from a sdf file""" + toolkit_wrapper = RDKitToolkitWrapper() + filename = get_data_filename('molecules/toluene.sdf') + molecule = Molecule.from_file(filename, toolkit_registry=toolkit_wrapper) + assert len(molecule._conformers) == 1 + assert molecule._conformers[0].shape == (15, 3) + assert_almost_equal(molecule.conformers[0][5][1] / unit.angstrom, 2.0104, decimal=4) + + # Find a multiconformer SDF file + @pytest.mark.skip + #@pytest.mark.skipif(not RDKitToolkitWrapper.toolkit_is_available(), reason='RDKit Toolkit not available') + def test_get_multiconformer_sdf_coordinates(self): + """Test RDKitToolkitWrapper for importing a single set of coordinates from a sdf file""" + raise NotImplementedError + toolkit_wrapper = RDKitToolkitWrapper() + filename = get_data_filename('molecules/toluene.sdf') + molecule = Molecule.from_file(filename, toolkit_registry=toolkit_wrapper) + assert len(molecule._conformers) == 1 + assert molecule._conformers[0].shape == (15,3) + + # Unskip this when we implement PDB-reading support for RDKitToolkitWrapper + @pytest.mark.skip + @pytest.mark.skipif(not RDKitToolkitWrapper.toolkit_is_available(), reason='RDKit Toolkit not available') + def test_get_pdb_coordinates(self): + """Test RDKitToolkitWrapper for importing a single set of coordinates from a pdb file""" + toolkit_wrapper = RDKitToolkitWrapper() + filename = get_data_filename('molecules/toluene.pdb') + molecule = Molecule.from_file(filename, toolkit_registry=toolkit_wrapper) + assert len(molecule._conformers) == 1 + assert molecule._conformers[0].shape == (15,3) + + # Unskip this when we implement PDB-reading support for RDKitToolkitWrapper + @pytest.mark.skip + @pytest.mark.skipif(not RDKitToolkitWrapper.toolkit_is_available(), reason='RDKit Toolkit not available') + def test_load_aromatic_pdb(self): + """Test OpenEyeToolkitWrapper for importing molecule conformers""" + toolkit_wrapper = RDKitToolkitWrapper() + filename = get_data_filename('molecules/toluene.pdb') + molecule = Molecule.from_file(filename, toolkit_registry=toolkit_wrapper) + assert len(molecule._conformers) == 1 + assert molecule._conformers[0].shape == (15,3) + + @pytest.mark.skipif(not RDKitToolkitWrapper.toolkit_is_available(), reason='RDKit Toolkit not available') + def test_generate_conformers(self): + """Test RDKitToolkitWrapper generate_conformers()""" + toolkit_wrapper = RDKitToolkitWrapper() + smiles = '[H]C([H])([H])C([H])([H])[H]' + molecule = toolkit_wrapper.from_smiles(smiles) + molecule.generate_conformers() + # TODO: Make this test more robust + + + + + + + # TODO: Add test for higher bonds orders + # TODO: Add test for aromaticity + # TODO: Add test and molecule functionality for isotopes + # TODO: Add read tests for MOL/SDF, SMI + # TODO: Add read tests fpr multi-SMI files + # TODO: Add read tests for both files and file-like objects + # TODO: Add read/write tests for gzipped files + # TODO: Add write tests for all formats + + + + +class TestAmberToolsToolkitWrapper: + """Test the AmberToolsToolkitWrapper""" + + @pytest.mark.skipif(not RDKitToolkitWrapper.toolkit_is_available() or not AmberToolsToolkitWrapper.toolkit_is_available(), + reason='RDKitToolkit and AmberToolsToolkit not available') + def test_compute_partial_charges(self): + """Test OpenEyeToolkitWrapper compute_partial_charges()""" + toolkit_registry = ToolkitRegistry(toolkit_precedence=[AmberToolsToolkitWrapper, RDKitToolkitWrapper]) + + smiles = '[H]C([H])([H])C([H])([H])[H]' + molecule = Molecule.from_smiles(smiles, toolkit_registry=toolkit_registry) + molecule.generate_conformers(toolkit_registry=toolkit_registry) + + # TODO: Implementation of these tests is pending a decision on the API for our charge model + with pytest.raises(NotImplementedError) as excinfo: + charge_model = 'notARealChargeModel' + molecule.compute_partial_charges(toolkit_registry=toolkit_registry)#, charge_model=charge_model) + + # ['cm1', 'cm2'] + for charge_model in ['gas', 'mul', 'bcc']: + with pytest.raises(NotImplementedError) as excinfo: + molecule.compute_partial_charges(toolkit_registry=toolkit_registry)#, charge_model=charge_model) + charge_sum = 0 * unit.elementary_charge + for pc in molecule._partial_charges: + charge_sum += pc + assert charge_sum < 0.01 * unit.elementary_charge + + # For now, just test AM1-BCC while the SMIRNOFF spec for other charge models gets worked out + molecule.compute_partial_charges_am1bcc(toolkit_registry=toolkit_registry) # , charge_model=charge_model) + charge_sum = 0 * unit.elementary_charge + for pc in molecule._partial_charges: + charge_sum += pc + assert charge_sum < 0.002 * unit.elementary_charge + + + + @pytest.mark.skipif(not RDKitToolkitWrapper.toolkit_is_available() or not AmberToolsToolkitWrapper.toolkit_is_available(), + reason='RDKitToolkit and AmberToolsToolkit not available') + def test_compute_partial_charges_net_charge(self): + """Test OpenEyeToolkitWrapper compute_partial_charges() on a molecule with a net +1 charge""" + toolkit_registry = ToolkitRegistry(toolkit_precedence=[AmberToolsToolkitWrapper, RDKitToolkitWrapper]) + smiles = '[H]C([H])([H])[N+]([H])([H])[H]' + molecule = Molecule.from_smiles(smiles, toolkit_registry=toolkit_registry) + molecule.generate_conformers(toolkit_registry=toolkit_registry) + + + with pytest.raises(NotImplementedError) as excinfo: + charge_model = 'notARealChargeModel' + molecule.compute_partial_charges(toolkit_registry=toolkit_registry)#, charge_model=charge_model) + + # TODO: Figure out why ['cm1', 'cm2'] fail + for charge_model in ['gas', 'mul', 'bcc']: + with pytest.raises(NotImplementedError) as excinfo: + molecule.compute_partial_charges(toolkit_registry=toolkit_registry)#, charge_model=charge_model) + charge_sum = 0 * unit.elementary_charge + for pc in molecule._partial_charges: + charge_sum += pc + assert 0.99 * unit.elementary_charge < charge_sum < 1.01 * unit.elementary_charge + + # For now, I'm just testing AM1-BCC (will test more when the SMIRNOFF spec for other charges is finalized) + molecule.compute_partial_charges_am1bcc(toolkit_registry=toolkit_registry) + charge_sum = 0 * unit.elementary_charge + for pc in molecule._partial_charges: + charge_sum += pc + assert 0.999 * unit.elementary_charge < charge_sum < 1.001 * unit.elementary_charge + + +class TestToolkitRegistry: + """Test the ToolkitRegistry""" + + @pytest.mark.skipif(not OpenEyeToolkitWrapper.toolkit_is_available(), reason='OpenEye Toolkit not available') + def test_register_openeye(self): + """Test creation of toolkit registry with OpenEye toolkit""" + # Test registration of OpenEyeToolkitWrapper + toolkit_precedence = [OpenEyeToolkitWrapper] + registry = ToolkitRegistry(toolkit_precedence=toolkit_precedence, register_imported_toolkit_wrappers=False) + #registry.register_toolkit(OpenEyeToolkitWrapper) + assert set([type(c) for c in registry.registered_toolkits]) == set([OpenEyeToolkitWrapper]) + + # Test ToolkitRegistry.resolve() + assert registry.resolve('to_smiles') == registry.registered_toolkits[0].to_smiles + + # Test ToolkitRegistry.call() + smiles = '[H]C([H])([H])C([H])([H])[H]' + molecule = registry.call('from_smiles', smiles) + smiles2 = registry.call('to_smiles', molecule) + assert smiles == smiles2 + + @pytest.mark.skipif(not RDKitToolkitWrapper.toolkit_is_available(), reason='RDKit Toolkit not available') + def test_register_rdkit(self): + """Test creation of toolkit registry with RDKit toolkit""" + # Test registration of RDKitToolkitWrapper + toolkit_precedence = [RDKitToolkitWrapper] + registry = ToolkitRegistry(toolkit_precedence=toolkit_precedence, + register_imported_toolkit_wrappers=False) + #registry.register_toolkit(RDKitToolkitWrapper) + assert set([ type(c) for c in registry.registered_toolkits]) == set([RDKitToolkitWrapper]) + + # Test ToolkitRegistry.resolve() + assert registry.resolve('to_smiles') == registry.registered_toolkits[0].to_smiles + + # Test ToolkitRegistry.call() + smiles = '[H][C]([H])([H])[C]([H])([H])[H]' + molecule = registry.call('from_smiles', smiles) + smiles2 = registry.call('to_smiles', molecule) + assert smiles == smiles2 + + @pytest.mark.skipif( + not RDKitToolkitWrapper.toolkit_is_available() or not AmberToolsToolkitWrapper.toolkit_is_available(), + reason='RDKitToolkit and AmberToolsToolkit not available') + def test_register_ambertools(self): + """Test creation of toolkit registry with AmberToolsToolkitWrapper and RDKitToolkitWrapper + """ + # Test registration of AmberToolsToolkitWrapper + toolkit_precedence = [AmberToolsToolkitWrapper, RDKitToolkitWrapper] + registry = ToolkitRegistry(toolkit_precedence=toolkit_precedence, + register_imported_toolkit_wrappers=False) + #registry.register_toolkit(AmberToolsToolkitWrapper) + assert set([ type(c) for c in registry.registered_toolkits]) == set([AmberToolsToolkitWrapper,RDKitToolkitWrapper]) + + # Test ToolkitRegistry.resolve() + registry.resolve('compute_partial_charges') + assert registry.resolve('compute_partial_charges') == registry.registered_toolkits[0].compute_partial_charges + + # Test ToolkitRegistry.call() + registry.register_toolkit(RDKitToolkitWrapper) + smiles = '[H]C([H])([H])C([H])([H])[H]' + molecule = registry.call('from_smiles', smiles) + #partial_charges = registry.call('compute_partial_charges', molecule) + diff --git a/openforcefield/tests/test_topology.py b/openforcefield/tests/test_topology.py new file mode 100644 index 000000000..100591f5a --- /dev/null +++ b/openforcefield/tests/test_topology.py @@ -0,0 +1,480 @@ +#!/usr/bin/env python + +#============================================================================================= +# MODULE DOCSTRING +#============================================================================================= + +""" +Tests for Topology + +""" + +#============================================================================================= +# GLOBAL IMPORTS +#============================================================================================= + +from unittest import TestCase + +import pytest +import numpy as np +from simtk import unit +from openforcefield.utils import (BASIC_CHEMINFORMATICS_TOOLKITS, RDKIT_AVAILABLE, OPENEYE_AVAILABLE, + RDKitToolkitWrapper, OpenEyeToolkitWrapper) +from openforcefield.tests.utils import get_data_filename +from openforcefield.topology import Topology, ValenceDict, ImproperDict, DuplicateUniqueMoleculeError +from openforcefield.topology import Molecule + + +#============================================================================================= +# UTILITY FUNCTIONS +#============================================================================================= + +def assert_tuple_of_atoms_equal(atom_tuples1, atom_tuples2, transformed_dict_cls=ValenceDict): + """Check that two lists of atoms are the same. + + The function compares that the parent molecules are isomorphic and + that the molecule index is the same. + """ + assert len(atom_tuples1) == len(atom_tuples2) + + # They are atoms of isomorphic molecules. We assume here that all + # atoms in the same list of tuples belong to the same molecule so + # that we can perform the check only once. + molecule1 = atom_tuples1[0][0]._molecule + molecule2 = atom_tuples2[0][0]._molecule + assert molecule1 == molecule2 + for atom_tuple in atom_tuples1: + for a in atom_tuple: + assert a._molecule is molecule1 + for atom_tuple in atom_tuples2: + for a in atom_tuple: + assert a._molecule is molecule2 + + # All atoms are equal. Use ValenceDict for this + atom_indices = [] + for atom_tuples in [atom_tuples1, atom_tuples2]: + valence_dict = transformed_dict_cls() + for atom_tuple in atom_tuples: + key = tuple(a.molecule_atom_index for a in atom_tuple) + valence_dict[key] = atom_tuple + atom_indices.append(valence_dict) + assert set(atom_indices[0]) == set(atom_indices[1]) + + +#============================================================================================= +# TESTS +#============================================================================================= + +# IF we've done our jobs right, it shouldn't matter which toolkit the tests for Topology run using (both's behaviors +# should be indistinguishable) +def test_cheminformatics_toolkit_is_installed(): + """Ensure that at least one supported cheminformatics toolkit is installed.""" + if not(RDKIT_AVAILABLE) and not(OPENEYE_AVAILABLE): + msg = 'No supported cheminformatics toolkits are installed. Please install a supported toolkit:\n' + msg += str(BASIC_CHEMINFORMATICS_TOOLKITS) + raise Exception(msg) + + +class TestTopology(TestCase): + + def setUp(self): + self.empty_molecule = Molecule() + self.ethane_from_smiles = Molecule.from_smiles('CC') + self.ethene_from_smiles = Molecule.from_smiles('C=C') + self.propane_from_smiles = Molecule.from_smiles('CCC') + + filename = get_data_filename('molecules/toluene.sdf') + self.toluene_from_sdf = Molecule.from_file(filename) + if OpenEyeToolkitWrapper.toolkit_is_available(): + filename = get_data_filename('molecules/toluene_charged.mol2') + # TODO: This will require openeye to load + self.toluene_from_charged_mol2 = Molecule.from_file(filename) + self.charged_methylamine_from_smiles = Molecule.from_smiles('[H]C([H])([H])[N+]([H])([H])[H]') + + molecule = Molecule.from_smiles('CC') + carbons = [atom for atom in molecule.atoms if atom.atomic_number == 6] + c0_hydrogens = [atom for atom in carbons[0].bonded_atoms if atom.atomic_number == 1] + molecule.add_bond_charge_virtual_site((carbons[0], carbons[1]), + 0.1*unit.angstrom, + charge_increments=[0.1, 0.05] * unit.elementary_charge + ) + molecule.add_monovalent_lone_pair_virtual_site((c0_hydrogens[0], carbons[0], carbons[1]), + 0.2*unit.angstrom, + 20*unit.degree, + 25*unit.degree, + charge_increments=[0.01, 0.02, 0.03] * unit.elementary_charge + ) + self.ethane_from_smiles_w_vsites = Molecule(molecule) + + # Make a propane with virtual sites + molecule = Molecule.from_smiles('CCC') + carbons = [atom for atom in molecule.atoms if atom.atomic_number == 6] + c0_hydrogens = [atom for atom in carbons[0].bonded_atoms if atom.atomic_number == 1] + molecule.add_bond_charge_virtual_site((carbons[0], carbons[1]), + 0.1*unit.angstrom, + charge_increments=[0.1, 0.05] * unit.elementary_charge + ) + molecule.add_monovalent_lone_pair_virtual_site((c0_hydrogens[0], carbons[0], carbons[1]), + 0.2*unit.angstrom, + 20*unit.degree, + 25*unit.degree, + charge_increments=[0.01, 0.02, 0.03] * unit.elementary_charge + ) + self.propane_from_smiles_w_vsites = Molecule(molecule) + + def test_empty(self): + """Test creation of empty topology""" + topology = Topology() + assert topology.n_reference_molecules == 0 + assert topology.n_topology_molecules == 0 + assert topology.n_topology_atoms == 0 + assert topology.n_topology_bonds == 0 + assert topology.n_topology_particles == 0 + assert topology.n_topology_virtual_sites == 0 + assert topology.box_vectors is None + assert len(topology.constrained_atom_pairs.items()) == 0 + + def test_box_vectors(self): + """Test the getter and setter for box_vectors""" + topology = Topology() + good_box_vectors = unit.Quantity(np.array([10,20,30]), unit.angstrom) + bad_box_vectors = np.array([10,20,30]) # They're bad because they're unitless + assert topology.box_vectors is None + + with self.assertRaises(ValueError) as context: + topology.box_vectors = bad_box_vectors + assert topology.box_vectors is None + + topology.box_vectors = good_box_vectors + assert (topology.box_vectors == good_box_vectors).all() + + + def test_from_smiles(self): + """Test creation of a openforcefield Topology object from a SMILES string""" + topology = Topology.from_molecules(self.ethane_from_smiles) + + assert topology.n_reference_molecules == 1 + assert topology.n_topology_molecules == 1 + assert topology.n_topology_atoms == 8 + assert topology.n_topology_bonds == 7 + assert topology.n_topology_particles == 8 + assert topology.n_topology_virtual_sites == 0 + assert topology.box_vectors is None + assert len(topology.constrained_atom_pairs.items()) == 0 + + topology.add_molecule(self.ethane_from_smiles) + + assert topology.n_reference_molecules == 1 + assert topology.n_topology_molecules == 2 + assert topology.n_topology_atoms == 16 + assert topology.n_topology_bonds == 14 + assert topology.n_topology_particles == 16 + assert topology.n_topology_virtual_sites == 0 + assert topology.box_vectors is None + assert len(topology.constrained_atom_pairs.items()) == 0 + + def test_from_smiles_unique_mols(self): + """Test the addition of two different molecules to a topology""" + topology = Topology.from_molecules([self.ethane_from_smiles, self.propane_from_smiles]) + assert topology.n_topology_molecules == 2 + assert topology.n_reference_molecules == 2 + + + def test_n_topology_atoms(self): + """Test n_atoms function""" + topology = Topology() + assert topology.n_topology_atoms == 0 + assert topology.n_topology_bonds == 0 + topology.add_molecule(self.ethane_from_smiles) + assert topology.n_topology_atoms == 8 + assert topology.n_topology_bonds == 7 + + def test_get_atom(self): + """Test Topology.atom function (atom lookup from index)""" + topology = Topology() + topology.add_molecule(self.ethane_from_smiles) + with self.assertRaises(Exception) as context: + topology_atom = topology.atom(-1) + + # Make sure we get 2 carbons and 8 hydrogens + n_carbons = 0 + n_hydrogens = 0 + for index in range(8): + if topology.atom(index).atomic_number == 6: + n_carbons += 1 + if topology.atom(index).atomic_number == 1: + n_hydrogens += 1 + assert n_carbons == 2 + assert n_hydrogens == 6 + + with self.assertRaises(Exception) as context: + topology_atom = topology.atom(8) + + def test_get_bond(self): + """Test Topology.bond function (bond lookup from index)""" + topology = Topology() + topology.add_molecule(self.ethane_from_smiles) + topology.add_molecule(self.ethene_from_smiles) + with self.assertRaises(Exception) as context: + topology_atom = topology.bond(-1) + + n_single_bonds = 0 + n_double_bonds = 0 + n_ch_bonds = 0 + n_cc_bonds = 0 + for index in range(12): # 7 from ethane, 5 from ethene + topology_bond = topology.bond(index) + if topology_bond.bond_order == 1: + n_single_bonds += 1 + if topology_bond.bond_order == 2: + n_double_bonds += 1 + n_bond_carbons = 0 + n_bond_hydrogens = 0 + for atom in topology_bond.atoms: + if atom.atomic_number == 6: + n_bond_carbons += 1 + if atom.atomic_number == 1: + n_bond_hydrogens += 1 + if n_bond_carbons == 2: + n_cc_bonds += 1 + if n_bond_carbons == 1 and n_bond_hydrogens == 1: + n_ch_bonds += 1 + + assert n_single_bonds == 11 + assert n_double_bonds == 1 + assert n_cc_bonds == 2 + assert n_ch_bonds == 10 + + with self.assertRaises(Exception) as context: + topology_bond = topology.bond(12) + + + def test_get_virtual_site(self): + """Test Topology.virtual_site function (get virtual site from index) + """ + topology = Topology() + topology.add_molecule(self.ethane_from_smiles_w_vsites) + assert topology.n_topology_virtual_sites == 2 + topology.add_molecule(self.propane_from_smiles_w_vsites) + assert topology.n_topology_virtual_sites == 4 + with self.assertRaises(Exception) as context: + topology_vsite = topology.virtual_site(-1) + with self.assertRaises(Exception) as context: + topology_vsite = topology.virtual_site(4) + topology_vsite1 = topology.virtual_site(0) + topology_vsite2 = topology.virtual_site(1) + topology_vsite3 = topology.virtual_site(2) + topology_vsite4 = topology.virtual_site(3) + assert topology_vsite1.type == "BondChargeVirtualSite" + assert topology_vsite2.type == "MonovalentLonePairVirtualSite" + assert topology_vsite3.type == "BondChargeVirtualSite" + assert topology_vsite4.type == "MonovalentLonePairVirtualSite" + + n_equal_atoms = 0 + for topology_atom in topology.topology_atoms: + for vsite in topology.topology_virtual_sites: + for vsite_atom in vsite.atoms: + if topology_atom == vsite_atom: + n_equal_atoms += 1 + + # There are four virtual sites -- Two BondCharges with 2 atoms, and two MonovalentLonePairs with 3 atoms + assert n_equal_atoms == 10 + + def test_is_bonded(self): + """Test Topology.virtual_site function (get virtual site from index) + """ + topology = Topology() + topology.add_molecule(self.propane_from_smiles_w_vsites) + #raise Exception([str(topology.atom(i).atom) for i in range(6)]) + topology.assert_bonded(0, 1) + topology.assert_bonded(1, 0) + topology.assert_bonded(1, 2) + # C-H bond + topology.assert_bonded(0,4) + with self.assertRaises(Exception) as context: + topology.assert_bonded(0, 2) + + def test_angles(self): + """Topology.angles should return image angles of all topology molecules.""" + molecule1 = self.ethane_from_smiles + molecule2 = self.propane_from_smiles + + # Create topology. + topology = Topology() + topology.add_molecule(molecule1) + topology.add_molecule(molecule1) + topology.add_molecule(molecule2) + + # The topology should have the correct number of angles. + topology_angles = list(topology.angles) + assert len(topology_angles) == topology.n_angles + assert topology.n_angles == 2*molecule1.n_angles + molecule2.n_angles + + # Check that the topology angles are the correct ones. + mol_angle_atoms1 = list(molecule1.angles) + mol_angle_atoms2 = list(molecule2.angles) + top_angle_atoms1 = [tuple(a._atom for a in atoms) + for atoms in topology_angles[:molecule1.n_angles]] + top_angle_atoms2 = [tuple(a._atom for a in atoms) + for atoms in topology_angles[molecule1.n_angles:2*molecule1.n_angles]] + top_angle_atoms3 = [tuple(a._atom for a in atoms) + for atoms in topology_angles[2*molecule1.n_angles:]] + + assert_tuple_of_atoms_equal(top_angle_atoms1, mol_angle_atoms1) + assert_tuple_of_atoms_equal(top_angle_atoms2, mol_angle_atoms1) + assert_tuple_of_atoms_equal(top_angle_atoms3, mol_angle_atoms2) + + def test_propers(self): + """Topology.propers should return image propers torsions of all topology molecules.""" + molecule1 = self.ethane_from_smiles + molecule2 = self.propane_from_smiles + + # Create topology. + topology = Topology() + topology.add_molecule(molecule1) + topology.add_molecule(molecule1) + topology.add_molecule(molecule2) + + # The topology should have the correct number of propers. + topology_propers = list(topology.propers) + assert len(topology_propers) == topology.n_propers + assert topology.n_propers == 2*molecule1.n_propers + molecule2.n_propers + + # Check that the topology propers are the correct ones. + mol_proper_atoms1 = list(molecule1.propers) + mol_proper_atoms2 = list(molecule2.propers) + top_proper_atoms1 = [tuple(a._atom for a in atoms) + for atoms in topology_propers[:molecule1.n_propers]] + top_proper_atoms2 = [tuple(a._atom for a in atoms) + for atoms in topology_propers[molecule1.n_propers:2*molecule1.n_propers]] + top_proper_atoms3 = [tuple(a._atom for a in atoms) + for atoms in topology_propers[2*molecule1.n_propers:]] + + assert_tuple_of_atoms_equal(top_proper_atoms1, mol_proper_atoms1) + assert_tuple_of_atoms_equal(top_proper_atoms2, mol_proper_atoms1) + assert_tuple_of_atoms_equal(top_proper_atoms3, mol_proper_atoms2) + + def test_impropers(self): + """Topology.impropers should return image impropers torsions of all topology molecules.""" + molecule1 = self.ethane_from_smiles + molecule2 = self.propane_from_smiles + + # Create topology. + topology = Topology() + topology.add_molecule(molecule1) + topology.add_molecule(molecule1) + topology.add_molecule(molecule2) + + # The topology should have the correct number of impropers. + topology_impropers = list(topology.impropers) + assert len(topology_impropers) == topology.n_impropers + assert topology.n_impropers == 2*molecule1.n_impropers + molecule2.n_impropers + + # Check that the topology impropers are the correct ones. + mol_improper_atoms1 = list(molecule1.impropers) + mol_improper_atoms2 = list(molecule2.impropers) + top_improper_atoms1 = [tuple(a._atom for a in atoms) + for atoms in topology_impropers[:molecule1.n_impropers]] + top_improper_atoms2 = [tuple(a._atom for a in atoms) + for atoms in topology_impropers[molecule1.n_impropers:2*molecule1.n_impropers]] + top_improper_atoms3 = [tuple(a._atom for a in atoms) + for atoms in topology_impropers[2*molecule1.n_impropers:]] + + assert_tuple_of_atoms_equal(top_improper_atoms1, mol_improper_atoms1) + assert_tuple_of_atoms_equal(top_improper_atoms2, mol_improper_atoms1) + assert_tuple_of_atoms_equal(top_improper_atoms3, mol_improper_atoms2) + + + # test_get_fractional_bond_order + # test_two_of_same_molecule + # test_two_different_molecules + # test_to_from_dict + # test_get_molecule + # test_get_topology_atom + # test_get_topology_bond + # test_get_topology_virtual_site + # test_get_topology_molecule + # test_is_bonded + # TODO: Test serialization + + + def test_from_openmm(self): + """Test creation of an openforcefield Topology object from an OpenMM Topology and component molecules""" + from simtk.openmm import app + pdbfile = app.PDBFile(get_data_filename('systems/packmol_boxes/cyclohexane_ethanol_0.4_0.6.pdb')) + #toolkit_wrapper = RDKitToolkitWrapper() + #molecules = [ Molecule.from_file(get_data_filename(name)) for name in ('molecules/ethanol.mol2', + # 'molecules/cyclohexane.mol2')] + molecules = [] + molecules.append(Molecule.from_smiles('CCO')) + molecules.append(Molecule.from_smiles('C1CCCCC1')) + + topology = Topology.from_openmm(pdbfile.topology, unique_molecules=molecules) + assert topology.n_reference_molecules == 2 + assert topology.n_topology_molecules == 239 + + @pytest.mark.skipif( not(OpenEyeToolkitWrapper.toolkit_is_available()), reason='Test requires OE toolkit') + def test_from_openmm_duplicate_unique_mol(self): + """Check that a DuplicateUniqueMoleculeError is raised if we try to pass in two indistinguishably unique mols""" + from simtk.openmm import app + pdbfile = app.PDBFile(get_data_filename('systems/packmol_boxes/cyclohexane_ethanol_0.4_0.6.pdb')) + #toolkit_wrapper = RDKitToolkitWrapper() + molecules = [ Molecule.from_file(get_data_filename(name)) for name in ('molecules/ethanol.mol2', + 'molecules/ethanol_reordered.mol2', + 'molecules/cyclohexane.mol2')] + with self.assertRaises(DuplicateUniqueMoleculeError) as context: + topology = Topology.from_openmm(pdbfile.topology, unique_molecules=molecules) + + @pytest.mark.skip + def test_from_openmm_distinguish_using_stereochemistry(self): + """Test creation of an openforcefield Topology object from an OpenMM topology with stereoisomers""" + # From Jeff: The graph representation created from OMM molecules during the matching + # process doesn't encode stereochemistry. + raise NotImplementedError + + @pytest.mark.skipif( not(OpenEyeToolkitWrapper.toolkit_is_available()), reason='Test requires OE toolkit') + def test_chemical_environments_matches_OE(self): + """Test Topology.chemical_environment_matches""" + from simtk.openmm import app + toolkit_wrapper = OpenEyeToolkitWrapper() + pdbfile = app.PDBFile(get_data_filename('systems/packmol_boxes/cyclohexane_ethanol_0.4_0.6.pdb')) + # toolkit_wrapper = RDKitToolkitWrapper() + molecules = [Molecule.from_file(get_data_filename(name)) for name in ('molecules/ethanol.mol2', + 'molecules/cyclohexane.mol2')] + topology = Topology.from_openmm(pdbfile.topology, unique_molecules=molecules) + # Test for substructure match + matches = topology.chemical_environment_matches("[C:1]-[C:2]-[O:3]", toolkit_registry=toolkit_wrapper) + assert len(matches) == 143 + assert tuple(i.topology_atom_index for i in matches[0]) == (1728, 1729, 1730) + # Test for whole-molecule match + matches = topology.chemical_environment_matches("[H][C:1]([H])([H])-[C:2]([H])([H])-[O:3][H]", toolkit_registry=toolkit_wrapper) + assert len(matches) == 1716 # 143 * 12 (there are 12 possible hydrogen mappings) + assert tuple(i.topology_atom_index for i in matches[0]) == (1728, 1729, 1730) + # Search for a substructure that isn't there + matches = topology.chemical_environment_matches("[C][C:1]-[C:2]-[O:3]", toolkit_registry=toolkit_wrapper) + assert len(matches) == 0 + + @pytest.mark.skipif( not(RDKitToolkitWrapper.toolkit_is_available()), reason='Test requires RDKit') + def test_chemical_environments_matches_RDK(self): + """Test Topology.chemical_environment_matches""" + from simtk.openmm import app + toolkit_wrapper = RDKitToolkitWrapper() + pdbfile = app.PDBFile(get_data_filename('systems/packmol_boxes/cyclohexane_ethanol_0.4_0.6.pdb')) + # toolkit_wrapper = RDKitToolkitWrapper() + #molecules = [Molecule.from_file(get_data_filename(name)) for name in ('molecules/ethanol.mol2', + # 'molecules/cyclohexane.mol2')] + molecules = [] + molecules.append(Molecule.from_smiles('CCO')) + molecules.append(Molecule.from_smiles('C1CCCCC1')) + topology = Topology.from_openmm(pdbfile.topology, unique_molecules=molecules) + # Count CCO matches + matches = topology.chemical_environment_matches("[C:1]-[C:2]-[O:3]", toolkit_registry=toolkit_wrapper) + assert len(matches) == 143 + assert tuple(i.topology_atom_index for i in matches[0]) == (1728, 1729, 1730) + matches = topology.chemical_environment_matches("[H][C:1]([H])([H])-[C:2]([H])([H])-[O:3][H]", toolkit_registry=toolkit_wrapper) + assert len(matches) == 1716 # 143 * 12 (there are 12 possible hydrogen mappings) + assert tuple(i.topology_atom_index for i in matches[0]) == (1728, 1729, 1730) + # Search for a substructure that isn't there + matches = topology.chemical_environment_matches("[C][C:1]-[C:2]-[O:3]", toolkit_registry=toolkit_wrapper) + assert len(matches) == 0 + diff --git a/openforcefield/tests/test_utils.py b/openforcefield/tests/test_utils.py index 75955a1aa..1d6b1ca4d 100644 --- a/openforcefield/tests/test_utils.py +++ b/openforcefield/tests/test_utils.py @@ -1,24 +1,94 @@ -from functools import partial -from unittest import TestCase -import parmed +#!/usr/bin/env python + +#============================================================================================= +# MODULE DOCSTRING +#============================================================================================= + +""" +Tests for utility methods + +""" + +#============================================================================================= +# GLOBAL IMPORTS +#============================================================================================= + +import ast +import os + +import pytest +from simtk import unit + from openforcefield import utils -class TestUtils(TestCase): - def test_read_molecules(self): - molecules = utils.read_molecules('zinc-subset-tripos.mol2.gz', verbose=False) - def test_positions(self): - """Test ability to extract and set positions.""" - molecules = utils.read_molecules('zinc-subset-tripos.mol2.gz', verbose=False) - positions = utils.extractPositionsFromOEMol(molecules[0]) - utils.setPositionsInOEMol(molecules[0], positions) - def test_smirnoff_structure(self): - """Test function that generates the SMIRNOFF parmed.Structure.""" - molecule = utils.read_molecules('toluene.pdb', verbose=False)[0] - molecule_structure = utils.generateSMIRNOFFStructure(molecule) - self.assertIsInstance(molecule_structure, parmed.structure.Structure) - def test_protein_structure(self): - from simtk.openmm import app - pdbfile = utils.get_data_filename('proteins/T4-protein.pdb') - proteinpdb = app.PDBFile(pdbfile) - protein_structure = utils.generateProteinStructure(proteinpdb) - self.assertIsInstance(protein_structure, parmed.structure.Structure) + +#============================================================================================= +# TESTS +#============================================================================================= + +def test_subclasses(): + """Test that all subclasses (and descendents) are correctly identified by all_subclasses()""" + class Foo(object): + pass + class FooSubclass1(Foo): + pass + class FooSubclass2(Foo): + pass + class FooSubSubclass(FooSubclass1): + pass + + subclass_names = [ cls.__name__ for cls in utils.all_subclasses(Foo) ] + assert set(subclass_names) == set(['FooSubclass1', 'FooSubclass2', 'FooSubSubclass']) + +def test_temporary_cd(): + """Test temporary_cd() context manager""" + initial_dir = os.getcwd() + temporary_dir = '/' + from openforcefield.utils import temporary_cd + with temporary_cd(temporary_dir): + assert os.getcwd() == temporary_dir + assert os.getcwd() == initial_dir + +def test_temporary_directory(): + """Test temporary_directory() context manager""" + from openforcefield.utils import temporary_directory + initial_dir = os.getcwd() + with temporary_directory() as tmp_dir: + # Make sure the temporary directory is not the current directory + assert tmp_dir != initial_dir + + # Make sure the temporary directory is writeable + output_filename = os.path.join(tmp_dir, 'test.out') + outfile = open(output_filename,'w') + outfile.write('test') + outfile.close() + + # Make sure the file we created exists + assert os.path.exists(output_filename) + + # Make sure the directory has been cleaned up + assert not os.path.exists(tmp_dir), "Temporary directory was not automatically cleaned up." + assert not os.path.exists(output_filename), "Temporary directory was not automatically cleaned up." + +def test_get_data_filename(): + """Test get_data_filename()""" + from openforcefield.utils import get_data_filename + filename = get_data_filename('forcefield/tip3p.offxml') + assert os.path.exists(filename) + + +@pytest.mark.parametrize('unit_string,expected_unit',[ + ('kilocalories_per_mole', unit.kilocalories_per_mole), + ('kilocalories_per_mole/angstrom**2', unit.kilocalories_per_mole/unit.angstrom**2), + ('joule/(mole * nanometer**2)', unit.joule/(unit.mole * unit.nanometer**2)), + ('picosecond**(-1)', unit.picosecond**(-1)), + ('300.0 * kelvin', 300*unit.kelvin), + ('1 * kilojoule + 500 * joule', 1.5*unit.kilojoule), + ('1 / meter', 1.0 / unit.meter) +]) +def test_ast_eval(unit_string, expected_unit): + """Test that _ast_eval() correctly parses string quantities.""" + from openforcefield.utils.utils import _ast_eval + ast_root_node = ast.parse(unit_string, mode='eval').body + parsed_units = _ast_eval(ast_root_node) + assert parsed_units == expected_unit diff --git a/openforcefield/tests/test_utils_serialization.py b/openforcefield/tests/test_utils_serialization.py new file mode 100644 index 000000000..61369f773 --- /dev/null +++ b/openforcefield/tests/test_utils_serialization.py @@ -0,0 +1,146 @@ +#!/usr/bin/env python + +#============================================================================================= +# MODULE DOCSTRING +#============================================================================================= + +""" +Tests for utility methods for serialization + +""" + +#============================================================================================= +# GLOBAL IMPORTS +#============================================================================================= + +import pytest + + +#============================================================================================= +# TESTS +#============================================================================================= + +from openforcefield.utils.serialization import Serializable + +class Thing(Serializable): + + def __init__(self, description, mylist): + self.description = description + self.mylist = mylist + + def to_dict(self): + return { + 'description' : self.description, + 'mylist' : self.mylist + } + + @classmethod + def from_dict(cls, d): + return cls(d['description'], d['mylist']) + + def __eq__(self, other): + """Comparator for asserting object field equality.""" + equality = self.description == other.description + equality &= self.mylist == other.mylist + return equality + + +# DEBUG +def write(filename, contents): + if type(contents) == str: + mode = 'w' + elif type(contents) == bytes: + mode = 'wb' + else: + raise Exception('Cannot handle contents of type {}'.format(type(contents))) + with open(filename, mode) as outfile: + outfile.write(contents) + + +class TestUtilsSerialization: + """Test serialization and deserialization of a simple class.""" + + @classmethod + def setup_class(cls): + cls.thing = Thing('blorb', [1, 2, 3]) + + def test_json(self): + """Test JSON serialization""" + json_thing = self.thing.to_json() + thing_from_json = self.thing.__class__.from_json(json_thing) + assert self.thing == thing_from_json + + def test_yaml(self): + """Test YAML serialization""" + yaml_thing = self.thing.to_yaml() + thing_from_yaml = self.thing.__class__.from_yaml(yaml_thing) + assert self.thing == thing_from_yaml + + def test_bson(self): + """Test BSON serialization""" + bson_thing = self.thing.to_bson() + thing_from_bson = self.thing.__class__.from_bson(bson_thing) + assert self.thing == thing_from_bson + + @pytest.mark.wip(reason=("the current implementation of to_toml cannot handle dict " + "keys associated to None (e.g. the ToolkitAM1BCC tag in the " + "TestUtilsSMIRNOFFSerialization suite).")) + def test_toml(self): + """Test TOML serialization""" + toml_thing = self.thing.to_toml() + thing_from_toml = self.thing.__class__.from_toml(toml_thing) + assert self.thing == thing_from_toml + + def test_messagepack(self): + """Test MessagePack serialization""" + messagepack_thing = self.thing.to_messagepack() + thing_from_messagepack = self.thing.__class__.from_messagepack(messagepack_thing) + assert self.thing == thing_from_messagepack + + @pytest.mark.wip(reason='from/to_xml is not implemented yet. This test fails ' + 'because the list of integers is saved in the XML as ' + 'a list of numeric strings.') + def test_xml(self): + """Test XML serialization""" + xml_thing = self.thing.to_xml() + thing_from_xml = self.thing.__class__.from_xml(xml_thing) + assert self.thing == thing_from_xml + + def test_pickle(self): + """Test pickle serialization""" + pkl_thing = self.thing.to_pickle() + thing_from_pkl = self.thing.__class__.from_pickle(pkl_thing) + assert self.thing == thing_from_pkl + + +class DictionaryContainer(Serializable): + def __init__(self, dictionary): + import copy + self.dictionary = copy.deepcopy(dictionary) + + def to_dict(self): + return self.dictionary + + @staticmethod + def from_dict(dictionary): + return DictionaryContainer(dictionary) + + def __eq__(self, other): + """Comparator for asserting object field equality.""" + return self.dictionary == other.dictionary + + +class TestUtilsSMIRNOFFSerialization(TestUtilsSerialization): + """Test serialization and deserialization of smirnoff99Frosst.""" + + @classmethod + def setup_class(cls): + cls.thing = Thing('blorb', [1, 2, 3]) + # Create an example object holding the SMIRNOFF xmltodict dictionary representation + import xmltodict + from openforcefield.utils import get_data_filename + filename = get_data_filename('forcefield/smirnoff99Frosst.offxml') + with open(filename, 'r') as f: + xml = f.read() + dictionary = xmltodict.parse(xml) + cls.thing = DictionaryContainer(dictionary) diff --git a/openforcefield/tests/test_utils_structure.py b/openforcefield/tests/test_utils_structure.py new file mode 100644 index 000000000..451c3f1df --- /dev/null +++ b/openforcefield/tests/test_utils_structure.py @@ -0,0 +1,151 @@ +#!/usr/bin/env python + +#============================================================================================= +# MODULE DOCSTRING +#============================================================================================= + +""" +Tests for utility methods that involve parmed Structure manipulation + +""" + +#============================================================================================= +# GLOBAL IMPORTS +#============================================================================================= + +import os + +import parmed +import pytest + +from openforcefield.typing.engines.smirnoff import ForceField +from openforcefield.topology import Molecule, Topology +from openforcefield import utils +import openforcefield.utils.structure as structure + + +#============================================================================================= +# TESTS +#============================================================================================= + +requires_openeye_mol2 = pytest.mark.skipif(not utils.OpenEyeToolkitWrapper.is_available(), + reason='OpenEye is required to parse mol2 files') + +class TestUtilsStructure: + + @requires_openeye_mol2 + def test_read_molecules(self): + molecules = structure.read_molecules('zinc-subset-tripos.mol2.gz', verbose=False) + + @requires_openeye_mol2 + def test_positions(self): + """Test ability to extract and set positions.""" + molecules = structure.read_molecules('zinc-subset-tripos.mol2.gz', verbose=False) + positions = structure.extractPositionsFromOEMol(molecules[0]) + structure.setPositionsInOEMol(molecules[0], positions) + + @requires_openeye_mol2 + def test_smirnoff_structure(self): + """Test function that generates the SMIRNOFF parmed.Structure.""" + molecule = structure.read_molecules('toluene.pdb', verbose=False)[0] + molecule_structure = structure.generateSMIRNOFFStructure(molecule) + assert isinstance(molecule_structure, parmed.structure.Structure) + + def test_protein_structure(self): + from simtk.openmm import app + pdbfile = utils.get_data_filename('proteins/T4-protein.pdb') + proteinpdb = app.PDBFile(pdbfile) + protein_structure = structure.generateProteinStructure(proteinpdb) + assert isinstance(protein_structure, parmed.structure.Structure) + + +@requires_openeye_mol2 +def test_merge_system(): + """Test merging of a system created from AMBER and another created from SMIRNOFF.""" + from .utils import create_system_from_amber, get_amber_filepath, get_alkethoh_filepath + + # Create System from AMBER + prmtop_filename, inpcrd_filename = get_amber_filepath('cyclohexane_ethanol_0.4_0.6') + system0, topology0, positions0 = create_system_from_amber(prmtop_filename, inpcrd_filename) + + # TODO: + from openeye import oechem + # Load simple OEMol + alkethoh_mol2_filepath = get_alkethoh_filepath('AlkEthOH_c100')[0] + ifs = oechem.oemolistream(alkethoh_mol2_filepath) + mol = oechem.OEMol() + flavor = oechem.OEIFlavor_Generic_Default | oechem.OEIFlavor_MOL2_Default | oechem.OEIFlavor_MOL2_Forcefield + ifs.SetFlavor(oechem.OEFormat_MOL2, flavor) + oechem.OEReadMolecule(ifs, mol) + oechem.OETriposAtomNames(mol) + + # Load forcefield file. + AlkEthOH_offxml_filename = utils.get_data_filename('forcefield/Frosst_AlkEthOH.offxml') + forcefield = ForceField(AlkEthOH_offxml_filename) + + # Create OpenMM System and Topology. + off_mol = Molecule.from_openeye(mol, allow_undefined_stereo=True) + off_top = Topology.from_molecules([off_mol]) + system1 = forcefield.create_openmm_system(off_top) + topology1 = structure.generateTopologyFromOEMol(mol) + positions1 = structure.extractPositionsFromOEMol(mol) + + structure.merge_system(topology0, topology1, system0, system1, positions0, positions1, verbose=True) + + +@pytest.mark.slow +@requires_openeye_mol2 +def test_component_combination(): + """Test that a system still yields the same energy after rebuilding it out of its components + """ + from simtk import openmm + from .utils import compare_system_energies, get_packmol_pdbfile + + # We've had issues where subsequent instances of a molecule might have zero charges + # Here we'll try to catch this (and also explicitly check the charges) by re-building + # a system out of its components + + # Create an OpenMM System from mol2 files containing a cyclohexane-ethanol mixture. + AlkEthOH_offxml_filename = utils.get_data_filename('forcefield/Frosst_AlkEthOH.offxml') + forcefield = ForceField(AlkEthOH_offxml_filename) + pdbfile = openmm.app.PDBFile(get_packmol_pdbfile('cyclohexane_ethanol_0.4_0.6')) + sdf_file_paths = [utils.get_data_filename(os.path.join('systems', 'monomers', name+'.sdf')) + for name in ('ethanol', 'cyclohexane')] + molecules = [Molecule.from_file(file_path) for file_path in sdf_file_paths] + topology = Topology.from_openmm(pdbfile.topology, unique_molecules=molecules) + system = forcefield.create_openmm_system(topology) + + # Convert System to a ParmEd Structure + structure = parmed.openmm.topsystem.load_topology(topology.to_openmm(), system, pdbfile.positions) + + # Split the Structure into components, then re-compose it out of its components + tmp = structure.split() + strs, nums = [], [] + for s, n in tmp: + strs.append(s) + nums.append(n) + nums = [len(n) for n in nums] + + # Re-compose Structure from components + new_structure = strs[0]*nums[0] + for idx in range(1,len(nums)): + new_structure += strs[idx]*nums[idx] + # Swap in coordinates again + new_structure.positions = structure.positions + + # Create System + newsys = new_structure.createSystem(nonbondedMethod=openmm.app.NoCutoff, constraints=None, implicitSolvent=None) + + # Cross check energies + groups0, groups1, energy0, energy1 = compare_system_energies(pdbfile.topology, pdbfile.topology, system, newsys, pdbfile.positions, verbose = False) + + # Also check that that the number of components is equal to the number I expect + if not len(nums) == 2: + print("Error: Test system has incorrect number of components.") + raise Exception('Incorrect number of components in cyclohexane/ethanol test system.') + + # Also check that none of residues have zero charge + for resnr in range(len(structure.residues)): + abscharges = [ abs(structure.residues[resnr].atoms[idx].charge) for idx in range(len(structure.residues[resnr].atoms))] + if sum(abscharges)==0: + raise Exception('Error: Residue %s in cyclohexane-ethanol test system has a charge of zero, which is incorrect.' % resnr) diff --git a/openforcefield/tests/utils.py b/openforcefield/tests/utils.py new file mode 100644 index 000000000..37ee320c3 --- /dev/null +++ b/openforcefield/tests/utils.py @@ -0,0 +1,1314 @@ +#!/usr/bin/env python + +#============================================================================================= +# MODULE DOCSTRING +#============================================================================================= + +""" +Utilities for testing. + +""" + +#============================================================================================= +# GLOBAL IMPORTS +#============================================================================================= + +import collections +import copy +import functools +import itertools +import os +import pprint +import textwrap + +import numpy as np +from simtk import unit, openmm + +from openforcefield.utils import get_data_filename + + +#============================================================================================= +# Shortcut functions to get file paths to test data. +#============================================================================================= + +def get_amber_filepath(prefix): + """Get AMBER prmtop and inpcrd test data filepaths. + + Parameters + ---------- + prefix : str + The file name without extension of .prmtop and .inpcrd + files to retrieve from testdata/systems/amber. + + Returns + ------- + prmtop_filepath : str + Absolute path to the AMBER prmtop filepath in testdata/systems/amber + inpcrd_filepath : str + Absolute path to the AMBER inpcrd filepath in testdata/systems/amber + + """ + prefix = os.path.join('systems', 'amber', prefix) + prmtop_filepath = get_data_filename(prefix+'.prmtop') + inpcrd_filepath = get_data_filename(prefix+'.inpcrd') + return prmtop_filepath, inpcrd_filepath + + +def get_packmol_pdbfile(prefix='cyclohexane_ethanol_0.4_0.6'): + """Get PDB filename for a packmol-generated box + + Parameters + ---------- + prefix : str, optional, default='cyclohexane_ethanol_0.4_0.6' + The prefix of .pdb file to retrieve from testdata/systems/packmol_boxes + + Returns + ------- + pdb_filename : str + Absolute path to the PDB file + """ + prefix = os.path.join('systems', 'packmol_boxes', prefix) + pdb_filename = get_data_filename(prefix+'.pdb') + return pdb_filename + + +def get_monomer_mol2file(prefix='ethanol'): + """Get absolute filepath for a mol2 file denoting a small molecule monomer in testdata + + Parameters + ---------- + prefix : str, optional, default='ethanol' + The prefix of .mol2 file to retrieve from systems/monomers/ + + Returns + ------- + mol2_filename : str + Absolute path to the mol2 file + """ + # TODO: The mol2 files in this folder are not tripos mol2 files. Delete or convert them. + prefix = os.path.join('systems', 'monomers', prefix) + mol2_filename = get_data_filename(prefix + '.mol2') + return mol2_filename + + +def extract_compressed_molecules(tar_file_name, file_subpaths=None, filter_func=None): + if (file_subpaths is None) == (filter_func is None): + raise ValueError('Only one between file_subpaths and filter_func must be specified.') + + # Find the path of the tarfile with respect to the data/molecules/ folder. + molecules_dir_path = get_data_filename('molecules') + tar_file_path = os.path.join(molecules_dir_path, tar_file_name) + tar_root_dir_name = tar_file_name.split('.')[0] + + # Return value: Paths to the extracted molecules. + extracted_file_paths = None + + # Handle subpaths search. + if file_subpaths is not None: + # We can already check the paths of the extracted files + # and skipping opening the tarball if not necessary. + extracted_file_paths = [os.path.join(molecules_dir_path, tar_root_dir_name, file_subpath) + for file_subpath in file_subpaths] + + # Remove files that we have already extracted. + # Also, we augument the subpath with its root directory. + file_subpaths_set = {os.path.join(tar_root_dir_name, subpath) + for subpath, fullpath in zip(file_subpaths, extracted_file_paths) + if not os.path.isfile(fullpath)} + + # If everything was already extracted, we don't need to open the tarball. + if len(file_subpaths_set) == 0: + return extracted_file_paths + + # Otherwise, create a filter matching only the subpaths. + filter_func = lambda x: x in file_subpaths_set + + # If no filter was specified, just create one matching everything. + if filter_func is None: + filter_func = lambda x: True + + # Determine opening mode. + if '.gz' in tar_file_name: + mode = 'r:gz' + else: + mode = 'r' + + # Extract required files. + import tarfile + with tarfile.open(tar_file_path, mode) as tar_file: + # Gather the paths to extract. Remove the + members = [m for m in tar_file.getmembers() if filter_func(m.name)] + + # Built the paths to the extracted molecules we didn't already. + if extracted_file_paths is None: + extracted_file_paths = [os.path.join(molecules_dir_path, m.name) + for m in members] + + # Extract only the members that we haven't already extracted. + members = [member for member, fullpath in zip(members, extracted_file_paths) + if not os.path.isfile(fullpath)] + tar_file.extractall(path=molecules_dir_path, members=members) + + return extracted_file_paths + + +def get_alkethoh_filepath(alkethoh_name, get_amber=False): + """Retrieve the mol2, top and crd files of a molecule in the AlkEthOH set. + + Parameters + ---------- + alkethoh_name : str + The name of the AlkEthOH molecule (e.g. "AlkEthOH_r0", "AlkEthOH_c1266"). + get_amber : bool, optional + If True, the paths to the top and crd files are returned. + + Returns + ------- + molecule_file_paths : str or List[str] + All the requested paths. If ``get_amber`` is False, only a single string + pointing to the path of the mol2 file is returned, otherwise this is a + list ``[mol2_path, top_path, crd_path]``. + + """ + # Determine if this is a ring or a chain molecule and the subfolder name. + is_ring = alkethoh_name[9] == 'r' + alkethoh_subdir_name = 'rings' if is_ring else 'chain' + alkethoh_subdir_name = 'AlkEthOH_' + alkethoh_subdir_name + '_filt1' + + # Determine which paths have to be returned. + file_base_subpath = os.path.join(alkethoh_subdir_name, alkethoh_name) + # We always return the mol2 file. + file_subpaths = [file_base_subpath + '_tripos.mol2'] + # Check if we need to return also Amber files. + if get_amber: + file_subpaths.append(file_base_subpath + '.top') + file_subpaths.append(file_base_subpath + '.crd') + + return extract_compressed_molecules('AlkEthOH_tripos.tar.gz', file_subpaths=file_subpaths) + + +def get_freesolv_filepath(freesolv_id, ff_version): + file_base_name = 'mobley_' + freesolv_id + mol2_file_subpath = os.path.join('mol2files_sybyl', file_base_name + '.mol2') + xml_dir = 'xml_' + ff_version.replace('.', '_') + xml_file_subpath = os.path.join(xml_dir, file_base_name + '_vacuum.xml') + + # Extract the files if needed. + file_subpaths = [mol2_file_subpath, xml_file_subpath] + return extract_compressed_molecules('FreeSolv.tar.gz', file_subpaths=file_subpaths) + + +#============================================================================================= +# Shortcut functions to create System objects from system files. +#============================================================================================= + +def create_system_from_amber(prmtop_filepath, inpcrd_filepath, *args, **kwargs): + """Create an OpenMM System and Topology from the AMBER files. + + Parameters + ---------- + prmtop_filepath : str + Path to the topology/parameter file in AMBER prmtop format. + inpcrd_filepath : str + Path to the coordinates file in AMBER inpcrd or rst7 format. + *args + **kwargs + Other parameters to pass to ``simtk.openmm.app.AmberPrmtopFile.createSystem``. + + Returns + ------- + system : simtk.openmm.System + The OpenMM ``System`` object with the parameters. + topology : simtk.openmm.app.Topology + The OpenMM ``Topology`` object loaded from the AMBER files. + positions : simtk.unit.Quantity + Initial positions loaded from the inpcrd or restart file. + + """ + prmtop_file = openmm.app.AmberPrmtopFile(prmtop_filepath) + # AmberInpcrdFile parses also rst7 files. + inpcrd_file = openmm.app.AmberInpcrdFile(inpcrd_filepath) + # Create system and update box vectors (if needed) + system = prmtop_file.createSystem(*args, **kwargs) + if inpcrd_file.boxVectors is not None: + system.setDefaultPeriodicBoxVectors(*inpcrd_file.boxVectors) + # Store numpy positions. + positions = inpcrd_file.getPositions(asNumpy=True) + return system, prmtop_file.topology, positions + + +#============================================================================================= +# Utility functions for energy comparisons. +#============================================================================================= + +def quantities_allclose(quantity1, quantity2, **kwargs): + """Check if two Quantity objects are close. + + If the quantities are arrays, all their elements must be close. + If the given arguments are unitless, this simply calls numpy.allclose(). + + Parameters + ---------- + quantity1 : simtk.unit.Quantity + The first unit to compare. + quantity2 : simtk.unit.Quantity + The second unit to compare. + **kwargs + Other parameters passed to ``numpy.allclose()``. + + Returns + ------- + is_close : bool + True if the two quantities are close, False otherwise. + + """ + if isinstance(quantity1, unit.Quantity): + # Check that the two Quantities have compatible units. + if not quantity1.unit.is_compatible(quantity2.unit): + raise ValueError("The two quantities don't have compatible units: " + "{} and {}".format(quantity1.unit, quantity2.unit)) + # Compare the values stripped of the units. + quantity1 = quantity1.value_in_unit_system(unit.md_unit_system) + quantity2 = quantity2.value_in_unit_system(unit.md_unit_system) + return np.allclose(quantity1, quantity2, **kwargs) + + +def get_context_potential_energy(context, positions, box_vectors=None, + by_force_group=True): + """Compute the potential energy of a System in a Context object. + + This is simply a shortcut that takes care of setting + box vectors and positions before computing the energy. + + Parameters + ---------- + context : simtk.openmm.Context + The Context object containing the system. + positions : simtk.unit.Quantity + A n_atoms x 3 arrays of coordinates with units of length. + box_vectors : simtk.unit.Quantity, optional + If specified, this should be a 3 x 3 array. Each row should + be a box vector. + by_force_group : bool, optional + If True, it returns a dictionary mapping force groups to + their potential energies. Default is True. + + Returns + ------- + potential_energy : simtk.unit.Quantity or Dict[type, Quantity] + The potential energy of the system at the given coordinates. + If ``by_force_group`` is True, then this is a dictionary + mapping force groups to their potential energy. + + """ + # Box vectors must be updated before positions are set. + if box_vectors is not None: + context.setPeriodicBoxVectors(*box_vectors) + context.setPositions(positions) + + # If we don't have energies by force group, + # just return the energy of the full System. + if not by_force_group: + return context.getState(getEnergy=True).getPotentialEnergy() + + # Determine how many force groups we need to compute. + force_groups = {f.getForceGroup() for f in context.getSystem().getForces()} + + # Compute potential energies of all groups. + potential_energies = {} + for force_group in force_groups: + state = context.getState(getEnergy=True, groups={force_group}) + potential_energies[force_group] = state.getPotentialEnergy() + return potential_energies + + +class FailedEnergyComparisonError(AssertionError): + """Error raised when the energy comparison between two system fails. + + Attributes + ---------- + potential_energy1 + potential_energy2 + + """ + def __init__(self, err_msg, potential_energy1, potential_energy2): + super().__init__(err_msg) + self.potential_energy1 = potential_energy1 + self.potential_energy2 = potential_energy2 + + +def compare_context_energies(context1, context2, *args, rtol=1.e-5, atol=1.e-8, **kwargs): + """Compare energies of two Contexts given the same positions. + + Parameters + ---------- + context1 : simtk.openmm.Context + The first Context object to compare containing the system. + context2 : simtk.openmm.Context + The second Context object to compare containing the system. + positions : simtk.unit.Quantity + A n_atoms x 3 arrays of coordinates with units of length. + rtol : float, optional, default=1e-5 + The relative tolerance parameter used for the energy comparisons. + atol : float, optional, default=1e-8 + The absolute tolerance parameter used for the energy comparisons. + box_vectors : simtk.unit.Quantity, optional + If specified, this should be a 3 x 3 array. Each row should + be a box vector. + by_force_group : bool, optional + If True, the energies of each force groups are compared. + Default is True. + + Returns + ------- + potential_energy1 : simtk.unit.Quantity or Dict[int, Quantity] + The potential energy of context1 at the given coordinates. + If ``by_force_group`` is True, then this is a dictionary + mapping force groups to their potential energy. + potential_energy2 : simtk.unit.Quantity or Dict[int, Quantity] + The potential energy of context2 at the given coordinates. + If ``by_force_group`` is True, then this is a dictionary + mapping force groups to their potential energy. + + Raises + ------ + FailedEnergyComparisonError + If the potential energies of the two contexts are different + or if the two Systems in the contexts have forces divided into + different force groups. The potential energies of context1 and + context2 can be accessed in the Exception through the attributes + potential_energy1 and potential_energy2 respectively. + + """ + potential_energy1 = get_context_potential_energy(context1, *args, **kwargs) + potential_energy2 = get_context_potential_energy(context2, *args, **kwargs) + + def raise_assert(assertion, err_msg, format_args): + """Shortcut to raise a custom error and format the error message.""" + if not assertion: + raise FailedEnergyComparisonError( + err_msg.format(*format_args), potential_energy1, potential_energy2 + ) + + # If by_force_group is True, then the return value will be a + # dictionary and we need to compare force group by force group. + if isinstance(potential_energy1, unit.Quantity): + raise_assert( + assertion=quantities_allclose(potential_energy1, potential_energy2, + rtol=rtol, atol=atol), + err_msg='potential energy 1 {}, potential energy 2: {}', + format_args=(potential_energy1, potential_energy2) + ) + else: # potential_energy1 is a dict. + # If the two context expose different force groups raise an error. + raise_assert( + assertion=set(potential_energy1) == set(potential_energy2), + err_msg='The two contexts have different force groups: context1 {}, context2 {}', + format_args=(sorted(potential_energy1), sorted(potential_energy2)) + ) + + # Check the potential energies of all force groups. + for force_group in potential_energy1: + energy1 = potential_energy1[force_group] + energy2 = potential_energy2[force_group] + raise_assert( + assertion=quantities_allclose(energy1, energy2, rtol=rtol, atol=atol), + err_msg='Force group {} do not have the same energies: context1 {}, context2 {}', + format_args=(force_group, energy1, energy2) + ) + + return potential_energy1, potential_energy2 + + +def compare_system_energies(system1, system2, positions, box_vectors=None, + by_force_type=True, ignore_charges=False, + modify_system=False, rtol=1.e-5, atol=1.e-8): + """Compare energies of two Systems given the same positions. + + Parameters + ---------- + system1 : simtk.openmm.System + The first Context object to compare containing the system. + system2 : simtk.openmm.System + The second Context object to compare containing the system. + positions : simtk.unit.Quantity + A n_atoms x 3 arrays of coordinates with units of length. + box_vectors : simtk.unit.Quantity, optional + If specified, this should be a 3 x 3 array. Each row should + be a box vector. + by_force_type : bool, optional + If True, the contribution to the energy of each force type + is compared instead of just the overall potential energy. + Default is True. + ignore_charges : bool, optional + If True, particle and exception charges are ignored during + the comparison. Default is False. + modify_system : bool, optional + If either ``by_force_type`` or ``ignore_charges`` are True, + the function will change the force groups of two ``Systems`` + to compute the separate contributions. Set this to False to + work on a copy and avoid modifying the original objects. + Default is False. + rtol : float, optional, default=1e-5 + The relative tolerance parameter used for the energy comparisons. + atol : float, optional, default=1e-8 + The absolute tolerance parameter used for the energy comparisons. + + Returns + ------- + potential_energy1 : simtk.unit.Quantity or Dict[str, Quantity] + The potential energy of context1 at the given coordinates. + If ``by_force_type`` is True, then this is a dictionary + mapping force names to their potential energy. + potential_energy2 : simtk.unit.Quantity or Dict[str, Quantity] + The potential energy of context2 at the given coordinates. + If ``by_force_type`` is True, then this is a dictionary + mapping force names to their potential energy. + + Raises + ------ + FailedEnergyComparisonError + If the potential energies of the two contexts are different + or if the two Systems in the contexts have forces divided into + different force groups. The potential energies of context1 and + context2 can be accessed in the Exception through the attributes + potential_energy1 and potential_energy2 respectively. + + """ + # Make a copy of the systems if requested. + if not modify_system and (by_force_type or ignore_charges): + system1 = copy.deepcopy(system1) + system2 = copy.deepcopy(system2) + + # Group force types into OpenMM force groups. + if by_force_type: + # Remove eventual CMMotionRemover forces that do not affect energies. + for system in [system1, system2]: + for force_idx, force in enumerate(system.getForces()): + if isinstance(force, openmm.CMMotionRemover): + system.removeForce(force_idx) + break + + # First check that the two systems have the same force types. + force_names1 = {f.__class__.__name__ for f in system1.getForces()} + force_names2 = {f.__class__.__name__ for f in system2.getForces()} + if set(force_names1) != set(force_names2): + err_msg = 'The two Systems have different forces to compare:\n - system1 {}\n - system2 {}' + raise ValueError(err_msg.format(sorted(force_names1), sorted(force_names2))) + + # Create a map from force group to force class and viceversa. + group_to_force = {i: force_name for i, force_name in enumerate(force_names1)} + force_to_group = {force_name: i for i, force_name in group_to_force.items()} + + # Assign force groups. + for system in [system1, system2]: + for force in system.getForces(): + force.setForceGroup(force_to_group[force.__class__.__name__]) + + # If we need to ignore the charges, turn off particle and exceptions charges. + if ignore_charges: + for system in [system1, system2]: + # Find the NonbondedForce. + nonbonded_force = None + for force in system.getForces(): + if isinstance(force, openmm.NonbondedForce): + nonbonded_force = force + + # We checked before that the two systems have the same force + # types so we can break the loop if there are no NonbondedForces. + if nonbonded_force is None: + break + + # Set particle charges to 0.0. + for particle_idx in range(nonbonded_force.getNumParticles()): + charge, sigma, epsilon = nonbonded_force.getParticleParameters(particle_idx) + nonbonded_force.setParticleParameters(particle_idx, 0.0, sigma, epsilon) + + # Set particle exceptions charge products to 0.0. + for exception_idx in range(nonbonded_force.getNumExceptions()): + atom1, atom2, chargeprod, sigma, epsilon = nonbonded_force.getExceptionParameters(exception_idx) + nonbonded_force.setExceptionParameters(exception_idx, atom1, atom2, 0.0, sigma, epsilon) + + # Create Contexts and compare the energies. + integrator = openmm.VerletIntegrator(1.0*unit.femtoseconds) + context1 = openmm.Context(system1, integrator) + context2 = openmm.Context(system2, copy.deepcopy(integrator)) + + def map_energies_by_force_type(potential_energy1, potential_energy2): + """Convert dictionary force_group -> energy to force_type -> energy.""" + potential_energy1 = {group_to_force[group]: energy + for group, energy in potential_energy1.items()} + potential_energy2 = {group_to_force[group]: energy + for group, energy in potential_energy2.items()} + return potential_energy1, potential_energy2 + + # Catch the exception and log table force type -> energy. + try: + potential_energy1, potential_energy2 = compare_context_energies( + context1, context2, positions, box_vectors, + by_force_group=by_force_type, rtol=rtol, atol=atol + ) + except FailedEnergyComparisonError as e: + # We don't need to convert force groups into force types + if not by_force_type: + raise + # Add to the error message the table of energies by force type. + potential_energy1, potential_energy2 = map_energies_by_force_type( + e.potential_energy1, e.potential_energy2 + ) + # Pretty-print the dictionaries. + table = '\n\npotential energy system1:\n' + pprint.pformat(potential_energy1) + table += '\n\npotential energy system2:\n' + pprint.pformat(potential_energy2) + raise type(e)(str(e) + table, e.potential_energy1, e.potential_energy2) + + if by_force_type: + return map_energies_by_force_type(potential_energy1, potential_energy2) + return potential_energy1, potential_energy2 + + +#============================================================================================= +# Utility functions for parameters comparisons. +#============================================================================================= + +class _ParametersComparer: + """This is just a convenience class to compare and print parameters. + + Parameters + ---------- + **kwargs + All the parameters to compare. + + Attributes + ---------- + parameters : dict + The dictionary of parameters. + + Examples + -------- + >>> import copy + >>> from simtk import unit + >>> par1 = _ParametersComparer(charge=1.0*unit.elementary_charge, + ... rmin_half=1.5*unit.angstrom) + >>> par2 = copy.deepcopy(par1) + >>> par3 = _ParametersComparer(charge=-1.0*unit.elementary_charge, + ... rmin_half=0.15*unit.nanometers) + >>> par1 == par2 + True + >>> par1 == par3 + False + >>> str(par1) + '(charge: 1.0 e, rmin_half: 1.5 A)' + + """ + + def __init__(self, **parameters): + self.parameters = parameters + + def remove_parameters(self, parameter_names): + for parameter_name in parameter_names: + try: + del self.parameters[parameter_name] + except KeyError: + pass + + def pretty_format_diff(self, other, new_line=True, indent=True): + """Return a pretty-formatted string describing the differences between parameters. + + Parameters + ---------- + other : _ParametersComparer + new_line : bool, optional + Separate different parameters with new lines. + indent : bool, optional + Indent the formatting. + + Returns + ------- + diff_str : str + + """ + diff = self._get_diff(other) + diff_list = [] + for par_name in sorted(diff.keys()): + par1, par2 = diff[par_name] + diff_list.append('{par_name}: {par1} != {par2}'.format( + par_name=par_name, par1=par1, par2=par2)) + separator = '\n' if new_line else '' + diff_str = separator.join(diff_list) + if indent: + diff_str = textwrap.indent(diff_str, prefix=' ') + return diff_str + + def _get_diff(self, other): + """Build a 'diff' including only the parameters that are different. + """ + assert set(self.parameters.keys()) == set(other.parameters.keys()) + diff = {} + for par_name, par1_value in self.parameters.items(): + par2_value = other.parameters[par_name] + # Determine whether this parameter is close or not. + if not quantities_allclose(par1_value, par2_value): + diff[par_name] = (par1_value, par2_value) + return diff + + def __eq__(self, other): + return len(self._get_diff(other)) == 0 + + def __str__(self): + # Reorder the parameters to print in deterministic order. + parameter_order = sorted(self.parameters) + # Quantities in a dictionary are normally printed in the + # format "Quantity(value, unit=unit)" so we make it prettier. + par_str = ', '.join('{}: {}'.format(p, self.parameters[p]) for p in parameter_order) + return '(' + par_str + ')' + + +class _TorsionParametersComparer: + """A ParametersComparer class for torsions. + + Torsions require a different comparison because multiple set of + (periodicity, phase, k) parameters can be associated to the same + four atoms. + + Parameters + ---------- + *parameters + Variable length arguments. Each is a _ParametersComparer instance. + + Attributes + ---------- + parameters : List[_ParametersComparer] + The list of _ParametersComparer instances. + + Examples + -------- + >>> from simtk import unit + >>> par1 = _ParametersComparer(periodicity=2, phase=0.0*unit.degrees) + >>> par2 = _ParametersComparer(periodicity=4, phase=180.0*unit.degrees) + >>> torsion_par = _TorsionParametersComparer(par1, par2) + + """ + + def __init__(self, *parameters): + # *args is a tuple. Convert it to a list to make it appendable. + self.parameters = list(parameters) + + def pretty_format_diff(self, other, new_line=True, indent=True): + """Return a pretty-formatted string describing the differences between parameters. + + Parameters + ---------- + other : _TorsionParametersComparer + new_line : bool, optional + Separate different parameters with new lines. + indent : bool, optional + Indent the formatting. + + Returns + ------- + diff_str : str + + """ + diff_str = 'Parameters in first system:\n' + diff_str += self._pretty_format_parameters(self.parameters, new_line=new_line) + diff_str += '\nParameters in second system:\n' + diff_str += self._pretty_format_parameters(other.parameters, new_line=new_line) + if indent: + diff_str = textwrap.indent(diff_str, ' ') + return diff_str + + def _pretty_format_parameters(self, parameters, new_line=True, indent=True): + # Reorder the parameters by periodicity and then phase to print in deterministic order. + sort_key = lambda x: (x.parameters['periodicity'], x.parameters['phase']) + parameters = sorted(parameters, key=sort_key) + # Quantities in a dictionary are normally printed in the + # format "Quantity(value, unit=unit)" so we make it prettier. + separator = '\n' if new_line else ', ' + prefix = '[' + if indent and new_line: + separator += ' ' + elif indent: + prefix += ' ' + return prefix + separator.join(str(pars) for pars in parameters) + ']' + + def __eq__(self, other): + # Look for self.parameters that don't match any other.parameters. + for parameters1 in self.parameters: + # Find at least 1 set of parameters in the list that are equal. + if all(parameters1 != parameters2 for parameters2 in other.parameters): + return False + + # Look for other.parameters that don't match any other self.parameters. + for parameters2 in other.parameters: + # Find at least 1 set of parameters in the list that are equal. + if all(parameters1 != parameters2 for parameters1 in self.parameters): + return False + return True + + def __str__(self): + return self._pretty_format_parameters(self.parameters, new_line=False, indent=False) + + +class FailedParameterComparisonError(AssertionError): + """Error raised when the parameter comparison between two forces fails. + + Attributes + ---------- + different_parameters : Dict[Hashable, Tuple[_ParameterComparer]] + All the parameters for which a differences was detected. + different_parameters[atom_indices] is a tuple + (parameter_force1, parameter_force2). + + """ + def __init__(self, err_msg, different_parameters): + super().__init__(err_msg) + self.different_parameters = different_parameters + + +def _compare_parameters(parameters_force1, parameters_force2, interaction_type, + force_name='', systems_labels=None): + """Compare the parameters of 2 forces and raises an exception if they are different. + + Parameters + ---------- + parameters_force1 : Dict[Hashable, _ParametersComparer] + A dictionary associating a _ParametersComparer entry to a key + that is usually a set of atom indices (e.g., the atom index + for nonbonded interactions, two atom indices for bonds and + 1-4 exceptions, 3 indices for angles, and 4 for torsions). + parameters_force2 : Dict[Hashable, _ParametersComparer] + The parameters of the force to compare. + interaction_type : str + A string describing the type of interactions (e.g., "bond", + "particle exception", "proper torsion"). This is only used to + improve the error message where differences between the two + forces are detected. + force_name : str, optional + The name of the force to optionally include in the eventual + error message. + systems_labels : Tuple[str], optional + A pair of strings with a meaningful name for the system. If + specified, this will be included in the error message to + improve its readability. + + Raises + ------ + FailedParameterComparisonError + If there are differences in the parameters of the two forces. + The exceptions exposes an attribute ``different_parameters`` + with the different parameters. + + """ + diff_msg = '' + + # First check the parameters that are unique to only one of the forces. + unique_keys1 = set(parameters_force1) - set(parameters_force2) + unique_keys2 = set(parameters_force2) - set(parameters_force1) + err_msg = '\n\n{} force has the following unique ' + interaction_type + 's: {}\n' + if len(unique_keys1) != 0: + force_label = systems_labels[0] if systems_labels is not None else 'First' + diff_msg += err_msg.format(force_label, sorted(unique_keys1)) + if len(unique_keys2) != 0: + force_label = systems_labels[1] if systems_labels is not None else 'Second' + diff_msg += err_msg.format(force_label, sorted(unique_keys2)) + + # Create a diff for entries that have same keys but different parameters. + different_parameters = {} + for key in set(parameters_force1).intersection(set(parameters_force2)): + if parameters_force1[key] != parameters_force2[key]: + different_parameters[key] = (parameters_force1[key], parameters_force2[key]) + + # Handle force and systems labels default arguments. + if force_name != '': + force_name += ' ' # Add space after. + if systems_labels is not None: + systems_labels = ' for the {} and {} systems respectively'.format(*systems_labels) + else: + systems_labels = '' + + # Print error. + if len(different_parameters) > 0: + diff_msg += ('\n\nThe following {interaction}s have different parameters ' + 'in the two {force_name}forces{systems_labels}:'.format( + interaction=interaction_type, force_name=force_name, + systems_labels=systems_labels) + ) + for key in sorted(different_parameters.keys()): + param1, param2 = different_parameters[key] + parameters_diff = param1.pretty_format_diff(param2) + diff_msg += '\n{} {}:\n{}'.format(interaction_type, key, parameters_diff) + + if diff_msg != '': + diff_msg = ('A difference between {} was detected. ' + 'Details follow.').format(interaction_type) + diff_msg + raise FailedParameterComparisonError(diff_msg + '\n', different_parameters) + + +@functools.singledispatch +def _get_force_parameters(force, system, ignored_parameters): + """This function builds a _ParameterComparer representation of the + force parameters that can be used for comparison to other forces + with _compare_parameters. + + Each _ParameterComparer must be associated to a key, which is usually + a tuple of atom indices (e.g., the atom index for nonbonded interactions, + two atom indices for bonds and 1-4 exceptions, 3 indices for angles, + and 4 for torsions). + + A single force can generate multiple representations (e.g., a NonbondedForce + can generate one representations for particle parameters and one for + parameter exceptions. + + Parameters + ---------- + force + The OpenMM Force object. + system : simtk.openmm.System + The System to which this force belongs to. + ignored_parameters : Iterable[str] + The parameters to ignore in the comparison. + + Returns + ------- + force_parameters : Dict[str, Dict[Hashable, _ParameterComparer]] + The parameter representation. force_parameters[interaction_type] + is a dictionary mapping a tuple of atom indices to the + associated parameters. interaction_type can be any string + identifying the type of parameters (e.g. "particle exception", + "proper torsion", "bond"). + + """ + raise NotImplementedError('Comparison between {}s is not currently ' + 'supported.'.format(type(force))) + +@_get_force_parameters.register(openmm.HarmonicBondForce) +def _get_bond_force_parameters(force, _, ignored_parameters): + """Implementation of _get_force_parameters for HarmonicBondForces.""" + # Build the dictionary of the parameters of a single force. + force_parameters = {} + for bond_idx in range(force.getNumBonds()): + atom1, atom2, r0, k = force.getBondParameters(bond_idx) + + # Ignore bonds with 0.0 spring constant that don't affect the energy. + if (k / k.unit) == 0.0: + continue + + # Reorder the bond to have a canonical key. + bond_key = tuple(sorted([atom1, atom2])) + force_parameters[bond_key] = _ParametersComparer(r0=r0, k=k) + force_parameters[bond_key].remove_parameters(ignored_parameters) + + return {'bond': force_parameters} + + +@_get_force_parameters.register(openmm.HarmonicAngleForce) +def _get_angle_force_parameters(force, _, ignored_parameters): + """Implementation of _get_force_parameters for HarmonicAngleForces.""" + # Build the dictionary of the parameters of a single force. + force_parameters = {} + for angle_idx in range(force.getNumAngles()): + atom1, atom2, atom3, theta0, k = force.getAngleParameters(angle_idx) + + # Ignore angles with 0.0 spring constant that don't affect the energy. + if (k / k.unit) == 0.0: + continue + + # Reorder the bond to have a canonical key. + angle_key = min(atom1, atom3), atom2, max(atom1, atom3) + force_parameters[angle_key] = _ParametersComparer(theta0=theta0, k=k) + force_parameters[angle_key].remove_parameters(ignored_parameters) + + return {'angle': force_parameters} + + +@_get_force_parameters.register(openmm.NonbondedForce) +def _get_nonbonded_force_parameters(force, _, ignored_parameters): + """Implementation of _get_force_parameters for NonbondedForces.""" + # Build the dictionary of the particle parameters of the force. + particle_parameters = {} + for particle_idx in range(force.getNumParticles()): + charge, sigma, epsilon = force.getParticleParameters(particle_idx) + + # Ignore sigma parameter if epsilon is 0.0. + particle_parameters[particle_idx] = _ParametersComparer( + charge=charge, epsilon=epsilon) + if (epsilon / epsilon.unit) != 0.0: + particle_parameters[particle_idx].parameters['sigma'] = sigma + particle_parameters[particle_idx].remove_parameters(ignored_parameters) + + # Build the dictionary representation of the particle exceptions. + exception_parameters = {} + for exception_idx in range(force.getNumExceptions()): + atom1, atom2, chargeprod, sigma, epsilon = force.getExceptionParameters(exception_idx) + + # Reorder the atom indices to have a canonical key. + exception_key = tuple(sorted([atom1, atom2])) + # Ignore sigma parameter if epsilon is 0.0. + exception_parameters[exception_key] = _ParametersComparer( + charge=chargeprod, epsilon=epsilon) + if (epsilon / epsilon.unit) != 0.0: + exception_parameters[exception_key].parameters['sigma'] = sigma + exception_parameters[exception_key].remove_parameters(ignored_parameters) + + return {'particle': particle_parameters, 'particle exception': exception_parameters} + + +def _merge_impropers_folds(improper_parameters): + """Merge impropers with same periodicities and phases into a single folds. + + See _get_torsion_force_parameters. + + """ + for improper_key, improper_comparer in improper_parameters.items(): + # Group parameters by periodicity and phase and sum force constants. + for comparer2_idx in reversed(range(1, len(improper_comparer.parameters))): + parameter_comparer2 = improper_comparer.parameters[comparer2_idx] + parameters2 = parameter_comparer2.parameters + + # parameter_comparer1 comes before parameter_comparer2 in the list. + for parameter_comparer1 in improper_comparer.parameters[:comparer2_idx]: + parameters1 = parameter_comparer1.parameters + + # If phase and periodicity match, sum the force constants + # and remove one _ParametersComparer object from the list. + if (parameters1['phase'] == parameters2['phase'] and + parameters1['periodicity'] == parameters2['periodicity']): + # Update the force constant of the first parameter. + parameters1['k'] += parameters2['k'] + # Remove the second parameter from the list. + del improper_comparer.parameters[comparer2_idx] + break + + +@_get_force_parameters.register(openmm.PeriodicTorsionForce) +def _get_torsion_force_parameters(force, system, ignored_parameters): + """Implementation of _get_force_parameters for NonbondedForces. + + If the special attribute 'n_improper_folds' is in ignored_parameters, + then impropers with same periodicity and phases are merged into a + single set of parameters having the sum of the force constants as k. + This allows to compare parameters before and after the 0.1 version of + the toolkit, in which the six-fold implementation was changed into + the current three-fold. + + """ + if 'n_improper_folds' not in ignored_parameters: + ignore_n_folds = False + else: + ignore_n_folds = True + # Create a copy of ignored_parameters without n_improper_folds + # that must be removed later from the _ParametersComparer object. + ignored_parameters = copy.deepcopy(ignored_parameters) + ignored_parameters.remove('n_improper_folds') + + # Find all bonds. We'll use this to distinguish + # between proper and improper torsions. + bond_set = _find_all_bonds(system) + + proper_parameters = {} + improper_parameters = {} + for torsion_idx in range(force.getNumTorsions()): + atom1, atom2, atom3, atom4, periodicity, phase, k = force.getTorsionParameters(torsion_idx) + + # Ignore torsions that don't contribute to the energy. + if (k / k.unit) == 0.0: + continue + + torsion_key = [atom1, atom2, atom3, atom4] + if len(set(torsion_key)) != 4: + raise ValueError('Torsion {} is defined on less than 4 atoms: {}'.format(torsion_key)) + + # Check if this is proper or not. + torsion_bonds = [(torsion_key[i], torsion_key[i+1]) for i in range(3)] + is_proper = all(bond in bond_set for bond in torsion_bonds) + + # Determine the canonical order of the torsion key. + if is_proper: + torsion_key = _get_proper_torsion_canonical_order(*torsion_key) + force_parameters = proper_parameters + else: + torsion_key = _get_improper_torsion_canonical_order(bond_set, *torsion_key) + force_parameters = improper_parameters + + # Update the dictionary representation. + parameters = _ParametersComparer(periodicity=periodicity, phase=phase, k=k) + parameters.remove_parameters(ignored_parameters) + # Each set of 4 atoms can have multiple torsion terms. + try: + force_parameters[torsion_key].parameters.append(parameters) + except KeyError: + force_parameters[torsion_key] = _TorsionParametersComparer(parameters) + + # Sum the force constants of all the improper torsion folds. This + # is fundamental to compare parameters with versions of the toolkit + # previous to 0.1, where the trefoil improper was six-fold rather + # than three-fold as in the current version. + if ignore_n_folds: + _merge_impropers_folds(improper_parameters) + + return {'proper torsion': proper_parameters, 'improper torsion': improper_parameters} + + +def _find_all_bonds(system): + """Find all bonds in the given system + + Parameters + ---------- + system : simtk.openmm.System + A System object containing a HarmonicBondForce from which the + bonds are inferred. + + Returns + ------- + bond_set : Set[Tuple[int]] + A set of pairs (atom_index1, atom_index2) associated to bonds. + For each bond two pairs are created with the atom indices in + inverse order. + + """ + # Find the force with information on the bonds. + bond_force = [f for f in system.getForces() if isinstance(f, openmm.HarmonicBondForce)] + assert len(bond_force) == 1 + bond_force = bond_force[0] + + # Create a set of all bonds. + bond_set = set() + for bond_idx in range(bond_force.getNumBonds()): + atom1, atom2, _, _ = bond_force.getBondParameters(bond_idx) + bond_set.add((atom1, atom2)) + bond_set.add((atom2, atom1)) + + # Find all the constrained bonds, which do not have a HarmonicBondForce term. + for constraint_idx in range(system.getNumConstraints()): + atom1, atom2, distance = system.getConstraintParameters(constraint_idx) + bond_set.add((atom1, atom2)) + bond_set.add((atom2, atom1)) + + return bond_set + + +def _get_proper_torsion_canonical_order(i0, i1, i2, i3): + """Create a unique order of the 4 atom indices of a proper torsion. + + The atom indices of a proper torsion are reordered so that the + first atom is the smallest index. + + Parameters + ---------- + i0, i1, i2, i3 : int + Atom indices of the proper torsion. + + Returns + ------- + j0, j1, j2, j3 : int + Reordered atom indices of the proper torsion. + + """ + if i0 < i3: + return i0, i1, i2, i3 + else: + return i3, i2, i1, i0 + + +def _get_improper_torsion_canonical_order(bond_set, i0, i1, i2, i3): + """Create a unique order of the 4 atom indices of an improper torsion. + + Return j0, j1, j2, j3, where j0 is the central index and j1, j2, j3 + are in sorted() order. The centrality is determined by the maximum + counts in the adjacency matrix. + + Parameters + ---------- + bond_set : set + The set of all bonds as determined by _find_all_bonds. + i0, i1, i2, i3 : int, + Atom indices of the improper torsion. + + Returns + ------- + j0, j1, j2, j3 : int + Reordered atom indices of the improper torsion, with j0 being + the central index. + + """ + connections = np.zeros((4, 4)) + + mapping = {i0: 0, i1: 1, i2: 2, i3: 3} + inv_mapping = dict([(val, key) for key, val in mapping.items()]) + + for (a, b) in itertools.combinations([i0, i1, i2, i3], 2): + if (a, b) in bond_set: + i, j = mapping[a], mapping[b] + connections[i, j] += 1. + connections[j, i] += 1. + + central_ind = connections.sum(0).argmax() + central_ind = inv_mapping[central_ind] + other_ind = sorted([i0, i1, i2, i3]) + other_ind.remove(central_ind) + + return central_ind, other_ind[0], other_ind[1], other_ind[2] + + +def compare_system_parameters(system1, system2, systems_labels=None, + ignore_charges=False, ignore_improper_folds=False): + """Check that two OpenMM systems have the same parameters. + + Parameters + ---------- + system1 : simtk.openmm.System + The first system to compare. + system2 : simtk.openmm.System + The second system to compare. + systems_labels : Tuple[str], optional + A pair of strings with a meaningful name for the system. If + specified, this will be included in the error message to + improve its readability. + ignore_charges : bool, optional + If True, particle and exception charges are ignored during + the comparison. Default is False. + ignore_improper_folds : bool, optional + If True, all the folds of the same impropers are merged into + a single one for the purpose of parameter comparison. Default + is False. + + Raises + ------ + FailedParameterComparisonError + If there are differences in the parameters of the two forces. + The exceptions exposes an attribute ``different_parameters`` + with the different parameters. + + """ + # Determine parameters to ignore. + ignored_parameters_by_force = {} + if ignore_charges: + ignored_parameters_by_force['NonbondedForce'] = ['charge', 'chargeprod'] + if ignore_improper_folds: + ignored_parameters_by_force['PeriodicTorsionForce'] = ['n_improper_folds'] + + # We need to perform some checks on the type and number of forces in the Systems. + force_names1 = collections.Counter(f.__class__.__name__ for f in system1.getForces()) + force_names2 = collections.Counter(f.__class__.__name__ for f in system2.getForces()) + err_msg = 'Only systems having 1 force per type are supported.' + assert set(force_names1.values()) == {1}, err_msg + assert set(force_names2.values()) == {1}, err_msg + + # Remove the center-of-mass motion remover force from comparison. + for force_names in [force_names1, force_names2]: + if 'CMMotionRemover' in force_names: + del force_names['CMMotionRemover'] + + # Check that the two systems have the same forces. + if set(force_names1) != set(force_names2): + err_msg = 'The two Systems have different forces to compare:\n - system1 {}\n - system2 {}' + raise ValueError(err_msg.format(sorted(force_names1), sorted(force_names2))) + + # Find all the pair of forces to compare. + force_pairs = {force_name: [] for force_name in force_names1} + for system in [system1, system2]: + for force in system.getForces(): + # Skip CMMotionRemover. + if force.__class__.__name__ == 'CMMotionRemover': + continue + force_pairs[force.__class__.__name__].append(force) + + # Compare all pairs of forces + for force_name, (force1, force2) in force_pairs.items(): + # Select the parameters to ignore. + try: + ignored_parameters = ignored_parameters_by_force[force_name] + except KeyError: + ignored_parameters = () + + # Get a dictionary representation of the parameters. + parameters_force1 = _get_force_parameters(force1, system1, ignored_parameters) + parameters_force2 = _get_force_parameters(force2, system2, ignored_parameters) + + # Compare the forces and raise an error if a difference is detected. + for parameter_type, parameters1 in parameters_force1.items(): + parameters2 = parameters_force2[parameter_type] + _compare_parameters(parameters1, parameters2, + interaction_type=parameter_type, + force_name=force_name, + systems_labels=systems_labels) + + +#============================================================================================= +# Utility functions to compare SMIRNOFF and AMBER force fields. +#============================================================================================= + +def compare_amber_smirnoff(prmtop_filepath, inpcrd_filepath, forcefield, molecule, + check_parameters=True, check_energies=True, **kwargs): + """ + Compare energies and parameters for OpenMM Systems/topologies created + from an AMBER prmtop and crd versus from a SMIRNOFF forcefield file which + should parameterize the same system with same parameters. + + Parameters + ---------- + prmtop_filepath : str + Path to the topology/parameter file in AMBER prmtop format + inpcrd_filepath : str + Path to the coordinates file in AMBER inpcrd or rst7 format + forcefield : ForceField + Force field instance used to create the system to compare. + molecule : topology.molecule.Molecule + The molecule object to test. + check_parameters : bool, optional + If False, parameters are not compared. Energies are still comapred + if ``check_energies`` is ``True`` (default is ``True``). + check_parameters : bool, optional + If False, energies are not compared and they are not returned. + Parameters are not compared if ``check_energies`` is ``True`` + (default is ``True``). + ignore_charges : bool, optional + If True, particle and exception charges are ignored during + the comparison. Default is False. + + Returns + ------- + energies : Dict[str, Dict[str, simtk.unit.Quantity]] or None + If ``check_energies`` is ``False``, nothing is returned. Otherwise, + this is a dictionary with two keys: 'AMBER' and 'SMIRNOFF', each + pointing to another dictionary mapping forces to their total + contribution to the potential energy. + + Raises + ------ + FailedEnergyComparisonError + If the potential energies of the two systems are different + or if the two Systems in the contexts have forces divided into + different force groups. The potential energies of the AMBER and + ForceField systems can be accessed in the Exception through the + attributes potential_energy1 and potential_energy2 respectively. + FailedParameterComparisonError + If there are differences in the parameters of the two systems. + The exceptions exposes an attribute ``different_parameters`` + with the different parameters. + + """ + from openforcefield.topology import Topology + + # Create System from AMBER files. By default, contrarily to ForceField, + # systems from AMBER files are created with removeCMMotion=True + amber_system, openmm_topology, positions = create_system_from_amber( + prmtop_filepath, inpcrd_filepath, removeCMMotion=False) + box_vectors = amber_system.getDefaultPeriodicBoxVectors() + + # Create System from forcefield. + openff_topology = Topology.from_openmm(openmm_topology, unique_molecules=[molecule]) + ff_system = forcefield.create_openmm_system(openff_topology) + + # Test energies and parameters. + if check_parameters: + compare_system_parameters(amber_system, ff_system, + systems_labels=('AMBER', 'SMIRNOFF'), + **kwargs) + + if check_energies: + amber_energies, forcefield_energies = compare_system_energies( + amber_system, ff_system, positions, box_vectors, **kwargs) + + return {'AMBER': amber_energies, 'SMIRNOFF': forcefield_energies} + return None diff --git a/openforcefield/topology/__init__.py b/openforcefield/topology/__init__.py new file mode 100644 index 000000000..1c424bb59 --- /dev/null +++ b/openforcefield/topology/__init__.py @@ -0,0 +1,2 @@ +from openforcefield.topology.molecule import * +from openforcefield.topology.topology import * diff --git a/openforcefield/topology/molecule.py b/openforcefield/topology/molecule.py new file mode 100644 index 000000000..959c31090 --- /dev/null +++ b/openforcefield/topology/molecule.py @@ -0,0 +1,3706 @@ +#!/usr/bin/env python + +#============================================================================================= +# MODULE DOCSTRING +#============================================================================================= +""" +Molecular chemical entity representation and routines to interface with cheminformatics toolkits + +.. todo:: + + * Our main philosophy here is to keep the object contents of topology objects easily serializable/deserializable + + * Have ``Molecule`` raise an exception if loading/creating molecules with unspecified stereochemistry? + * Create ``FrozenMolecule`` to represent immutable molecule + * Make ``Atom`` and ``Bond`` an inner class of Molecule? + * Add ``Molecule.from_smarts()`` or ``.from_tagged_smiles()`` to allow a tagged SMARTS string + (where tags are zero-indexed atom indices) to be used to create a molecule with the given atom numbering. + * How can we make the ``Molecule`` API more useful to codes like perses that modify molecules on the fly? + * Use `attrs `_ for convenient class initialization? + * JSON/BSON representations of objects? + * Generalize Molecule infrastructure to provide "plug-in" support for cheminformatics toolkits + * Do we need a way to write a bunch of molecules to a file, or serialize a set of molecules to a file? + We currently don't have a way to do that through the ``Molecule`` API, even though there is a way to + read multiple molecules via ``Molecules.from_file()``. + * Should we allow the removal of atoms too? + * Should invalidation of cached properties be handled via something like a tracked list? + * Refactor toolkit encapsulation to generalize and provide only a few major toolkit methods and toolkit objects that can be queried for features + * Speed up overall import time by putting non-global imports only where they are needed + +""" + +#============================================================================================= +# GLOBAL IMPORTS +#============================================================================================= + +import numpy as np +from collections import OrderedDict +from copy import deepcopy + +from simtk import unit +from simtk.openmm.app import element + +import openforcefield +from openforcefield.utils import serialize_numpy, deserialize_numpy, quantity_to_string, string_to_quantity +from openforcefield.utils.toolkits import ToolkitRegistry, ToolkitWrapper, RDKitToolkitWrapper, OpenEyeToolkitWrapper,\ + InvalidToolkitError, GLOBAL_TOOLKIT_REGISTRY +from openforcefield.typing.chemistry import ChemicalEnvironment +from openforcefield.utils.toolkits import DEFAULT_AROMATICITY_MODEL +from openforcefield.utils.serialization import Serializable + + + +#============================================================================================= +# GLOBAL PARAMETERS +#============================================================================================= + +# TODO: Can we have the `ALLOWED_*_MODELS` list automatically appear in the docstrings below? +# TODO: Should `ALLOWED_*_MODELS` be objects instead of strings? +# TODO: Should these be imported from `openforcefield.cheminformatics.aromaticity_models` and `.bondorder_models`? + +# TODO: Allow all OpenEye aromaticity models to be used with OpenEye names? +# Only support OEAroModel_MDL in RDKit version? + +#============================================================================================= +# PRIVATE SUBROUTINES +#============================================================================================= + +#============================================================================================= +# Particle +#============================================================================================= + + +class Particle(Serializable): + """ + Base class for all particles in a molecule. + + A particle object could be an ``Atom`` or a ``VirtualSite``. + + .. warning :: This API is experimental and subject to change. + """ + + @property + def molecule(self): + """ + The ``Molecule`` this atom is part of. + + .. todo:: + + * Should we have a single unique ``Molecule`` for each molecule type in the system, + or if we have multiple copies of the same molecule, should we have multiple ``Molecule``s? + """ + return self._molecule + + @molecule.setter + def molecule(self, molecule): + """ + Set the particle's molecule pointer. Note that this will only work if the particle currently + doesn't have a molecule + """ + #TODO: Add informative exception here + assert self._molecule == None + self._molecule = molecule + + @property + def molecule_particle_index(self): + """ + Returns the index of this particle in its molecule + """ + return self._molecule.particles.index(self) + + + @property + def name(self): + """ + The name of the particle + """ + return self._name + + def to_dict(self): + """Convert to dictionary representation.""" + # Implement abstract method Serializable.to_dict() + raise NotImplementedError() # TODO + + @classmethod + def from_dict(cls, d): + """Static constructor from dictionary representation.""" + # Implement abstract method Serializable.to_dict() + raise NotImplementedError() # TODO + + +#============================================================================================= +# Atom +#============================================================================================= + + +class Atom(Particle): + """ + A particle representing a chemical atom. + + Note that non-chemical virtual sites are represented by the ``VirtualSite`` object. + + .. todo:: + + * Should ``Atom`` objects be immutable or mutable? + * Do we want to support the addition of arbitrary additional properties, + such as floating point quantities (e.g. ``charge``), integral quantities (such as ``id`` or ``serial`` index in a PDB file), + or string labels (such as Lennard-Jones types)? + + .. todo :: Allow atoms to have associated properties. + + .. warning :: This API is experimental and subject to change. + """ + + def __init__(self, + atomic_number, + formal_charge, + is_aromatic, + name=None, + molecule=None, + stereochemistry=None): + """ + Create an immutable Atom object. + + Object is serializable and immutable. + + .. todo :: Use attrs to validate? + + .. todo :: We can add setters if we need to. + + Parameters + ---------- + atomic_number : int + Atomic number of the atom + formal_charge : int + Formal charge of the atom + is_aromatic : bool + If True, atom is aromatic; if False, not aromatic + stereochemistry : str, optional, default=None + Either 'R' or 'S' for specified stereochemistry, or None for ambiguous stereochemistry + name : str, optional, default=None + An optional name to be associated with the atom + + Examples + -------- + + Create a non-aromatic carbon atom + + >>> atom = Atom(6, 0, False) + + Create a chiral carbon atom + + >>> atom = Atom(6, 0, False, stereochemistry='R', name='CT') + + """ + self._atomic_number = atomic_number + self._formal_charge = formal_charge + self._is_aromatic = is_aromatic + self._stereochemistry = stereochemistry + if name is None: + name = '' + self._name = name + self._molecule = molecule + ## From Jeff: I'm going to assume that this is implicit in the parent Molecule's ordering of atoms + #self._molecule_atom_index = molecule_atom_index + self._bonds = list() + self._virtual_sites = list() + + # TODO: We can probably avoid an explicit call and determine this dynamically + # from self._molecule (maybe caching the result) to get rid of some bookkeeping. + def add_bond(self, bond): + """Adds a bond that this atom is involved in + .. todo :: Is this how we want to keep records? + + Parameters + ---------- + bond: an openforcefield.topology.molecule.Bond + A bond involving this atom + +""" + + self._bonds.append(bond) + #self._stereochemistry = None + + def add_virtual_site(self, vsite): + """Adds a bond that this atom is involved in + .. todo :: Is this how we want to keep records? + + Parameters + ---------- + bond: an openforcefield.topology.molecule.Bond + A bond involving this atom + +""" + + self._virtual_sites.append(vsite) + + def to_dict(self): + """Return a dict representation of the atom. + +""" + # TODO + atom_dict = OrderedDict() + atom_dict['atomic_number'] = self._atomic_number + atom_dict['formal_charge'] = self._formal_charge + atom_dict['is_aromatic'] = self._is_aromatic + atom_dict['stereochemistry'] = self._stereochemistry + # TODO: Should we let atoms have names? + atom_dict['name'] = self._name + # TODO: Should this be implicit in the atom ordering when saved? + #atom_dict['molecule_atom_index'] = self._molecule_atom_index + return atom_dict + + @classmethod + def from_dict(cls, atom_dict): + """Create an Atom from a dict representation. + +""" + ## TODO: classmethod or static method? Classmethod is needed for Bond, so it have + ## its _molecule set and then look up the Atom on each side of it by ID + return cls.__init__(*atom_dict) + + @property + def formal_charge(self): + """ + The atom's formal charge + """ + return self._formal_charge + + @property + def partial_charge(self): + """ + The partial charge of the atom, if any. + + Returns + ------- + float or None + """ + if self._molecule._partial_charges is None: + return None + else: + index = self.molecule_atom_index + return self._molecule._partial_charges[index] + + @property + def is_aromatic(self): + """ + The atom's is_aromatic flag + """ + return self._is_aromatic + + @property + def stereochemistry(self): + """ + The atom's stereochemistry (if defined, otherwise None) + """ + return self._stereochemistry + + @stereochemistry.setter + def stereochemistry(self, value): + """Set the atoms stereochemistry + Parameters + ---------- + value : str + The stereochemistry around this atom, allowed values are "CW", "CCW", or None, + """ + + #if (value != 'CW') and (value != 'CCW') and not(value is None): + # raise Exception("Atom stereochemistry setter expected 'CW', 'CCW', or None. Received {} (type {})".format(value, type(value))) + self._stereochemistry = value + + @property + def element(self): + """ + The element name + + """ + return element.Element.getByAtomicNumber(self._atomic_number) + + @property + def atomic_number(self): + """ + The integer atomic number of the atom. + + """ + return self._atomic_number + + @property + def mass(self): + """ + The standard atomic weight (abundance-weighted isotopic mass) of the atomic site. + + .. todo :: Should we discriminate between standard atomic weight and most abundant isotopic mass? + TODO (from jeff): Are there atoms that have different chemical properties based on their isotopes? + + """ + return self.element.mass + + @property + def name(self): + """ + The name of this atom, if any + """ + return self._name + + @name.setter + def name(self, other): + """ + + Parameters + ---------- + other : string + The new name for this atom + """ + if not (type(other) is str): + raise Exception( + "In setting atom name. Expected str, received {} (type {})". + format(other, type(other))) + self._name = other + + # TODO: How are we keeping track of bonds, angles, etc? + + @property + def bonds(self): + """ + The list of ``Bond`` objects this atom is involved in. + + """ + return self._bonds + #for bond in self._bonds: + # yield bond + + @property + #def bonded_to(self): + def bonded_atoms(self): + """ + The list of ``Atom`` objects this atom is involved in bonds with + + """ + for bond in self._bonds: + for atom in bond.atoms: + if not (atom == self): + # TODO: This seems dangerous. Ask John for a better way + yield atom + + def is_bonded_to(self, atom2): + """ + Determine whether this atom is bound to another atom + + Parameters + ---------- + atom2: openforcefield.topology.molecule.Atom + a different atom in the same molecule + + Returns + ------- + bool + Whether this atom is bound to atom2 + """ + #TODO: Sanity check (check for same molecule?) + assert self != atom2 + for bond in self._bonds: + for bonded_atom in bond.atoms: + if atom2 == bonded_atom: + return True + return False + + @property + def virtual_sites(self): + """ + The list of ``VirtualSite`` objects this atom is involved in. + + """ + return self._virtual_sites + #for vsite in self._vsites: + # yield vsite + + @property + def molecule_atom_index(self): + """ + The index of this Atom within the the list of atoms in ``Molecules``. + Note that this can be different from ``molecule_particle_index``. + + """ + if self._molecule is None: + raise ValueError('This Atom does not belong to a Molecule object') + return self._molecule.atoms.index(self) + + @property + def molecule_particle_index(self): + """ + The index of this Atom within the the list of particles in the parent ``Molecule``. + Note that this can be different from ``molecule_atom_index``. + + """ + if self._molecule is None: + raise ValueError('This Atom does not belong to a Molecule object') + return self._molecule.particles.index(self) + + # ## From Jeff: Not sure if we actually need this + # @property + # def topology_atom_index(self): + # """ + # The index of this Atom within the the list of atoms in ``Topology``. + # Note that this can be different from ``particle_index``. + # + # """ + # if self._topology is None: + # raise ValueError('This Atom does not belong to a Topology object') + # # TODO: This will be slow; can we cache this and update it only when needed? + # # Deleting atoms/molecules in the Topology would have to invalidate the cached index. + # return self._topology.atoms.index(self) + + def __repr__(self): + # TODO: Also include particle_index and which molecule this atom belongs to? + return "Atom(name={}, atomic number={})".format( + self._name, self._atomic_number) + + def __str__(self): + # TODO: Also include particle_index and which molecule this atom belongs to? + return "".format( + self._name, self._atomic_number) + + +#============================================================================================= +# VirtualSite +#============================================================================================= + + +class VirtualSite(Particle): + """ + A particle representing a virtual site whose position is defined in terms of ``Atom`` positions. + + Note that chemical atoms are represented by the ``Atom``. + + + .. warning :: This API is experimental and subject to change. + + .. todo:: + + * Should a virtual site be able to belong to more than one Topology? + * Should virtual sites be immutable or mutable? + + """ + + def __init__(self, + atoms, + charge_increments=None, + epsilon=None, + sigma=None, + rmin_half=None, + name=None): + """ + Base class for VirtualSites + + .. todo :: + + * This will need to be generalized for virtual sites to allow out-of-plane sites, which are not simply a linear combination of atomic positions + * Add checking for allowed virtual site types + * How do we want users to specify virtual site types? + + Parameters + ---------- + atoms : list of Atom of shape [N] + atoms[index] is the corresponding Atom for weights[index] + charge_increments : list of floats of shape [N], optional, default=None + The amount of charge to remove from the VirtualSite's atoms and put in the VirtualSite. Indexing in this list should match the ordering in the atoms list. Default is None. + sigma : float, default=None + Sigma term for VdW properties of virtual site. Default is None. + epsilon : float + Epsilon term for VdW properties of virtual site. Default is None. + rmin_half : float + Rmin_half term for VdW properties of virtual site. Default is None. + name : string or None, default=None + The name of this virtual site. Default is None. + + + virtual_site_type : str + Virtual site type. + name : str or None, default=None + The name of this virtual site. Default is None + +""" + + # Ensure we have as many charge_increments as we do atoms + if not (charge_increments == None): + if not (len(charge_increments) == len(atoms)): + raise Exception( + "VirtualSite definition must have same number of charge_increments ({}) and atoms({})" + .format(len(charge_increments), len(atoms))) + + # VdW parameters can either be epsilon+rmin_half or epsilon+sigma, but not both + if not (epsilon == None): + if ((rmin_half != None) and (sigma != None)): + raise Exception( + "VirtualSite constructor given epsilon (value : {}), rmin_half (value : {}), and sigma (value : {}). If epsilon is nonzero, it should receive either rmin_half OR sigma" + .format(epsilon, rmin_half, sigma)) + if ((rmin_half == None) and (sigma == None)): + raise Exception( + "VirtualSite constructor given epsilon (value : {}) but not given rmin_half (value : {}) or sigma (value : {})" + .format(epsilon, rmin_half, sigma)) + if (sigma == None): + # TODO: Save the 6th root of 2 if this starts being slow. + sigma = (2. * rmin_half) / (2.**(1. / 6)) + + elif epsilon == None: + if ((rmin_half != None) or (sigma != None)): + raise Exception( + "VirtualSite constructor given rmin_half (value : {}) or sigma (value : {}), but not epsilon (value : {})" + .format(rmin_half, sigma, epsilon)) + + # Perform type-checking + for atom in atoms: + assert isinstance(atom, Atom) + for atom_index in range(len(atoms) - 1): + assert atoms[atom_index].molecule is atoms[atom_index + 1].molecule + assert isinstance(atoms[1].molecule, FrozenMolecule) + + if sigma == None: + self._sigma = None + else: + assert hasattr(sigma, 'unit') + assert unit.angstrom.is_compatible(sigma.unit) + self._sigma = sigma.in_units_of(unit.angstrom) + + if epsilon == None: + self._epsilon = None + else: + assert hasattr(epsilon, 'unit') + assert (unit.kilojoule_per_mole).is_compatible(epsilon.unit) + self._epsilon = epsilon.in_units_of(unit.kilojoule_per_mole) + + if charge_increments == None: + self._charge_increments = None + else: + assert hasattr(charge_increments, 'unit') + assert unit.elementary_charges.is_compatible( + charge_increments.unit) + self._charge_increments = charge_increments.in_units_of( + unit.elementary_charges) + + self._atoms = list() + for atom in atoms: + atom.add_virtual_site(self) + self._atoms.append(atom) + self._molecule = atoms[0].molecule + + self._name = name + + # Subclassing makes _type unnecessary + #self._type = None + # TODO: Validate site types against allowed values + + #self._weights = np.array(weights) # make a copy and convert to array internally + + def to_dict(self): + """Return a dict representation of the virtual site. + +""" + # Each subclass should have its own to_dict + vsite_dict = OrderedDict() + vsite_dict['name'] = self._name + vsite_dict['atoms'] = tuple( + [i.molecule_atom_index for i in self.atoms]) + vsite_dict['charge_increments'] = quantity_to_string(self._charge_increments) + + + vsite_dict['epsilon'] = quantity_to_string(self._epsilon) + + + vsite_dict['sigma'] = quantity_to_string(self._sigma) + + return vsite_dict + + + @staticmethod + def from_dict(vsite_dict): + """Create a virtual site from a dict representation. + +""" + # Each subclass needs to have its own from_dict + + # Make a copy of the vsite_dict, where we'll unit-wrap the appropriate values + vsite_dict_units = deepcopy(vsite_dict) + + # Attach units to epsilon term + vsite_dict_units['epsilon'] = string_to_quantity( + vsite_dict['epsilon']) + vsite_dict_units['sigma'] = string_to_quantity(vsite_dict['sigma']) + vsite_dict_units['charge_increments'] = string_to_quantity( + vsite_dict['charge_increments']) + + return VirtualSite(**vsite_dict_units) + + @property + def molecule_virtual_site_index(self): + """ + The index of this VirtualSite within the list of virtual sites within ``Molecule`` + Note that this can be different from ``particle_index``. + """ + #if self._topology is None: + # raise ValueError('This VirtualSite does not belong to a Topology object') + # TODO: This will be slow; can we cache this and update it only when needed? + # Deleting atoms/molecules in the Topology would have to invalidate the cached index. + return self._molecule.virtual_sites.index(self) + + @property + def molecule_particle_index(self): + """ + The index of this VirtualSite within the the list of particles in the parent ``Molecule``. + Note that this can be different from ``molecule_virtual_site_index``. + + """ + if self._molecule is None: + raise ValueError( + 'This VirtualSite does not belong to a Molecule object') + return self._molecule.particles.index(self) + + @property + def atoms(self): + """ + Atoms on whose position this VirtualSite depends. + """ + return self._atoms + #for atom in self._atoms: + # yield atom + + @property + def charge_increments(self): + """ + Charges taken from this VirtualSite's atoms and given to the VirtualSite + """ + return self._charge_increments + + @property + def epsilon(self): + """ + The VdW epsilon term of this VirtualSite + """ + return self._epsilon + + @property + def sigma(self): + """ + The VdW sigma term of this VirtualSite + """ + return self._sigma + + @property + def rmin_half(self): + """ + The VdW rmin_half term of this VirtualSite + """ + rmin = 2.**(1. / 6) * self._sigma + rmin_half = rmin / 2 + return rmin_half + + @property + def name(self): + """ + The name of this VirtualSite + """ + return self._name + + @property + def type(self): + """The type of this VirtualSite (returns the class name as string)""" + return self.__class__.__name__ + + def __repr__(self): + # TODO: Also include particle_index, which molecule this atom belongs to? + return "VirtualSite(name={}, type={}, atoms={})".format( + self.name, self.type, self.atoms) + + def __str__(self): + # TODO: Also include particle_index, which molecule this atom belongs to? + return "".format( + self.name, self.type, self.atoms) + + +class BondChargeVirtualSite(VirtualSite): + """ + A particle representing a "Bond Charge"-type virtual site, in which the location of the charge is specified by the positions of two atoms. This supports placement of a virtual site S along a vector between two specified atoms, e.g. to allow for a sigma hole for halogens or similar contexts. With positive values of the distance, the virtual site lies outside the first indexed atom. + + .. warning :: This API is experimental and subject to change. + """ + + def __init__(self, + atoms, + distance, + charge_increments=None, + weights=None, + epsilon=None, + sigma=None, + rmin_half=None, + name=None): + """ + Create a bond charge-type virtual site, in which the location of the charge is specified by the position of two atoms. This supports placement of a virtual site S along a vector between two specified atoms, e.g. to allow for a sigma hole for halogens or similar contexts. With positive values of the distance, the virtual site lies outside the first indexed atom. + + TODO: One of the examples on https://open-forcefield-toolkit.readthedocs.io/en/topology/smirnoff.html#virtualsites-virtual-sites-for-off-atom-charges has a BondCharge defined with three atoms -- How does that work? + + Parameters + ---------- + atoms : list of openforcefield.topology.molecule.Atom objects of shape [N] + The atoms defining the virtual site's position + distance : float + + weights : list of floats of shape [N] or None, optional, default=None + weights[index] is the weight of particles[index] contributing to the position of the virtual site. Default is None + charge_increments : list of floats of shape [N], optional, default=None + The amount of charge to remove from the VirtualSite's atoms and put in the VirtualSite. Indexing in this list should match the ordering in the atoms list. Default is None. + epsilon : float + Epsilon term for VdW properties of virtual site. Default is None. + sigma : float, default=None + Sigma term for VdW properties of virtual site. Default is None. + rmin_half : float + Rmin_half term for VdW properties of virtual site. Default is None. + name : string or None, default=None + The name of this virtual site. Default is None. + """ + assert hasattr(distance, 'unit') + assert unit.angstrom.is_compatible(distance.unit) + + super().__init__( + atoms, + charge_increments=charge_increments, + epsilon=epsilon, + sigma=sigma, + rmin_half=rmin_half, + name=name) + self._distance = distance.in_units_of(unit.angstrom) + + def to_dict(self): + vsite_dict = super().to_dict() + vsite_dict['distance'] = quantity_to_string(self._distance) + + #type = self.type + vsite_dict['vsite_type'] = self.type + #vsite_dict['vsite_type'] = 'BondChargeVirtualSite' + return vsite_dict + + @staticmethod + def from_dict(vsite_dict): + base_dict = deepcopy(vsite_dict) + # Make sure it's the right type of virtual site + assert vsite_dict['vsite_type'] == "BondChargeVirtualSite" + base_dict.pop('vsite_type') + base_dict.pop('distance') + vsite = super().from_dict(**base_dict) + vsite._distance = string_to_quantity(vsite_dict['distance']) + return vsite + + @property + def distance(self): + """The distance parameter of the virtual site""" + return self._distance + + +class MonovalentLonePairVirtualSite(VirtualSite): + """ + A particle representing a "Monovalent Lone Pair"-type virtual site, in which the location of the charge is specified by the positions of three atoms. This is originally intended for situations like a carbonyl, and allows placement of a virtual site S at a specified distance d, in_plane_angle, and out_of_plane_angle relative to a central atom and two connected atoms. + + .. warning :: This API is experimental and subject to change. + """ + + def __init__(self, + atoms, + distance, + out_of_plane_angle, + in_plane_angle, + charge_increments=None, + weights=None, + epsilon=None, + sigma=None, + rmin_half=None, + name=None): + """ + Create a bond charge-type virtual site, in which the location of the charge is specified by the position of three atoms. + + TODO : Do "weights" have any meaning here? + + Parameters + ---------- + atoms : list of three openforcefield.topology.molecule.Atom objects + The three atoms defining the virtual site's position + distance : float + + out_of_plane_angle : float + + in_plane_angle : float + + epsilon : float + Epsilon term for VdW properties of virtual site. Default is None. + sigma : float, default=None + Sigma term for VdW properties of virtual site. Default is None. + rmin_half : float + Rmin_half term for VdW properties of virtual site. Default is None. + name : string or None, default=None + The name of this virtual site. Default is None. + + + """ + #assert isinstance(distance, unit.Quantity) + # TODO: Check for proper number of atoms + assert hasattr(distance, 'unit') + assert unit.angstrom.is_compatible(distance.unit) + assert hasattr(in_plane_angle, 'unit') + assert unit.degree.is_compatible(in_plane_angle.unit) + assert hasattr(out_of_plane_angle, 'unit') + assert unit.degree.is_compatible(out_of_plane_angle.unit) + + assert len(atoms) == 3 + super().__init__( + atoms, + charge_increments=charge_increments, + epsilon=epsilon, + sigma=sigma, + rmin_half=rmin_half, + name=name) + self._distance = distance.in_units_of(unit.angstrom) + self._out_of_plane_angle = out_of_plane_angle.in_units_of(unit.degree) + self._in_plane_angle = in_plane_angle.in_units_of(unit.degree) + + def to_dict(self): + vsite_dict = super().to_dict() + vsite_dict['distance'] = quantity_to_string(self._distance) + vsite_dict['out_of_plane_angle'] = quantity_to_string( + self._out_of_plane_angle) + vsite_dict['in_plane_angle'] = quantity_to_string(self._in_plane_angle) + #vsite_dict['vsite_type'] = self.type.fget() + vsite_dict['vsite_type'] = self.type + #vsite_dict['vsite_type'] = 'MonovalentLonePairVirtualSite' + return vsite_dict + + @staticmethod + def from_dict(vsite_dict): + base_dict = deepcopy(vsite_dict) + + # Make sure it's the right type of virtual site + assert vsite_dict['vsite_type'] == "MonovalentLonePairVirtualSite" + base_dict.pop('vsite_type') + base_dict.pop('distance') + base_dict.pop('out_of_plane_angle') + base_dict.pop('in_plane_angle') + vsite = super().from_dict(**base_dict) + vsite._distance = string_to_quantity(vsite_dict['distance']) + vsite._in_plane_angle = string_to_quantity( + vsite_dict['in_plane_angle']) + vsite._out_of_plane_angle = string_to_quantity( + vsite_dict['out_of_plane_angle']) + return vsite + + @property + def distance(self): + """The distance parameter of the virtual site""" + return self._distance + + @property + def in_plane_angle(self): + """The in_plane_angle parameter of the virtual site""" + return self._in_plane_angle + + @property + def out_of_plane_angle(self): + """The out_of_plane_angle parameter of the virtual site""" + return self._out_of_plane_angle + + +class DivalentLonePairVirtualSite(VirtualSite): + """ + A particle representing a "Divalent Lone Pair"-type virtual site, in which the location of the charge is specified by the positions of three atoms. This is suitable for cases like four-point and five-point water models as well as pyrimidine; a charge site S lies a specified distance d from the central atom among three atoms along the bisector of the angle between the atoms (if out_of_plane_angle is zero) or out of the plane by the specified angle (if out_of_plane_angle is nonzero) with its projection along the bisector. For positive values of the distance d the virtual site lies outside the 2-1-3 angle and for negative values it lies inside. + + .. warning :: This API is experimental and subject to change. + """ + + def __init__(self, + atoms, + distance, + out_of_plane_angle, + in_plane_angle, + charge_increments=None, + weights=None, + epsilon=None, + sigma=None, + rmin_half=None, + name=None): + """ + Create a divalent lone pair-type virtual site, in which the location of the charge is specified by the position of three atoms. + + TODO : Do "weights" have any meaning here? + + Parameters + ---------- + atoms : list of 3 openforcefield.topology.molecule.Atom objects + The three atoms defining the virtual site's position + distance : float + + out_of_plane_angle : float + + in_plane_angle : float + + epsilon : float + Epsilon term for VdW properties of virtual site. Default is None. + sigma : float, default=None + Sigma term for VdW properties of virtual site. Default is None. + rmin_half : float + Rmin_half term for VdW properties of virtual site. Default is None. + name : string or None, default=None + The name of this virtual site. Default is None. + """ + #assert isinstance(distance, unit.Quantity) + assert hasattr(distance, 'unit') + assert unit.angstrom.is_compatible(distance.unit) + assert hasattr(in_plane_angle, 'unit') + assert unit.degree.is_compatible(in_plane_angle.unit) + assert hasattr(out_of_plane_angle, 'unit') + assert unit.degree.is_compatible(out_of_plane_angle.unit) + assert len(atoms) == 3 + super().__init__( + atoms, + charge_increments=charge_increments, + epsilon=epsilon, + sigma=sigma, + rmin_half=rmin_half, + name=name) + self._distance = distance.in_units_of(unit.angstrom) + self._out_of_plane_angle = out_of_plane_angle.in_units_of(unit.degree) + self._in_plane_angle = in_plane_angle.in_units_of(unit.degree) + + def to_dict(self): + vsite_dict = super().to_dict() + vsite_dict['distance'] = quantity_to_string(self._distance) + vsite_dict['out_of_plane_angle'] = quantity_to_string( + self._out_of_plane_angle) + vsite_dict['in_plane_angle'] = quantity_to_string(self._in_plane_angle) + vsite_dict['vsite_type'] = self.type + return vsite_dict + + @staticmethod + def from_dict(vsite_dict): + """ + Construct a new DivalentPairVirtualSite from an serialized dictionary representation. + + Parameters + ---------- + vsite_dict : dict + The VirtualSite to deserialize. + + Returns + ------- + The newly created DivalentLonePairVirtualSite + + """ + base_dict = deepcopy(vsite_dict) + + # Make sure it's the right type of virtual site + assert vsite_dict['vsite_type'] == "DivalentLonePairVirtualSite" + base_dict.pop('vsite_type') + base_dict.pop('distance') + base_dict.pop('out_of_plane_angle') + base_dict.pop('in_plane_angle') + vsite = super().from_dict(**base_dict) + vsite._distance = string_to_quantity(vsite_dict['distance']) + vsite._in_plane_angle = string_to_quantity( + vsite_dict['in_plane_angle']) + vsite._out_of_plane_angle = string_to_quantity( + vsite_dict['out_of_plane_angle']) + + return vsite + + @property + def distance(self): + """The distance parameter of the virtual site""" + return self._distance + + @property + def in_plane_angle(self): + """The in_plane_angle parameter of the virtual site""" + return self._in_plane_angle + + @property + def out_of_plane_angle(self): + """The out_of_plane_angle parameter of the virtual site""" + return self._out_of_plane_angle + + +class TrivalentLonePairVirtualSite(VirtualSite): + """ + A particle representing a "Trivalent Lone Pair"-type virtual site, in which the location of the charge is specified by the positions of four atoms. This is suitable for planar or tetrahedral nitrogen lone pairs; a charge site S lies above the central atom (e.g. nitrogen a distance d along the vector perpendicular to the plane of the three connected atoms (2,3,4). With positive values of d the site lies above the nitrogen and with negative values it lies below the nitrogen. + + .. warning :: This API is experimental and subject to change. + """ + + def __init__(self, + atoms, + distance, + out_of_plane_angle, + in_plane_angle, + charge_increments=None, + weights=None, + epsilon=None, + sigma=None, + rmin_half=None, + name=None): + """ + Create a trivalent lone pair-type virtual site, in which the location of the charge is specified by the position of four atoms. + + TODO : Do "weights" have any meaning here? + + Parameters + ---------- + atoms : list of 4 openforcefield.topology.molecule.Atom objects + The three atoms defining the virtual site's position + distance : float + + out_of_plane_angle : float + + in_plane_angle : float + + epsilon : float + Epsilon term for VdW properties of virtual site. Default is None. + sigma : float, default=None + Sigma term for VdW properties of virtual site. Default is None. + rmin_half : float + Rmin_half term for VdW properties of virtual site. Default is None. + name : string or None, default=None + The name of this virtual site. Default is None. + + """ + assert len(atoms) == 4 + assert hasattr(distance, 'unit') + assert unit.angstrom.is_compatible(distance.unit) + assert hasattr(in_plane_angle, 'unit') + assert unit.degree.is_compatible(in_plane_angle.unit) + assert hasattr(out_of_plane_angle, 'unit') + assert unit.degree.is_compatible(out_of_plane_angle.unit) + + super().__init__( + atoms, + charge_increments=charge_increments, + epsilon=epsilon, + sigma=sigma, + rmin_half=rmin_half, + name=name) + self._distance = distance.in_units_of(unit.angstrom) + self._out_of_plane_angle = out_of_plane_angle.in_units_of(unit.degree) + self._in_plane_angle = in_plane_angle.in_units_of(unit.degree) + + def to_dict(self): + vsite_dict = super().to_dict() + vsite_dict['distance'] = quantity_to_string(self._distance) + vsite_dict['out_of_plane_angle'] = quantity_to_string( + self._out_of_plane_angle) + vsite_dict['in_plane_angle'] = quantity_to_string(self._in_plane_angle) + vsite_dict['vsite_type'] = self.type + return vsite_dict + + @staticmethod + def from_dict(vsite_dict): + """ + Construct a new TrivalentPairVirtualSite from an serialized dictionary representation. + + Parameters + ---------- + vsite_dict : dict + The VirtualSite to deserialize. + + + Returns + ------- + The newly created TrivalentLonePairVirtualSite + + """ + base_dict = deepcopy(vsite_dict) + + # Make sure it's the right type of virtual site + assert vsite_dict['vsite_type'] == "TrivalentLonePairVirtualSite" + base_dict.pop('vsite_type') + base_dict.pop('distance') + base_dict.pop('out_of_plane_angle') + base_dict.pop('in_plane_angle') + vsite = super().from_dict(**base_dict) + vsite._distance = string_to_quantity(vsite_dict['distance']) + vsite._in_plane_angle = string_to_quantity( + vsite_dict['in_plane_angle']) + vsite._out_of_plane_angle = string_to_quantity( + vsite_dict['out_of_plane_angle']) + + return vsite + + @property + def distance(self): + """The distance parameter of the virtual site""" + return self._distance + + @property + def in_plane_angle(self): + """The in_plane_angle parameter of the virtual site""" + return self._in_plane_angle + + @property + def out_of_plane_angle(self): + """The out_of_plane_angle parameter of the virtual site""" + return self._out_of_plane_angle + + +# ============================================================================================= +# Bond Stereochemistry +# ============================================================================================= + +#class BondStereochemistry(Serializable): +#""" +#Bond stereochemistry representation +#""" +#def __init__(self, stereo_type, neighbor1, neighbor2): +# """ +# +# Parameters +# ---------- +# stereo_type +# neighbor1 +# neighbor2 +# """ +# assert isinstance(neighbor1, Atom) +# assert isinstance(neighbor2, Atom) +# # Use stereo_type @setter to check stereo type is a permitted value +# self.stereo_type = stereo_type +# self._neighbor1 = neighbor1 +# self._neighbor2 = neighbor2 + +#def to_dict(self): +# bs_dict = OrderedDict() +# bs_dict['stereo_type'] = self._stereo_type +# bs_dict['neighbor1_index'] = self._neighbor1.molecule_atom_index +# bs_dict['neighbor2_index'] = self._neighbor2.molecule_atom_index +# return bs_dict + +#classmethod +#def from_dict(cls, molecule, bs_dict): +# neighbor1 = molecule.atoms[bs_dict['neighbor1_index']] +# neighbor2 = molecule.atoms[bs_dict['neighbor2_index']] +# return cls.__init__(bs_dict['stereo_type'], neighbor1, neighbor2) + +#@property +#def stereo_type(self): +# return self._stereo_type + +#@stereo_type.setter +#def stereo_type(self, value): +# assert (value == 'CIS') or (value == 'TRANS') or (value is None) +# self._stereo_type = value + +#@property +#def neighbor1(self): +# return self._neighbor1 + +#@property +#def neighbor2(self): +# return self._neighbor2 + +#@property +#def neighbors(self): +# return (self._neighbor1, self._neighbor2) + +# ============================================================================================= +# Bond +# ============================================================================================= + + +class Bond(Serializable): + """ + Chemical bond representation. + + .. warning :: This API is experimental and subject to change. + + .. todo :: Allow bonds to have associated properties. + + Attributes + ---------- + atom1, atom2 : openforcefield.topology.Atom + Atoms involved in the bond + bondtype : int + Discrete bond type representation for the Open Forcefield aromaticity model + TODO: Do we want to pin ourselves to a single standard aromaticity model? + type : str + String based bond type + order : int + Integral bond order + fractional_bond_order : float, optional + Fractional bond order, or None. + + + .. warning :: This API is experimental and subject to change. + """ + + def __init__(self, + atom1, + atom2, + bond_order, + is_aromatic, + fractional_bond_order=None, + stereochemistry=None): + """ + Create a new chemical bond. + + """ + assert type(atom1) == Atom + assert type(atom2) == Atom + assert atom1.molecule is atom2.molecule + assert isinstance(atom1.molecule, FrozenMolecule) + self._molecule = atom1.molecule + + self._atom1 = atom1 + self._atom2 = atom2 + + atom1.add_bond(self) + atom2.add_bond(self) + # TODO: Check bondtype and fractional_bond_order are valid? + # TODO: Dative bonds + #self._type = bondtype + self._fractional_bond_order = fractional_bond_order + self._bond_order = bond_order + self._is_aromatic = is_aromatic + self._stereochemistry = stereochemistry + + def to_dict(self): + """ + Return a dict representation of the bond. + + """ + bond_dict = OrderedDict() + bond_dict['atom1'] = self.atom1.molecule_atom_index + bond_dict['atom2'] = self.atom2.molecule_atom_index + bond_dict['bond_order'] = self._bond_order + bond_dict['is_aromatic'] = self._is_aromatic + bond_dict['stereochemistry'] = self._stereochemistry + bond_dict['fractional_bond_order'] = self._fractional_bond_order + return bond_dict + + @classmethod + def from_dict(cls, molecule, d): + """Create a Bond from a dict representation.""" + # TODO + d['molecule'] = molecule + d['atom1'] = molecule.atoms[d['atom1']] + d['atom2'] = molecule.atoms[d['atom2']] + return cls(*d) + + @property + def atom1(self): + return self._atom1 + + @property + def atom2(self): + return self._atom2 + + @property + def atom1_index(self): + return self.molecule.atoms.index(self._atom1) + + @property + def atom2_index(self): + return self.molecule.atoms.index(self._atom2) + + @property + def atoms(self): + return (self._atom1, self._atom2) + + @property + def bond_order(self): + return self._bond_order + + @bond_order.setter + def bond_order(self, value): + self._bond_order = value + + @property + def fractional_bond_order(self): + return self._fractional_bond_order + + @fractional_bond_order.setter + def fractional_bond_order(self, value): + self._fractional_bond_order = value + + @property + def stereochemistry(self): + return self._stereochemistry + + @property + def is_aromatic(self): + return self._is_aromatic + + @property + def molecule(self): + return self._molecule + + @molecule.setter + def molecule(self, value): + """ + Sets the Bond's parent molecule. Can not be changed after assignment + """ + assert self._molecule == None + self._molecule = value + + @property + def molecule_bond_index(self): + """ + The index of this Bond within the the list of bonds in ``Molecules``. + + """ + if self._molecule is None: + raise ValueError('This Atom does not belong to a Molecule object') + return self._molecule.bonds.index(self) + + +#============================================================================================= +# Molecule +#============================================================================================= + +# TODO: How do we automatically trigger invalidation of cached properties if an ``Atom``, ``Bond``, or ``VirtualSite`` is modified, +# rather than added/deleted via the API? The simplest resolution is simply to make them immutable. + + +class FrozenMolecule(Serializable): + """ + Immutable chemical representation of a molecule, such as a small molecule or biopolymer. + + .. todo :: What other API calls would be useful for supporting biopolymers as small molecules? Perhaps iterating over chains and residues? + + Examples + -------- + + Create a molecule from a sdf file + + >>> from openforcefield.utils import get_data_filename + >>> sdf_filepath = get_data_filename('molecules/ethanol.sdf') + >>> molecule = FrozenMolecule.from_file(sdf_filepath) + + Convert to OpenEye OEMol object + + >>> oemol = molecule.to_openeye() + + Create a molecule from an OpenEye molecule + + >>> molecule = FrozenMolecule.from_openeye(oemol) + + Convert to RDKit Mol object + + >>> rdmol = molecule.to_rdkit() + + Create a molecule from an RDKit molecule + + >>> molecule = FrozenMolecule.from_rdkit(rdmol) + + Create a molecule from IUPAC name (requires the OpenEye toolkit) + + >>> molecule = FrozenMolecule.from_iupac('imatinib') + + Create a molecule from SMILES + + >>> molecule = FrozenMolecule.from_smiles('Cc1ccccc1') + + .. warning :: This API is experimental and subject to change. + + + """ + + def __init__(self, + other=None, + file_format=None, + toolkit_registry=GLOBAL_TOOLKIT_REGISTRY, + allow_undefined_stereo=False): + """ + Create a new FrozenMolecule object + + .. todo :: + + * If a filename or file-like object is specified but the file contains more than one molecule, what is the proper behavior? + Read just the first molecule, or raise an exception if more than one molecule is found? + + * Should we also support SMILES strings or IUPAC names for ``other``? + + Parameters + ---------- + other : optional, default=None + If specified, attempt to construct a copy of the Molecule from the specified object. + This can be any one of the following: + + * a :class:`Molecule` object + * a file that can be used to construct a :class:`Molecule` object + * an ``openeye.oechem.OEMol`` + * an ``rdkit.Chem.rdchem.Mol`` + * a serialized :class:`Molecule` object + file_format : str, optional, default=None + If providing a file-like object, you must specify the format + of the data. If providing a file, the file format will attempt + to be guessed from the suffix. + toolkit_registry : a :class:`ToolkitRegistry` or :class:`ToolkitWrapper` object, optional, default=GLOBAL_TOOLKIT_REGISTRY + :class:`ToolkitRegistry` or :class:`ToolkitWrapper` to use for I/O operations + allow_undefined_stereo : bool, default=False + If loaded from a file and ``False``, raises an exception if + undefined stereochemistry is detected during the molecule's + construction. + + Examples + -------- + + Create an empty molecule: + + >>> empty_molecule = FrozenMolecule() + + Create a molecule from a file that can be used to construct a molecule, + using either a filename or file-like object: + + >>> from openforcefield.utils import get_data_filename + >>> sdf_filepath = get_data_filename('molecules/ethanol.sdf') + >>> molecule = FrozenMolecule(sdf_filepath) + >>> molecule = FrozenMolecule(open(sdf_filepath, 'r'), file_format='sdf') + + >>> import gzip + >>> mol2_gz_filepath = get_data_filename('molecules/toluene.mol2.gz') + >>> molecule = FrozenMolecule(gzip.GzipFile(mol2_gz_filepath, 'r'), file_format='mol2') + + Create a molecule from another molecule: + + >>> molecule_copy = FrozenMolecule(molecule) + + Convert to OpenEye OEMol object + + >>> oemol = molecule.to_openeye() + + Create a molecule from an OpenEye molecule: + + >>> molecule = FrozenMolecule(oemol) + + Convert to RDKit Mol object + + >>> rdmol = molecule.to_rdkit() + + Create a molecule from an RDKit molecule: + + >>> molecule = FrozenMolecule(rdmol) + + Create a molecule from a serialized molecule object: + + >>> serialized_molecule = molecule.__getstate__() + >>> molecule_copy = Molecule(serialized_molecule) + + """ + + # Figure out if toolkit_registry is a whole registry, or just a single wrapper + if isinstance(toolkit_registry, ToolkitRegistry): + pass + elif isinstance(toolkit_registry, ToolkitWrapper): + toolkit = toolkit_registry + toolkit_registry = ToolkitRegistry(toolkit_precedence=[]) + toolkit_registry.add_toolkit(toolkit) + else: + raise ValueError( + "'toolkit_registry' must be either a ToolkitRegistry or a ToolkitWrapper" + ) + + if other is None: + self._initialize() + else: + loaded = False + if isinstance( + other, + openforcefield.topology.FrozenMolecule) and not (loaded): + self._copy_initializer(other) + loaded = True + if isinstance(other, + openforcefield.topology.Molecule) and not (loaded): + # TODO: This will need to be updated once FrozenMolecules and Molecules are significantly different + self._copy_initializer(other) + loaded = True + if isinstance(other, OrderedDict) and not (loaded): + self.__setstate__(other) + loaded = True + # Check through the toolkit registry to find a compatible wrapper for loading + if not loaded: + try: + result = toolkit_registry.call('from_object', other) + except NotImplementedError: + pass + else: + self._copy_initializer(result) + loaded = True + # TODO: Make this compatible with file-like objects (I couldn't figure out how to make an oemolistream + # from a fileIO object) + if (isinstance(other, str) + or hasattr(other, 'read')) and not (loaded): + mol = Molecule.from_file( + other, + file_format=file_format, + toolkit_registry=toolkit_registry, + allow_undefined_stereo=allow_undefined_stereo + ) # returns a list only if multiple molecules are found + if type(mol) == list: + raise ValueError( + 'Specified file or file-like object must contain exactly one molecule' + ) + + self._copy_initializer(mol) + loaded = True + if not (loaded): + msg = 'Cannot construct openforcefield.topology.Molecule from {}\n'.format( + other) + raise Exception(msg) + + #################################################################################################### + # Safe serialization + #################################################################################################### + + def to_dict(self): + """ + Return a dictionary representation of the molecule. + + .. todo :: + + * Document the representation standard. + * How do we do version control with this standard? + + Returns + ------- + molecule_dict : OrderedDict + A dictionary representation of the molecule. + + """ + molecule_dict = OrderedDict() + molecule_dict['name'] = self._name + ## From Jeff: If we go the properties-as-dict route, then _properties should, at + ## the top level, be a dict. Should we go through recursively and ensure all values are dicts too? + molecule_dict['atoms'] = [atom.to_dict() for atom in self._atoms] + molecule_dict['virtual_sites'] = [ + vsite.to_dict() for vsite in self._virtual_sites + ] + molecule_dict['bonds'] = [bond.to_dict() for bond in self._bonds] + # TODO: Charges + # TODO: Properties + # From Jeff: We could have the onerous requirement that all "properties" have to_dict() functions. + # Or we could restrict properties to simple stuff (ints, strings, floats, and the like) + # Or pickle anything unusual + # Or not allow user-defined properties at all (just use our internal _cached_properties) + #molecule_dict['properties'] = dict([(key, value._to_dict()) for key.value in self._properties]) + # TODO: Assuming "simple stuff" properties right now, figure out a better standard + molecule_dict['properties'] = self._properties + if hasattr(self, '_cached_properties'): + molecule_dict['cached_properties'] = self._cached_properties + # TODO: Conformers + if self._conformers == None: + molecule_dict['conformers'] = None + else: + molecule_dict['conformers'] = [] + molecule_dict[ + 'conformers_unit'] = 'angstrom' # Have this defined as a class variable? + for conf in self._conformers: + conf_unitless = (conf / unit.angstrom) + conf_serialized, conf_shape = serialize_numpy((conf_unitless)) + molecule_dict['conformers'].append(conf_serialized) + if self._partial_charges == None: + molecule_dict['partial_charges'] = None + molecule_dict['partial_charges_unit'] = None + + else: + charges_unitless = self._partial_charges / unit.elementary_charge + charges_serialized, charges_shape = serialize_numpy( + charges_unitless) + molecule_dict['partial_charges'] = charges_serialized + molecule_dict['partial_charges_unit'] = 'elementary_charge' + + return molecule_dict + + def __hash__(self): + """ + Returns a hash of this molecule. Used when checking molecule uniqueness in Topology creation. + + Returns + ------- + string + """ + return hash(self.to_smiles()) + + @classmethod + def from_dict(cls, molecule_dict): + """ + Create a new Molecule from a dictionary representation + + Parameters + ---------- + molecule_dict : OrderedDict + A dictionary representation of the molecule. + + Returns + ------- + molecule : Molecule + A Molecule created from the dictionary representation + + """ + # This implementation is a compromise to let this remain as a classmethod + mol = cls() + mol._initialize_from_dict(molecule_dict) + return mol + + def _initialize_from_dict(self, molecule_dict): + """ + Initialize this Molecule from a dictionary representation + + Parameters + ---------- + molecule_dict : OrderedDict + A dictionary representation of the molecule. + """ + # TODO: Provide useful exception messages if there are any failures + + self._initialize() + self.name = molecule_dict['name'] + for atom_dict in molecule_dict['atoms']: + self._add_atom(**atom_dict) + + # Handle virtual site unit reattachment and molecule tagging + for vsite_dict in molecule_dict['virtual_sites']: + vsite_dict_units = deepcopy(vsite_dict) + + # Attach units to epsilon term + vsite_dict_units['epsilon'] = string_to_quantity( + vsite_dict['epsilon']) + vsite_dict_units['sigma'] = string_to_quantity( + vsite_dict['sigma']) + vsite_dict_units['charge_increments'] = string_to_quantity( + vsite_dict['charge_increments']) + + # Call the correct molecule._add_X_virtual_site function, based on the stated type + if vsite_dict_units['vsite_type'] == "BondChargeVirtualSite": + del vsite_dict_units['vsite_type'] + vsite_dict_units['distance'] = string_to_quantity( + vsite_dict['distance']) + self._add_bond_charge_virtual_site(**vsite_dict_units) + + elif vsite_dict_units[ + 'vsite_type'] == "MonovalentLonePairVirtualSite": + del vsite_dict_units['vsite_type'] + vsite_dict_units['distance'] = string_to_quantity( + vsite_dict['distance']) + vsite_dict_units['in_plane_angle'] = string_to_quantity( + vsite_dict['in_plane_angle']) + vsite_dict_units['out_of_plane_angle'] = string_to_quantity( + vsite_dict['out_of_plane_angle']) + self._add_monovalent_lone_pair_virtual_site(**vsite_dict_units) + + elif vsite_dict_units[ + 'vsite_type'] == "DivalentLonePairVirtualSite": + del vsite_dict_units['vsite_type'] + vsite_dict_units['distance'] = string_to_quantity( + vsite_dict['distance']) + vsite_dict_units['in_plane_angle'] = string_to_quantity( + vsite_dict['in_plane_angle']) + vsite_dict_units['out_of_plane_angle'] = string_to_quantity( + vsite_dict['out_of_plane_angle']) + self._add_divalent_lone_pair_virtual_site(**vsite_dict_units) + + elif vsite_dict_units[ + 'vsite_type'] == "TrivalentLonePairVirtualSite": + del vsite_dict_units['vsite_type'] + vsite_dict_units['distance'] = string_to_quantity( + vsite_dict['distance']) + vsite_dict_units['in_plane_angle'] = string_to_quantity( + vsite_dict['in_plane_angle']) + vsite_dict_units['out_of_plane_angle'] = string_to_quantity( + vsite_dict['out_of_plane_angle']) + self._add_trivalent_lone_pair_virtual_site(**vsite_dict_units) + + else: + raise Exception("Vsite type {} not recognized".format( + vsite_dict['vsite_type'])) + + for bond_dict in molecule_dict['bonds']: + bond_dict['atom1'] = int(bond_dict['atom1']) + bond_dict['atom2'] = int(bond_dict['atom2']) + self._add_bond(**bond_dict) + + if molecule_dict['partial_charges'] == None: + self._partial_charges = None + else: + charges_shape = (self.n_atoms, ) + partial_charges_unitless = deserialize_numpy( + molecule_dict['partial_charges'], charges_shape) + pc_unit = getattr(unit, molecule_dict['partial_charges_unit']) + partial_charges = unit.Quantity(partial_charges_unitless, pc_unit) + self._partial_charges = partial_charges + + if molecule_dict['conformers'] == None: + self._conformers = None + else: + self._conformers = list() + for ser_conf in molecule_dict['conformers']: + # TODO: Update to use string_to_quantity + conformers_shape = ((self.n_atoms, 3)) + conformer_unitless = deserialize_numpy(ser_conf, + conformers_shape) + c_unit = getattr(unit, molecule_dict['conformers_unit']) + conformer = unit.Quantity(conformer_unitless, c_unit) + self._conformers.append(conformer) + + self._properties = molecule_dict['properties'] + + def __repr__(self): + """Return the SMILES of this molecule""" + return "Molecule with name '{}' and SMILES '{}'".format( + self.name, self.to_smiles()) + + def __getstate__(self): + return self.to_dict() + + def __setstate__(self, state): + return self._initialize_from_dict(state) + + def _initialize(self): + """ + Clear the contents of the current molecule. + """ + self._name = '' + self._atoms = list() + self._virtual_sites = list() + self._bonds = list() # List of bonds between Atom objects + self._properties = {} # Attached properties to be preserved + #self._cached_properties = None # Cached properties (such as partial charges) can be recomputed as needed + self._partial_charges = None + self._conformers = None # Optional conformers + + def _copy_initializer(self, other): + """ + Copy contents of the specified molecule + + .. todo :: Should this be a ``@staticmethod`` where we have an explicit copy constructor? + + Parameters + ---------- + other : optional + Overwrite the state of this FrozenMolecule with the specified FrozenMolecule object. + A deep copy is made. + + """ + #assert isinstance(other, type(self)), "can only copy instances of {}".format(type(self)) + other_dict = other.to_dict() + self._initialize_from_dict(other_dict) + + def __eq__(self, other): + """Test two molecules for equality to see if they are the chemical species, but do not check other annotated properties. + + .. note :: + + Note that this method simply tests whether two molecules are identical chemical species using equivalence of their canonical isomeric SMILES. + No effort is made to ensure that the atoms are in the same order or that any annotated properties are preserved. + + """ + return self.is_isomorphic(other) + + def to_smiles(self, toolkit_registry=GLOBAL_TOOLKIT_REGISTRY): + """ + Return a canonical isomeric SMILES representation of the current molecule + + .. note :: RDKit and OpenEye versions will not necessarily return the same representation. + + Parameters + ---------- + toolkit_registry : openforcefield.utils.toolkits.ToolRegistry or openforcefield.utils.toolkits.ToolkitWrapper, optional, default=None + :class:`ToolkitRegistry` or :class:`ToolkitWrapper` to use for SMILES conversion + + Returns + ------- + smiles : str + Canonical isomeric explicit-hydrogen SMILES + + Examples + -------- + + >>> from openforcefield.utils import get_data_filename + >>> sdf_filepath = get_data_filename('molecules/ethanol.sdf') + >>> molecule = Molecule(sdf_filepath) + >>> smiles = molecule.to_smiles() + + """ + if isinstance(toolkit_registry, ToolkitRegistry): + return toolkit_registry.call('to_smiles', self) + elif isinstance(toolkit_registry, ToolkitWrapper): + toolkit = toolkit_registry + return toolkit.to_smiles(self) + else: + raise Exception( + 'Invalid toolkit_registry passed to to_smiles. Expected ToolkitRegistry or ToolkitWrapper. Got {}' + .format(type(toolkit_registry))) + + @staticmethod + def from_smiles(smiles, hydrogens_are_explicit=False, toolkit_registry=GLOBAL_TOOLKIT_REGISTRY): + """ + Construct a Molecule from a SMILES representation + + Parameters + ---------- + smiles : str + The SMILES representation of the molecule. + hydrogens_are_explicit : bool, default = False + If False, the cheminformatics toolkit will perform hydrogen addition + toolkit_registry : openforcefield.utils.toolkits.ToolRegistry or openforcefield.utils.toolkits.ToolkitWrapper, optional, default=None + :class:`ToolkitRegistry` or :class:`ToolkitWrapper` to use for SMILES-to-molecule conversion + + Returns + ------- + molecule : openforcefield.topology.Molecule + + Examples + -------- + + >>> molecule = Molecule.from_smiles('Cc1ccccc1') + + """ + if isinstance(toolkit_registry, ToolkitRegistry): + return toolkit_registry.call('from_smiles', smiles) + elif isinstance(toolkit_registry, ToolkitWrapper): + toolkit = toolkit_registry + return toolkit.from_smiles(smiles, hydrogens_are_explicit=hydrogens_are_explicit) + else: + raise Exception( + 'Invalid toolkit_registry passed to from_smiles. Expected ToolkitRegistry or ToolkitWrapper. Got {}' + .format(type(toolkit_registry))) + + def is_isomorphic( + self, other, + compare_atom_stereochemistry=True, + compare_bond_stereochemistry=True, + ): + """ + Determines whether the molecules are isomorphic by comparing their graphs. + + Parameters + ---------- + other : an openforcefield.topology.molecule.FrozenMolecule + The molecule to test for isomorphism. + compare_atom_stereochemistry : bool, optional + If ``False``, atoms' stereochemistry is ignored for the + purpose of determining equality. Default is ``True``. + compare_bond_stereochemistry : bool, optional + If ``False``, bonds' stereochemistry is ignored for the + purpose of determining equality. Default is ``True``. + + Returns + ------- + molecules_are_isomorphic : bool + """ + import networkx as nx + + def node_match_func(x, y): + is_equal = ( + (x['atomic_number'] == y['atomic_number']) and + (x['is_aromatic'] == y['is_aromatic']) and + (x['formal_charge'] == y['formal_charge']) + ) + if compare_atom_stereochemistry: + is_equal &= x['stereochemistry'] == y['stereochemistry'] + return is_equal + + def edge_match_func(x, y): + # We don't need to check the exact bond order (which is 1 or 2) + # if the bond is aromatic. This way we avoid missing a match only + # if the alternate bond orders 1 and 2 are assigned differently. + is_equal = x['is_aromatic'] == y['is_aromatic'] or x['bond_order'] == y['bond_order'] + if compare_bond_stereochemistry: + is_equal &= x['stereochemistry'] == y['stereochemistry'] + return is_equal + + return nx.is_isomorphic(self.to_networkx(), + other.to_networkx(), + node_match=node_match_func, + edge_match=edge_match_func + ) + #if not (isinstance(other, FrozenMolecule)): + # other_fm = FrozenMolecule(other) + #else: + # other_fm = other + #self_smiles = self.to_smiles(toolkit_registry=toolkit_registry) + #other_smiles = other_fm.to_smiles(toolkit_registry=toolkit_registry) + #return self_smiles == other_smiles + + def generate_conformers(self, + toolkit_registry=GLOBAL_TOOLKIT_REGISTRY, + num_conformers=10, + clear_existing=True): + """ + Generate conformers for this molecule using an underlying toolkit + + Parameters + ---------- + toolkit_registry : openforcefield.utils.toolkits.ToolRegistry or openforcefield.utils.toolkits.ToolkitWrapper, optional, default=None + :class:`ToolkitRegistry` or :class:`ToolkitWrapper` to use for SMILES-to-molecule conversion + num_conformers : int, default=1 + The maximum number of conformers to produce + clear_existing : bool, default=True + Whether to overwrite existing conformers for the molecule + + Examples + -------- + + >>> molecule = Molecule.from_smiles('CCCCCC') + >>> molecule.generate_conformers() + + Raises + ------ + InvalidToolkitError + If an invalid object is passed as the toolkit_registry parameter + + """ + if isinstance(toolkit_registry, ToolkitRegistry): + return toolkit_registry.call('generate_conformers', self, num_conformers=num_conformers, + clear_existing=clear_existing) + elif isinstance(toolkit_registry, ToolkitWrapper): + toolkit = toolkit_registry + return toolkit.generate_conformers(self, num_conformers=num_conformers, clear_existing=clear_existing) + else: + raise InvalidToolkitError( + 'Invalid toolkit_registry passed to generate_conformers. Expected ToolkitRegistry or ToolkitWrapper. Got {}' + .format(type(toolkit_registry))) + + def compute_partial_charges_am1bcc(self, toolkit_registry=GLOBAL_TOOLKIT_REGISTRY): + """ + Calculate partial atomic charges for this molecule using AM1-BCC run by an underlying toolkit + + Parameters + ---------- + toolkit_registry : openforcefield.utils.toolkits.ToolRegistry or openforcefield.utils.toolkits.ToolkitWrapper, optional, default=None + :class:`ToolkitRegistry` or :class:`ToolkitWrapper` to use for the calculation + + Examples + -------- + + >>> molecule = Molecule.from_smiles('CCCCCC') + >>> molecule.generate_conformers() + >>> molecule.compute_partial_charges_am1bcc() + + Raises + ------ + InvalidToolkitError + If an invalid object is passed as the toolkit_registry parameter + + """ + if isinstance(toolkit_registry, ToolkitRegistry): + charges = toolkit_registry.call( + 'compute_partial_charges_am1bcc', + self + ) + elif isinstance(toolkit_registry, ToolkitWrapper): + toolkit = toolkit_registry + charges = toolkit.compute_partial_charges_am1bcc(self) + else: + raise InvalidToolkitError( + 'Invalid toolkit_registry passed to compute_partial_charges_am1bcc. Expected ToolkitRegistry or ToolkitWrapper. Got {}' + .format(type(toolkit_registry))) + self.partial_charges = charges + + + def compute_partial_charges(self, + #quantum_chemical_method='AM1-BCC', + #partial_charge_method='None', + toolkit_registry=GLOBAL_TOOLKIT_REGISTRY): + """ + **Warning! Not Implemented!** + Calculate partial atomic charges for this molecule using an underlying toolkit + + Parameters + ---------- + quantum_chemical_method : string, default='AM1-BCC' + The quantum chemical method to use for partial charge calculation. + partial_charge_method : string, default='None' + The partial charge calculation method to use for partial charge calculation. + toolkit_registry : openforcefield.utils.toolkits.ToolRegistry or openforcefield.utils.toolkits.ToolkitWrapper, optional, default=None + :class:`ToolkitRegistry` or :class:`ToolkitWrapper` to use for SMILES-to-molecule conversion + + Examples + -------- + + molecule = Molecule.from_smiles('CCCCCC') + molecule.generate_conformers() + molecule.compute_partial_charges() + + Raises + ------ + InvalidToolkitError + If an invalid object is passed as the toolkit_registry parameter + + """ + raise NotImplementedError + # TODO: Implement this in a way that's compliant with SMIRNOFF's tag when the spec gets finalized + if isinstance(toolkit_registry, ToolkitRegistry): + charges = toolkit_registry.call( + 'compute_partial_charges_am1bcc', + self, + ) + elif isinstance(toolkit_registry, ToolkitWrapper): + toolkit = toolkit_registry + charges = toolkit.compute_partial_charges_am1bcc( + self, + #quantum_chemical_method=quantum_chemical_method, + #partial_charge_method=partial_charge_method + ) + else: + raise InvalidToolkitError( + 'Invalid toolkit_registry passed to compute_partial_charges_am1bcc. Expected ToolkitRegistry or ToolkitWrapper. Got {}' + .format(type(toolkit_registry))) + + def compute_wiberg_bond_orders(self, + charge_model=None, + toolkit_registry=GLOBAL_TOOLKIT_REGISTRY): + """ + Calculate wiberg bond orders for this molecule using an underlying toolkit + + Parameters + ---------- + toolkit_registry : openforcefield.utils.toolkits.ToolRegistry or openforcefield.utils.toolkits.ToolkitWrapper, optional, default=None + :class:`ToolkitRegistry` or :class:`ToolkitWrapper` to use for SMILES-to-molecule conversion + charge_model : string, optional + The charge model to use for partial charge calculation + Examples + -------- + + >>> molecule = Molecule.from_smiles('CCCCCC') + >>> molecule.generate_conformers() + >>> molecule.compute_wiberg_bond_orders() + + Raises + ------ + InvalidToolkitError + If an invalid object is passed as the toolkit_registry parameter + + """ + if isinstance(toolkit_registry, ToolkitRegistry): + return toolkit_registry.call( + 'compute_wiberg_bond_orders', self, charge_model=charge_model) + elif isinstance(toolkit_registry, ToolkitWrapper): + toolkit = toolkit_registry + return toolkit.compute_wiberg_bond_orders( + self, charge_model=charge_model) + else: + raise Exception( + 'Invalid toolkit_registry passed to compute_wiberg_bond_orders. Expected ToolkitRegistry or ToolkitWrapper. Got {}' + .format(type(toolkit_registry))) + + def _invalidate_cached_properties(self): + """ + Indicate that the chemical entity has been altered. + """ + #if hasattr(self, '_cached_properties'): + # delattr(self, '_cached_properties') + self._conformers = None + self._partial_charges = None + self._propers = None + self._impropers = None + # TODO: Clear fractional bond orders + + def to_networkx(self): + """Generate a NetworkX undirected graph from the Molecule. + + Nodes are Atoms labeled with particle indices and atomic elements (via the ``element`` node atrribute). + Edges denote chemical bonds between Atoms. + Virtual sites are not included, since they lack a concept of chemical connectivity. + + .. todo :: + + * Do we need a ``from_networkx()`` method? If so, what would the Graph be required to provide? + * Should edges be labeled with discrete bond types in some aromaticity model? + * Should edges be labeled with fractional bond order if a method is specified? + * Should we add other per-atom and per-bond properties (e.g. partial charges) if present? + * Can this encode bond/atom chirality? + + + Returns + ------- + graph : networkx.Graph + The resulting graph, with nodes (atoms) labeled with atom indices, elements, stereochemistry and aromaticity + flags and bonds with two atom indices, bond order, stereochemistry, and aromaticity flags + + Examples + -------- + Retrieve the bond graph for imatinib (OpenEye toolkit required) + + >>> molecule = Molecule.from_iupac('imatinib') + >>> nxgraph = molecule.to_networkx() + + """ + import networkx as nx + G = nx.Graph() + for atom in self.atoms: + G.add_node( + atom.molecule_atom_index, atomic_number=atom.atomic_number, is_aromatic=atom.is_aromatic, + stereochemistry=atom.stereochemistry, formal_charge=atom.formal_charge) + #G.add_node(atom.molecule_atom_index, attr_dict={'atomic_number': atom.atomic_number}) + for bond in self.bonds: + G.add_edge( + bond.atom1_index, bond.atom2_index, bond_order=bond.bond_order, is_aromatic=bond.is_aromatic, + stereochemistry = bond.stereochemistry) + #G.add_edge(bond.atom1_index, bond.atom2_index, attr_dict={'order':bond.bond_order}) + + return G + + def _add_atom(self, + atomic_number, + formal_charge, + is_aromatic, + stereochemistry=None, + name=None): + """ + Add an atom + + Parameters + ---------- + atomic_number : int + Atomic number of the atom + formal_charge : int + Formal charge of the atom + is_aromatic : bool + If True, atom is aromatic; if False, not aromatic + stereochemistry : str, optional, default=None + Either 'R' or 'S' for specified stereochemistry, or None if stereochemistry is irrelevant + name : str, optional, default=None + An optional name for the atom + + Returns + ------- + index : int + The index of the atom in the molecule + + Examples + -------- + + Define a methane molecule + + >>> molecule = Molecule() + >>> molecule.name = 'methane' + >>> C = molecule.add_atom(6, 0, False) + >>> H1 = molecule.add_atom(1, 0, False) + >>> H2 = molecule.add_atom(1, 0, False) + >>> H3 = molecule.add_atom(1, 0, False) + >>> H4 = molecule.add_atom(1, 0, False) + >>> bond_idx = molecule.add_bond(C, H1, False, 1) + >>> bond_idx = molecule.add_bond(C, H2, False, 1) + >>> bond_idx = molecule.add_bond(C, H3, False, 1) + >>> bond_idx = molecule.add_bond(C, H4, False, 1) + + """ + # Create an atom + atom = Atom( + atomic_number, + formal_charge, + is_aromatic, + stereochemistry=stereochemistry, + name=name, + molecule=self) + self._atoms.append(atom) + #self._particles.append(atom) + self._invalidate_cached_properties() + return self._atoms.index(atom) + + def _add_bond_charge_virtual_site(self, atoms, distance, **kwargs): + """ + Create a bond charge-type virtual site, in which the location of the charge is specified by the position of two + atoms. This supports placement of a virtual site S along a vector between two specified atoms, e.g. to allow + for a sigma hole for halogens or similar contexts. With positive values of the distance, the virtual site lies + outside the first indexed atom. + + Parameters + ---------- + atoms : list of openforcefield.topology.molecule.Atom objects of shape [N] + The atoms defining the virtual site's position + distance : float + + weights : list of floats of shape [N] or None, optional, default=None + weights[index] is the weight of particles[index] contributing to the position of the virtual site. Default + is None + charge_increments : list of floats of shape [N], optional, default=None + The amount of charge to remove from the VirtualSite's atoms and put in the VirtualSite. Indexing in this + list should match the ordering in the atoms list. Default is None. + epsilon : float + Epsilon term for VdW properties of virtual site. Default is None. + sigma : float, default=None + Sigma term for VdW properties of virtual site. Default is None. + rmin_half : float + Rmin_half term for VdW properties of virtual site. Default is None. + name : string or None, default=None + The name of this virtual site. Default is None. + + Returns + ------- + index : int + The index of the newly-added virtual site in the molecule + """ + # Check if function was passed list of atoms or atom indices + if all([isinstance(atom, int) for atom in atoms]): + atom_list = [self.atoms[atom_index] for atom_index in atoms] + elif all([isinstance(atom, Atom) for atom in atoms]): + atom_list = atoms + else: + raise Exception( + 'Invalid inputs to molecule._add_bond_charge_virtual_site.' + ' Expected ints or Atoms. Received types {} '.format( + [type(i) for i in atoms])) + # TODO: Check to make sure bond does not already exist + vsite = BondChargeVirtualSite(atom_list, distance, **kwargs) + self._virtual_sites.append(vsite) + self._invalidate_cached_properties() + return self._virtual_sites.index(vsite) + + def _add_monovalent_lone_pair_virtual_site(self, atoms, distance, + out_of_plane_angle, + in_plane_angle, **kwargs): + """ + Create a bond charge-type virtual site, in which the location of the charge is specified by the position of + three atoms. + + TODO : Do "weights" have any meaning here? + + Parameters + ---------- + atoms : list of three openforcefield.topology.molecule.Atom objects + The three atoms defining the virtual site's position + distance : float + + out_of_plane_angle : float + + in_plane_angle : float + + epsilon : float + Epsilon term for VdW properties of virtual site. Default is None. + sigma : float, default=None + Sigma term for VdW properties of virtual site. Default is None. + rmin_half : float + Rmin_half term for VdW properties of virtual site. Default is None. + name : string or None, default=None + The name of this virtual site. Default is None. + + Returns + ------- + index : int + The index of the newly-added virtual site in the molecule + """ + # Check if function was passed list of atoms or atom indices + if all([isinstance(atom, int) for atom in atoms]): + atom_list = [self.atoms[atom_index] for atom_index in atoms] + elif all([isinstance(atom, Atom) for atom in atoms]): + atom_list = atoms + else: + raise Exception( + 'Invalid inputs to molecule._add_monovalent_lone_pair_virtual_site. Expected ints or Atoms.' + ' Received types {} '.format([type(i) for i in atoms])) + # TODO: Check to make sure bond does not already exist + vsite = MonovalentLonePairVirtualSite( + atom_list, distance, out_of_plane_angle, in_plane_angle, **kwargs) + self._virtual_sites.append(vsite) + self._invalidate_cached_properties() + return self._virtual_sites.index(vsite) + + def _add_divalent_lone_pair_virtual_site(self, atoms, distance, + out_of_plane_angle, + in_plane_angle, **kwargs): + """ + Create a divalent lone pair-type virtual site, in which the location of the charge is specified by the position + of three atoms. + + TODO : Do "weights" have any meaning here? + + Parameters + ---------- + atoms : list of 3 openforcefield.topology.molecule.Atom objects + The three atoms defining the virtual site's position + distance : float + + out_of_plane_angle : float + + in_plane_angle : float + + epsilon : float + Epsilon term for VdW properties of virtual site. Default is None. + sigma : float, default=None + Sigma term for VdW properties of virtual site. Default is None. + rmin_half : float + Rmin_half term for VdW properties of virtual site. Default is None. + name : string or None, default=None + The name of this virtual site. Default is None. + + Returns + ------- + index : int + The index of the newly-added virtual site in the molecule + """ + # Check if function was passed list of atoms or atom indices + if all([isinstance(atom, int) for atom in atoms]): + atom_list = [self.atoms[atom_index] for atom_index in atoms] + elif all([isinstance(atom, Atom) for atom in atoms]): + atom_list = atoms + else: + raise Exception( + 'Invalid inputs to molecule._add_divalent_lone_pair_virtual_site. Expected ints or Atoms. ' + 'Received types {} '.format([type(i) for i in atoms])) + # TODO: Check to make sure bond does not already exist + vsite = DivalentLonePairVirtualSite( + atom_list, distance, out_of_plane_angle, in_plane_angle, **kwargs) + self._virtual_sites.append(vsite) + self._invalidate_cached_properties() + return self._virtual_sites.index(vsite) + + def _add_trivalent_lone_pair_virtual_site(self, atoms, distance, + out_of_plane_angle, + in_plane_angle, **kwargs): + """ + Create a trivalent lone pair-type virtual site, in which the location of the charge is specified by the position + of four atoms. + + TODO : Do "weights" have any meaning here? + + Parameters + ---------- + atoms : list of 4 openforcefield.topology.molecule.Atom objects or atom indices + The three atoms defining the virtual site's position + distance : float + + out_of_plane_angle : float + + in_plane_angle : float + + epsilon : float + Epsilon term for VdW properties of virtual site. Default is None. + sigma : float, default=None + Sigma term for VdW properties of virtual site. Default is None. + rmin_half : float + Rmin_half term for VdW properties of virtual site. Default is None. + name : string or None, default=None + The name of this virtual site. Default is None. + """ + # Check if function was passed list of atoms or atom indices + if all([isinstance(atom, int) for atom in atoms]): + atom_list = [self.atoms[atom_index] for atom_index in atoms] + elif all([isinstance(atom, Atom) for atom in atoms]): + atom_list = atoms + else: + raise Exception( + 'Invalid inputs to molecule._add_trivalent_lone_pair_virtual_site. Expected ints or Atoms. Received types {} ' + .format([type(i) for i in atoms])) + vsite = TrivalentLonePairVirtualSite( + atom_list, distance, out_of_plane_angle, in_plane_angle, **kwargs) + self._virtual_sites.append(vsite) + self._invalidate_cached_properties() + return self._virtual_sites.index(vsite) + + def _add_bond(self, + atom1, + atom2, + bond_order, + is_aromatic, + stereochemistry=None, + fractional_bond_order=None): + """ + Add a bond between two specified atom indices + + Parameters + ---------- + atom1 : int or openforcefield.topology.molecule.Atom + Index of first atom or first atom + atom2_index : int or openforcefield.topology.molecule.Atom + Index of second atom or second atom + bond_order : int + Integral bond order of Kekulized form + is_aromatic : bool + True if this bond is aromatic, False otherwise + stereochemistry : str, optional, default=None + Either 'E' or 'Z' for specified stereochemistry, or None if stereochemistry is irrelevant + fractional_bond_order : float, optional, default=None + The fractional (eg. Wiberg) bond order + Returns + ------- + index : int + The index of the bond in the molecule + + """ + if isinstance(atom1, int) and isinstance(atom2, int): + atom1_atom = self.atoms[atom1] + atom2_atom = self.atoms[atom2] + elif isinstance(atom1, Atom) and isinstance(atom2, Atom): + atom1_atom = atom1 + atom2_atom = atom2 + else: + raise Exception( + 'Invalid inputs to molecule._add_bond. Expected ints or Atoms. ' + 'Received {} (type {}) and {} (type {}) '.format( + atom1, type(atom1), atom2, type(atom2))) + # TODO: Check to make sure bond does not already exist + if atom1_atom.is_bonded_to(atom2_atom): + raise Exception('Bond already exists between {} and {}'.format( + atom1_atom, atom2_atom)) + bond = Bond( + atom1_atom, + atom2_atom, + bond_order, + is_aromatic, + stereochemistry=stereochemistry, + fractional_bond_order=fractional_bond_order) + self._bonds.append(bond) + self._invalidate_cached_properties() + # TODO: This is a bad way to get bond index + return self._bonds.index(bond) + + def _add_conformer(self, coordinates): + """ + Add a conformation of the molecule + + Parameters + ---------- + coordinates: A simtk vector wrapped unit quantity + The coordinates of the conformer to add. + + Returns + ------- + index: int + The index of this conformer + + + """ + new_conf = unit.Quantity( + np.zeros((self.n_atoms, 3), np.float), unit.angstrom) + if not (new_conf.shape == coordinates.shape): + raise Exception( + "molecule.add_conformer given input of the wrong shape: " + "Given {}, expected {}".format(coordinates.shape, + new_conf.shape)) + + try: + new_conf[:] = coordinates + except AttributeError as e: + print(e) + raise Exception( + 'Coordinates passed to Molecule._add_conformer without units. Ensure that coordinates are ' + 'of type simtk.units.Quantity') + + if self._conformers == None: + self._conformers = [] + self._conformers.append(new_conf) + return len(self._conformers) + + @property + def partial_charges(self): + """ + Returns the partial charges (if present) on the molecule + + Returns + ------- + partial_charges : a simtk.unit.Quantity - wrapped numpy array [1 x n_atoms] + The partial charges on this Molecule's atoms. + """ + return self._partial_charges + + @partial_charges.setter + def partial_charges(self, charges): + """ + Set the atomic partial charges for this molecule + + Parameters + ---------- + charges : a simtk.unit.Quantity - wrapped numpy array [1 x n_atoms] + The partial charges to assign to the molecule. Must be in units compatible with simtk.unit.elementary_charge + + """ + assert hasattr(charges, 'unit') + assert unit.elementary_charge.is_compatible(charges.unit) + assert charges.shape == (self.n_atoms, ) + + charges_ec = charges.in_units_of(unit.elementary_charge) + self._partial_charges = charges_ec + + @property + def n_particles(self): + """ + The number of Particle objects, which corresponds to how many positions must be used. + """ + return sum([1 for particle in self.particles]) + + @property + def n_atoms(self): + """ + The number of Atom objects. + """ + return sum([1 for atom in self.atoms]) + + @property + def n_virtual_sites(self): + """ + The number of VirtualSite objects. + """ + return sum([1 for virtual_site in self.virtual_sites]) + + @property + def n_bonds(self): + """ + The number of Bond objects. + """ + return sum([1 for bond in self.bonds]) + + @property + def n_angles(self): + """int: number of angles in the Molecule.""" + self._construct_angles() + return len(self._angles) + + @property + def n_propers(self): + """int: number of proper torsions in the Molecule.""" + self._construct_torsions() + return len(self._propers) + + @property + def n_impropers(self): + """int: number of improper torsions in the Molecule.""" + self._construct_torsions() + return len(self._impropers) + + @property + def particles(self): + """ + Iterate over all Particle objects. + """ + # TODO: Re-implement this when we see how it interfaces with Topology + return self._atoms + self._virtual_sites + + @property + def atoms(self): + """ + Iterate over all Atom objects. + """ + return self._atoms + + @property + def conformers(self): + """ + Iterate over all conformers in this molecule. + """ + return self._conformers + + @property + def n_conformers(self): + """ + Iterate over all Atom objects. + """ + if self._conformers == None: + return 0 + return len(self._conformers) + + @property + def virtual_sites(self): + """ + Iterate over all VirtualSite objects. + """ + return self._virtual_sites + + @property + def bonds(self): + """ + Iterate over all Bond objects. + """ + return self._bonds + + @property + def angles(self): + """ + Get an iterator over all i-j-k angles. + """ + self._construct_angles() + return self._angles + + @property + def torsions(self): + """ + Get an iterator over all i-j-k-l torsions. + Note that i-j-k-i torsions (cycles) are excluded. + + Returns + ------- + torsions : iterable of 4-Atom tuples + """ + self._construct_torsions() + return self._torsions + + @property + def propers(self): + """ + Iterate over all proper torsions in the molecule + + .. todo:: + + * Do we need to return a ``Torsion`` object that collects information about fractional bond orders? + """ + self._construct_torsions() + return self._propers + + @property + def impropers(self): + """ + Iterate over all proper torsions in the molecule + + .. todo:: + + * Do we need to return a ``Torsion`` object that collects information about fractional bond orders? + """ + self._construct_torsions() + return self._impropers + + @property + def total_charge(self): + """ + Return the total charge on the molecule + """ + return sum([atom.formal_charge for atom in self.atoms]) + + @property + def name(self): + """ + The name (or title) of the molecule + """ + return self._name + + @name.setter + def name(self, other): + """ + Set the name of this molecule + """ + if other is None: + self._name = '' + elif type(other) is str: + self._name = other + else: + raise Exception("Molecule name must be a string") + + @property + def properties(self): + """ + The properties dictionary of the molecule + """ + return self._properties + + def chemical_environment_matches(self, + query, + toolkit_registry=GLOBAL_TOOLKIT_REGISTRY): + """Retrieve all matches for a given chemical environment query. + + Parameters + ---------- + query : str or ChemicalEnvironment + SMARTS string (with one or more tagged atoms) or ``ChemicalEnvironment`` query + Query will internally be resolved to SMIRKS using ``query.asSMIRKS()`` if it has an ``.asSMIRKS`` method. + toolkit_registry : openforcefield.utils.toolkits.ToolRegistry or openforcefield.utils.toolkits.ToolkitWrapper, optional, default=GLOBAL_TOOLKIT_REGISTRY + :class:`ToolkitRegistry` or :class:`ToolkitWrapper` to use for chemical environment matches + + + Returns + ------- + matches : list of Atom tuples + A list of all matching Atom tuples + + Examples + -------- + Retrieve all the carbon-carbon bond matches in a molecule + + >>> molecule = Molecule.from_iupac('imatinib') + >>> matches = molecule.chemical_environment_matches('[#6X3:1]~[#6X3:2]') + + .. todo :: + + * Do we want to generalize ``query`` to allow other kinds of queries, such as mdtraj DSL, pymol selections, atom index slices, etc? + We could call it ``topology.matches(query)`` instead of ``chemical_environment_matches`` + + """ + # Resolve to SMIRKS if needed + # TODO: Update this to use updated ChemicalEnvironment API + if hasattr(query, 'asSMIRKS'): + smirks = query.asSMIRKS() + elif type(query) == str: + smirks = query + else: + raise ValueError( + "'query' must be either a string or a ChemicalEnvironment") + + # Use specified cheminformatics toolkit to determine matches with specified aromaticity model + # TODO: Simplify this by requiring a toolkit registry for the molecule? + # TODO: Do we have to pass along an aromaticity model? + if isinstance(toolkit_registry, ToolkitRegistry): + matches = toolkit_registry.call('find_smarts_matches', self, + smirks) + elif isinstance(toolkit_registry, ToolkitWrapper): + matches = toolkit_registry.find_smarts_matches(self, smirks) + else: + raise ValueError( + "'toolkit_registry' must be either a ToolkitRegistry or a ToolkitWrapper" + ) + + return matches + + # TODO: Move OE-dependent parts of this to toolkits.py + @classmethod + @OpenEyeToolkitWrapper.requires_toolkit() + def from_iupac(cls, iupac_name, **kwargs): + """Generate a molecule from IUPAC or common name + + Parameters + ---------- + iupac_name : str + IUPAC name of molecule to be generated + allow_undefined_stereo : bool, default=False + If false, raises an exception if molecule contains undefined stereochemistry. + + Returns + ------- + molecule : Molecule + The resulting molecule with position + + .. note :: This method requires the OpenEye toolkit to be installed. + + Examples + -------- + + Create a molecule from a common name + + >>> molecule = Molecule.from_iupac('4-[(4-methylpiperazin-1-yl)methyl]-N-(4-methyl-3-{[4-(pyridin-3-yl)pyrimidin-2-yl]amino}phenyl)benzamide') + + Create a molecule from a common name + + >>> molecule = Molecule.from_iupac('imatinib') + + """ + from openeye import oechem, oeiupac + oemol = oechem.OEMol() + oeiupac.OEParseIUPACName(oemol, iupac_name) + oechem.OETriposAtomNames(oemol) + result = oechem.OEAddExplicitHydrogens(oemol) + if result == False: + raise Exception( + "Addition of explicit hydrogens failed in from_iupac") + return cls.from_openeye(oemol, **kwargs) + + # TODO: Move OE-dependent parts of this to toolkits.py + @OpenEyeToolkitWrapper.requires_toolkit() + def to_iupac(self): + """Generate IUPAC name from Molecule + + Returns + ------- + iupac_name : str + IUPAC name of the molecule + + .. note :: This method requires the OpenEye toolkit to be installed. + + Examples + -------- + + >>> from openforcefield.utils import get_data_filename + >>> sdf_filepath = get_data_filename('molecules/ethanol.sdf') + >>> molecule = Molecule(sdf_filepath) + >>> iupac_name = molecule.to_iupac() + + """ + from openeye import oeiupac + return oeiupac.OECreateIUPACName(self.to_openeye()) + + @staticmethod + def from_topology(topology): + """Return a Molecule representation of an openforcefield Topology containing a single Molecule object. + + Parameters + ---------- + topology : openforcefield.topology.Topology + The :class:`Topology` object containing a single :class:`Molecule` object. + Note that OpenMM and MDTraj ``Topology`` objects are not supported. + + Returns + ------- + molecule : openforcefield.topology.Molecule + The Molecule object in the topology + + Raises + ------ + ValueError + If the topology does not contain exactly one molecule. + + Examples + -------- + + Create a molecule from a Topology object that contains exactly one molecule + + >>> molecule = Molecule.from_topology(topology) # doctest: +SKIP + + """ + # TODO: Ensure we are dealing with an openforcefield Topology object + if topology.n_topology_molecules != 1: + raise ValueError('Topology must contain exactly one molecule') + molecule = [i for i in topology.reference_molecules][0] + return Molecule(molecule) + + def to_topology(self): + """ + Return an openforcefield Topology representation containing one copy of this molecule + + Returns + ------- + topology : openforcefield.topology.Topology + A Topology representation of this molecule + + Examples + -------- + + >>> molecule = Molecule.from_iupac('imatinib') + >>> topology = molecule.to_topology() + + """ + from openforcefield.topology import Topology + return Topology.from_molecules(self) + + @staticmethod + def from_file(filename, + file_format=None, + toolkit_registry=GLOBAL_TOOLKIT_REGISTRY, + allow_undefined_stereo=False): + """ + Create one or more molecules from a file + + .. todo:: + + * Extend this to also include some form of .offmol Open Force Field Molecule format? + * Generalize this to also include file-like objects? + + Parameters + ---------- + filename : str or file-like object + The name of the file or file-like object to stream one or more molecules from. + file_format : str, optional, default=None + Format specifier, usually file suffix (eg. 'MOL2', 'SMI') + Note that not all toolkits support all formats. Check ToolkitWrapper.toolkit_file_read_formats for your + loaded toolkits for details. + toolkit_registry : openforcefield.utils.toolkits.ToolRegistry or openforcefield.utils.toolkits.ToolkitWrapper, + optional, default=GLOBAL_TOOLKIT_REGISTRY + :class:`ToolkitRegistry` or :class:`ToolkitWrapper` to use for file loading. If a Toolkit is passed, only + the highest-precedence toolkit is used + allow_undefined_stereo : bool, default=False + If false, raises an exception if oemol contains undefined stereochemistry. + + Returns + ------- + molecules : Molecule or list of Molecules + If there is a single molecule in the file, a Molecule is returned; + otherwise, a list of Molecule objects is returned. + + Examples + -------- + >>> from openforcefield.tests.utils import get_monomer_mol2file + >>> mol2_filename = get_monomer_mol2file('cyclohexane') + >>> molecule = Molecule.from_file(mol2_filename) + + """ + + if file_format == None: + if not (isinstance(filename, str)): + raise Exception( + "If providing a file-like object for reading molecules, the format must be specified" + ) + # Assume that files ending in ".gz" should use their second-to-last suffix for compatibility check + # TODO: Will all cheminformatics packages be OK with gzipped files? + if filename[-3:] == '.gz': + file_format = filename.split('.')[-2] + else: + file_format = filename.split('.')[-1] + file_format = file_format.upper() + + # Determine which toolkit to use (highest priority that's compatible with input type) + if isinstance(toolkit_registry, ToolkitRegistry): + # TODO: Encapsulate this logic into ToolkitRegistry.call()? + toolkit = None + supported_read_formats = {} + for query_toolkit in toolkit_registry.registered_toolkits: + if file_format in query_toolkit.toolkit_file_read_formats: + toolkit = query_toolkit + break + supported_read_formats[ + query_toolkit. + toolkit_name] = query_toolkit.toolkit_file_read_formats + if toolkit == None: + raise NotImplementedError( + "No toolkits in registry can read file {} (format {}). Supported formats in the " + "provided ToolkitRegistry are {}".format( + filename, file_format, supported_read_formats)) + + elif isinstance(toolkit_registry, ToolkitWrapper): + # TODO: Encapsulate this logic in ToolkitWrapper? + toolkit = toolkit_registry + if file_format not in toolkit.toolkit_file_read_formats: + raise NotImplementedError( + "Toolkit {} can not read file {} (format {}). Supported formats for this toolkit " + "are {}".format(toolkit.toolkit_name, filename, + file_format, + toolkit.toolkit_file_read_formats)) + else: + raise ValueError( + "'toolkit_registry' must be either a ToolkitRegistry or a ToolkitWrapper" + ) + + mols = list() + + if isinstance(filename, str): + mols = toolkit.from_file( + filename, + file_format=file_format, + allow_undefined_stereo=allow_undefined_stereo) + elif hasattr(filename, 'read'): + file_obj = filename + mols = toolkit.from_file_obj( + file_obj, + file_format=file_format, + allow_undefined_stereo=allow_undefined_stereo) + + if len(mols) == 0: + raise Exception( + 'Unable to read molecule from file: {}'.format(filename)) + elif len(mols) == 1: + return mols[0] + return mols + + def to_file(self, + outfile, + outfile_format, + toolkit_registry=GLOBAL_TOOLKIT_REGISTRY): + """Write the current molecule to a file or file-like object + + Parameters + ---------- + outfile : str or file-like object + A file-like object or the filename of the file to be written to + outfile_format : str + Format specifier, one of ['MOL2', 'MOL2H', 'SDF', 'PDB', 'SMI', 'CAN', 'TDT'] + Note that not all toolkits support all formats + toolkit_registry : openforcefield.utils.toolkits.ToolRegistry or openforcefield.utils.toolkits.ToolkitWrapper, + optional, default=GLOBAL_TOOLKIT_REGISTRY + :class:`ToolkitRegistry` or :class:`ToolkitWrapper` to use for file writing. If a Toolkit is passed, only + the highest-precedence toolkit is used + + Raises + ------ + ValueError + If the requested outfile_format is not supported by one of the installed cheminformatics toolkits + + Examples + -------- + + >>> molecule = Molecule.from_iupac('imatinib') + >>> molecule.to_file('imatinib.mol2', outfile_format='mol2') # doctest: +SKIP + >>> molecule.to_file('imatinib.sdf', outfile_format='sdf') # doctest: +SKIP + >>> molecule.to_file('imatinib.pdb', outfile_format='pdb') # doctest: +SKIP + + """ + + if isinstance(toolkit_registry, ToolkitRegistry): + pass + elif isinstance(toolkit_registry, ToolkitWrapper): + toolkit = toolkit_registry + toolkit_registry = ToolkitRegistry(toolkit_precedence=[]) + toolkit_registry.add_toolkit(toolkit) + else: + raise ValueError( + "'toolkit_registry' must be either a ToolkitRegistry or a ToolkitWrapper" + ) + + outfile_format = outfile_format.upper() + + # Take the first toolkit that can write the desired output format + toolkit = None + for query_toolkit in toolkit_registry.registered_toolkits: + if outfile_format in query_toolkit.toolkit_file_write_formats: + toolkit = query_toolkit + break + + # Raise an exception if no toolkit was found to provide the requested outfile_format + if toolkit == None: + supported_formats = {} + for toolkit in toolkit_registry.registered_toolkits: + supported_formats[ + toolkit.toolkit_name] = toolkit.toolkit_file_write_formats + raise ValueError( + 'The requested file format ({}) is not available from any of the installed toolkits ' + '(supported formats: {})'.format(outfile_format, + supported_formats)) + + # Write file + if type(outfile) == str: + # Open file for writing + toolkit.to_file(self, outfile, outfile_format) + else: + toolkit.to_file_obj(self, outfile, outfile_format) + + @staticmethod + @RDKitToolkitWrapper.requires_toolkit() + def from_rdkit(rdmol, allow_undefined_stereo=False): + """ + Create a Molecule from an RDKit molecule. + + Requires the RDKit to be installed. + + Parameters + ---------- + rdmol : rkit.RDMol + An RDKit molecule + allow_undefined_stereo : bool, default=False + If false, raises an exception if oemol contains undefined stereochemistry. + + Returns + ------- + molecule : openforcefield.Molecule + An openforcefield molecule + + Examples + -------- + + Create a molecule from an RDKit molecule + + >>> from rdkit import Chem + >>> from openforcefield.tests.utils import get_data_filename + >>> rdmol = Chem.MolFromMolFile(get_data_filename('systems/monomers/ethanol.sdf')) + >>> molecule = Molecule.from_rdkit(rdmol) + + """ + toolkit = RDKitToolkitWrapper() + return toolkit.from_rdkit( + rdmol, allow_undefined_stereo=allow_undefined_stereo) + + @RDKitToolkitWrapper.requires_toolkit() + def to_rdkit(self, aromaticity_model=DEFAULT_AROMATICITY_MODEL): + """ + Create an RDKit molecule + + Requires the RDKit to be installed. + + Parameters + ---------- + aromaticity_model : str, optional, default=DEFAULT_AROMATICITY_MODEL + The aromaticity model to use + + Returns + ------- + rdmol : rkit.RDMol + An RDKit molecule + + Examples + -------- + + Convert a molecule to RDKit + + >>> from openforcefield.utils import get_data_filename + >>> sdf_filepath = get_data_filename('molecules/ethanol.sdf') + >>> molecule = Molecule(sdf_filepath) + >>> rdmol = molecule.to_rdkit() + + """ + toolkit = RDKitToolkitWrapper() + return toolkit.to_rdkit(self, aromaticity_model=aromaticity_model) + + @staticmethod + @OpenEyeToolkitWrapper.requires_toolkit() + def from_openeye(oemol, allow_undefined_stereo=False): + """ + Create a Molecule from an OpenEye molecule. + + Requires the OpenEye toolkit to be installed. + + Parameters + ---------- + oemol : openeye.oechem.OEMol + An OpenEye molecule + allow_undefined_stereo : bool, default=False + If false, raises an exception if oemol contains undefined stereochemistry. + + Returns + ------- + molecule : openforcefield.topology.Molecule + An openforcefield molecule + + Examples + -------- + + Create a Molecule from an OpenEye OEMol + + >>> from openeye import oechem + >>> from openforcefield.tests.utils import get_data_filename + >>> ifs = oechem.oemolistream(get_data_filename('systems/monomers/ethanol.mol2')) + >>> oemols = list(ifs.GetOEGraphMols()) + >>> molecule = Molecule.from_openeye(oemols[0]) + + """ + toolkit = OpenEyeToolkitWrapper() + return toolkit.from_openeye( + oemol, allow_undefined_stereo=allow_undefined_stereo) + + @OpenEyeToolkitWrapper.requires_toolkit() + def to_openeye(self, aromaticity_model=DEFAULT_AROMATICITY_MODEL): + """ + Create an OpenEye molecule + + Requires the OpenEye toolkit to be installed. + + .. todo :: + + * Use stored conformer positions instead of an argument. + * Should the aromaticity model be specified in some other way? + + Parameters + ---------- + aromaticity_model : str, optional, default=DEFAULT_AROMATICITY_MODEL + The aromaticity model to use + + Returns + ------- + oemol : openeye.oechem.OEMol + An OpenEye molecule + + Examples + -------- + + Create an OpenEye molecule from a Molecule + + >>> molecule = Molecule.from_smiles('CC') + >>> oemol = molecule.to_openeye() + + """ + toolkit = OpenEyeToolkitWrapper() + return toolkit.to_openeye(self, aromaticity_model=aromaticity_model) + + + def get_fractional_bond_orders(self, + method='Wiberg', + toolkit_registry=GLOBAL_TOOLKIT_REGISTRY): + """Get fractional bond orders. + + method : str, optional, default='Wiberg' + The name of the charge method to use. + Options are: + * 'Wiberg' : Wiberg bond order + toolkit_registry : openforcefield.utils.toolkits ToolkitRegistry + The toolkit registry to use for molecule operations + + Examples + -------- + + Get fractional Wiberg bond orders + + >>> molecule = Molecule.from_iupac('imatinib') + >>> molecule.generate_conformers() + >>> fractional_bond_orders = molecule.get_fractional_bond_orders(method='Wiberg') + + + .. todo:: + * Is it OK that the ``Molecule`` object does not store geometry, but will create it using ``openeye.omega`` or ``rdkit``? + * Should this method assign fractional bond orders to the ``Bond``s in the molecule, a separate ``bond_orders`` molecule property, + or just return the array of bond orders? + * How do we add enough flexibility to specify the toolkit and optional parameters, such as: + ``oequacpac.OEAssignPartialCharges(charged_copy, getattr(oequacpac, 'OECharges_AM1BCCSym'), False, False)`` + * Generalize to allow user to specify both QM method and bond order computation approach (e.g. ``AM1`` and ``Wiberg``) + + + """ + # TODO: Let ToolkitRegistry handle this once compute_fractional_bond_orders will be added to the Wrappers API. + if method != 'Wiberg': + raise NotImplementedError('Only Wiberg bond order is currently implemented') + # TODO: Use memoization to speed up subsequent calls; use decorator? + fractional_bond_orders = toolkit_registry.call( + 'compute_wiberg_bond_orders', molecule=self) + return fractional_bond_orders + + def _construct_angles(self): + """ + Get an iterator over all i-j-k angles. + """ + # TODO: Build Angle objects instead of tuple of atoms. + if not hasattr(self, '_angles'): + self._construct_bonded_atoms_list() + self._angles = set() + for atom1 in self._atoms: + for atom2 in self._bondedAtoms[atom1]: + for atom3 in self._bondedAtoms[atom2]: + if atom1 == atom3: + continue + # TODO: Encapsulate this logic into an Angle class. + if atom1.molecule_atom_index < atom3.molecule_atom_index: + self._angles.add((atom1, atom2, atom3)) + else: + self._angles.add((atom3, atom2, atom1)) + + def _construct_torsions(self): + """ + Construct sets containing the atoms improper and proper torsions + """ + # TODO: Build Proper/ImproperTorsion objects instead of tuple of atoms. + if not hasattr(self, '_torsions'): + self._construct_bonded_atoms_list() + + #self._torsions = set() + self._propers = set() + self._impropers = set() + for atom1 in self._atoms: + for atom2 in self._bondedAtoms[atom1]: + for atom3 in self._bondedAtoms[atom2]: + if atom1 == atom3: + continue + for atom4 in self._bondedAtoms[atom3]: + if atom4 == atom2: + continue + # Exclude i-j-k-i + if atom1 == atom4: + continue + + if atom1.molecule_atom_index < atom4.molecule_atom_index: + torsion = (atom1, atom2, atom3, atom4) + else: + torsion = (atom4, atom3, atom2, atom1) + + self._propers.add(torsion) + + for atom3i in self._bondedAtoms[atom2]: + if atom3i == atom3: + continue + if atom3i == atom1: + continue + + improper = (atom1, atom2, atom3, atom3i) + self._impropers.add(improper) + + self._torsions = self._propers | self._impropers + #return iter(self._torsions) + + def _construct_bonded_atoms_list(self): + """ + Construct list of all atoms each atom is bonded to. + + """ + # TODO: Add this to cached_properties + if not hasattr(self, '_bondedAtoms'): + #self._atoms = [ atom for atom in self.atoms() ] + self._bondedAtoms = dict() + for atom in self._atoms: + self._bondedAtoms[atom] = set() + for bond in self._bonds: + atom1 = self.atoms[bond.atom1_index] + atom2 = self.atoms[bond.atom2_index] + self._bondedAtoms[atom1].add(atom2) + self._bondedAtoms[atom2].add(atom1) + + def _is_bonded(self, atom_index_1, atom_index_2): + """Return True if atoms are bonded, False if not. + + Parameters + ---------- + atom_index_1 : int + atom_index_2 : int + Atom indices + + Returns + ------- + is_bonded : bool + True if atoms are bonded, False otherwise + + + """ + self._construct_bonded_atoms_list() + atom1 = self._atoms[atom_index_1] + atom2 = self._atoms[atom_index_2] + return atom2 in self._bondedAtoms[atom1] + + +class Molecule(FrozenMolecule): + """ + Mutable chemical representation of a molecule, such as a small molecule or biopolymer. + + .. todo :: What other API calls would be useful for supporting biopolymers as small molecules? Perhaps iterating over chains and residues? + + Examples + -------- + + Create a molecule from an sdf file + + >>> from openforcefield.utils import get_data_filename + >>> sdf_filepath = get_data_filename('molecules/ethanol.sdf') + >>> molecule = Molecule(sdf_filepath) + + Convert to OpenEye OEMol object + + >>> oemol = molecule.to_openeye() + + Create a molecule from an OpenEye molecule + + >>> molecule = Molecule.from_openeye(oemol) + + Convert to RDKit Mol object + + >>> rdmol = molecule.to_rdkit() + + Create a molecule from an RDKit molecule + + >>> molecule = Molecule.from_rdkit(rdmol) + + Create a molecule from IUPAC name (requires the OpenEye toolkit) + + >>> molecule = Molecule.from_iupac('imatinib') + + Create a molecule from SMILES + + >>> molecule = Molecule.from_smiles('Cc1ccccc1') + + .. warning :: This API is experimental and subject to change. + + """ + + def __init__(self, *args, **kwargs): + """ + Create a new Molecule object + + Parameters + ---------- + other : optional, default=None + If specified, attempt to construct a copy of the Molecule from the specified object. + This can be any one of the following: + + * a :class:`Molecule` object + * a file that can be used to construct a :class:`Molecule` object + * an ``openeye.oechem.OEMol`` + * an ``rdkit.Chem.rdchem.Mol`` + * a serialized :class:`Molecule` object + + Examples + -------- + + Create an empty molecule: + + >>> empty_molecule = Molecule() + + Create a molecule from a file that can be used to construct a molecule, + using either a filename or file-like object: + + >>> from openforcefield.utils import get_data_filename + >>> sdf_filepath = get_data_filename('molecules/ethanol.sdf') + >>> molecule = Molecule(sdf_filepath) + >>> molecule = Molecule(open(sdf_filepath, 'r'), file_format='sdf') + + >>> import gzip + >>> mol2_gz_filepath = get_data_filename('molecules/toluene.mol2.gz') + >>> molecule = Molecule(gzip.GzipFile(mol2_gz_filepath, 'r'), file_format='mol2') + + Create a molecule from another molecule: + + >>> molecule_copy = Molecule(molecule) + + Convert to OpenEye OEMol object + + >>> oemol = molecule.to_openeye() + + Create a molecule from an OpenEye molecule: + + >>> molecule = Molecule(oemol) + + Convert to RDKit Mol object + + >>> rdmol = molecule.to_rdkit() + + Create a molecule from an RDKit molecule: + + >>> molecule = Molecule(rdmol) + + Create a molecule from a serialized molecule object: + + >>> serialized_molecule = molecule.__getstate__() + >>> molecule_copy = Molecule(serialized_molecule) + + .. todo :: + + * If a filename or file-like object is specified but the file contains more than one molecule, what is the + proper behavior? Read just the first molecule, or raise an exception if more than one molecule is found? + + * Should we also support SMILES strings or IUPAC names for ``other``? + + """ + #super(self, Molecule).__init__(*args, **kwargs) + super(Molecule, self).__init__(*args, **kwargs) + + # TODO: Change this to add_atom(Atom) to improve encapsulation and extensibility? + def add_atom(self, + atomic_number, + formal_charge, + is_aromatic, + stereochemistry=None, + name=None): + """ + Add an atom + + Parameters + ---------- + atomic_number : int + Atomic number of the atom + formal_charge : int + Formal charge of the atom + is_aromatic : bool + If True, atom is aromatic; if False, not aromatic + stereochemistry : str, optional, default=None + Either 'R' or 'S' for specified stereochemistry, or None if stereochemistry is irrelevant + name : str, optional, default=None + An optional name for the atom + + Returns + ------- + index : int + The index of the atom in the molecule + + Examples + -------- + + Define a methane molecule + + >>> molecule = Molecule() + >>> molecule.name = 'methane' + >>> C = molecule.add_atom(6, 0, False) + >>> H1 = molecule.add_atom(1, 0, False) + >>> H2 = molecule.add_atom(1, 0, False) + >>> H3 = molecule.add_atom(1, 0, False) + >>> H4 = molecule.add_atom(1, 0, False) + >>> bond_idx = molecule.add_bond(C, H1, False, 1) + >>> bond_idx = molecule.add_bond(C, H2, False, 1) + >>> bond_idx = molecule.add_bond(C, H3, False, 1) + >>> bond_idx = molecule.add_bond(C, H4, False, 1) + + """ + atom_index = self._add_atom( + atomic_number, + formal_charge, + is_aromatic, + stereochemistry=stereochemistry, + name=name) + return atom_index + + def add_bond_charge_virtual_site(self, + atoms, + distance, + charge_increments=None, + weights=None, + epsilon=None, + sigma=None, + rmin_half=None, + name=''): + """ + Create a bond charge-type virtual site, in which the location of the charge is specified by the position of two atoms. This supports placement of a virtual site S along a vector between two specified atoms, e.g. to allow for a sigma hole for halogens or similar contexts. With positive values of the distance, the virtual site lies outside the first indexed atom. + Parameters + ---------- + atoms : list of openforcefield.topology.molecule.Atom objects or ints of shape [N + The atoms defining the virtual site's position or their indices + distance : float + + weights : list of floats of shape [N] or None, optional, default=None + weights[index] is the weight of particles[index] contributing to the position of the virtual site. Default is None + charge_increments : list of floats of shape [N], optional, default=None + The amount of charge to remove from the VirtualSite's atoms and put in the VirtualSite. Indexing in this list should match the ordering in the atoms list. Default is None. + epsilon : float + Epsilon term for VdW properties of virtual site. Default is None. + sigma : float, default=None + Sigma term for VdW properties of virtual site. Default is None. + rmin_half : float + Rmin_half term for VdW properties of virtual site. Default is None. + name : string or None, default='' + The name of this virtual site. Default is ''. + + Returns + ------- + index : int + The index of the newly-added virtual site in the molecule + + """ + + vsite_index = self._add_bond_charge_virtual_site( + atoms, + distance, + weights=weights, + charge_increments=charge_increments, + epsilon=epsilon, + sigma=sigma, + rmin_half=rmin_half, + name=name) + return vsite_index + + def add_monovalent_lone_pair_virtual_site(self, atoms, distance, + out_of_plane_angle, + in_plane_angle, **kwargs): + """ + Create a bond charge-type virtual site, in which the location of the charge is specified by the position of three atoms. + + TODO : Do "weights" have any meaning here? + + Parameters + ---------- + atoms : list of three openforcefield.topology.molecule.Atom objects or ints + The three atoms defining the virtual site's position or their molecule atom indices + distance : float + + out_of_plane_angle : float + + in_plane_angle : float + + epsilon : float + Epsilon term for VdW properties of virtual site. Default is None. + sigma : float, default=None + Sigma term for VdW properties of virtual site. Default is None. + rmin_half : float + Rmin_half term for VdW properties of virtual site. Default is None. + name : string or None, default='' + The name of this virtual site. Default is ''. + + Returns + ------- + index : int + The index of the newly-added virtual site in the molecule + + + """ + + #vsite_index = self._add_monovalent_lone_pair_virtual_site(self, atoms, distance, out_of_plane_angle, in_plane_angle, charge_increments=charge_increments, weights=weights, epsilon=epsilon, sigma=sigma, rmin_half=rmin_half, name=name) + vsite_index = self._add_monovalent_lone_pair_virtual_site( + atoms, distance, out_of_plane_angle, in_plane_angle, **kwargs) + return vsite_index + + #def add_divalent_lone_pair_virtual_site(self, atoms, distance, out_of_plane_angle, in_plane_angle, charge_increments=None, weights=None, epsilon=None, sigma=None, rmin_half=None, name=None): + def add_divalent_lone_pair_virtual_site(self, atoms, distance, + out_of_plane_angle, in_plane_angle, + **kwargs): + """ + Create a divalent lone pair-type virtual site, in which the location of the charge is specified by the position of three atoms. + + TODO : Do "weights" have any meaning here? + + Parameters + ---------- + atoms : list of 3 openforcefield.topology.molecule.Atom objects or ints + The three atoms defining the virtual site's position or their molecule atom indices + distance : float + + out_of_plane_angle : float + + in_plane_angle : float + + epsilon : float + Epsilon term for VdW properties of virtual site. Default is None. + sigma : float, default=None + Sigma term for VdW properties of virtual site. Default is None. + rmin_half : float + Rmin_half term for VdW properties of virtual site. Default is None. + name : string or None, default='' + The name of this virtual site. Default is ''. + + Returns + ------- + index : int + The index of the newly-added virtual site in the molecule + + """ + #vsite_index = self._add_divalent_lone_pair_virtual_site(self, atoms, distance, out_of_plane_angle, in_plane_angle, charge_increments=charge_increments, weights=weights, epsilon=epsilon, sigma=sigma, rmin_half=rmin_half, name=name) + vsite_index = self._add_divalent_lone_pair_virtual_site( + atoms, distance, out_of_plane_angle, in_plane_angle, **kwargs) + return vsite_index + + def add_trivalent_lone_pair_virtual_site(self, atoms, distance, + out_of_plane_angle, + in_plane_angle, **kwargs): + """ + Create a trivalent lone pair-type virtual site, in which the location of the charge is specified by the position of four atoms. + + TODO : Do "weights" have any meaning here? + + Parameters + ---------- + atoms : list of 4 openforcefield.topology.molecule.Atom objects or ints + The three atoms defining the virtual site's position or their molecule atom indices + distance : float + + out_of_plane_angle : float + + in_plane_angle : float + + epsilon : float + Epsilon term for VdW properties of virtual site. Default is None. + sigma : float, default=None + Sigma term for VdW properties of virtual site. Default is None. + rmin_half : float + Rmin_half term for VdW properties of virtual site. Default is None. + name : string or None, default='' + The name of this virtual site. Default is ''. + + Returns + ------- + index : int + The index of the newly-added virtual site in the molecule + + """ + vsite_index = self._add_trivalent_lone_pair_virtual_site( + atoms, distance, out_of_plane_angle, in_plane_angle, **kwargs) + return vsite_index + + def add_bond(self, + atom1, + atom2, + bond_order, + is_aromatic, + stereochemistry=None, + fractional_bond_order=None): + """ + Add a bond between two specified atom indices + + + Parameters + ---------- + atom1 : int or openforcefield.topology.molecule.Atom + Index of first atom + atom2 : int or openforcefield.topology.molecule.Atom + Index of second atom + bond_order : int + Integral bond order of Kekulized form + is_aromatic : bool + True if this bond is aromatic, False otherwise + stereochemistry : str, optional, default=None + Either 'E' or 'Z' for specified stereochemistry, or None if stereochemistry is irrelevant + fractional_bond_order : float, optional, default=None + The fractional (eg. Wiberg) bond order + + Returns + ------- + index: int + Index of the bond in this molecule + +""" + bond_index = self._add_bond( + atom1, + atom2, + bond_order, + is_aromatic, + stereochemistry=stereochemistry, + fractional_bond_order=fractional_bond_order) + return bond_index + + def add_conformer(self, coordinates): + """ + # TODO: Should this not be public? + Adds a conformer of the molecule + + Parameters + ---------- + coordinates: simtk.unit.Quantity(np.array) with shape (n_atoms, 3) + Coordinates of the new conformer, with the first dimension of the array corresponding to the atom index in + the Molecule's indexing system. + Returns + ------- + index: int + Index of the conformer in the Molecule + + +""" + return self._add_conformer(coordinates) diff --git a/openforcefield/topology/topology.py b/openforcefield/topology/topology.py new file mode 100644 index 000000000..c8eb0c8d8 --- /dev/null +++ b/openforcefield/topology/topology.py @@ -0,0 +1,2198 @@ +#!/usr/bin/env python + +#============================================================================================= +# MODULE DOCSTRING +#============================================================================================= +""" +Class definitions to represent a molecular system and its chemical components + +.. todo:: + + * Create MoleculeImage, ParticleImage, AtomImage, VirtualSiteImage here. (Or ``MoleculeInstance``?) + * Create ``MoleculeGraph`` to represent fozen set of atom elements and bonds that can used as a key for compression + * Add hierarchical way of traversing Topology (chains, residues) + * Make all classes hashable and serializable. + * JSON/BSON representations of objects? + * Use `attrs `_ for object setter boilerplate? + +""" + +#============================================================================================= +# GLOBAL IMPORTS +#============================================================================================= + +import itertools + +from collections import MutableMapping +from collections import OrderedDict + +from simtk import unit +from simtk.openmm import app + +from openforcefield.typing.chemistry import ChemicalEnvironment, SMIRKSParsingError +from openforcefield.utils.toolkits import DEFAULT_AROMATICITY_MODEL, ALLOWED_AROMATICITY_MODELS, DEFAULT_FRACTIONAL_BOND_ORDER_MODEL, ALLOWED_FRACTIONAL_BOND_ORDER_MODELS, DEFAULT_CHARGE_MODEL, GLOBAL_TOOLKIT_REGISTRY, ALLOWED_CHARGE_MODELS +from openforcefield.utils.serialization import Serializable +from openforcefield.utils import MessageException + +#============================================================================================= +# Exceptions +#============================================================================================= + + +class DuplicateUniqueMoleculeError(MessageException): + """ + Exception for when the user provides indistinguishable unique molecules when trying to identify atoms from a PDB + """ + pass + +class NotBondedError(MessageException): + """ + Exception for when a function requires a bond between two atoms, but none is present + """ + pass + + +#============================================================================================= +# PRIVATE SUBROUTINES +#============================================================================================= + +class _TransformedDict(MutableMapping): + """A dictionary that transform and sort keys. + + The function __keytransform__ can be inherited to apply an arbitrary + key-altering function before accessing the keys. + + The function __sortfunc__ can be inherited to specify a particular + order over which to iterate over the dictionary. + + """ + + def __init__(self, *args, **kwargs): + self.store = OrderedDict() + self.update(dict(*args, **kwargs)) # use the free update to set keys + + def __getitem__(self, key): + return self.store[self.__keytransform__(key)] + + def __setitem__(self, key, value): + self.store[self.__keytransform__(key)] = value + + def __delitem__(self, key): + del self.store[self.__keytransform__(key)] + + def __iter__(self): + return iter(sorted(self.store, key=self.__sortfunc__)) + + def __len__(self): + return len(self.store) + + def __keytransform__(self, key): + return key + + @staticmethod + def __sortfunc__(key): + return key + +# TODO: Encapsulate this atom ordering logic directly into Atom/Bond/Angle/Torsion classes? +class ValenceDict(_TransformedDict): + """Enforce uniqueness in atom indices.""" + + def __keytransform__(self, key): + """Reverse tuple if first element is larger than last element.""" + # Ensure key is a tuple. + key = tuple(key) + # Reverse the key if the first element is bigger than the last. + if key[0] > key[-1]: + key = tuple(reversed(key)) + return key + + +class ImproperDict(_TransformedDict): + """Symmetrize improper torsions.""" + + def __keytransform__(self, key): + """Reorder tuple in numerical order except for element[1] which is the central atom; it retains its position.""" + # Ensure key is a tuple + key = tuple(key) + # Retrieve connected atoms + connectedatoms = [key[0], key[2], key[3]] + # Sort connected atoms + connectedatoms.sort() + # Re-store connected atoms + key = tuple( + [connectedatoms[0], key[1], connectedatoms[1], connectedatoms[2]]) + return (key) + + +#============================================================================================= +# TOPOLOGY OBJECTS +#============================================================================================= + +# ============================================================================================= +# TopologyAtom +# ============================================================================================= + + +class TopologyAtom(Serializable): + """ + A TopologyAtom is a lightweight data structure that represents a single openforcefield.topology.molecule.Atom in + a Topology. A TopologyAtom consists of two references -- One to its fully detailed "atom", an + openforcefield.topology.molecule.Atom, and another to its parent "topology_molecule", which occupies a spot in + the parent Topology's TopologyMolecule list. + + As some systems can be very large, there is no always-existing representation of a TopologyAtom. They are created on + demand as the user requests them. + + .. warning :: This API is experimental and subject to change. + + """ + + def __init__(self, atom, topology_molecule): + """ + Create a new TopologyAtom. + + Parameters + ---------- + atom : An openforcefield.topology.molecule.Atom + The reference atom + topology_molecule : An openforcefield.topology.TopologyMolecule + The TopologyMolecule that this TopologyAtom belongs to + """ + # TODO: Type checks + self._atom = atom + self._topology_molecule = topology_molecule + + @property + def atom(self): + """ + Get the reference Atom for this TopologyAtom. + + Returns + ------- + an openforcefield.topology.molecule.Atom + """ + return self._atom + + @property + def atomic_number(self): + """ + Get the atomic number of this atom + + Returns + ------- + int + """ + return self._atom.atomic_number + + @property + def topology_molecule(self): + """ + Get the TopologyMolecule that this TopologyAtom belongs to. + + Returns + ------- + openforcefield.topology.TopologyMolecule + """ + return self._topology_molecule + + @property + def molecule(self): + """ + Get the reference Molecule that this TopologyAtom belongs to. + + Returns + ------- + openforcefield.topology.molecule.Molecule + """ + return self._topology_molecule.molecule + + @property + def topology_atom_index(self): + """ + Get the index of this atom in its parent Topology. + + Returns + ------- + int + The index of this atom in its parent topology. + """ + mapped_molecule_atom_index = self._topology_molecule._ref_to_top_index[ + self._atom.molecule_atom_index] + return self._topology_molecule.atom_start_topology_index + mapped_molecule_atom_index + + @property + def topology_particle_index(self): + """ + Get the index of this particle in its parent Topology. + + Returns + ------- + int + The index of this atom in its parent topology. + """ + # This assumes that particles in a molecule are ordered with all the Atoms first and VirtualSites last. + mapped_molecule_particle_index = self._topology_molecule._ref_to_top_index[ + self._atom.molecule_atom_index] + return self._topology_molecule.particle_start_topology_index + mapped_molecule_particle_index + + @property + def topology_bonds(self): + """ + Get the TopologyBonds connected to this TopologyAtom. + + Returns + ------- + iterator of openforcefield.topology.TopologyBonds + """ + + for bond in self._atom.bonds: + reference_mol_bond_index = bond.molecule_bond_index + yield self._topology_molecule.bond(reference_mol_bond_index) + + def __eq__(self, other): + return ((self._atom == other._atom) + and (self._topology_molecule == other._topology_molecule)) + + def __repr__(self): + return "TopologyAtom {} with reference atom {} and parent TopologyMolecule {}".format( + self.topology_atom_index, self._atom, self._topology_molecule) + + def to_dict(self): + """Convert to dictionary representation.""" + # Implement abstract method Serializable.to_dict() + raise NotImplementedError() # TODO + + @classmethod + def from_dict(cls, d): + """Static constructor from dictionary representation.""" + # Implement abstract method Serializable.to_dict() + raise NotImplementedError() # TODO + + #@property + #def bonds(self): + # """ + # Get the Bonds connected to this TopologyAtom. + # + # Returns + # ------- + # iterator of openforcefield.topology.molecule.Bonds + # """ + # for bond in self._atom.bonds: + # yield bond + + # TODO: Add all atom properties here? Or just make people use TopologyAtom.atom for that? + + +#============================================================================================= +# TopologyBond +#============================================================================================= + + +class TopologyBond(Serializable): + """ + A TopologyBond is a lightweight data structure that represents a single openforcefield.topology.molecule.Bond in + a Topology. A TopologyBond consists of two references -- One to its fully detailed "bond", an + openforcefield.topology.molecule.Bond, and another to its parent "topology_molecule", which occupies a spot in + the parent Topology's TopologyMolecule list. + + As some systems can be very large, there is no always-existing representation of a TopologyBond. They are created on + demand as the user requests them. + + .. warning :: This API is experimental and subject to change. + + """ + + def __init__(self, bond, topology_molecule): + """ + + Parameters + ---------- + bond : An openforcefield.topology.molecule.Bond + The reference bond. + topology_molecule : An openforcefield.topology.TopologyMolecule + The TopologyMolecule that this TopologyBond belongs to. + """ + # TODO: Type checks + self._bond = bond + self._topology_molecule = topology_molecule + + @property + def bond(self): + """ + Get the reference Bond for this TopologyBond. + + Returns + ------- + an openforcefield.topology.molecule.Bond + """ + return self._bond + + @property + def topology_molecule(self): + """ + Get the TopologyMolecule that this TopologyBond belongs to. + + Returns + ------- + openforcefield.topology.TopologyMolecule + """ + return self._topology_molecule + + @property + def topology_bond_index(self): + """ + Get the index of this bond in its parent Topology. + + Returns + ------- + int + The index of this bond in its parent topology. + """ + return self._topology_molecule.bond_start_topology_index + self._bond.molecule_bond_index + + @property + def molecule(self): + """ + Get the reference Molecule that this TopologyBond belongs to. + + Returns + ------- + openforcefield.topology.molecule.Molecule + """ + return self._topology_molecule.molecule + + @property + def bond_order(self): + """ + Get the order of this TopologyBond. + + Returns + ------- + int : bond order + """ + return self._bond.bond_order + + @property + def atoms(self): + """ + Get the TopologyAtoms connected to this TopologyBond. + + Returns + ------- + iterator of openforcefield.topology.TopologyAtom + """ + for ref_atom in self._bond.atoms: + yield TopologyAtom(ref_atom, self._topology_molecule) + + def to_dict(self): + """Convert to dictionary representation.""" + # Implement abstract method Serializable.to_dict() + raise NotImplementedError() # TODO + + @classmethod + def from_dict(cls, d): + """Static constructor from dictionary representation.""" + # Implement abstract method Serializable.to_dict() + raise NotImplementedError() # TODO + + +#============================================================================================= +# TopologyVirtualSite +#============================================================================================= + + +class TopologyVirtualSite(Serializable): + """ + A TopologyVirtualSite is a lightweight data structure that represents a single + openforcefield.topology.molecule.VirtualSite in a Topology. A TopologyVirtualSite consists of two references -- + One to its fully detailed "VirtualSite", an openforcefield.topology.molecule.VirtualSite, and another to its parent + "topology_molecule", which occupies a spot in the parent Topology's TopologyMolecule list. + + As some systems can be very large, there is no always-existing representation of a TopologyVirtualSite. They are + created on demand as the user requests them. + + .. warning :: This API is experimental and subject to change. + + """ + + def __init__(self, virtual_site, topology_molecule): + """ + + Parameters + ---------- + virtual_site : An openforcefield.topology.molecule.VirtualSite + The reference virtual site + topology_molecule : An openforcefield.topology.TopologyMolecule + The TopologyMolecule that this TopologyVirtualSite belongs to + """ + # TODO: Type checks + self._virtual_site = virtual_site + self._topology_molecule = topology_molecule + + def atom(self, index): + """ + Get the atom at a specific index in this TopologyVirtualSite + + Parameters + ---------- + index : int + The index of the atom in the reference VirtualSite to retrieve + + Returns + ------- + TopologyAtom + + """ + return TopologyAtom(self._virtual_site.atoms[index], + self.topology_molecule) + #for atom in self._virtual_site.atoms: + # reference_mol_atom_index = atom.molecule_atom_index + # yield self._topology_molecule.atom(reference_mol_atom_index) + + @property + def atoms(self): + """ + Get the TopologyAtoms involved in this TopologyVirtualSite. + + Returns + ------- + iterator of openforcefield.topology.TopologyAtom + """ + for atom in self._virtual_site.atoms: + reference_mol_atom_index = atom.molecule_atom_index + yield self._topology_molecule.atom(reference_mol_atom_index) + + @property + def virtual_site(self): + """ + Get the reference VirtualSite for this TopologyVirtualSite. + + Returns + ------- + an openforcefield.topology.molecule.VirtualSite + """ + return self._virtual_site + + @property + def topology_molecule(self): + """ + Get the TopologyMolecule that this TopologyVirtualSite belongs to. + + Returns + ------- + openforcefield.topology.TopologyMolecule + """ + return self._topology_molecule + + @property + def topology_virtual_site_index(self): + """ + Get the index of this virtual site in its parent Topology. + + Returns + ------- + int + The index of this virtual site in its parent topology. + """ + return self._topology_molecule.virtual_site_start_topology_index + self._virtual_site.molecule_virtual_site_index + + @property + def topology_particle_index(self): + """ + Get the index of this particle in its parent Topology. + + Returns + ------- + int + The index of this particle in its parent topology. + """ + return self._topology_molecule.particle_start_topology_index + self._virtual_site.molecule_particle_index + + @property + def molecule(self): + """ + Get the reference Molecule that this TopologyVirtualSite belongs to. + + Returns + ------- + openforcefield.topology.molecule.Molecule + """ + return self._topology_molecule.molecule + + @property + def type(self): + """ + Get the type of this virtual site + + Returns + ------- + str : The class name of this virtual site + """ + return self._virtual_site.type + + def __eq__(self, other): + return ((self._virtual_site == other._virtual_site) + and (self._topology_molecule == other._topology_molecule)) + + def to_dict(self): + """Convert to dictionary representation.""" + # Implement abstract method Serializable.to_dict() + raise NotImplementedError() # TODO + + @classmethod + def from_dict(cls, d): + """Static constructor from dictionary representation.""" + # Implement abstract method Serializable.to_dict() + raise NotImplementedError() # TODO + + +# ============================================================================================= +# TopologyMolecule +# ============================================================================================= + + +class TopologyMolecule: + """ + TopologyMolecules are built to be an efficient way to store large numbers of copies of the same molecule for + parameterization and system preparation. + + .. warning :: This API is experimental and subject to change. + + """ + + def __init__(self, + reference_molecule, + topology, + local_topology_to_reference_index=None): + """ + Create a new TopologyMolecule. + + Parameters + ---------- + reference_molecule : an openforcefield.topology.molecule.Molecule + The reference molecule, with details like formal charges, partial charges, bond orders, partial bond orders, + and atomic symbols. + topology : an openforcefield.topology.Topology + The topology that this TopologyMolecule belongs to + local_topology_to_reference_index : dict, optional, default=None + Dictionary of {TopologyMolecule_atom_index : Molecule_atom_index} for the TopologyMolecule that will be built + """ + # TODO: Type checks + self._reference_molecule = reference_molecule + self._topology = topology + if local_topology_to_reference_index is None: + local_topology_to_reference_index = dict( + [(i, i) for i in range(reference_molecule.n_atoms)]) + self._top_to_ref_index = local_topology_to_reference_index + self._ref_to_top_index = dict( + (k, j) for j, k in local_topology_to_reference_index.items()) + + @property + def topology(self): + """ + Get the topology that this TopologyMolecule belongs to + + Returns + ------- + an openforcefield.topology.Topology + """ + return self._topology + + @property + def reference_molecule(self): + """ + Get the reference molecule for this TopologyMolecule + + Returns + ------- + an openforcefield.topology.molecule.Molecule + """ + return self._reference_molecule + + @property + def n_atoms(self): + """ + The number of atoms in this topology. + + Returns + ------- + int + """ + return self._reference_molecule.n_atoms + + def atom(self, index): + """ + Get the TopologyAtom with a given topology molecule index in this TopologyMolecule. + + Parameters + ---------- + index : int + Index of the TopologyAtom within this TopologyMolecule to retrieve + + Returns + ------- + an openforcefield.topology.TopologyAtom + """ + ref_mol_atom_index = self._top_to_ref_index[index] + return TopologyAtom(self._reference_molecule.atoms[ref_mol_atom_index], + self) + + @property + def atoms(self): + """ + Return an iterator of all the TopologyAtoms in this TopologyMolecule + + Returns + ------- + an iterator of openforcefield.topology.TopologyAtoms + """ + iterate_order = list(self._top_to_ref_index.items()) + # Sort by topology index + iterate_order.sort(key=lambda x: x[0]) + for top_index, ref_index in iterate_order: + #self._reference_molecule.atoms: + yield TopologyAtom(self._reference_molecule.atoms[ref_index], self) + + @property + def atom_start_topology_index(self): + """ + Get the topology index of the first atom in this TopologyMolecule + + """ + atom_start_topology_index = 0 + for topology_molecule in self._topology.topology_molecules: + if self == topology_molecule: + return atom_start_topology_index + atom_start_topology_index += topology_molecule.n_atoms + + def bond(self, index): + """ + Get the TopologyBond with a given reference molecule index in this TopologyMolecule + + Parameters + ---------- + index : int + Index of the TopologyBond within this TopologyMolecule to retrieve + + Returns + ------- + an openforcefield.topology.TopologyBond + """ + return TopologyBond(self.reference_molecule.bonds[index], self) + + @property + def bonds(self): + """ + Return an iterator of all the TopologyBonds in this TopologyMolecule + + Returns + ------- + an iterator of openforcefield.topology.TopologyBonds + """ + for bond in self._reference_molecule.bonds: + yield TopologyBond(bond, self) + + @property + def n_bonds(self): + """Get the number of bonds in this TopologyMolecule + + Returns + ------- + int : number of bonds + """ + return self._reference_molecule.n_bonds + + @property + def bond_start_topology_index(self): + """Get the topology index of the first bond in this TopologyMolecule + + """ + bond_start_topology_index = 0 + for topology_molecule in self._topology.topology_molecules: + if self == topology_molecule: + return bond_start_topology_index + bond_start_topology_index += topology_molecule.n_bonds + + def particle(self, index): + """ + Get the TopologyParticle with a given reference molecule index in this TopologyMolecule + + Parameters + ---------- + index : int + Index of the TopologyParticle within this TopologyMolecule to retrieve + + Returns + ------- + an openforcefield.topology.TopologyParticle + """ + return TopologyParticle(self.reference_molecule.particles[index], self) + + @property + def particles(self): + """ + Return an iterator of all the TopologyParticles in this TopologyMolecules + + Returns + ------- + an iterator of openforcefield.topology.TopologyParticle + """ + # Note: This assumes that particles are all Atoms (in topology map order), and then virtualsites + yield_order = list(self._top_to_ref_index.items()) + # Sort by topology atom index + yield_order.sort(key=lambda x: x[0]) + for top_atom_index, ref_mol_atom_index in yield_order: + ref_atom = self._reference_molecule.atoms[ref_mol_atom_index] + yield TopologyAtom(ref_atom, self) + + # TODO: Add ordering scheme here + for vsite in self.reference_molecule.virtual_sites: + yield TopologyVirtualSite(vsite, self) + + #for particle in self._reference_molecule.particles: + # if isinstance(particle, Atom): + # yield TopologyAtom(particle, self) + # elif isinstance(particle, VirtualSite): + # yield TopologyVirtualSite(particle, self) + + @property + def n_particles(self): + """Get the number of particles in this TopologyMolecule + + Returns + ------- + int : The number of particles + """ + return self._reference_molecule.n_particles + + @property + def particle_start_topology_index(self): + """Get the topology index of the first particle in this TopologyMolecule. + """ + particle_start_topology_index = 0 + for topology_molecule in self._topology.topology_molecules: + if self == topology_molecule: + return particle_start_topology_index + particle_start_topology_index += topology_molecule.n_particles + + def virtual_site(self, index): + """ + Get the TopologyVirtualSite with a given reference molecule index in this TopologyMolecule + + Parameters + ---------- + index : int + Index of the TopologyVirtualSite within this TopologyMolecule to retrieve + + Returns + ------- + an openforcefield.topology.TopologyVirtualSite + """ + return TopologyVirtualSite( + self.reference_molecule.virtual_sites[index], self) + + @property + def virtual_sites(self): + """ + Return an iterator of all the TopologyVirtualSites in this TopologyMolecules + + Returns + ------- + an iterator of openforcefield.topology.TopologyVirtualSite + """ + for vs in self._reference_molecule.virtual_sites: + yield TopologyVirtualSite(vs, self) + + @property + def n_virtual_sites(self): + """Get the number of virtual sites in this TopologyMolecule + + Returns + ------- + int + """ + return self._reference_molecule.n_virtual_sites + + @property + def angles(self): + """Iterable of Tuple[TopologyAtom]: iterator over the angles in this Topology.""" + return self._convert_to_topology_atom_tuples(self._reference_molecule.angles) + + @property + def n_angles(self): + """int: number of angles in this Topology.""" + return self._reference_molecule.n_angles + + @property + def propers(self): + """Iterable of Tuple[TopologyAtom]: iterator over the proper torsions in this Topology.""" + return self._convert_to_topology_atom_tuples(self._reference_molecule.propers) + + @property + def n_propers(self): + """int: number of proper torsions in this Topology.""" + return self._reference_molecule.n_propers + + @property + def impropers(self): + """Iterable of Tuple[TopologyAtom]: iterator over the improper torsions in this Topology.""" + return self._convert_to_topology_atom_tuples(self._reference_molecule.impropers) + + @property + def n_impropers(self): + """int: number of proper torsions in this Topology.""" + return self._reference_molecule.n_impropers + + @property + def virtual_site_start_topology_index(self): + """Get the topology index of the first virtual site in this TopologyMolecule + """ + virtual_site_start_topology_index = 0 + for topology_molecule in self._topology.topology_molecules: + if self == topology_molecule: + return virtual_site_start_topology_index + virtual_site_start_topology_index += topology_molecule.n_virtual_sites + + def to_dict(self): + """Convert to dictionary representation.""" + # Implement abstract method Serializable.to_dict() + raise NotImplementedError() # TODO + + @classmethod + def from_dict(cls, d): + """Static constructor from dictionary representation.""" + # Implement abstract method Serializable.to_dict() + raise NotImplementedError() # TODO + + def _convert_to_topology_atom_tuples(self, molecule_atom_tuples): + for atom_tuple in molecule_atom_tuples: + mol_atom_indices = (a.molecule_atom_index for a in atom_tuple) + top_mol_atom_indices = (self._ref_to_top_index[mol_idx] for mol_idx in mol_atom_indices) + yield tuple(self.atom(i) for i in top_mol_atom_indices) + + +# TODO: pick back up figuring out how we want TopologyMolecules to know their starting TopologyParticle indices + +# ============================================================================================= +# Topology +# ============================================================================================= + +# TODO: Revise documentation and remove chains + + +class Topology(Serializable): + """ + A Topology is a chemical representation of a system containing one or more molecules appearing in a specified order. + + .. warning :: This API is experimental and subject to change. + + Examples + -------- + + Import some utilities + + >>> from simtk.openmm import app + >>> from openforcefield.tests.utils import get_data_filename, get_packmol_pdbfile + >>> pdb_filepath = get_packmol_pdbfile('cyclohexane_ethanol_0.4_0.6') + >>> monomer_names = ('cyclohexane', 'ethanol') + + Create a Topology object from a PDB file and sdf files defining the molecular contents + + >>> from openforcefield.topology import Molecule, Topology + >>> pdbfile = app.PDBFile(pdb_filepath) + >>> sdf_filepaths = [get_data_filename(f'systems/monomers/{name}.sdf') for name in monomer_names] + >>> unique_molecules = [Molecule.from_file(sdf_filepath) for sdf_filepath in sdf_filepaths] + >>> topology = Topology.from_openmm(pdbfile.topology, unique_molecules=unique_molecules) + + Create a Topology object from a PDB file and IUPAC names of the molecular contents + + >>> pdbfile = app.PDBFile(pdb_filepath) + >>> unique_molecules = [Molecule.from_iupac(name) for name in monomer_names] + >>> topology = Topology.from_openmm(pdbfile.topology, unique_molecules=unique_molecules) + + Create an empty Topology object and add a few copies of a single benzene molecule + + >>> topology = Topology() + >>> molecule = Molecule.from_iupac('benzene') + >>> molecule_topology_indices = [topology.add_molecule(molecule) for index in range(10)] + + """ + + def __init__(self, other=None): + """ + Create a new Topology. + + Parameters + ---------- + other : optional, default=None + If specified, attempt to construct a copy of the Topology from the specified object. + This might be a Topology object, or a file that can be used to construct a Topology object + or serialized Topology object. + + """ + from openforcefield.topology.molecule import FrozenMolecule + + # Assign cheminformatics models + model = DEFAULT_AROMATICITY_MODEL + self._aromaticity_model = model + #self._fractional_bond_order_model = DEFAULT_FRACTIONAL_BOND_ORDER_MODEL + #self._charge_model = DEFAULT_CHARGE_MODEL + + # Initialize storage + self._initialize() + + # TODO: Try to construct Topology copy from `other` if specified + if isinstance(other, Topology): + self.copy_initializer(other) + elif isinstance(other, FrozenMolecule): + self.from_molecules([other]) + elif isinstance(other, OrderedDict): + self._initialize_from_dict(other) + + def _initialize(self): + """ + Initializes a blank Topology. + """ + self._aromaticity_model = DEFAULT_AROMATICITY_MODEL + self._constrained_atom_pairs = dict() + self._box_vectors = None + #self._is_periodic = False + #self._reference_molecule_dicts = set() + # TODO: Look into weakref and what it does. Having multiple topologies might cause a memory leak. + self._reference_molecule_to_topology_molecules = OrderedDict() + self._topology_molecules = list() + + @property + def reference_molecules(self): + """ + Get an iterator of reference molecules in this Topology. + + Returns + ------- + iterable of openforcefield.topology.Molecule + """ + for ref_mol in self._reference_molecule_to_topology_molecules.keys(): + yield ref_mol + + @classmethod + def from_molecules(cls, molecules): + """ + Create a new Topology object containing one copy of each of the specified molecule(s). + + Parameters + ---------- + molecules : Molecule or iterable of Molecules + One or more molecules to be added to the Topology + + Returns + ------- + topology : Topology + The Topology created from the specified molecule(s) + """ + # Ensure that we are working with an iterable + try: + some_object_iterator = iter(molecules) + except TypeError as te: + # Make iterable object + molecules = [molecules] + + # Create Topology and populate it with specified molecules + topology = cls() + for molecule in molecules: + topology.add_molecule(molecule) + + return topology + + def assert_bonded(self, atom1, atom2): + """ + Raise an exception if the specified atoms are not bonded in the topology. + + Parameters + ---------- + atom1, atom2 : openforcefield.topology.Atom or int + The atoms or atom topology indices to check to ensure they are bonded + + """ + if (type(atom1) is int) and (type(atom2) is int): + atom1 = self.atom(atom1) + atom2 = self.atom(atom2) + + #else: + if not (self.is_bonded(atom1, atom2)): + # TODO: Raise more specific exception. + raise Exception( + 'Atoms {} and {} are not bonded in topology'.format( + atom1, atom2)) + + @property + def aromaticity_model(self): + """ + Get the aromaticity model applied to all molecules in the topology. + + Returns + ------- + aromaticity_model : str + Aromaticity model in use. + """ + return self._aromaticity_model + + @aromaticity_model.setter + def aromaticity_model(self, aromaticity_model): + """ + Set the aromaticity model applied to all molecules in the topology. + + Parameters + ---------- + aromaticity_model : str + Aromaticity model to use. One of: ['OEAroModel_MDL'] + """ + + if not aromaticity_model in ALLOWED_AROMATICITY_MODELS: + msg = "Aromaticity model must be one of {}; specified '{}'".format( + ALLOWED_AROMATICITY_MODELS, aromaticity_model) + raise ValueError(msg) + self._aromaticity_model = aromaticity_model + + @property + def box_vectors(self): + """Return the box vectors of the topology, if specified + Returns + ------- + box_vectors : simtk.unit.Quantity wrapped numpy array + The unit-wrapped box vectors of this topology + """ + return self._box_vectors + + @box_vectors.setter + def box_vectors(self, box_vectors): + """ + Sets the box vectors to be used for this topology. + + Parameters + ---------- + box_vectors : simtk.unit.Quantity wrapped numpy array + The unit-wrapped box vectors + + """ + if box_vectors is None: + self._box_vectors = None + return + if not hasattr(box_vectors, 'unit'): + raise ValueError("Given unitless box vectors") + if not (unit.angstrom.is_compatible(box_vectors.unit)): + raise ValueError( + "Attempting to set box vectors in units that are incompatible with simtk.unit.Angstrom" + ) + + if hasattr(box_vectors, 'shape'): + assert box_vectors.shape == (3, ) + else: + assert len(box_vectors) == 3 + self._box_vectors = box_vectors + + @property + def charge_model(self): + """ + Get the partial charge model applied to all molecules in the topology. + + Returns + ------- + charge_model : str + Charge model used for all molecules in the Topology. + + """ + return self._charge_model + + @charge_model.setter + def charge_model(self, charge_model): + """ + Set the partial charge model used for all molecules in the topology. + + Parameters + ---------- + charge_model : str + Charge model to use for all molecules in the Topology. + Allowed values: ['AM1-BCC'] + * ``AM1-BCC``: Canonical AM1-BCC scheme + """ + if not charge_model in ALLOWED_CHARGE_MODELS: + raise ValueError( + "Charge model must be one of {}; specified '{}'".format( + ALLOWED_CHARGE_MODELS, charge_model)) + self._charge_model = charge_model + + @property + def constrained_atom_pairs(self): + """Returns the constrained atom pairs of the Topology + + Returns + ------- + constrained_atom_pairs : dict + dictionary of the form d[(atom1_topology_index, atom2_topology_index)] = distance (float) + """ + return self._constrained_atom_pairs + + @property + def fractional_bond_order_model(self): + """ + Get the fractional bond order model for the Topology. + + Returns + ------- + fractional_bond_order_model : str + Fractional bond order model in use. + + """ + return self._fractional_bond_order_model + + @fractional_bond_order_model.setter + def fractional_bond_order_model(self, fractional_bond_order_model): + """ + Set the fractional bond order model applied to all molecules in the topology. + + Parameters + ---------- + fractional_bond_order_model : str + Fractional bond order model to use. One of: ['Wiberg'] + + """ + if not fractional_bond_order_model in ALLOWED_FRACTIONAL_BOND_ORDER_MODELS: + raise ValueError( + "Fractional bond order model must be one of {}; specified '{}'" + .format(ALLOWED_FRACTIONAL_BOND_ORDER_MODELS, + fractional_bond_order_model)) + self._fractional_bond_order_model = fractional_bond_order_model + + @property + def n_reference_molecules(self): + """ + Returns the number of reference (unique) molecules in in this Topology. + + Returns + ------- + n_reference_molecules : int + """ + count = 0 + for i in self.reference_molecules: + count += 1 + return count + + @property + def n_topology_molecules(self): + """ + Returns the number of topology molecules in in this Topology. + + Returns + ------- + n_topology_molecules : int + """ + return len(self._topology_molecules) + + @property + def topology_molecules(self): + """Returns an iterator over all the TopologyMolecules in this Topology + + Returns + ------- + topology_molecules : Iterable of TopologyMolecule + """ + return self._topology_molecules + + @property + def n_topology_atoms(self): + """ + Returns the number of topology atoms in in this Topology. + + Returns + ------- + n_topology_atoms : int + """ + n_atoms = 0 + for reference_molecule in self.reference_molecules: + n_atoms_per_topology_molecule = reference_molecule.n_atoms + n_instances_of_topology_molecule = len( + self. + _reference_molecule_to_topology_molecules[reference_molecule]) + n_atoms += n_atoms_per_topology_molecule * n_instances_of_topology_molecule + return n_atoms + + @property + def topology_atoms(self): + """Returns an iterator over the atoms in this Topology. These will be in ascending order of topology index (Note + that this is not necessarily the same as the reference molecule index) + + Returns + ------- + topology_atoms : Iterable of TopologyAtom + """ + for topology_molecule in self._topology_molecules: + for atom in topology_molecule.atoms: + yield atom + + @property + def n_topology_bonds(self): + """ + Returns the number of TopologyBonds in in this Topology. + + Returns + ------- + n_bonds : int + """ + n_bonds = 0 + for reference_molecule in self.reference_molecules: + n_bonds_per_topology_molecule = reference_molecule.n_bonds + n_instances_of_topology_molecule = len( + self. + _reference_molecule_to_topology_molecules[reference_molecule]) + n_bonds += n_bonds_per_topology_molecule * n_instances_of_topology_molecule + return n_bonds + + @property + def topology_bonds(self): + """Returns an iterator over the bonds in this Topology + + Returns + ------- + topology_bonds : Iterable of TopologyBond + """ + for topology_molecule in self._topology_molecules: + for bond in topology_molecule.bonds: + yield bond + + @property + def n_topology_particles(self): + """ + Returns the number of topology particles (TopologyAtoms and TopologyVirtualSites) in in this Topology. + + Returns + ------- + n_topology_particles : int + """ + n_particles = 0 + for reference_molecule in self.reference_molecules: + n_particles_per_topology_molecule = reference_molecule.n_particles + n_instances_of_topology_molecule = len( + self. + _reference_molecule_to_topology_molecules[reference_molecule]) + n_particles += n_particles_per_topology_molecule * n_instances_of_topology_molecule + return n_particles + + @property + def topology_particles(self): + """Returns an iterator over the particles (TopologyAtoms and TopologyVirtualSites) in this Topology. The + TopologyAtoms will be in order of ascending Topology index (Note that this may differ from the + order of atoms in the reference molecule index). + + Returns + -------- + topology_particles : Iterable of TopologyAtom and TopologyVirtualSite + """ + for topology_molecule in self._topology_molecules: + for particle in topology_molecule.particles: + yield particle + + @property + def n_topology_virtual_sites(self): + """ + Returns the number of TopologyVirtualSites in in this Topology. + + Returns + ------- + n_virtual_sites : iterable of TopologyVirtualSites + """ + n_virtual_sites = 0 + for reference_molecule in self.reference_molecules: + n_virtual_sites_per_topology_molecule = reference_molecule.n_virtual_sites + n_instances_of_topology_molecule = len( + self. + _reference_molecule_to_topology_molecules[reference_molecule]) + n_virtual_sites += n_virtual_sites_per_topology_molecule * n_instances_of_topology_molecule + return n_virtual_sites + + @property + def topology_virtual_sites(self): + """Get an iterator over the virtual sites in this Topology + + Returns + ------- + topology_virtual_sites : Iterable of TopologyVirtualSite + """ + for topology_molecule in self._topology_molecules: + for virtual_site in topology_molecule.virtual_sites: + yield virtual_site + + @property + def n_angles(self): + """int: number of angles in this Topology.""" + return sum(mol.n_angles for mol in self._topology_molecules) + + @property + def angles(self): + """Iterable of Tuple[TopologyAtom]: iterator over the angles in this Topology.""" + for topology_molecule in self._topology_molecules: + for angle in topology_molecule.angles: + yield angle + + @property + def n_propers(self): + """int: number of proper torsions in this Topology.""" + return sum(mol.n_propers for mol in self._topology_molecules) + + @property + def propers(self): + """Iterable of Tuple[TopologyAtom]: iterator over the proper torsions in this Topology.""" + for topology_molecule in self._topology_molecules: + for proper in topology_molecule.propers: + yield proper + + @property + def n_impropers(self): + """int: number of improper torsions in this Topology.""" + return sum(mol.n_impropers for mol in self._topology_molecules) + + @property + def impropers(self): + """Iterable of Tuple[TopologyAtom]: iterator over the improper torsions in this Topology.""" + for topology_molecule in self._topology_molecules: + for improper in topology_molecule.impropers: + yield improper + + def chemical_environment_matches(self, + query, + aromaticity_model='MDL', + toolkit_registry=GLOBAL_TOOLKIT_REGISTRY): + """ + Retrieve all matches for a given chemical environment query. + + TODO: + * Do we want to generalize this to other kinds of queries too, like mdtraj DSL, pymol selections, atom index slices, etc? + We could just call it topology.matches(query) + + Parameters + ---------- + query : str or ChemicalEnvironment + SMARTS string (with one or more tagged atoms) or ``ChemicalEnvironment`` query + Query will internally be resolved to SMARTS using ``query.as_smarts()`` if it has an ``.as_smarts`` method. + aromaticity_model : str + Override the default aromaticity model for this topology and use the specified aromaticity model instead. + Allowed values: ['MDL'] + + Returns + ------- + matches : list of TopologyAtom tuples + A list of all matching Atom tuples + + """ + # Render the query to a SMARTS string + if type(query) is str: + smarts = query + elif type(query) is ChemicalEnvironment: + smarts = query.as_smarts() + else: + raise ValueError( + "Don't know how to convert query '%s' into SMARTS string" % + query) + + # Perform matching on each unique molecule, unrolling the matches to all matching copies of that molecule in the Topology object. + matches = list() + for ref_mol in self.reference_molecules: + # Find all atomsets that match this definition in the reference molecule + # This will automatically attempt to match chemically identical atoms in a canonical order within the Topology + refmol_matches = ref_mol.chemical_environment_matches( + smarts, toolkit_registry=toolkit_registry) + + # Loop over matches + for reference_match in refmol_matches: + #mol_dict = molecule.to_dict + # Unroll corresponding atom indices over all instances of this molecule + for topology_molecule in self._reference_molecule_to_topology_molecules[ + ref_mol]: + match = list() + # Create match TopologyAtoms. + for reference_molecule_atom_index in reference_match: + reference_atom = topology_molecule._reference_molecule.atoms[ + reference_molecule_atom_index] + topology_atom = TopologyAtom(reference_atom, + topology_molecule) + match.append(topology_atom) + #topology_molecule_atom_index = topology_molecule._ref_to_top_index[reference_molecule_atom_index] + #atom_topology_index = topology_molecule.atom_start_topology_index+topology_molecule_atom_index + #match.append(self.atom(atom_topology_index)) + match = tuple(match) + #match = tuple([topology_molecule.atom_start_topology_index+ref_mol_atom_index for ref_mol_atom_index in reference_match]) + matches.append(match) + + return matches + + def to_dict(self): + """Convert to dictionary representation.""" + # Implement abstract method Serializable.to_dict() + raise NotImplementedError() # TODO + + @classmethod + def from_dict(cls, d): + """Static constructor from dictionary representation.""" + # Implement abstract method Serializable.to_dict() + raise NotImplementedError() # TODO + + @classmethod + def from_openmm(cls, openmm_topology, unique_molecules=None): + """ + Construct an openforcefield Topology object from an OpenMM Topology object. + + Parameters + ---------- + openmm_topology : simtk.openmm.app.Topology + An OpenMM Topology object + unique_molecules : iterable of objects that can be used to construct unique Molecule objects + All unique molecules must be provided, in any order, though multiple copies of each molecule are allowed. + The atomic elements and bond connectivity will be used to match the reference molecules + to molecule graphs appearing in the OpenMM ``Topology``. If bond orders are present in the + OpenMM ``Topology``, these will be used in matching as well. + If all bonds have bond orders assigned in ``mdtraj_topology``, these bond orders will be used to attempt to construct + the list of unique Molecules if the ``unique_molecules`` argument is omitted. + + Returns + ------- + topology : openforcefield.topology.Topology + An openforcefield Topology object + """ + import networkx as nx + from networkx.algorithms.isomorphism import GraphMatcher + + # Check to see if the openMM system has defined bond orders, by looping over all Bonds in the Topology. + omm_has_bond_orders = True + for omm_bond in openmm_topology.bonds(): + if omm_bond.order is None: + omm_has_bond_orders = False + + # Set functions for determining equality between nodes and edges + node_match_func = lambda x, y: x['atomic_number'] == y['atomic_number'] + if omm_has_bond_orders: + edge_match_func = lambda x, y: x['order'] == y['order'] + else: + edge_match_func = None + + # Convert all unique mols to graphs + topology = cls() + graph_to_unq_mol = {} + for unq_mol in unique_molecules: + unq_mol_graph = unq_mol.to_networkx() + for existing_graph in graph_to_unq_mol.keys(): + if nx.is_isomorphic( + existing_graph, + unq_mol_graph, + node_match=node_match_func, + edge_match=edge_match_func): + msg = "Error: Two unique molecules have indistinguishable " \ + "graphs: {} and {}".format(unq_mol, graph_to_unq_mol[existing_graph]) + raise DuplicateUniqueMoleculeError(msg) + graph_to_unq_mol[unq_mol_graph] = unq_mol + + # Convert all openMM mols to graphs + omm_topology_G = nx.Graph() + for atom in openmm_topology.atoms(): + omm_topology_G.add_node( + atom.index, atomic_number=atom.element.atomic_number) + for bond in openmm_topology.bonds(): + omm_topology_G.add_edge( + bond.atom1.index, bond.atom2.index, order=bond.order) + + # For each connected subgraph (molecule) in the topology, find its match in unique_molecules + topology_molecules_to_add = list() + for omm_mol_G in (omm_topology_G.subgraph(c).copy() + for c in nx.connected_components(omm_topology_G)): + match_found = False + for unq_mol_G in graph_to_unq_mol.keys(): + if nx.is_isomorphic( + unq_mol_G, + omm_mol_G, + node_match=node_match_func, + edge_match=edge_match_func): + # Take the first valid atom indexing map + GM = GraphMatcher( + omm_mol_G, + unq_mol_G, + node_match=node_match_func, + edge_match=edge_match_func) + for mapping in GM.isomorphisms_iter(): + topology_atom_map = mapping + break + first_topology_atom_index = min(topology_atom_map.keys()) + topology_molecules_to_add.append( + (first_topology_atom_index, unq_mol_G, + topology_atom_map.items())) + match_found = True + break + if not (match_found): + # TODO: We should make this message way more informative. Maybe take the unmatched subgraph and + # print the result of Molecule.from_networkx (which we need to implement)? + raise ValueError('No match found for molecule {}') + + # The connected_component_subgraph function above may have scrambled the molecule order, so sort molecules + # by their first atom's topology index + topology_molecules_to_add.sort(key=lambda x: x[0]) + for first_index, unq_mol_G, top_to_ref_index in topology_molecules_to_add: + local_top_to_ref_index = dict( + [(top_index - first_index, ref_index) + for top_index, ref_index in top_to_ref_index]) + topology.add_molecule( + graph_to_unq_mol[unq_mol_G], + local_topology_to_reference_index=local_top_to_ref_index) + + topology.box_vectors = openmm_topology.getPeriodicBoxVectors() + # TODO: How can we preserve metadata from the openMM topology when creating the OFF topology? + return topology + + # TODO: Jeff prepended an underscore on this before 0.2.0 release to remove it from the API. + # Given the recent (2019_04) discussions about potential loss of parameters during conversion, we should + # revisit this function to determine what sorts of guarantees we can put on system correctness before + # we expose it. + def _to_openmm(self): + """ + Create an OpenMM Topology object. + + Parameters + ---------- + openmm_topology : simtk.openmm.app.Topology + An OpenMM Topology object + """ + raise NotImplementedError + + @staticmethod + def from_mdtraj(mdtraj_topology, unique_molecules=None): + """ + Construct an openforcefield Topology object from an MDTraj Topology object. + + Parameters + ---------- + mdtraj_topology : mdtraj.Topology + An MDTraj Topology object + unique_molecules : iterable of objects that can be used to construct unique Molecule objects + All unique molecules mult be provided, in any order, though multiple copies of each molecule are allowed. + The atomic elements and bond connectivity will be used to match the reference molecules + to molecule graphs appearing in the MDTraj ``Topology``. If bond orders are present in the + MDTraj ``Topology``, these will be used in matching as well. + If all bonds have bond orders assigned in ``mdtraj_topology``, these bond orders will be used to attempt to construct + the list of unique Molecules if the ``unique_molecules`` argument is omitted. + + Returns + ------- + topology : openforcefield.Topology + An openforcefield Topology object + """ + return Topology.from_openmm( + mdtraj_topology.to_openmm(), unique_molecules=unique_molecules) + + # TODO: Jeff prepended an underscore on this before 0.2.0 release to remove it from the API. + # Before exposing this, we should look carefully at the information that is preserved/lost during this + # conversion, and make it clear what would happen to this information in a round trip. For example, + # we should know what would happen to formal and partial bond orders and charges, stereochemistry, and + # multi-conformer information. It will be important to document these risks to users, as all of these + # factors could lead to unintended behavior during system parameterization. + def _to_mdtraj(self): + """ + Create an MDTraj Topology object. + + Returns + ---------- + mdtraj_topology : mdtraj.Topology + An MDTraj Topology object + """ + import mdtraj as md + return md.Topology.from_openmm(self.to_openmm()) + + @staticmethod + def from_parmed(parmed_structure, unique_molecules=None): + """ + .. warning:: This functionality will be implemented in a future toolkit release. + + Construct an openforcefield Topology object from a ParmEd Structure object. + + Parameters + ---------- + parmed_structure : parmed.Structure + A ParmEd structure object + unique_molecules : iterable of objects that can be used to construct unique Molecule objects + All unique molecules mult be provided, in any order, though multiple copies of each molecule are allowed. + The atomic elements and bond connectivity will be used to match the reference molecules + to molecule graphs appearing in the structure's ``topology`` object. If bond orders are present in the + structure's ``topology`` object, these will be used in matching as well. + If all bonds have bond orders assigned in the structure's ``topology`` object, + these bond orders will be used to attempt to construct + the list of unique Molecules if the ``unique_molecules`` argument is omitted. + + Returns + ------- + topology : openforcefield.Topology + An openforcefield Topology object + """ + import parmed + # TODO: Implement functionality + raise NotImplementedError + + def to_parmed(self): + """ + + .. warning:: This functionality will be implemented in a future toolkit release. + + Create a ParmEd Structure object. + + Returns + ---------- + parmed_structure : parmed.Structure + A ParmEd Structure objecft + """ + import parmed + # TODO: Implement functionality + raise NotImplementedError + + # TODO: Jeff prepended an underscore on this before 0.2.0 release to remove it from the API. + # This function is deprecated and expects the OpenEye toolkit. We need to discuss what + # to do with this functionality in light of our move to the ToolkitWrapper architecture. + # Also, as written, this function implies several things about our toolkit's ability to + # handle biopolymers. We need to discuss how much of this functionality we will expose + # and how we can make our toolkit's current scope clear to users.. + @staticmethod + def _from_openeye(oemol): + """ + Create a Molecule from an OpenEye molecule. + + Requires the OpenEye toolkit to be installed. + + Parameters + ---------- + oemol : openeye.oechem.OEMol + An OpenEye molecule + + Returns + ------- + molecule : openforcefield.Molecule + An openforcefield molecule + + """ + # TODO: Convert this to cls.from_molecules(Molecule.from_openeye())? + # OE Hierarchical molecule view + hv = oechem.OEHierView( + oemol, oechem.OEAssumption_BondedResidue + + oechem.OEAssumption_ResPerceived + oechem.OEAssumption_PDBOrder) + + # Create empty OpenMM Topology + topology = app.Topology() + # Dictionary used to map oe atoms to openmm atoms + oe_atom_to_openmm_at = {} + + for chain in hv.GetChains(): + # TODO: Fail if hv contains more than one molecule. + + # Create empty OpenMM Chain + openmm_chain = topology.addChain(chain.GetChainID()) + + for frag in chain.GetFragments(): + + for hres in frag.GetResidues(): + + # Get OE residue + oe_res = hres.GetOEResidue() + # Create OpenMM residue + openmm_res = topology.addResidue(oe_res.GetName(), + openmm_chain) + + for oe_at in hres.GetAtoms(): + # Select atom element based on the atomic number + element = app.element.Element.getByAtomicNumber( + oe_at.GetAtomicNum()) + # Add atom OpenMM atom to the topology + openmm_at = topology.addAtom(oe_at.GetName(), element, + openmm_res) + openmm_at.index = oe_at.GetIdx() + # Add atom to the mapping dictionary + oe_atom_to_openmm_at[oe_at] = openmm_at + + if topology.getNumAtoms() != mol.NumAtoms(): + oechem.OEThrow.Error( + "OpenMM topology and OEMol number of atoms mismatching: " + "OpenMM = {} vs OEMol = {}".format(topology.getNumAtoms(), + mol.NumAtoms())) + + # Count the number of bonds in the openmm topology + omm_bond_count = 0 + + def IsAmideBond(oe_bond): + # TODO: Can this be replaced by a SMARTS query? + + # This supporting function checks if the passed bond is an amide bond or not. + # Our definition of amide bond C-N between a Carbon and a Nitrogen atom is: + # O + # ║ + # CA or O-C-N- + # | + + # The amide bond C-N is a single bond + if oe_bond.GetOrder() != 1: + return False + + atomB = oe_bond.GetBgn() + atomE = oe_bond.GetEnd() + + # The amide bond is made by Carbon and Nitrogen atoms + if not (atomB.IsCarbon() and atomE.IsNitrogen() or + (atomB.IsNitrogen() and atomE.IsCarbon())): + return False + + # Select Carbon and Nitrogen atoms + if atomB.IsCarbon(): + C_atom = atomB + N_atom = atomE + else: + C_atom = atomE + N_atom = atomB + + # Carbon and Nitrogen atoms must have 3 neighbour atoms + if not (C_atom.GetDegree() == 3 and N_atom.GetDegree() == 3): + return False + + double_bonds = 0 + single_bonds = 0 + + for bond in C_atom.GetBonds(): + # The C-O bond can be single or double. + if (bond.GetBgn() == C_atom and bond.GetEnd().IsOxygen()) or \ + (bond.GetBgn().IsOxygen() and bond.GetEnd() == C_atom): + if bond.GetOrder() == 2: + double_bonds += 1 + if bond.GetOrder() == 1: + single_bonds += 1 + # The CA-C bond is single + if (bond.GetBgn() == C_atom and bond.GetEnd().IsCarbon()) or \ + (bond.GetBgn().IsCarbon() and bond.GetEnd() == C_atom): + if bond.GetOrder() == 1: + single_bonds += 1 + # Just one double and one single bonds are connected to C + # In this case the bond is an amide bond + if double_bonds == 1 and single_bonds == 1: + return True + else: + return False + + # Creating bonds + for oe_bond in mol.GetBonds(): + # Set the bond type + if oe_bond.GetType() is not "": + if oe_bond.GetType() in [ + 'Single', 'Double', 'Triple', 'Aromatic', 'Amide' + ]: + off_bondtype = oe_bond.GetType() + else: + off_bondtype = None + else: + if oe_bond.IsAromatic(): + oe_bond.SetType("Aromatic") + off_bondtype = "Aromatic" + elif oe_bond.GetOrder() == 2: + oe_bond.SetType("Double") + off_bondtype = "Double" + elif oe_bond.GetOrder() == 3: + oe_bond.SetType("Triple") + off_bond_type = "Triple" + elif IsAmideBond(oe_bond): + oe_bond.SetType("Amide") + off_bond_type = "Amide" + elif oe_bond.GetOrder() == 1: + oe_bond.SetType("Single") + off_bond_type = "Single" + else: + off_bond_type = None + + molecule.add_bond( + oe_atom_to_openmm_at[oe_bond.GetBgn()], + oe_atom_to_openmm_at[oe_bond.GetEnd()], + type=off_bondtype, + order=oe_bond.GetOrder()) + + if molecule.n_bondsphe != mol.NumBonds(): + oechem.OEThrow.Error( + "OpenMM topology and OEMol number of bonds mismatching: " + "OpenMM = {} vs OEMol = {}".format(omm_bond_count, + mol.NumBonds())) + + dic = mol.GetCoords() + positions = [Vec3(v[0], v[1], v[2]) + for k, v in dic.items()] * unit.angstrom + + return topology, positions + + # TODO: Jeff prepended an underscore on this before 0.2.0 release to remove it from the API. + # This function is deprecated and expects the OpenEye toolkit. We need to discuss what + # to do with this functionality in light of our move to the ToolkitWrapper architecture. + # It also expects Topology to be organized by chain, which is not currently the case. + # Bringing this function back would require non-trivial engineering and testing, and we + # would want to discuss what "guarantee" of correctness it could offer. + def _to_openeye(self, + positions=None, + aromaticity_model=DEFAULT_AROMATICITY_MODEL): + """ + Create an OpenEye OEMol from the topology + + Requires the OpenEye toolkit to be installed. + + Returns + ------- + oemol : openeye.oechem.OEMol + An OpenEye molecule + positions : simtk.unit.Quantity with shape [nparticles,3], optional, default=None + Positions to use in constructing OEMol. + If virtual sites are present in the Topology, these indices will be skipped. + + NOTE: This comes from https://github.com/oess/oeommtools/blob/master/oeommtools/utils.py + + """ + oe_mol = oechem.OEMol() + molecule_atom_to_oe_atom = { + } # Mapping dictionary between Molecule atoms and oe atoms + + # Python set used to identify atoms that are not in protein residues + keep = set(proteinResidues).union(dnaResidues).union(rnaResidues) + + for chain in topology.chains(): + for res in chain.residues(): + # Create an OEResidue + oe_res = oechem.OEResidue() + # Set OEResidue name + oe_res.SetName(res.name) + # If the atom is not a protein atom then set its heteroatom + # flag to True + if res.name not in keep: + oe_res.SetFragmentNumber(chain.index + 1) + oe_res.SetHetAtom(True) + # Set OEResidue Chain ID + oe_res.SetChainID(chain.id) + # res_idx = int(res.id) - chain.index * len(chain._residues) + # Set OEResidue number + oe_res.SetResidueNumber(int(res.id)) + + for openmm_at in res.atoms(): + # Create an OEAtom based on the atomic number + oe_atom = oe_mol.NewAtom(openmm_at.element._atomic_number) + # Set atom name + oe_atom.SetName(openmm_at.name) + # Set Symbol + oe_atom.SetType(openmm_at.element.symbol) + # Set Atom index + oe_res.SetSerialNumber(openmm_at.index + 1) + # Commit the changes + oechem.OEAtomSetResidue(oe_atom, oe_res) + # Update the dictionary OpenMM to OE + openmm_atom_to_oe_atom[openmm_at] = oe_atom + + if self.n_atoms != oe_mol.NumAtoms(): + raise Exception( + "OEMol has an unexpected number of atoms: " + "Molecule has {} atoms, while OEMol has {} atoms".format( + topology.n_atom, oe_mol.NumAtoms())) + + # Create bonds + for off_bond in self.topology_bonds(): + oe_mol.NewBond(oe_atoms[bond.atom1], oe_atoms[bond.atom2], + bond.bond_order) + if off_bond.type: + if off_bond.type == 'Aromatic': + oe_atom0.SetAromatic(True) + oe_atom1.SetAromatic(True) + oe_bond.SetAromatic(True) + oe_bond.SetType("Aromatic") + elif off_bond.type in ["Single", "Double", "Triple", "Amide"]: + oe_bond.SetType(omm_bond.type) + else: + oe_bond.SetType("") + + if self.n_bonds != oe_mol.NumBonds(): + oechem.OEThrow.Erorr( + "OEMol has an unexpected number of bonds:: " + "Molecule has {} bonds, while OEMol has {} bonds".format( + self.n_bond, oe_mol.NumBonds())) + + if positions is not None: + # Set the OEMol positions + particle_indices = [ + atom.particle_index for atom in self.topology_atoms + ] # get particle indices + pos = positions[particle_indices].value_in_units_of(unit.angstrom) + pos = list(itertools.chain.from_iterable(pos)) + oe_mol.SetCoords(pos) + oechem.OESetDimensionFromCoords(oe_mol) + + return oe_mol + + def get_bond_between(self, i, j): + """Returns the bond between two atoms + + Parameters + ---------- + i, j : int or TopologyAtom + Atoms or atom indices to check + + Returns + ------- + bond : TopologyBond + The bond between i and j. + + """ + if (type(i) is int) and (type(j) is int): + atomi = self.atom(i) + atomj = self.atom(j) + elif (type(i) is TopologyAtom) and (type(j) is TopologyAtom): + atomi = i + atomj = j + else: + raise Exception( + "Invalid input passed to is_bonded(). Expected ints or TopologyAtoms, " + "got {} and {}".format(i, j)) + + for top_bond in atomi.topology_bonds: + for top_atom in top_bond.atoms: + if top_atom == atomi: + continue + if top_atom == atomj: + return top_bond + + raise NotBondedError('No bond between atom {} and {}'.format(i, j)) + + + def is_bonded(self, i, j): + """Returns True if the two atoms are bonded + + Parameters + ---------- + i, j : int or TopologyAtom + Atoms or atom indices to check + + Returns + ------- + is_bonded : bool + True if atoms are bonded, False otherwise. + + """ + try: + self.get_bond_between(i, j) + return True + except NotBondedError: + return False + + def atom(self, atom_topology_index): + """ + Get the TopologyAtom at a given Topology atom index. + + Parameters + ---------- + atom_topology_index : int + The index of the TopologyAtom in this Topology + + Returns + ------- + An openforcefield.topology.TopologyAtom + """ + assert type(atom_topology_index) is int + assert 0 <= atom_topology_index < self.n_topology_atoms + this_molecule_start_index = 0 + next_molecule_start_index = 0 + for topology_molecule in self._topology_molecules: + next_molecule_start_index += topology_molecule.n_atoms + if next_molecule_start_index > atom_topology_index: + atom_molecule_index = atom_topology_index - this_molecule_start_index + # NOTE: the index here should still be in the topology index order, NOT the reference molecule's + return topology_molecule.atom(atom_molecule_index) + this_molecule_start_index += topology_molecule.n_atoms + + # Potentially more computationally efficient lookup ( O(largest_molecule_natoms)? ) + # start_index_2_top_mol is an ordered dict of [starting_atom_index] --> [topology_molecule] + # search_range = range(atom_topology_index - largest_molecule_natoms, atom_topology_index) + # search_index = atom_topology_index + # while not(search_index in start_index_2_top_mol.keys()): # Only efficient if start_index_2_top_mol.keys() is a set (constant time lookups) + # search_index -= 1 + # topology_molecule = start_index_2_top_mol(search_index) + # atom_molecule_index = atom_topology_index - search_index + # return topology_molecule.atom(atom_molecule_index) + + def virtual_site(self, vsite_topology_index): + """ + Get the TopologyAtom at a given Topology atom index. + + Parameters + ---------- + vsite_topology_index : int + The index of the TopologyVirtualSite in this Topology + + Returns + ------- + An openforcefield.topology.TopologyVirtualSite + + """ + assert type(vsite_topology_index) is int + assert 0 <= vsite_topology_index < self.n_topology_virtual_sites + this_molecule_start_index = 0 + next_molecule_start_index = 0 + for topology_molecule in self._topology_molecules: + next_molecule_start_index += topology_molecule.n_virtual_sites + if next_molecule_start_index > vsite_topology_index: + vsite_molecule_index = vsite_topology_index - this_molecule_start_index + return topology_molecule.virtual_site(vsite_molecule_index) + this_molecule_start_index += topology_molecule.n_virtual_sites + + def bond(self, bond_topology_index): + """ + Get the TopologyBond at a given Topology bond index. + + Parameters + ---------- + bond_topology_index : int + The index of the TopologyBond in this Topology + + Returns + ------- + An openforcefield.topology.TopologyBond + """ + assert type(bond_topology_index) is int + assert 0 <= bond_topology_index < self.n_topology_bonds + this_molecule_start_index = 0 + next_molecule_start_index = 0 + for topology_molecule in self._topology_molecules: + next_molecule_start_index += topology_molecule.n_bonds + if next_molecule_start_index > bond_topology_index: + bond_molecule_index = bond_topology_index - this_molecule_start_index + return topology_molecule.bond(bond_molecule_index) + this_molecule_start_index += topology_molecule.n_bonds + + def add_particle(self, particle): + """Add a Particle to the Topology. + + Parameters + ---------- + particle : Particle + The Particle to be added. + The Topology will take ownership of the Particle. + + """ + pass + + def add_molecule(self, molecule, local_topology_to_reference_index=None): + """Add a Molecule to the Topology. + + Parameters + ---------- + molecule : Molecule + The Molecule to be added. + local_topology_to_reference_index: dict, optional, default = None + Dictionary of {TopologyMolecule_atom_index : Molecule_atom_index} for the TopologyMolecule that will be built + + Returns + ------- + index : int + The index of this molecule in the topology + """ + from openforcefield.topology.molecule import FrozenMolecule + #molecule.set_aromaticity_model(self._aromaticity_model) + + mol_smiles = molecule.to_smiles() + reference_molecule = None + for potential_ref_mol in self._reference_molecule_to_topology_molecules.keys( + ): + if mol_smiles == potential_ref_mol.to_smiles(): + # If the molecule is already in the Topology.reference_molecules, add another reference to it in + # Topology.molecules + reference_molecule = potential_ref_mol + break + if reference_molecule is None: + # If it's a new unique molecule, make and store an immutable copy of it + reference_molecule = FrozenMolecule(molecule) + self._reference_molecule_to_topology_molecules[ + reference_molecule] = list() + + topology_molecule = TopologyMolecule( + reference_molecule, self, local_topology_to_reference_index) + self._topology_molecules.append(topology_molecule) + self._reference_molecule_to_topology_molecules[ + reference_molecule].append(self._topology_molecules[-1]) + + index = len(self._topology_molecules) - 1 + return index + + def add_constraint(self, iatom, jatom, distance=True): + """ + Mark a pair of atoms as constrained. + + Constraints between atoms that are not bonded (e.g., rigid waters) are permissible. + + Parameters + ---------- + iatom, jatom : Atom + Atoms to mark as constrained + These atoms may be bonded or not in the Topology + distance : simtk.unit.Quantity, optional, default=True + Constraint distance + ``True`` if distance has yet to be determined + ``False`` if constraint is to be removed + + """ + # Check that constraint hasn't already been specified. + if (iatom, jatom) in self._constrained_atom_pairs: + existing_distance = self._constrained_atom_pairs[(iatom, jatom)] + if unit.is_quantity(existing_distance) and (distance is True): + raise Exception( + 'Atoms (%d,%d) already constrained with distance %s but attempting to override with unspecified distance' + % (iatom, jatom, existing_distance)) + if (existing_distance is True) and (distance is True): + raise Exception( + 'Atoms (%d,%d) already constrained with unspecified distance but attempting to override with unspecified distance' + % (iatom, jatom)) + if distance is False: + del self._constrained_atom_pairs[(iatom, jatom)] + del self._constrained_atom_pairs[(jatom, iatom)] + return + + self._constrained_atom_pairs[(iatom, jatom)] = distance + self._constrained_atom_pairs[(jatom, iatom)] = distance + + def is_constrained(self, iatom, jatom): + """ + Check if a pair of atoms are marked as constrained. + + Parameters + ---------- + iatom, jatom : int + Indices of atoms to mark as constrained. + + Returns + ------- + distance : simtk.unit.Quantity or bool + True if constrained but constraints have not yet been applied + Distance if constraint has already been added to System + + """ + if (iatom, jatom) in self._constrained_atom_pairs: + return self._constrained_atom_pairs[(iatom, jatom)] + else: + return False + + def get_fractional_bond_order(self, iatom, jatom): + """ + Retrieve the fractional bond order for a bond. + + An Exception is raised if it cannot be determined. + + Parameters + ---------- + iatom, jatom : Atom + Atoms for which a fractional bond order is to be retrieved. + + Returns + ------- + order : float + Fractional bond order between the two specified atoms. + + """ + # TODO: Look up fractional bond order in corresponding list of unique molecules, + # computing it lazily if needed. + + pass + diff --git a/openforcefield/typing/chemistry/environment.py b/openforcefield/typing/chemistry/environment.py index 9b28422af..745d8d5b0 100644 --- a/openforcefield/typing/chemistry/environment.py +++ b/openforcefield/typing/chemistry/environment.py @@ -7,6 +7,8 @@ """ environment.py +.. warning :: This file is will be updated to comply with PEP8. + Classes defining a chemical environment for atoms and how they are connected using networkx graph objects to organize and make changes to the structure. Output will be in the form of SMARTS and SMIRKS. @@ -19,19 +21,19 @@ """ -# QUESTION: should we ditch camelCase and go with PEP8 standard snake_case? - #============================================================================== # GLOBAL IMPORTS #============================================================================== -import networkx as nx import re import copy -import numpy as np +import networkx as nx from numpy import random +import openforcefield.utils + + #============================================================================== # Functions #============================================================================== @@ -82,11 +84,11 @@ def _convert_embedded_SMIRKS(smirks): a_out = 0 while smirks.find('$(') != -1: # Find first atom - atom, a_in, a_out = _find_embedded_brackets(smirks, '\[', '\]') + atom, a_in, a_out = _find_embedded_brackets(smirks, r'\[', r'\]') d = atom.find('$(') # Find atom with the $ string embedded while d == -1: - atom, temp_in, temp_out = _find_embedded_brackets(smirks[a_out+1:], '\[', '\]') + atom, temp_in, temp_out = _find_embedded_brackets(smirks[a_out+1:], r'\[', r'\]') a_in = a_out + temp_in + 1 a_out += temp_out + 1 d = atom.find('$(') @@ -104,11 +106,11 @@ def _convert_embedded_SMIRKS(smirks): else: ring_out = '' - embedded, p_in, p_out = _find_embedded_brackets(atom, '\(', '\)') + embedded, p_in, p_out = _find_embedded_brackets(atom, r'\(', r'\)') # two forms of embedded strings $(*~stuff) or $([..]~stuff) # in the latter case the first atom refers the current atom if embedded[1] == '[': - first, f_in, f_out = _find_embedded_brackets(embedded, '\[','\]') + first, f_in, f_out = _find_embedded_brackets(embedded, r'\[', r'\]') first = _convert_embedded_SMIRKS(first) new_atom = atom[:d]+first[1:-1]+atom[p_out+1:] embedded = embedded[f_out+1:] @@ -155,25 +157,26 @@ def _remove_blanks_repeats(init_list, remove_list = ['']): return list( set(final_list) ) -class SMIRKSMismatchError(Exception): +class SMIRKSMismatchError(openforcefield.utils.MessageException): """ Exception for cases where smirks are inappropriate for the environment type they are being parsed into """ - def __init__(self, msg): - super(SMIRKSMismatchError, self).__init__(self,msg) - self.msg = msg + pass + -class SMIRKSParsingError(Exception): +class SMIRKSParsingError(openforcefield.utils.MessageException): """ Exception for when SMIRKS are not parseable for any environment """ - def __init__(self, msg): - super(SMIRKSParsingError, self).__init__(self, msg) - self.msg = msg + pass + class ChemicalEnvironment(object): """Chemical environment abstract base class that matches an atom, bond, angle, etc. + + .. warning :: This class is largely redundant with the same one in the Chemper package, and will likely be removed. + """ class Atom(object): """Atom representation, which may have some ORtypes and ANDtypes properties. @@ -270,7 +273,7 @@ def asSMIRKS(self): # Add label to the end of SMARTS else: - sub_string, start, end = _find_embedded_brackets(smirks, '\[','\]') + sub_string, start, end = _find_embedded_brackets(smirks, r'\[', r'\]') if self.ring is not None: return sub_string[:-1] + ':' + str(self.index) + ']'+str(self.ring) else: @@ -281,7 +284,7 @@ def addORtype(self, ORbase, ORdecorators): Adds ORtype to the set for this atom. Parameters - -------- + ---------- ORbase: string, such as '#6' ORdecorators: list of strings, such as ['X4','+0'] """ @@ -293,7 +296,7 @@ def addANDtype(self, ANDtype): Adds ANDtype to the set for this atom. Parameters - -------- + ---------- ANDtype: string added to the list of ANDtypes for this atom """ @@ -376,7 +379,7 @@ def asSMARTS(self): """Return the atom representation as SMARTS. Returns - -------- + ------- smarts : str The SMARTS string for just this atom """ @@ -396,7 +399,7 @@ def asSMARTS(self): def asSMIRKS(self): """ Returns - -------- + ------- smarts : str The SMIRKS string for just this bond """ @@ -421,6 +424,27 @@ def getOrder(self): orderList = [orderDict[base] for (base, decor) in self.ORtypes] return min(orderList) + @staticmethod + def validate(smirks, ensure_valence_type=None, toolkit='openeye'): + """Validate the provided SMIRKS string is valid, and if requested, tags atoms appropriate to the specified valence type. + + Parameters + ---------- + smirks : str + The SMIRKS expression to validate + ensure_valence_type : str, optional, default=None + If specified, ensure the tagged atoms are appropriate to the specified valence type + + This method will raise a :class:`SMIRKSParsingError` if the provided SMIRKS string is not valid. + + """ + chemenv = ChemicalEnvironment(smirks, toolkit=toolkit) + + if ensure_valence_type: + valence_type = chemenv.getType() + if valence_type != ensure_valence_type: + raise SMIRKSParsingError("Tagged atoms in SMARTS string '%s' specifies valence type '%s', expected '%s'." % (smirks, valence_type, ensure_valence_type)) + def __init__(self, smirks = None, label = None, replacements = None, toolkit='openeye'): """Initialize a chemical environment abstract base class. @@ -433,39 +457,33 @@ def __init__(self, smirks = None, label = None, replacements = None, toolkit='op replacements = list of lists, optional, [substitution, smarts] form for parsing SMIRKS """ - if toolkit.lower() == 'openeye': - try: - from openeye import oechem - self.toolkit = 'openeye' - except: - raise Exception("Could not import openeye.oechem") - elif toolkit.lower() == 'rdkit': - try: - from rdkit import Chem - self.toolkit = 'rdkit' - except: - raise Exception("Could not import rdkit.Chem") + # TODO: Refactor all this class to use the ToolkitRegistry API. + if toolkit.lower() == 'openeye' and openforcefield.utils.OpenEyeToolkitWrapper.is_available(): + self.toolkit = 'openeye' + elif toolkit.lower() == 'rdkit' and openforcefield.utils.RDKitToolkitWrapper.is_available(): + self.toolkit = 'rdkit' else: - raise Exception("Toolkit %s was not recognized, please use openeye or rdkit" % toolkit) + raise ValueError("Could not find toolkit {}, please use/install " + "openeye or rdkit.".format(toolkit)) # Define the regular expressions used for all SMIRKS decorators # There are a limited number of descriptors for smirks string they are: # That is a # followed by one or more ints w/or w/o at ! in front '!#16' - element_num = "!?[#]\d+" + element_num = r"!?[#]\d+" # covers element symbols, i.e. N,C,O,Br not followed by a number element_sym = "!?[A-Z][a-z]?" # covers element symbols that are aromatic: aro_sym = "!?[cnops]" # replacement strings - replace_str = "\$\w+" + replace_str = r"\$\w+" # a or A w/ or w/o a ! in front 'A' aro_ali = "!?[aA]" # the decorators (D,H,j,r,V,X,^) followed by one or more integers - needs_int = "!?[DHjrVX^]\d+" + needs_int = r"!?[DHjrVX^]\d+" # R(x), +, - do not need to be followed by a integer w/ or w/o a ! 'R2' - optional_int = "!?[Rx+-]\d*" + optional_int = r"!?[Rx+-]\d*" # chirality options, "@", "@@", "@int" w/ or w/o a ! in front - chirality = "!?[@]\d+|!?[@]@?" + chirality = r"!?[@]\d+|!?[@]@?" # Generate RegEx string for decorators: self.no_bracket_atom_reg = r'('+'|'.join([element_sym, aro_sym, replace_str])+')' @@ -553,7 +571,7 @@ def _graph_get_edge_data(self, node1, node2): """ return self._graph.get_edge_data(node1, node2) - def isValid(self, smirks = None): + def isValid(self, smirks=None): """ Returns if the environment is valid, that is if it creates a parseable SMIRKS string. @@ -598,7 +616,7 @@ def _parse_smirks(self,input_smirks): store = list() # to store indices while branching bondingTo = idx # which atom are we going to bond to - atom_string, start, end = _find_embedded_brackets(smirks, '\[', '\]') + atom_string, start, end = _find_embedded_brackets(smirks, r'\[', r'\]') if start != 0: # first atom is not in square brackets if start != -1: @@ -650,7 +668,7 @@ def _parse_smirks(self,input_smirks): continue # find beginning and end of next [atom] - atom_string, start, end = _find_embedded_brackets(leftover, '\[', '\]') + atom_string, start, end = _find_embedded_brackets(leftover, r'\[', r'\]') if start != -1: # no more square brackets bond_string = leftover[:start] @@ -791,7 +809,7 @@ def _asSMIRKS(self, initialAtom = None, neighbors = None, smarts = False): """Return a SMIRKS representation of the chemical environment. Parameters - ----------- + ---------- initalAtom = optional, atom object This is randomly selected if not chosen. neighbors = optional, list of atom objects @@ -885,7 +903,7 @@ def getComponentList(self, component_type, descriptor = None): Returns a list of atoms or bonds matching the descriptor Parameters - ----------- + ---------- component_type: string: 'atom' or 'bond' descriptor: string, optional 'all', 'Indexed', 'Unindexed', 'Alpha', 'Beta' @@ -941,7 +959,7 @@ def selectBond(self, descriptor = None): 'Beta' - returns a random beta bond Returns - -------- + ------- a single Bond object fitting the description or None if no such atom exists """ @@ -1469,4 +1487,4 @@ def __init__(self, smirks = "[*:1]~[*:2](~[*:3])~[*:4]", label = None, replaceme self.bond3 = self._graph_get_edge_data(self.atom2, self.atom4)['bond'] def _checkType(self): - return (self.getType() == 'ImproperTorsion'), 'ImproperTorsion' + return (self.getType() == 'Improper'), 'Improper' diff --git a/openforcefield/typing/engines/smirnoff/__init__.py b/openforcefield/typing/engines/smirnoff/__init__.py index f06059159..dfb6e3a94 100644 --- a/openforcefield/typing/engines/smirnoff/__init__.py +++ b/openforcefield/typing/engines/smirnoff/__init__.py @@ -1,5 +1,6 @@ # The SMIRks Native Open Force Field (SMIRNOFF) -from openforcefield.typing.engines.smirnoff.forcefield import * -from openforcefield.typing.engines.smirnoff.forcefield_utils import * -from openforcefield.typing.engines.smirnoff.gbsaforces import * +from .forcefield import * +from .io import * +from .parameters import * +from .gbsaforces import * diff --git a/openforcefield/typing/engines/smirnoff/forcefield.py b/openforcefield/typing/engines/smirnoff/forcefield.py index fd1396e94..a0c38ea83 100644 --- a/openforcefield/typing/engines/smirnoff/forcefield.py +++ b/openforcefield/typing/engines/smirnoff/forcefield.py @@ -3,2390 +3,936 @@ #============================================================================================= # MODULE DOCSTRING #============================================================================================= - """ -forcefield.py - -OpenMM ForceField replacement using SMIRKS-based matching. +Parameter assignment tools for the SMIRNOFF (SMIRKS Native Open Force Field) format. -AUTHORS +.. codeauthor:: John D. Chodera +.. codeauthor:: David L. Mobley +.. codeauthor:: Peter K. Eastman -John D. Chodera -David L. Mobley +.. todo :: -Baseed on simtk.openmm.app.forcefield written by Peter Eastman. + * Speed up overall import time by putting non-global imports only where they are needed -TODO: -* Constraint handling -* Move utility functions like 'generateTopologyFromOEMol()' elsewhere? -* Use xml parser with 'sourceline' node attributes to aid debugging -http://stackoverflow.com/questions/6949395/is-there-a-way-to-get-a-line-number-from-an-elementtree-element """ + #============================================================================================= # GLOBAL IMPORTS #============================================================================================= -import ast -import operator as op -import collections -import sys -import string - -import lxml.etree as etree -from simtk.openmm.app import element as elem -from simtk.openmm.app import Topology -from openforcefield.utils import generateTopologyFromOEMol, get_data_filename - -import os -import math import copy -import re -import numpy -import random - -import openeye.oechem -import openeye.oeomega -import openeye.oequacpac +import logging +import os -from openeye import oechem, oequacpac +from collections import OrderedDict -from openforcefield.typing.chemistry import ChemicalEnvironment, SMIRKSParsingError from simtk import openmm, unit -import time - -import networkx - -import itertools +from openforcefield.utils import all_subclasses, MessageException +from openforcefield.topology import DEFAULT_AROMATICITY_MODEL +from openforcefield.typing.engines.smirnoff.parameters import ParameterList, ParameterHandler +from openforcefield.typing.engines.smirnoff.io import ParameterIOHandler #============================================================================================= -# PRIVATE SUBROUTINES +# CONFIGURE LOGGER #============================================================================================= -def getSMIRKSMatches_OEMol(oemol, smirks, aromaticity_model = None): - """Find all sets of atoms in the provided oemol that match the provided SMIRKS strings. - - Parameters - ---------- - oemol : OpenEye oemol - oemol to process with the SMIRKS in order to find matches - smirks : str - SMIRKS string with tagged atoms. - If there are N tagged atoms numbered 1..N, the resulting matches will be N-tuples of atoms that match the corresponding tagged atoms. - aromaticity_model : str (optional) - OpenEye aromaticity model designation as a string, such as "OEAroModel_MDL". Default: None. If none is provided, molecule is processed exactly as provided; otherwise it is prepared with this aromaticity model prior to querying. - - Returns - ------- - matches : list of tuples of atoms numbers - matches[index] is an N-tuple of atom numbers from the oemol - Matches are returned in no guaranteed order. - """ - - # Make a copy of molecule so we don't influence original (probably safer than deepcopy per C Bayly) - mol = oechem.OEMol(oemol) - - # Set up query. - qmol = oechem.OEQMol() - if not oechem.OEParseSmarts(qmol, smirks): - raise Exception("Error parsing SMIRKS '%s'" % smirks) - - # Determine aromaticity model - if aromaticity_model: - if type(aromaticity_model) == str: - # Check if the user has provided a manually-specified aromaticity_model - if hasattr(oechem, aromaticity_model): - oearomodel = getattr(oechem, aromaticity_model) - else: - raise ValueError("Error: provided aromaticity model not recognized by oechem.") - else: - raise ValueError("Error: provided aromaticity model must be a string.") - - # If aromaticity model was provided, prepare molecule - oechem.OEClearAromaticFlags( mol) - oechem.OEAssignAromaticFlags( mol, oearomodel) - # avoid running OEPrepareSearch or we lose desired aromaticity, so instead: - oechem.OEAssignHybridization( mol) - - # Perform matching on each mol - matches = list() - - # We require non-unique matches, i.e. all matches - unique = False - ss = oechem.OESubSearch(qmol) - matches = [] - for match in ss.Match( mol, unique): - # Compile list of atom indices that match the pattern tags - atom_indices = dict() - for ma in match.GetAtoms(): - if ma.pattern.GetMapIdx() != 0: - atom_indices[ma.pattern.GetMapIdx()-1] = ma.target.GetIdx() - # Compress into list - atom_indices = [ atom_indices[index] for index in range(len(atom_indices)) ] - # Store - matches.append( tuple(atom_indices) ) - - return matches +logger = logging.getLogger(__name__) #============================================================================================= -# Augmented Topology +# PRIVATE METHODS #============================================================================================= -def generateGraphFromTopology(topology): - """Geneate a NetworkX graph from a Topology object. - - Parameters - ---------- - topology : simtk.openmm.app.Topology - The source topology. +# TODO: Instead of having a global version number, alow each Force to have a separate version number +MAX_SUPPORTED_VERSION = '1.0' # maximum version of the SMIRNOFF spec supported by this SMIRNOFF forcefield - Returns - ------- - graph : networkx.Graph - The resulting graph, with nodes labeled with atom indices and elements +class ParameterHandlerRegistrationError(MessageException): """ - import networkx as nx - # Create graph of atoms connected by bonds. - G = nx.Graph() - for atom in topology.atoms(): - G.add_node(atom.index, element=atom.element) - for (atom1, atom2) in topology.bonds(): - G.add_edge(atom1.index, atom2.index) - - return G - -class _Topology(Topology): - """Augmented Topology object which adds: - - self._reference_molecules is a list of OEMol for the reference molecules - self._reference_to_topology_atom_mappings[reference_molecule] is a list of dicts, where each dict maps the atom indices of atoms in the reference molecule onto an equivalent atom index for a topology atom. - self._bondorders is a list of floating point bond orders for the bonds in the Topology. - self._bondorders_by_atomindices is a dict of floating point bond orders for the bonds in the Topology, keyed by indices of the atoms involved. - - Assumes class is immutable. - + Exception for errors in ParameterHandler registration """ - def __init__(self, topology, reference_molecules): - """ - Parameters - ---------- - topology : simtk.openmm.app.Topology - The Topology object to initialize this one from. - reference_molecules : list of openeye.oechem.OEMol - The list of reference molecules in the Topology. + pass - """ - # Initialize. - super(_Topology, self).__init__() - - # TODO: Find a way to avoid having this be fragile based on internal representation of Topology. - # TODO: Should this also use a deepcopy of 'topology' first? - self._chains = topology._chains - self._numResidues = topology._numResidues - self._numAtoms = topology._numAtoms - self._bonds = topology._bonds - self._periodicBoxVectors = topology._periodicBoxVectors - - # Store reference molecules. - # TODO: Deep copy? - self._reference_molecules = reference_molecules +class SMIRNOFFVersionError(MessageException): + """ + Exception thrown when an incompatible SMIRNOFF version data structure in attempted to be read. + """ + pass - # Identify all molecules and atom mappings. - self._identifyMolecules() +class SMIRNOFFAromaticityError(MessageException): + """ + Exception thrown when an incompatible SMIRNOFF aromaticity model is checked for compatibility. + """ + pass - # Get/initialize bond orders - self._updateBondOrders() +class ParseError(MessageException): + """ + Error for when a SMIRNOFF data structure is not parseable by a ForceField + """ + pass - # Track constraints - self._constrainedAtomPairs = dict() - def constrainAtomPair(self, iatom, jatom, distance=True): - """ - Mark a pair of atoms as constrained. - Parameters - ---------- - iatom, jatom : int - Indices of atoms to mark as constrained. - distance : simtk.unit.Quantity, optional, default=True - Constraint distance if constraint has been applied, - or True if no constraint has yet been applied - """ - # Check that constraint hasn't already been specified. - if (iatom,jatom) in self._constrainedAtomPairs: - existing_distance = self._constrainedAtomPairs[(iatom,jatom)] - if unit.is_quantity(existing_distance) and (distance is True): - raise Exception('Atoms (%d,%d) already constrained with distance %s but attempting to override with unspecified distance' % (iatom, jatom, existing_distance)) - if (existing_distance is True) and (distance is True): - raise Exception('Atoms (%d,%d) already constrained with unspecified distance but attempting to override with unspecified distance' % (iatom, jatom)) - - self._constrainedAtomPairs[(iatom,jatom)] = distance - self._constrainedAtomPairs[(jatom,iatom)] = distance - - def atomPairIsConstrained(self, iatom, jatom): - """ - Check if a pair of atoms are marked as constrained. - Parameters - ---------- - iatom, jatom : int - Indices of atoms to mark as constrained. +#============================================================================================= +# FORCEFIELD +#============================================================================================= - Returns - ------- - distance : simtk.unit.Quantity or bool - True if constrained but constraints have not yet been applied - Distance if constraint has already been added to System +# QUESTION: How should we document private object fields? - """ - if (iatom,jatom) in self._constrainedAtomPairs: - return self._constrainedAtomPairs[(iatom,jatom)] - else: - return False +# TODO: How do we serialize/deserialize `ForceField`'s object model? Can we rely on pickle? - def angles(self): - """ - Get an iterator over all i-j-k angles. - """ - if not hasattr(self, '_angles'): - self._construct_bonded_atoms_list() - self._angles = set() - for atom1 in self._atoms: - for atom2 in self._bondedAtoms[atom1]: - for atom3 in self._bondedAtoms[atom2]: - if atom1 == atom3: - continue - if atom1.index < atom3.index: - self._angles.add( (atom1, atom2, atom3) ) - else: - self._angles.add( (atom3, atom2, atom1) ) - - return iter(self._angles) - - def torsions(self): - """ - Get an iterator over all i-j-k-l torsions. - Note that i-j-k-i torsions are excluded. - """ - if not hasattr(self, '_torsions'): - self._construct_bonded_atoms_list() - - self._torsions = set() - for atom1 in self._atoms: - for atom2 in self._bondedAtoms[atom1]: - for atom3 in self._bondedAtoms[atom2]: - if atom1 == atom3: - continue - for atom4 in self._bondedAtoms[atom3]: - if atom4 == atom2: - continue - # Exclude i-j-k-i - if atom1 == atom4: - continue - if atom1.index < atom4.index: - self._torsions.add( (atom1, atom2, atom3, atom4) ) - else: - self._torsions.add( (atom4, atom3, atom2, atom1) ) - - return iter(self._torsions) - - def _construct_bonded_atoms_list(self): - """ - Construct list of all atoms each atom is bonded to. - """ - if not hasattr(self, '_bondedAtoms'): - self._atoms = [ atom for atom in self.atoms() ] - self._bondedAtoms = dict() - for atom in self._atoms: - self._bondedAtoms[atom] = set() - for bond in self._bonds: - self._bondedAtoms[bond[0]].add(bond[1]) - self._bondedAtoms[bond[1]].add(bond[0]) - - def _isBonded(self, atom_index_1, atom_index_2): - """Return True if atoms are bonded, False if not. - Parameters - ---------- - atom_index_1 : int - atom_index_2 : int - Atom indices +class ForceField(object): + """A factory that assigns SMIRNOFF parameters to a molecular system - Returns - ------- - is_bonded : bool - True if atoms are bonded, False otherwise + :class:`ForceField` is a factory that constructs an OpenMM :class:`simtk.openmm.System` object from a + :class:`openforcefield.topology.Topology` object defining a (bio)molecular system containing one or more molecules. - TODO - ---- - This assumes _Topology is immutable. - """ - self._construct_bonded_atoms_list() - atom1 = self._atoms[atom_index_1] - atom2 = self._atoms[atom_index_2] - return atom2 in self._bondedAtoms[atom1] + When a :class:`ForceField` object is created from one or more specified SMIRNOFF serialized representations, + all :class:`ParameterHandler` subclasses currently imported are identified and registered to handle different + sections of the SMIRNOFF force field definition file(s). - def _identifyMolecules(self): - """Identify all unique reference molecules and atom mappings to all instances in the Topology. - """ - import networkx as nx - from networkx.algorithms import isomorphism - - # Generate list of topology atoms. - atoms = [ atom for atom in self.atoms() ] - - # Generate graphs for reference molecules. - self._reference_molecule_graphs = list() - for reference_molecule in self._reference_molecules: - # Generate Topology - reference_molecule_topology = generateTopologyFromOEMol(reference_molecule) - # Generate Graph - reference_molecule_graph = generateGraphFromTopology(reference_molecule_topology) - self._reference_molecule_graphs.append(reference_molecule_graph) - - # Generate a graph for the current topology. - G = generateGraphFromTopology(self) - - # Extract molecules (as connected component subgraphs). - self._reference_to_topology_atom_mappings = { reference_molecule : list() for reference_molecule in self._reference_molecules } - for molecule_graph in nx.connected_component_subgraphs(G): - # Check if we have already stored a reference molecule for this molecule. - reference_molecule_exists = False - for (reference_molecule_graph, reference_molecule) in zip(self._reference_molecule_graphs, self._reference_molecules): - GM = isomorphism.GraphMatcher(molecule_graph, reference_molecule_graph) - if GM.is_isomorphic(): - # This molecule is present in the list of unique reference molecules. - reference_molecule_exists = True - # Add the reference atom mappings. - reference_to_topology_atom_mapping = dict() - for (topology_atom, reference_atom) in GM.mapping.items(): - reference_to_topology_atom_mapping[reference_atom] = topology_atom - self._reference_to_topology_atom_mappings[reference_molecule].append(reference_to_topology_atom_mapping) - # Break out of the search loop. - break + All :class:`ParameterIOHandler` subclasses currently imported are identified and registered to handle different + serialization formats (such as XML). - # If the reference molecule could not be found, throw an exception. - if not reference_molecule_exists: - msg = 'No provided molecule matches topology molecule:\n' - for index in sorted(list(molecule_graph)): - msg += 'Atom %8d %5s %5d %3s\n' % (atoms[index].index, atoms[index].name, atoms[index].residue.index, atoms[index].residue.name) - raise Exception(msg) + The force field definition is processed by these handlers to populate the ``ForceField`` object model data + structures that can easily be manipulated via the API: - def _updateBondOrders(self, Wiberg = False): - """Update and store list of bond orders for the molecules in this Topology. Can be used for initialization of bondorders list, or for updating bond orders in the list. + Processing a :class:`Topology` object defining a chemical system will then call all :class`ParameterHandler` + objects in an order guaranteed to satisfy the declared processing order constraints of each + :class`ParameterHandler`. - Parameters: - ---------- - Wiberg : bool (optional) - Default False. If False, uses bond orders OEChem assigns to bonds on the molecule. If True, instead uses Wiberg bond orders stored on bonds in the molecule. These must already be present, i.e. from assignPartialCharges with an AM1 method. + Attributes + ---------- + parameters : dict of str : list of ParameterType + ``parameters[tagname]`` is the instantiated :class:`ParameterHandler` class that handles parameters associated + with the force ``tagname``. + This is the primary means of retrieving and modifying parameters, such as + ``parameters['vdW'][0].sigma *= 1.1`` + parameter_object_handlers : dict of str : ParameterHandler class + Registered list of :class:`ParameterHandler` classes that will handle different forcefield tags to create the parameter object model. + ``parameter_object_handlers[tagname]`` is the :class:`ParameterHandler` that will be instantiated to process the force field definition section ``tagname``. + :class:`ParameterHandler` classes are registered when the ForceField object is created, but can be manipulated afterwards. + parameter_io_handlers : dict of str : ParameterIOHandler class + Registered list of :class:`ParameterIOHandler` classes that will handle serializing/deserializing the parameter object model to string or file representations, such as XML. + ``parameter_io_handlers[iotype]`` is the :class:`ParameterHandler` that will be instantiated to process the serialization scheme ``iotype``. + :class:`ParameterIOHandler` classes are registered when the ForceField object is created, but can be manipulated afterwards. - """ - # Initialize - self._bondorders=list() - self._bondorders_by_atomindices = {} - # Loop over reference molecules and pull bond orders - - for mol in self._reference_molecules: - # Pull mappings for this molecule - mappings = self._reference_to_topology_atom_mappings[mol] - # Loop over bonds - for idx,bond in enumerate(mol.GetBonds()): - # Get atom indices involved in bond - at1 = bond.GetBgn().GetIdx() - at2 = bond.GetEnd().GetIdx() - # Get bond order - if not Wiberg: - order = bond.GetOrder() - else: - order = bond.GetData('WibergBondOrder') - # Convert atom numbers to topology atom numbers; there may be multiple matches - for mapping in mappings: - topat1 = None - topat2 = None - for mapatom in mapping: - if mapatom==at1: - topat1 = mapping[mapatom] - elif mapatom==at2: - topat2 = mapping[mapatom] - if topat1==None or topat2==None: - raise ValueError("No mapping found for these topology atoms (indices %s-%s)." % (at1, at2)) - # Store bond order to re-use below and elsewhere; store in both directions - if not topat1 in self._bondorders_by_atomindices: - self._bondorders_by_atomindices[topat1] = {} - if not topat2 in self._bondorders_by_atomindices: - self._bondorders_by_atomindices[topat2] = {} - self._bondorders_by_atomindices[topat2][topat1] = order - self._bondorders_by_atomindices[topat1][topat2] = order - - # Loop over bonds in topology and store orders in the same order - for bond in self._bonds: - # See if we have in the 0-1 order and store - topat1 = bond[0].index - topat2 = bond[1].index - order = self._bondorders_by_atomindices[topat1][topat2] - self._bondorders.append(order) - - def unrollSMIRKSMatches(self, smirks, aromaticity_model = None): - """Find all sets of atoms in the topology that match the provided SMIRKS strings. + Examples + -------- - Parameters - ---------- - smirks : str - SMIRKS string with tagged atoms. - If there are N tagged atoms numbered 1..N, the resulting matches will be N-tuples of atoms that match the corresponding tagged atoms. - aromaticity_model : str (optional) - Default None. Aromaticity model used in SMIRKS matching, as per getSMIRKSMatches_OEMol docs. If provided, pre-processes molecule with this model prior to matching. Otherwise, uses provided oemol. + Create a new ForceField containing the smirnoff99Frosst parameter set: - Returns - ------- - matches : list of tuples of Atom - matches[index] is an N-tuple of Atom entries from the topology - Matches are returned in no guaranteed order. + >>> from openforcefield.typing.engines.smirnoff import ForceField + >>> forcefield = ForceField('smirnoff99Frosst.offxml') - """ + Create an OpenMM system from a :class:`openforcefield.topology.Topology` object: - # Perform matching on each unique molecule, unrolling the matches to all matching copies of that molecule in the Topology object. - matches = list() - for reference_molecule in self._reference_molecules: - # Find all atomsets that match this definition in the reference molecule - refmol_matches = getSMIRKSMatches_OEMol( reference_molecule, smirks, aromaticity_model = aromaticity_model) + >>> from openforcefield.topology import Molecule, Topology + >>> ethanol = Molecule.from_smiles('CCO') + >>> topology = Topology.from_molecules(molecules=[ethanol]) + >>> system = forcefield.create_openmm_system(topology) - # Loop over matches - for reference_atom_indices in refmol_matches: - # Unroll corresponding atom indices over all instances of this molecule - for reference_to_topology_atom_mapping in self._reference_to_topology_atom_mappings[reference_molecule]: - # Create match. - atom_indices = tuple([ reference_to_topology_atom_mapping[atom_index] for atom_index in reference_atom_indices ]) - matches.append(atom_indices) + Modify the long-range electrostatics method: - return matches + >>> forcefield.get_handler('Electrostatics').method = 'PME' + Inspect the first few vdW parameters: -#============================================================================================= -# FORCEFIELD -#============================================================================================= + >>> low_precedence_parameters = forcefield.get_handler('vdW').parameters[0:3] -# Enumerated values for nonbonded method + Retrieve the vdW parameters by SMIRKS string and manipulate it: -class NoCutoff(object): - def __repr__(self): - return 'NoCutoff' -NoCutoff = NoCutoff() + >>> parameter = forcefield.get_handler('vdW').parameters['[#1:1]-[#7]'] + >>> parameter.sigma += 0.1 * unit.angstroms + >>> parameter.epsilon *= 1.02 -class CutoffNonPeriodic(object): - def __repr__(self): - return 'CutoffNonPeriodic' -CutoffNonPeriodic = CutoffNonPeriodic() + Make a child vdW type more specific (checking modified SMIRKS for validity): -class CutoffPeriodic(object): - def __repr__(self): - return 'CutoffPeriodic' -CutoffPeriodic = CutoffPeriodic() + >>> forcefield.get_handler('vdW').parameters[-1].smirks += '~[#53]' -class Ewald(object): - def __repr__(self): - return 'Ewald' -Ewald = Ewald() + .. warning :: -class PME(object): - def __repr__(self): - return 'PME' -PME = PME() + While we check whether the modified SMIRKS is still valid and has the appropriate valence type, + we currently don't check whether the typing remains hierarchical, which could result in some types + no longer being assignable because more general types now come *below* them and preferentially match. -# Enumerated values for constraint type + Delete a parameter: -class HBonds(object): - def __repr__(self): - return 'HBonds' -HBonds = HBonds() + >>> del forcefield.get_handler('vdW').parameters['[#1:1]-[#6X4]'] -class AllBonds(object): - def __repr__(self): - return 'AllBonds' -AllBonds = AllBonds() + Insert a parameter at a specific point in the parameter tree: -class HAngles(object): - def __repr__(self): - return 'HAngles' -HAngles = HAngles() + >>> from openforcefield.typing.engines.smirnoff import vdWHandler + >>> new_parameter = vdWHandler.vdWType(smirks='[*:1]', epsilon=0.0157*unit.kilocalories_per_mole, rmin_half=0.6000*unit.angstroms) + >>> forcefield.get_handler('vdW').parameters.insert(0, new_parameter) -# A map of functions to parse elements of the XML file. + .. warning :: -parsers = {} + We currently don't check whether removing a parameter could accidentally remove the root type, so it's possible to no longer type all molecules this way. -class ForceField(object): - """A ForceField constructs OpenMM System objects based on a Topology. """ - def __init__(self, *files): - """Load one or more XML parameter definition files and create a SMIRNOFF ForceField object based on them. + def __init__(self, + *sources, + parameter_handler_classes=None, + parameter_io_handler_classes=None, + disable_version_check=False): + """Create a new :class:`ForceField` object from one or more SMIRNOFF parameter definition files. Parameters ---------- - files : list - A list of XML files defining the SMIRNOFF force field. - Each entry may be an absolute file path, a path relative to the current working directory, a path relative to this module's data subdirectory (for built in force fields), or an open file-like object with a read() method from which the forcefield XML data can be loaded. + sources : string or file-like object or open file handle or URL (or iterable of these) + A list of files defining the SMIRNOFF force field to be loaded + Currently, only `the SMIRNOFF XML format `_ is supported. + Each entry may be an absolute file path, a path relative to the current working directory, a path relative to this module's data subdirectory + (for built in force fields), or an open file-like object with a ``read()`` method from which the forcefield XML data can be loaded. + If multiple files are specified, any top-level tags that are repeated will be merged if they are compatible, + with files appearing later in the sequence resulting in parameters that have higher precedence. + Support for multiple files is primarily intended to allow solvent parameters to be specified by listing them last in the sequence. + parameter_handler_classes : iterable of ParameterHandler classes, optional, default=None + If not None, the specified set of ParameterHandler classes will be instantiated to create the parameter object model + By default, all imported subclasses of ParameterHandler are automatically registered + parameter_io_handler_classes : iterable of ParameterIOHandler classes + If not None, the specified set of ParameterIOHandler classes will be used to parse/generate serialized parameter sets + By default, all imported subclasses of ParameterIOHandler are automatically registered + disable_version_check : bool, optional, default=False + If True, will disable checks against the current highest supported forcefield version. + This option is primarily intended for forcefield development. - """ - self._forces = [] - self.loadFile(files) + Examples + -------- - def loadFile(self, files): - """Load a SMIRNOFF XML file and add the definitions from it to this ForceField. + Load one SMIRNOFF parameter set in XML format (searching the package data directory by default, which includes some standard parameter sets): - Parameters - ---------- - files : string or file or tuple - An XML file or tuple of XML files containing SMIRNOFF force field definitions. - Each entry may be an absolute file path, a path relative to the current working directory, a path relative to this module's data subdirectory (for built in force fields), or an open file-like object with a read() method from which the forcefield XML data can be loaded. - """ + >>> forcefield = ForceField('smirnoff99Frosst.offxml') - # Ensure that we are working with a tuple of files. - if not isinstance(files, tuple): - files = (files,) + Load multiple SMIRNOFF parameter sets: - # Load in all XML trees. - trees = list() - for file in files: - parser = etree.XMLParser(remove_blank_text=True) # For pretty print on write - try: - # this handles either filenames or open file-like objects - tree = etree.parse(file, parser) - except IOError: - temp_file = get_data_filename(file) - tree = etree.parse(temp_file, parser) - except Exception as e: - # Fail with an error message about which file could not be read. - # TODO: Also handle case where fallback to 'data' directory encounters problems, - # but this is much less worrisome because we control those files. - msg = str(e) + '\n' - if hasattr(file, 'name'): - filename = file.name - else: - filename = str(file) - msg += "ForceField.loadFile() encountered an error reading file '%s'\n" % filename - raise Exception(msg) - - trees.append(tree) - - # Retain XML trees internally - self._XMLTrees = trees - # Store whether this has been modified or not; if modified, it will - # trigger re-parsing/loading of XML on system creation - self._XMLModified = False - - # Parse XML, get force definitions - self.parseXMLTrees() - - def parseXMLTrees(self): - """Parse XML trees, load force definitions.""" - - trees = self._XMLTrees - - # We'll be creating all forces again from scratch by re-parsing - self._forces = [] - - # Store forcefield version info and, if present, aromaticity model - root = trees[0].getroot() - # Formerly known as SMIRFF, now SMIRNOFF - if root.tag=='SMIRFF' or root.tag=='SMIRNOFF': - if 'version' in root.attrib: - #TO DO: Should this be a float, a string, or something else? - self.version = float(root.attrib['version']) - else: - self.version = 0.0 - if 'aromaticity_model' in root.attrib: - self._aromaticity_model = root.attrib['aromaticity_model'] - else: - self._aromaticity_model = None - if 'use_fractional_bondorder' in root.attrib: - self._use_fractional_bondorder = root.attrib['use_fractional_bondorder'] == 'True' - else: - self._use_fractional_bondorder = False - else: - raise ValueError("Error: ForceField parses a SMIRNOFF forcefield, but this does not appear to be one as the root tag is %s." % root.tag) - - # Load force definitions - for tree in trees: - root = tree.getroot() - - # Before loading, do some error checking/consistency checking. - # Warn if version number is not consistent - if 'version' in root.attrib: - if float(root.attrib['version']) != self.version: - print("Warning: Inconsistent version number in parsed FFXML files.") - # Throw an exception if aromaticity model is not consistent - if 'aromaticity_model' in root.attrib: - if root.attrib['aromaticity_model'] != self._aromaticity_model: - raise ValueError("Error: Aromaticity model specified in FFXML files is inconsistent.") - - # Now actually load - for child in root: - if child.tag in parsers: - parsers[child.tag](child, self) - - - def getGenerators(self): - """Get the list of all registered generators.""" - return self._forces - - def registerGenerator(self, generator): - """Register a new generator.""" - # Special case: ConstraintGenerator has to come before HarmonicBondGenerator and HarmonicAngleGenerator. - # TODO: Figure out a more general way to allow generators to specify enforced orderings. - if isinstance(generator, ConstraintGenerator): - self._forces.insert(0, generator) - else: - self._forces.append(generator) + forcefield = ForceField('smirnoff99Frosst.offxml', 'tip3p.offxml') - def getParameter(self, smirks = None, paramID=None, force_type='Implied'): - """Get info associated with a particular parameter as specified by SMIRKS or parameter ID, and optionally force term. + Load a parameter set from a string: - Parameters - ---------- - smirks (optional) : str - Default None. If specified, will pull parameters on line containing this `smirks`. - paramID : str - Default None. If specified, will pull parameters on line with this `id` - force_type : str - Default "Implied". Optionally, specify a particular force type such as - "HarmonicBondForce" or "HarmonicAngleForce" etc. to search for a - matching ID or SMIRKS. + >>> offxml = '' + >>> forcefield = ForceField(offxml) + """ + # Clear all object fields + self._initialize() + + # Store initialization options + self.disable_version_check = disable_version_check + # if True, we won't check which SMIRNOFF version number we're parsing + + # Register all ParameterHandler objects that will process SMIRNOFF force definitions + # TODO: We need to change this to just find all ParameterHandler objects in this file; + # otherwise, we can't define two different ParameterHandler subclasses to compare for a new type of energy term + # since both will try to register themselves for the same XML tag and an Exception will be raised. + if parameter_handler_classes is None: + parameter_handlers = all_subclasses(ParameterHandler) + self._register_parameter_handler_classes(parameter_handlers) + + # Register all ParameterIOHandler objects that will process serialized parameter representations + if parameter_io_handler_classes is None: + parameter_io_handler_classes = all_subclasses(ParameterIOHandler) + self._register_parameter_io_handler_classes( + parameter_io_handler_classes) + + # Parse all sources containing SMIRNOFF parameter definitions + self.parse_sources(sources) + + def _initialize(self): + """ + Initialize all object fields. + """ + self._MAX_SUPPORTED_SMIRNOFF_VERSION = 0.2 + self._disable_version_check = False # if True, will disable checking compatibility version + self._aromaticity_model = DEFAULT_AROMATICITY_MODEL # aromaticity model + self._parameter_handler_classes = OrderedDict() # Parameter handler classes that _can_ be initialized if needed + self._parameter_handlers = OrderedDict() # ParameterHandler classes to be instantiated for each parameter type + self._parameter_io_handler_classes = OrderedDict() # ParameterIOHandler classes that _can_ be initialiazed if needed + self._parameter_io_handlers = OrderedDict() # ParameterIO classes to be used for each file type + self._parameters = ParameterList() # ParameterHandler objects instantiated for each parameter type + self._aromaticity_model = None + + + def _check_smirnoff_version_compatibility(self, version): + """ + Raise a parsing exception if the given file version is incompatible with this ForceField class. - Returns - ------- - params : dict - Dictionary of attributes (parameters and their descriptions) from XML + Parameters + ---------- + version : str + The SMIRNOFF version being read. + Raises + ------ + SMIRNOFFVersionError if an incompatible version is passed in. -Usage notes: SMIRKS or parameter ID must be specified. + """ + import packaging.version + # Use PEP-440 compliant version number comparison, if requested + if (not self.disable_version_check) and ( + packaging.version.parse(str(version)) > + packaging.version.parse(str(self._MAX_SUPPORTED_SMIRNOFF_VERSION))): + raise SMIRNOFFVersionError( + 'SMIRNOFF offxml file was written with version {}, but this version of ForceField only supports ' + 'up to version {}'.format(version, self._MAX_SUPPORTED_SMIRNOFF_VERSION)) -To do: Update behavior of "Implied" force_type so it raises an exception if the parameter is not uniquely identified by the provided info. -""" - # Check for valid input - if smirks and paramID: - raise ValueError("Error: Specify SMIRKS OR parameter ID but not both.") - if smirks==None and paramID==None: - raise ValueError("Error: Must specify SMIRKS or parameter ID.") - - - trees=self._XMLTrees - # Loop over XML files we read - for tree in trees: - # Loop over tree - for child in tree.getroot(): - # Check a particular section? - checksection = True - if force_type is not 'Implied': - # See whether this has the tag we want to check - checksection= (child.tag==force_type) - - if checksection: - #Loop over descendants - for elem in child.iterdescendants(tag=etree.Element): - if (smirks and elem.attrib['smirks']==smirks) or (paramID and elem.attrib['id']==paramID): - return copy.deepcopy(elem.attrib) - - - def setParameter(self, params, smirks=None, paramID=None, force_type="Implied"): - """Get info associated with a particular parameter as specified by SMIRKS or parameter ID, and optionally force term. - - Parameters - ---------- - params : dict - Dictionary of attributes (parameters and their descriptions) for XML, - i.e. as output by getParameter. - smirks (optional) : str - Default None. If specified, will set parameters on line containing this `smirks`. - paramID (optional) : str - Default None. If specified, will set parameters on line with this `id` - force_type (optional) : str - Default "Implied". Optionally, specify a particular force type such as - "HarmonicBondForce" or "HarmonicAngleForce" etc. to search for a - matching ID or SMIRKS. - - - Returns - ------- - status : bool - True/False as to whether that parameter was found and successfully set - -Usage notes: SMIRKS or parameter ID must be specified. - -To do: Update behavior of "Implied" force_type so it raises an exception if the parameter is not uniquely identified by the provided info. -""" - # Check for valid input - if smirks and paramID: - raise ValueError("Error: Specify SMIRKS OR parameter ID but not both.") - if smirks==None and paramID==None: - raise ValueError("Error: Must specify SMIRKS or parameter ID.") - if not params: - raise ValueError("Error, parameters must be specified.") - - # Below, we should do due dilegence that we're working on a parameter line which has - # roughly the same types of parameters (though for torsions (or bonds, if we have partial bond orders), - # the number of terms might differ), so define a utility function to give - # back the basic names of parameters (i.e. k) without suffixes - def get_param_names( param_keys ): - names = set() - for param in param_keys: - ct = 1 - while param[-ct].isdigit(): - ct+=1 - if ct > 1: - names.add( param[:-(ct-1)]) - else: - names.add( param ) - return names - - # Set parameters - trees=self._XMLTrees - status = False - # Loop over XML files we read - for tree in trees: - # Loop over tree - for child in tree.getroot(): - # Check a particular section? - checksection = True - if force_type is not 'Implied': - # See whether this has the tag we want to check - checksection= (child.tag==force_type) - - if checksection: - #Loop over descendants - for elem in child.iterdescendants(tag=etree.Element): - if (smirks and elem.attrib['smirks']==smirks) or (paramID and elem.attrib['id']==paramID): - # Try to set parameters - old_params=elem.attrib - if get_param_names(old_params.keys()) != get_param_names(params.keys()): - raise ValueError('Error: Provided parameters have different keys (%s) than existing parameters (%s).' % (', '.join(old_params.keys()), ', '.join(params.keys()))) - - # Loop over attributes, change values - for tag in params.keys(): - elem.set( tag, params[tag]) - - # Found parameters and set, so update status - status = True - - - # If we made any changes to XML, set flag so it will be reprocessed prior - # to system creation - if status: - self._XMLModified = True - - return status - - def addParameter(self, params, smirks, force_type, tag): - """Add specified SMIRKS/parameter in the section under the specified force type. - - Parameters - ---------- - params : dict - Dictionary of attributes (parameters and their descriptions) for XML, - i.e. as output by getParameter. - smirks : str - SMIRKS pattern to associate with this parameter - force_type : str - Specify a particular force type such as "HarmonicBondForce" or "HarmonicAngleForce" in which to add this parameter - tag : str - Tag to use identifying this parameter, i.e. 'Bond' for a HarmonicBondForce, etc. + def _set_aromaticity_model(self, aromaticity_model): + """ + Register that this forcefield is using an aromaticity model. Will check for + compatibility with other aromaticity model(s) already in use. - Returns - ------- - status : Bool - Successful? True or False. + Parameters + ---------- + aromaticity_model : str + The aromaticity model to register. + Raises + ------ + SMIRNOFFAromaticityError if an incompatible aromaticity model is passed in. -""" + """ + # Implement better logic here if we ever support another aromaticity model + if aromaticity_model != 'OEAroModel_MDL': + raise SMIRNOFFAromaticityError("Read aromaticity model {}. Currently only " + "OEAroModel_MDL is supported.".format(aromaticity_model)) - trees=self._XMLTrees - # Loop over XML files we read - found = False - for tree in trees: - # Loop over tree - for child in tree.getroot(): - if child.tag==force_type: - found = True - addl = etree.Element( tag, smirks=smirks, attrib = params) - child.append(addl) - return found + self._aromaticity_model = aromaticity_model - def writeFile(self, files): - """Write forcefield trees out to specified files.""" + def _register_parameter_handler_classes(self, parameter_handler_classes): + """ + Register multiple ParameterHandler classes, ensuring they specify unique tags to process - # Ensure that we are working with a tuple of files. - if not isinstance(files, tuple): - files = (files,) + .. warning :: This API is experimental and subject to change. - for idx, filenm in enumerate(files): - tree=self._XMLTrees[idx] - tree.write( filenm, xml_declaration=True, pretty_print=True) + Parameters + ---------- + parameter_handler_classes : iterable of ParameterHandler subclasses + List of ParameterHandler classes to register for this ForceField. + """ + for parameter_handler_class in parameter_handler_classes: + tagname = parameter_handler_class._TAGNAME + if tagname is not None: + if tagname in self._parameter_handler_classes: + raise Exception( + "Attempting to register ParameterHandler {}, which provides a parser for tag" + " '{}', but ParameterHandler {} has already been registered to handle that tag.".format( + parameter_handler_class, tagname, + self._parameter_handler_classes[tagname]) + ) + self._parameter_handler_classes[tagname] = parameter_handler_class + + def _register_parameter_io_handler_classes(self, + parameter_io_handler_classes): + """ + Register multiple ParameterIOHandler classes, ensuring they specify unique suffixes - def _assignPartialCharges(self, molecule, oechargemethod, modifycharges = True): - """Assign partial charges to the specified molecule using best practices. + .. warning :: This API is experimental and subject to change. Parameters ---------- - molecule : OEMol - The molecule to be charged. - NOTE: The molecule will be modified when charges are added. - oechargemethod : str - The name of the charge method from oequacpac to use (e.g. 'OECharges_AM1BCCSym') - modifycharges : bool (optional) - If False, don't actually assign partial charges; use the charge calculation solely to update the Wiberg bond orders. - - Notes: - As per Christopher Bayly and http://docs.eyesopen.com/toolkits/cookbook/python/modeling/am1-bcc.html, OEAssignPartialCharges needs multiple conformations to ensure well-behaved charges. This implements that recipe for conformer generation. - This conformer generation may or may not be necessary if the calculation is only to obtain bond orders; this will have to be investigated separately so it is retained for now. + parameter_io_handler_classes : iterable of ParameterIOHandler subclasses + All specified ParameterIOHandler classes will be registered as ways to translate to/from the object model + to serialized parameter sets. + + Raises + ------ + Exception if two ParameterIOHandlers are attempted to be registered for the same file format. + + """ + for parameter_io_handler_class in parameter_io_handler_classes: + serialization_format = parameter_io_handler_class._FORMAT + if serialization_format is not None: + if serialization_format in self._parameter_io_handler_classes.keys( + ): + raise Exception( + "Attempting to register ParameterIOHandler {}, which provides a IO parser for format " + "'{}', but ParameterIOHandler {} has already been registered to handle that tag.".format( + parameter_io_handler_class, serialization_format, + self._parameter_io_handler_classes[ + serialization_format]) + ) + self._parameter_io_handler_classes[ + serialization_format] = parameter_io_handler_class + + def register_parameter_handler(self, parameter_handler_class, + parameter_handler_kwargs): """ - # TODO: Cache charged molecules here to save time in future calls to createSystem - - # Expand conformers - if not openeye.oechem.OEChemIsLicensed(): raise(ImportError("Need License for OEChem!")) - if not openeye.oeomega.OEOmegaIsLicensed(): raise(ImportError("Need License for OEOmega!")) - omega = openeye.oeomega.OEOmega() - omega.SetMaxConfs(800) - omega.SetCanonOrder(False) - omega.SetSampleHydrogens(True) - omega.SetEnergyWindow(15.0) - omega.SetRMSThreshold(1.0) - omega.SetStrictStereo(True) #Don't generate random stereoisomer if not specified - charged_copy = openeye.oechem.OEMol(molecule) - status = omega(charged_copy) - if not status: - raise(RuntimeError("Omega returned error code %s" % status)) - - # Assign charges - status = openeye.oequacpac.OEAssignPartialCharges(charged_copy, getattr(oequacpac, oechargemethod), False, False) - if not status: - raise(RuntimeError("OEAssignPartialCharges returned error code %s" % status)) - # Our copy has the charges we want but not the right conformation. Copy charges over. Also copy over Wiberg bond orders if present - partial_charges = [] - partial_bondorders = [] - if modifycharges: - for atom in charged_copy.GetAtoms(): - partial_charges.append( atom.GetPartialCharge() ) - for (idx,atom) in enumerate(molecule.GetAtoms()): - atom.SetPartialCharge( partial_charges[idx] ) - for bond in charged_copy.GetBonds(): - partial_bondorders.append( bond.GetData("WibergBondOrder")) - for (idx, bond) in enumerate(molecule.GetBonds()): - bond.SetData("WibergBondOrder", partial_bondorders[idx]) - - - def createSystem(self, topology, molecules, nonbondedMethod=NoCutoff, nonbondedCutoff=1.0*unit.nanometer, - constraints=None, rigidWater=True, removeCMMotion=True, hydrogenMass=None, residueTemplates=dict(), - chargeMethod=None, verbose=False, **kwargs): - """Construct an OpenMM System representing a Topology with this force field. XML will be re-parsed if it is modified prior to system creation. + Register a new ParameterHandler from a specified class, instantiating the ParameterHandler object and making it + available for lookup in the ForceField. + + .. warning :: This API is experimental and subject to change. Parameters ---------- - topology : Topology - The Topology for which to create a System - molecules : list of openeye.oechem.OEMol - List of molecules appearing in the topology - nonbondedMethod : object=NoCutoff - The method to use for nonbonded interactions. Allowed values are - NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, or PME. - nonbondedCutoff : distance=1*nanometer - The cutoff distance to use for nonbonded interactions - constraints : object=None - Specifies which bonds and angles should be implemented with constraints. - Allowed values are None, HBonds, AllBonds, or HAngles. - rigidWater : boolean=True - If true, water molecules will be fully rigid regardless of the value - passed for the constraints argument - removeCMMotion : boolean=True - If true, a CMMotionRemover will be added to the System - hydrogenMass : mass=None - The mass to use for hydrogen atoms bound to heavy atoms. Any mass - added to a hydrogen is subtracted from the heavy atom to keep - their total mass the same. - residueTemplates : dict=dict() - Key: Topology Residue object - Value: string, name of _TemplateData residue template object to use for - (Key) residue - This allows user to specify which template to apply to particular Residues - in the event that multiple matching templates are available (e.g Fe2+ and Fe3+ - templates in the ForceField for a monoatomic iron ion in the topology). - chargeMethod : str, optional, default=None - If 'BCC' is specified, bond charge corrections defined the `ForceField` will be applied to AM1-derived charges, otherwise charges from provided `molecules` will be used. (DEFAULT) - If one of the `openeye.oequacpac.OECharges_` options is specified as a string (e.g. 'OECharges_AM1BCCSym'), this will be used and no bond charge corrections will be applied. - If `None`, charges from the provided `molecules` will be used and no bond charge corrections will be applied. - verbose : bool - If True, verbose output will be printed. - kwargs - Arbitrary additional keyword arguments may also be specified. - This allows extra parameters to be specified that are specific to - particular force fields. + parameter_handler_class : A ParameterHandler-derived object + The ParameterHandler to register Returns ------- - system - the newly created System + new_handler : an openforcefield.engines.typing.smirnoff.ParameterHandler-derived object. + The newly-created ParameterHandler """ - # XML modified? If so, re-parse by generators - if self._XMLModified: - if verbose: print("Re-parsing XML because it was modified.") - self.parseXMLTrees() - - # Make a deep copy of the input molecules so they are not modified by charging - molecules = copy.deepcopy(molecules) - - # Charge molecules, if needed - if chargeMethod == None: - # Don't charge molecules - if verbose: print('Charges specified in provided molecules will be used.') - oechargemethod = None - elif chargeMethod == 'BCC': - # Check if we have a BondChargeCorrectionGenerator populated - force_generators = { force.__class__.__name__ : force for force in self._forces } - if ('BondChargeCorrectionGenerator' in force_generators): - oechargemethod = force_generators['BondChargeCorrectionGenerator']._oechargemethod - if verbose: print('Applying oechem.oequacpac.OEAssignPartialCharges with initial charge method "%s" followed by bond charge corrections.' % oechargemethod) - else: - # Don't charge molecules if no bond charge corrections were found - oechargemethod = None - elif type(chargeMethod) == str: - # Check if the user has provided a manually-specified charge method - if hasattr(oequacpac, chargeMethod): - oechargemethod = chargeMethod - if verbose: print('Applying oechem.oequacpac.OEAssignPartialCharges with specified charge method "%s".' % oechargemethod) - else: - raise Exception("Unknown chargeMethod '%s'"% chargeMethod) - else: - raise Exception("Unknown chargeMethod ''%s'"% str(chargeMethod)) - - # Charge molecules if a valid charging method was identified - if oechargemethod is not None: - for molecule in molecules: - self._assignPartialCharges(molecule, oechargemethod) - - # Work with a modified form of the topology that provides additional accessors. - topology = _Topology(topology, molecules) + tagname = parameter_handler_class._TAGNAME + if tagname in self._parameter_handlers.keys(): + raise ParameterHandlerRegistrationError( + "Tried to register parameter handler '{}' for tag '{}', but " + "tag is already registered to {}".format( + parameter_handler_class, tagname, + self._parameter_handlers[tagname])) - # If the charge method was not an OpenEye AM1 method and we need Wiberg bond orders, obtain Wiberg bond orders - if not (type(chargeMethod) == str and 'AM1' in chargeMethod) and self._use_fractional_bondorder: - if verbose: print("Doing an AM1 calculation to get Wiberg bond orders.") - for molecule in molecules: - # Do AM1 calculation just to get bond orders on moleules (discarding charges) - self._assignPartialCharges(molecule, "OECharges_AM1", modifycharges = False) + new_handler = parameter_handler_class(**parameter_handler_kwargs) + self._parameter_handlers[new_handler._TAGNAME] = new_handler + return new_handler - # Update bond orders stored in the topology if needed - if self._use_fractional_bondorder: - topology._updateBondOrders(Wiberg = True ) - - # Create the System and add atoms - system = openmm.System() - for atom in topology.atoms(): - # Add the particle to the OpenMM system. - system.addParticle(atom.element.mass) # TODO: Add option to use a different mass than the integral elemental mass? - - # Adjust hydrogen masses if requested. - if hydrogenMass is not None: - if not unit.is_quantity(hydrogenMass): - hydrogenMass *= unit.dalton - for atom1, atom2 in topology.bonds(): - if atom1.element == elem.hydrogen: - (atom1, atom2) = (atom2, atom1) - if atom2.element == elem.hydrogen and atom1.element not in (elem.hydrogen, None): - transferMass = hydrogenMass-system.getParticleMass(atom2.index) - system.setParticleMass(atom2.index, hydrogenMass) - system.setParticleMass(atom1.index, system.getParticleMass(atom1.index)-transferMass) - - # Set periodic boundary conditions. - boxVectors = topology.getPeriodicBoxVectors() - if boxVectors is not None: - system.setDefaultPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]) - elif nonbondedMethod not in [NoCutoff, CutoffNonPeriodic]: - raise ValueError('Requested periodic boundary conditions for a Topology that does not specify periodic box dimensions') - - # TODO: Convert requested bonds and angles to use constraints - if constraints != None: - raise Exception("Constraints are not implemented yet.") - - # Set nonbonded method. - kwargs['nonbondedMethod'] = nonbondedMethod - kwargs['nonbondedCutoff'] = nonbondedCutoff - - # Set user-specified charge method. - kwargs['chargeMethod'] = chargeMethod - - # Add forces to the System - for force in self._forces: - if 'createForce' in dir(force): - force.createForce(system, topology, verbose=verbose, **kwargs) - - # Add center-of-mass motion removal, if requested - if removeCMMotion: - system.addForce(openmm.CMMotionRemover()) - - # Let force generators do postprocessing - for force in self._forces: - if 'postprocessSystem' in dir(force): - force.postprocessSystem(system, topology, **kwargs) - - return system + def register_parameter_io_handler(self, parameter_io_handler_class): + """ + Register a new ParameterIOHandler from a specified class, instantiating the ParameterIOHandler object and making + it available for lookup in the ForceField. - def labelMolecules(self, oemols, verbose = False): - """Return labels for a list of OEMols corresponding to parameters from this force field. For each oemol, a dictionary of force types is returned, and for each force type, each force term is provided with the atoms involved, the parameter id assigned, and the corresponding SMIRKS. + .. warning :: This API is experimental and subject to change. Parameters ---------- - oemols : list of OEMols - The OpenEye OEChem OEMol objects as a list; these will be labeled. Should include all atoms with the correct ordering atom atom numbers will be returned along with corresponding labeling. - verbose : bool - If True, verbose output will be printed - - Returns - ------- - molecule_labels : list - list of labels for molecules. Each entry in the list corresponds to - one molecule from the provided list of oemols and is a dictionary - keyed by force type, i.e. molecule_labels[0]['HarmonicBondForce'] - gives details for the harmonic bond parameters for the first - molecule. Each element is a list of the form [ ( [ atom1, ..., - atomN], parameter_id, SMIRKS), ... ] + parameter_io_handler_class : A subclass of ParameterIOHandler """ + io_format = parameter_io_handler_class._FORMAT + if io_format in self._parameter_io_handlers.keys(): + raise ParameterHandlerRegistrationError( + "Tried to register parameter IO handler '{}' for tag '{}', but " + "tag is already registered to {}".format( + parameter_io_handler_class, io_format, + self._parameter_io_handlers[io_format])) + new_io_handler = parameter_io_handler_class() - # XML modified? If so, re-parse by generators - if self._XMLModified: - if verbose: print("Re-parsing XML because it was modified.") - self.parseXMLTrees() + self._parameter_io_handlers[io_format] = new_io_handler + return new_io_handler - # Storage for labels - molecule_labels = [] + # TODO: Do we want to make this optional? - # Loop over molecules and label - for idx,mol in enumerate(oemols): - molecule_labels.append({}) - for force in self._forces: - # Initialize dictionary storage for this force type - forcelabel = force.__class__.__name__ - - # Grab force terms of this type for this molecule and store - molecule_labels[idx][forcelabel] = force.labelForce( mol, verbose=verbose ) - return molecule_labels + @staticmethod + def _check_for_missing_valence_terms(name, topology, assigned_terms, + topological_terms): + """ + Check to ensure there are no missing valence terms in the given topology, identifying potential gaps in parameter coverage. -#============================================================================================= -# The following classes are generators that know how to create Force subclasses and add them to a System that is being -# created. Each generator class must define three methods: 1) a static method that takes an etree Element and a ForceField, -# and returns the corresponding generator object; 2) a createForce() method that constructs the Force object and adds it -# to the System; and 3) a labelForce() method that provides access to which -# terms are applied to which atoms in specified oemols. -# The static method should be added to the parsers map. -#============================================================================================= + .. warning :: This API is experimental and subject to change. -def _validateSMIRKS(smirks, node=None): - """Validate the specified SMIRKS string. + Parameters + ---------- + name : str + Name of the calling force Handler + topology : openforcefield.topology.Topology + The Topology object + assigned_terms : iterable of ints or int tuples + Atom index tuples defining added valence terms + topological_terms : iterable of atoms or atom tuples + Atom tuples defining topological valence atomsets to which forces should be assigned - Parameters - ---------- - smirks : str - The SMIRKS string to be validated - node : xml.etree.ElementTree.Element - Node of etree with 'sourceline' attribute. + """ + # Convert assigned terms and topological terms to lists + assigned_terms = [item for item in assigned_terms] + topological_terms = [item for item in topological_terms] + + def ordered_tuple(atoms): + atoms = list(atoms) + if atoms[0] < atoms[-1]: + return tuple(atoms) + else: + return tuple(reversed(atoms)) + + try: + topology_set = set([ + ordered_tuple(atom.index for atom in atomset) + for atomset in topological_terms + ]) + assigned_set = set([ + ordered_tuple(index for index in atomset) + for atomset in assigned_terms + ]) + except TypeError as te: + topology_set = set([atom.index for atom in topological_terms]) + assigned_set = set([atomset[0] for atomset in assigned_terms]) + + def render_atoms(atomsets): + msg = "" + for atomset in atomsets: + msg += '%30s :' % str(atomset) + try: + for atom_index in atomset: + atom = atoms[atom_index] + msg += ' %5s %3s %3s' % (atom.residue.index, + atom.residue.name, atom.name) + except TypeError as te: + atom = atoms[atomset] + msg += ' %5s %3s %3s' % (atom.residue.index, + atom.residue.name, atom.name) + + msg += '\n' + return msg + + if set(assigned_set) != set(topology_set): + # Form informative error message + msg = '%s: Mismatch between valence terms added and topological terms expected.\n' % name + atoms = [atom for atom in topology.topology_atoms] + if len(assigned_set.difference(topology_set)) > 0: + msg += 'Valence terms created that are not present in Topology:\n' + msg += render_atoms(assigned_set.difference(topology_set)) + if len(topology_set.difference(assigned_set)) > 0: + msg += 'Topological atom sets not assigned parameters:\n' + msg += render_atoms(topology_set.difference(assigned_set)) + msg += 'topology_set:\n' + msg += str(topology_set) + '\n' + msg += 'assigned_set:\n' + msg += str(assigned_set) + '\n' + raise Exception( + msg) # TODO: Should we raise a more specific exception here? + + def get_handler(self, tagname, handler_kwargs=None): + """Retrieve the parameter handlers associated with the provided tagname. + + If the parameter handler has not yet been instantiated, it will be created. + If a parameter handler object already exists, it will be checked for compatibility + and an Exception raised if it is incompatible with the provided kwargs. - """ - qmol = oechem.OEQMol() - if not oechem.OEParseSmarts(qmol, smirks): - if (node is not None) and ('sourceline' in node.attrib): - raise Exception("Line %s: Error parsing SMIRKS '%s'" % (node.attrib['sourceline'], node.attrib['smirks'])) - else: - raise Exception("Error parsing SMIRKS '%s'" % (node.attrib['smirks'])) + Parameters + ---------- + tagame : str + The name of the parameter to be handled. + handler_kwargs : dict, optional. Default=None + Dict to be passed to the handler for construction or checking compatibility. If None, will be assumed + to represent handler defaults. - return smirks + Returns + ------- + handler : An openforcefield.engines.typing.smirnoff.ParameterHandler -def _ast_eval(node): - """ - Performs an algebraic syntax tree evaluation of a unit. - """ + Raises + ------ + KeyError if there is no ParameterHandler for the given tagname + """ - operators = {ast.Add: op.add, ast.Sub: op.sub, ast.Mult: op.mul, - ast.Div: op.truediv, ast.Pow: op.pow, ast.BitXor: op.xor, - ast.USub: op.neg} - - if isinstance(node, ast.Num): # - return node.n - elif isinstance(node, ast.BinOp): # - return operators[type(node.op)](_ast_eval(node.left), _ast_eval(node.right)) - elif isinstance(node, ast.UnaryOp): # e.g., -1 - return operators[type(node.op)](_ast_eval(node.operand)) - elif isinstance(node, ast.Name): - # see if this is a simtk unit - b = getattr(unit, node.id) - return b - else: - raise TypeError(node) - -def _extractQuantity(node, parent, name, unit_name=None): - """ - Form a (potentially unit-bearing) quantity from the specified attribute name. + if handler_kwargs is None: + handler_kwargs = dict() - node : xml.etree.ElementTree.Element - Node of etree corresponding to force type entry. - parent : xml.etree.ElementTree.Element - Node of etree corresponding to parent Force. - name : str - Name of parameter to extract from attributes. - unit_name : str, optional, default=None - If specified, use this attribute name of 'parent' to look up units + handler = None + if tagname in self._parameter_handlers: + # If handler already exists, make sure it is compatible + handler = self._parameter_handlers[tagname] + handler.check_handler_compatibility(handler_kwargs) + elif tagname in self._parameter_handler_classes: + new_ph_class = self._parameter_handler_classes[tagname] + handler = self.register_parameter_handler(new_ph_class, + handler_kwargs) - """ - # Check for expected attributes - if name not in node.attrib: - if 'sourceline' in node.attrib: - raise Exception("Line %d : Expected XML attribute '%s' not found" % (node.attrib['sourceline'], name)) - else: - raise Exception("Expected XML attribute '%s' not found" % (name)) - - # Most attributes will be converted to floats, but some are strings - string_names = ['parent_id', 'id'] - # Handle case where this is a normal quantity - if name not in string_names: - quantity = float(node.attrib[name]) - # Handle label or string - else: - quantity = node.attrib[name] - return quantity - - if unit_name is None: - unit_name = name + '_unit' - - if unit_name in parent.attrib: - a = node.attrib[name] - b = parent.attrib[unit_name] - parsed_units = _ast_eval(ast.parse(b, mode='eval').body) - result = float(a) * parsed_units - quantity = result.value_in_unit_system(unit.md_unit_system) - - return quantity - -def _check_for_missing_valence_terms(name, topology, assigned_terms, topological_terms): - """ - Check to ensure there are no missing valence terms. + if handler is None: + msg = "Cannot find a registered parameter handler for tag '{}'\n".format( + tagname) + msg += "Registered parameter handlers: {}\n".format( + self._parameter_handlers.keys()) + raise KeyError(msg) - Parameters - ---------- - name : str - Name of the calling force generator - topology : simtk.openmm.app.Topology - The Topology object - assigned_terms : iterable of ints or int tuples - Atom index tuples defining added valence terms - topological_terms : iterable of atoms or atom tuples - Atom tuples defining topological valence atomsets to which forces should be assigned + return handler - """ - # Convert to lists - assigned_terms = [ item for item in assigned_terms ] - topological_terms = [ item for item in topological_terms ] - - def ordered_tuple(atoms): - atoms = list(atoms) - if atoms[0] < atoms[-1]: - return tuple(atoms) - else: - return tuple(reversed(atoms)) - try: - topology_set = set([ ordered_tuple( atom.index for atom in atomset ) for atomset in topological_terms ]) - assigned_set = set([ ordered_tuple( index for index in atomset ) for atomset in assigned_terms ]) - except TypeError as te: - topology_set = set([ atom.index for atom in topological_terms ]) - assigned_set = set([ atomset[0] for atomset in assigned_terms ]) - - def render_atoms(atomsets): - msg = "" - for atomset in atomsets: - msg += '%30s :' % str(atomset) - try: - for atom_index in atomset: - atom = atoms[atom_index] - msg += ' %5s %3s %3s' % (atom.residue.index, atom.residue.name, atom.name) - except TypeError as te: - atom = atoms[atomset] - msg += ' %5s %3s %3s' % (atom.residue.index, atom.residue.name, atom.name) - - msg += '\n' - return msg - - if set(assigned_set) != set(topology_set): - msg = '%s: Mismatch between valence terms added and topological terms expected.\n' % name - atoms = [ atom for atom in topology.atoms() ] - if len(assigned_set.difference(topology_set)) > 0: - msg += 'Valence terms created that are not present in Topology:\n' - msg += render_atoms(assigned_set.difference(topology_set)) - if len(topology_set.difference(assigned_set)) > 0: - msg += 'Topological atom sets not assigned parameters:\n' - msg += render_atoms(topology_set.difference(assigned_set)) - msg += 'topology_set:\n' - msg += str(topology_set) + '\n' - msg += 'assigned_set:\n' - msg += str(assigned_set) + '\n' - raise Exception(msg) - -import collections -class TransformedDict(collections.MutableMapping): - """A dictionary that applies an arbitrary key-altering - function before accessing the keys""" - - def __init__(self, *args, **kwargs): - self.store = dict() - self.update(dict(*args, **kwargs)) # use the free update to set keys - - def __getitem__(self, key): - return self.store[self.__keytransform__(key)] - - def __setitem__(self, key, value): - self.store[self.__keytransform__(key)] = value - - def __delitem__(self, key): - del self.store[self.__keytransform__(key)] - - def __iter__(self): - return iter(self.store) - - def __len__(self): - return len(self.store) - - def __keytransform__(self, key): - return key - -class ValenceDict(TransformedDict): - """Enforce uniqueness in atom indices""" - def __keytransform__(self, key): - """Reverse tuple if first element is larger than last element.""" - # Ensure key is a tuple. - key = tuple(key) - # Reverse the key if the first element is bigger than the last. - if key[0] > key[-1]: - key = tuple(reversed(key)) - return key - -class ImproperDict(TransformedDict): - """Symmetrize improper torsions""" - def __keytransform__(self,key): - """Reorder tuple in numerical order except for element[1] which is the central atom; it retains its position.""" - # Ensure key is a tuple - key = tuple(key) - # Retrieve connected atoms - connectedatoms = [key[0], key[2], key[3]] - # Sort connected atoms - connectedatoms.sort() - # Re-store connected atoms - key = tuple( [connectedatoms[0], key[1], connectedatoms[1], connectedatoms[2]]) - return(key) + def get_io_handler(self, io_format): + """Retrieve the parameter handlers associated with the provided tagname. -#============================================================================================= -# Force generators -#============================================================================================= + If the parameter handler has not yet been instantiated, it will be created. + If a parameter handler object already exists, it will be checked for compatibility + and an Exception raised if it is incompatible with the provided kwargs. -#============================================================================================= -# Force generators -#============================================================================================= - -## @private -class ConstraintGenerator(object): - """A ConstraintGenerator adds constraints. - - The ConstraintGenerator must be applied before HarmonicBondGenerator and HarmonicAngleGenerator if constrained bonds are to not also have harmonic bond terms added. - - ConstraintGenerator will mark bonds as being constrained for HarmonicBondGenerator to assign constraints to equilibrium bond lengths, - while constraints with distances specified will be assigned by ConstraintGenerator. + Parameters + ---------- + io_format : str + The name of the io format to be handled. - """ + Returns + ------- + io_handler : An openforcefield.engines.typing.smirnoff.ParameterIOHandler - class ConstraintType(object): - """A SMIRNOFF constraint type.""" - def __init__(self, node, parent): - self.smirks = _validateSMIRKS(node.attrib['smirks'], node=node) - self.pid = _extractQuantity(node, parent, 'id') - if 'distance' in node.attrib: - # Constraint distance is specified, will be handled by ConstraintGenerator - self.distance = _extractQuantity(node, parent, 'distance') - else: - # Constraint to equilibrium bond length, handled by HarmonicBondGenerator - self.distance = True + Raises + ------ + KeyError if there is no ParameterIOHandler for the given tagname + """ + io_handler = None + if io_format in self._parameter_io_handlers.keys(): + io_handler = self._parameter_io_handlers[io_format] + elif io_format in self._parameter_io_handler_classes.keys(): + new_ph_class = self._parameter_io_handler_classes[io_format] + io_handler = self.register_parameter_io_handler(new_ph_class) + if io_handler is None: + msg = "Cannot find a registered parameter IO handler for format '{}'\n".format( + io_format) + msg += "Registered parameter IO handlers: {}\n".format( + self._parameter_io_handlers.keys()) + raise KeyError(msg) - def __init__(self, forcefield): - self.ff = forcefield - self._constraint_types = list() + return io_handler - def registerConstraint(self, node, parent): - """Register a SMIRNOFF constraint type definition.""" - constraint = ConstraintGenerator.ConstraintType(node, parent) - self._constraint_types.append(constraint) - @staticmethod - def parseElement(element, ff): - # Find existing force generator or create new one. - existing = [f for f in ff._forces if isinstance(f, ConstraintGenerator)] - if len(existing) == 0: - generator = ConstraintGenerator(ff) - ff.registerGenerator(generator) - else: - generator = existing[0] - - # Register all SMIRNOFF constraint definitions. - for constraint in element.findall('Constraint'): - generator.registerConstraint(constraint, element) - - def createForce(self, system, topology, verbose=False, **kwargs): - # Iterate over all defined constraint types, allowing later matches to override earlier ones. - constraints = ValenceDict() - for constraint in self._constraint_types: - for atom_indices in topology.unrollSMIRKSMatches(constraint.smirks, aromaticity_model = self.ff._aromaticity_model): - constraints[atom_indices] = constraint - - if verbose: - print('') - print('ConstraintGenerator:') - print('') - for constraint in self._constraint_types: - print('%64s : %8d matches' % (constraint.smirks, len(topology.unrollSMIRKSMatches(constraint.smirks, aromaticity_model = self.ff._aromaticity_model)))) - print('') - - for (atom_indices, constraint) in constraints.items(): - # Update constrained atom pairs in topology - topology.constrainAtomPair(atom_indices[0], atom_indices[1], constraint.distance) - # If a distance is specified, add the constraint here. - # Otherwise, the equilibrium bond length will be used to constrain the atoms in HarmonicBondGenerator - if constraint.distance is not True: - system.addConstraint(atom_indices[0], atom_indices[1], constraint.distance) - - if verbose: print('%d constraints added' % (len(constraints))) - - def labelForce(self, oemol, verbose=False, **kwargs): - """Take a provided OEMol and parse Constraint terms for this molecule. + def parse_sources(self, sources): + """Parse a SMIRNOFF force field definition. Parameters ---------- - oemol : OEChem OEMol object for molecule to be examined + sources : string or file-like object or open file handle or URL (or iterable of these) + A list of files defining the SMIRNOFF force field to be loaded + Currently, only `the SMIRNOFF XML format `_ is supported. + Each entry may be an absolute file path, a path relative to the current working directory, a path relative to this module's data subdirectory + (for built in force fields), or an open file-like object with a ``read()`` method from which the forcefield XML data can be loaded. + If multiple files are specified, any top-level tags that are repeated will be merged if they are compatible, + with files appearing later in the sequence resulting in parameters that have higher precedence. + Support for multiple files is primarily intended to allow solvent parameters to be specified by listing them last in the sequence. + + .. notes :: + + * New SMIRNOFF sections are handled independently, as if they were specified in the same file. + * If a SMIRNOFF section that has already been read appears again, its definitions are appended to the end of the previously-read + definitions if the sections are configured with compatible attributes; otherwise, an ``IncompatibleTagException`` is raised. - Returns - --------- - force_terms: list - Returns a list of tuples, [ ([atom id 1, ... atom id N], parameter id, smirks) , (....), ... ] for all forces of this type which would be applied. """ + # Ensure that we are working with an iterable + try: + sources = iter(sources) + except TypeError as te: + # Make iterable object + sources = [sources] - # Iterate over all defined constraint SMIRKS, allowing later matches to override earlier ones. - constraints = ValenceDict() - for constraint in self._constraint_types: - for atom_indices in getSMIRKSMatches_OEMol(oemol, constraint.smirks, aromaticity_model = self.ff._aromaticity_model): - constraints[atom_indices] = constraint - - if verbose: - print('') - print('ConstraintGenerator:') - print('') - for constraint in self._constraint_types: - print('%64s : %8d matches' % (constraint.smirks, len(getSMIRKSMatches_OEMol(oemol, constraint.smirks, aromaticity_model = self.ff._aromaticity_model)))) - print('') - - # Add all bonds to the output list - force_terms = [] - for (atom_indices, constraint) in constraints.items(): - force_terms.append( ([atom_indices[0], atom_indices[1]], constraint.pid, constraint.smirks) ) - - return force_terms - -parsers["Constraints"] = ConstraintGenerator.parseElement - -## @private -class HarmonicBondGenerator(object): - """A HarmonicBondGenerator constructs a HarmonicBondForce.""" - - class BondType(object): - """A SMIRNOFF bond type.""" - def __init__(self, node, parent): - self.smirks = _validateSMIRKS(node.attrib['smirks'], node=node) - self.pid = _extractQuantity(node, parent, 'id') - - # Determine if we are using fractional bond orders for this bond - # First, check if this force uses fractional bond orders - if 'fractional_bondorder' in parent.attrib: - # If it does, see if this parameter line provides fractional bond order parameters - if 'length_bondorder1' in node.attrib and 'k_bondorder1' in node.attrib: - # Store what interpolation scheme we're using - self.fractional_bondorder = parent.attrib['fractional_bondorder'] - # Store bondorder1 and bondorder2 parameters - self.k = list() - self.length = list() - for ct in range(1,3): - self.length.append( _extractQuantity(node, parent, 'length_bondorder%s' % ct, unit_name = 'length_unit') ) - self.k.append( _extractQuantity(node, parent, 'k_bondorder%s' % ct, unit_name = 'k_unit') ) - else: - self.fractional_bondorder = None - else: - self.fractional_bondorder = None + # TODO: If a non-first source fails here, the forcefield might be partially modified + for source in sources: + smirnoff_data = self.parse_smirnoff_from_source(source) + self.load_smirnoff_data(smirnoff_data) - # If no fractional bond orders, just get normal length and k - if self.fractional_bondorder == None: - self.length = _extractQuantity(node, parent, 'length') - self.k = _extractQuantity(node, parent, 'k') - def __init__(self, forcefield): - self.ff = forcefield - self._bondtypes = list() + def to_smirnoff_data(self): + """ + Convert this ForceField and all related ParameterHandlers to an OrderedDict representing a SMIRNOFF + data object. - def registerBond(self, node, parent): - """Register a SMIRNOFF bondtype definition.""" - bond = HarmonicBondGenerator.BondType(node, parent) - self._bondtypes.append(bond) + Returns + ------- + smirnoff_dict : OrderedDict + A nested OrderedDict representing this ForceField as a SMIRNOFF data object. + """ + l1_dict = OrderedDict() - @staticmethod - def parseElement(element, ff): - # Find existing force generator or create new one. - existing = [f for f in ff._forces if isinstance(f, HarmonicBondGenerator)] - if len(existing) == 0: - generator = HarmonicBondGenerator(ff) - ff.registerGenerator(generator) - else: - generator = existing[0] - - # Register all SMIRNOFF bond definitions. - for bond in element.findall('Bond'): - generator.registerBond(bond, element) - - def createForce(self, system, topology, verbose=False, **kwargs): - # Find existing force or create new one. - existing = [system.getForce(i) for i in range(system.getNumForces())] - existing = [f for f in existing if type(f) == openmm.HarmonicBondForce] - if len(existing) == 0: - force = openmm.HarmonicBondForce() - system.addForce(force) - else: - force = existing[0] - - # Iterate over all defined bond types, allowing later matches to override earlier ones. - bonds = ValenceDict() - bondorders = ValenceDict() - for bond in self._bondtypes: - for atom_indices in topology.unrollSMIRKSMatches(bond.smirks, aromaticity_model = self.ff._aromaticity_model): - bonds[atom_indices] = bond - # Retrieve bond orders - bondorders[atom_indices] = topology._bondorders_by_atomindices[atom_indices[0]][atom_indices[1]] - - if verbose: - print('') - print('HarmonicBondGenerator:') - print('') - for bond in self._bondtypes: - print('%64s : %8d matches' % (bond.smirks, len(topology.unrollSMIRKSMatches(bond.smirks, aromaticity_model = self.ff._aromaticity_model)))) - print('') - - # Add all bonds to the system. - skipped_constrained_bonds = 0 # keep track of how many bonds were constrained (and hence skipped) - for (atom_indices, bond) in bonds.items(): - # Ensure atoms are actually bonded correct pattern in Topology - assert topology._isBonded(atom_indices[0], atom_indices[1]), 'Atom indices %d and %d are not bonded in topology' % (atom_indices[0], atom_indices[1]) - - # Compute equilibrium bond length and spring constant. - if bond.fractional_bondorder==None: - [k, length] = [bond.k, bond.length] - else: - # This bond uses partial bond orders - # Make sure forcefield asks for fractional bond orders - if not self.ff._use_fractional_bondorder: - raise ValueError("Error: your forcefield file does not request to use fractional bond orders in its header, but a harmonic bond attempts to use them.") - # Proceed to do interpolation - order = bondorders[atom_indices] - if bond.fractional_bondorder=='interpolate-linear': - k = bond.k[0] + (bond.k[1]-bond.k[0])*(order-1.) - length = bond.length[0] + (bond.length[1]-bond.length[0])*(order-1.) - else: - raise Exception("Partial bondorder treatment %s is not implemented." % bond.fractional_bondorder) - - # Handle constraints. - if topology.atomPairIsConstrained(*atom_indices): - # Atom pair is constrained; we don't need to add a bond term. - skipped_constrained_bonds += 1 - # Check if we need to add the constraint here to the equilibrium bond length. - if topology.atomPairIsConstrained(*atom_indices) is True: - # Mark that we have now assigned a specific constraint distance to this constraint. - topology.constrainAtomPair(atom_indices[0], atom_indices[1], length) - # Add the constraint to the System. - system.addConstraint(atom_indices[0], atom_indices[1], length) - continue + # Assume we will write out SMIRNOFF data in compliance with the max supported spec version + l1_dict['version'] = self._MAX_SUPPORTED_SMIRNOFF_VERSION - # Add bond - force.addBond(atom_indices[0], atom_indices[1], length, k) + # Write out the aromaticity model used + l1_dict['aromaticity_model'] = self._aromaticity_model - if verbose: print('%d bonds added (%d skipped due to constraints)' % (len(bonds) - skipped_constrained_bonds, skipped_constrained_bonds)) + for handler_format, parameter_handler in self._parameter_handlers.items(): + handler_tag = parameter_handler._TAGNAME + l1_dict[handler_tag] = parameter_handler.to_dict() - # Check that no topological bonds are missing force parameters - _check_for_missing_valence_terms('HarmonicBondForce', topology, bonds.keys(), topology.bonds()) + smirnoff_dict = OrderedDict() + smirnoff_dict['SMIRNOFF'] = l1_dict + return smirnoff_dict - def labelForce(self, oemol, verbose=False, **kwargs): - """Take a provided OEMol and parse HarmonicBondForce terms for this molecule. + # TODO: Should we call this "from_dict"? + def load_smirnoff_data(self, smirnoff_data): + """ + Add parameters from a SMIRNOFF-format data structure to this ForceField. Parameters ---------- - oemol : OEChem OEMol object for molecule to be examined + smirnoff_data : OrderedDict + A representation of a SMIRNOFF-format data structure. Begins at top-level 'SMIRNOFF' key. - Returns - --------- - force_terms: list - Returns a list of tuples, [ ([atom id 1, ... atom id N], parameter id, smirks) , (....), ... ] for all forces of this type which would be applied. """ - # Iterate over all defined bond SMIRKS, allowing later matches to override earlier ones. - bonds = ValenceDict() - for bond in self._bondtypes: - for atom_indices in getSMIRKSMatches_OEMol( oemol, bond.smirks, aromaticity_model = self.ff._aromaticity_model ): - bonds[atom_indices] = bond + # Ensure that SMIRNOFF is a top-level key of the dict + if not('SMIRNOFF' in smirnoff_data): + raise ParseError("'SMIRNOFF' must be a top-level key in the SMIRNOFF object model") - if verbose: - print('') - print('HarmonicBondGenerator:') - print('') - for bond in self._bondtypes: - print('%64s : %8d matches' % (bond.smirks, len(getSMIRKSMatches_OEMol(oemol, bond.smirks, aromaticity_model = self.ff._aromaticity_model)))) - print('') + l1_dict = smirnoff_data['SMIRNOFF'] + # Check that the aromaticity model required by this parameter set is compatible with + # others loaded by this ForceField + if 'aromaticity_model' in l1_dict: + aromaticity_model = l1_dict['aromaticity_model'] + self._set_aromaticity_model(aromaticity_model) - # Add all bonds to the output list - force_terms = [] - for (atom_indices, bond) in bonds.items(): - force_terms.append( ([atom_indices[0], atom_indices[1]], bond.pid, bond.smirks) ) + elif self._aromaticity_model == None: + raise ParseError("'aromaticity_model' attribute must be specified in SMIRNOFF " + "tag, or contained in a previously-loaded SMIRNOFF data source") - return force_terms -parsers["HarmonicBondForce"] = HarmonicBondGenerator.parseElement -#============================================================================================= -## @private -class HarmonicAngleGenerator(object): - """A HarmonicAngleGenerator constructs a HarmonicAngleForce.""" - - class AngleType(object): - """A SMIRNOFF angle type.""" - def __init__(self, node, parent): - self.smirks = _validateSMIRKS(node.attrib['smirks'], node=node) - self.angle = _extractQuantity(node, parent, 'angle') - self.k = _extractQuantity(node, parent, 'k') - self.pid = _extractQuantity(node, parent, 'id') - if 'fractional_bondorder' in parent.attrib: - self.fractional_bondorder = parent.attrib['fractional_bondorder'] - else: - self.fractional_bondorder = None - def __init__(self, forcefield): - self.ff = forcefield - self._angletypes = list() + # Check that the SMIRNOFF version of this data structure is supported by this ForceField implementation + if 'version' in l1_dict: + version = l1_dict['version'] + else: + raise ParseError("'version' attribute must be specified in SMIRNOFF tag") + self._check_smirnoff_version_compatibility(str(version)) - def registerAngle(self, node, parent): - """Register a SMIRNOFF angletype definition.""" - angle = HarmonicAngleGenerator.AngleType(node, parent) - self._angletypes.append(angle) - @staticmethod - def parseElement(element, ff): - # Find existing force generator or create new one. - existing = [f for f in ff._forces if isinstance(f, HarmonicAngleGenerator)] - if len(existing) == 0: - generator = HarmonicAngleGenerator(ff) - ff.registerGenerator(generator) - else: - generator = existing[0] - - # Register all SMIRNOFF angle definitions. - for angle in element.findall('Angle'): - generator.registerAngle(angle, element) - - def createForce(self, system, topology, verbose=False, **kwargs): - # Find existing force or create new one. - existing = [system.getForce(i) for i in range(system.getNumForces())] - existing = [f for f in existing if type(f) == openmm.HarmonicAngleForce] - if len(existing) == 0: - force = openmm.HarmonicAngleForce() - system.addForce(force) - else: - force = existing[0] - - # Iterate over all defined angle types, allowing later matches to override earlier ones. - angles = ValenceDict() - for angle in self._angletypes: - for atom_indices in topology.unrollSMIRKSMatches(angle.smirks, aromaticity_model = self.ff._aromaticity_model): - angles[atom_indices] = angle - - if verbose: - print('') - print('HarmonicAngleGenerator:') - print('') - for angle in self._angletypes: - print('%64s : %8d matches' % (angle.smirks, len(topology.unrollSMIRKSMatches(angle.smirks, aromaticity_model = self.ff._aromaticity_model)))) - print('') - - # Add all angles to the system. - skipped_constrained_angles = 0 # keep track of how many angles were constrained (and hence skipped) - for (atom_indices, angle) in angles.items(): - # Ensure atoms are actually bonded correct pattern in Topology - assert topology._isBonded(atom_indices[0], atom_indices[1]), 'Atom indices %d and %d are not bonded in topology' % (atom_indices[0], atom_indices[1]) - assert topology._isBonded(atom_indices[1], atom_indices[2]), 'Atom indices %d and %d are not bonded in topology' % (atom_indices[1], atom_indices[2]) - - if topology.atomPairIsConstrained(atom_indices[0], atom_indices[1]) and topology.atomPairIsConstrained(atom_indices[1], atom_indices[2]) and topology.atomPairIsConstrained(atom_indices[0], atom_indices[2]): - # Angle is constrained; we don't need to add an angle term. - skipped_constrained_angles += 1 + # Go through the subsections, delegating each to the proper ParameterHandler + + # Define keys which are expected from the spec, but are not parameter sections + l1_spec_keys = ['Author', 'Date', 'version', 'aromaticity_model'] + + for parameter_name in l1_dict: + # Skip (for now) cosmetic l1 items + if parameter_name in l1_spec_keys: continue + # Handle cases where a parameter name has no info (eg. ToolkitAM1BCC) + if l1_dict[parameter_name] is None: + handler = self.get_handler(parameter_name, {}) + continue + + # Otherwise, we expect this l1_key to correspond to a ParameterHandler + section_dict = l1_dict[parameter_name] + # In the OFFXML format, attributes and sub-elements are distinguished by whether they're a list - force.addAngle(atom_indices[0], atom_indices[1], atom_indices[2], angle.angle, angle.k) + # Retrieve or create parameter handler + handler = self.get_handler(parameter_name, + # handler_kwargs) + section_dict) - if verbose: print('%d angles added (%d skipped due to constraints)' % (len(angles) - skipped_constrained_angles, skipped_constrained_angles)) - # Check that no topological angles are missing force parameters - _check_for_missing_valence_terms('HarmonicAngleForce', topology, angles.keys(), topology.angles()) - def labelForce(self, oemol, verbose=False, **kwargs): - """Take a provided OEMol and parse HarmonicAngleForce terms for this molecule. + def parse_smirnoff_from_source(self, source): + """ + Reads a SMIRNOFF data structure from a source, which can be one of many types. Parameters ---------- - oemol : OEChem OEMol object for molecule to be examined + source : str or bytes + sources : string or file-like object or open file handle or URL (or iterable of these) + A list of files defining the SMIRNOFF force field to be loaded + Currently, only `the SMIRNOFF XML format `_ is supported. + Each entry may be an absolute file path, a path relative to the current working directory, a path relative to this module's data subdirectory + (for built in force fields), or an open file-like object with a ``read()`` method from which the forcefield XML data can be loaded. Returns - --------- - force_terms: list - Returns a list of tuples, [ ([atom id 1, ... atom id N], parameter id, smirks) , (....), ... ] for all forces of this type which would be applied. - """ + ------- + smirnoff_data : OrderedDict + A representation of a SMIRNOFF-format data structure. Begins at top-level 'SMIRNOFF' key. - # Iterate over all defined angle types, allowing later matches to override earlier ones. - angles = ValenceDict() - for angle in self._angletypes: - for atom_indices in getSMIRKSMatches_OEMol(oemol, angle.smirks, aromaticity_model = self.ff._aromaticity_model): - angles[atom_indices] = angle + """ - if verbose: - print('') - print('HarmonicAngleGenerator:') - print('') - for angle in self._angletypes: - print('%64s : %8d matches' % (angle.smirks, len(getSMIRKSMatches_OEMol(oemol, angle.smirks, aromaticity_model = self.ff._aromaticity_model)))) - print('') + # Process all SMIRNOFF definition files or objects + # QUESTION: Allow users to specify forcefield URLs so they can pull forcefield definitions from the web too? + io_formats_to_try = self._parameter_io_handler_classes.keys() - # Add all angles to the output list - force_terms = [] - for (atom_indices, angle) in angles.items(): - force_terms.append( ([atom_indices[0], atom_indices[1], atom_indices[2]], angle.pid, angle.smirks) ) + # Parse content depending on type + for parameter_io_format in io_formats_to_try: + parameter_io_handler = self.get_io_handler(parameter_io_format) - return force_terms + # Try parsing as a forcefield file or file-like object + try: + smirnoff_data = parameter_io_handler.parse_file(source) + return smirnoff_data + except ParseError as e: + exception_msg = str(e) + # TODO: Have parse_file() raise a different error type for file not found. + # If the file exists but there are syntax errors, don't + # parse as string to avoid overwriting the errors. + if os.path.exists(source): + break -parsers["HarmonicAngleForce"] = HarmonicAngleGenerator.parseElement + # Try parsing as a forcefield string + try: + smirnoff_data = parameter_io_handler.parse_string(source) + return smirnoff_data + except ParseError as e: + exception_msg = str(e) + # If we haven't returned by now, the parsing was unsuccessful + valid_formats = [ + input_format + for input_format in self._parameter_io_handlers.keys() + ] + msg = f"Source {source} does not appear to be in a known SMIRNOFF encoding.\n" + msg += f"Valid formats are: {valid_formats}\n" + msg += f"Parsing vailed with the following error:\n{exception_msg}\n" + raise IOError(msg) -#============================================================================================= -## @private -class PeriodicTorsionGenerator(object): - """A PeriodicTorsionForceGenerator constructs a PeriodicTorsionForce.""" + def _resolve_parameter_handler_order(self): + """Resolve the order in which ParameterHandler objects should execute to satisfy constraints. - class ProperTorsionType(object): + Returns + ------- + Iterable of ParameterHandlers + The ParameterHandlers in this ForceField, in the order that they should be called to satisfy constraints. + """ - """A SMIRNOFF torsion type for proper torsions.""" - def __init__(self, node, parent): - self.smirks = _validateSMIRKS(node.attrib['smirks'], node=node) - self.periodicity = list() - self.phase = list() - self.k = list() - self.pid = _extractQuantity(node, parent, 'id') + # Create a DAG expressing dependencies + import networkx as nx + G = nx.DiGraph() + for tagname, parameter_handler in self._parameter_handlers.items(): + G.add_node(tagname) + if parameter_handler._DEPENDENCIES is not None: + for dependency in parameter_handler._DEPENDENCIES: + G.add_edge(dependency._TAGNAME, parameter_handler._TAGNAME) + # TODO: Check to make sure DAG isn't cyclic + # Resolve order + ordered_parameter_handlers = list() + for tagname in nx.topological_sort(G): + if tagname in self._parameter_handlers: + ordered_parameter_handlers.append( + self._parameter_handlers[tagname]) + else: + # TODO: Is it safe to pass "{}" as the handler_kwargs? If the handler doesn't exist, do we want to assume default values? + ordered_parameter_handlers.append( + self.get_handler(tagname, {})) + #ordered_parameter_handlers = [ self.get_handler(tagname, {}) for tagname in nx.topological_sort(G) ] + return ordered_parameter_handlers - # Doublecheck type of torsion - if node.tag != 'Proper': - raise ValueError("Error: Attempting to process an invalid torsion type as a Proper.") + # TODO: Should we add convenience methods to parameterize a Topology and export directly to AMBER, gromacs, CHARMM, etc.? + # Or should we create an "enhanced" openforcefield System object that knows how to convert to all of these formats? + # We could even create a universal applyParameters(format='AMBER') method that allows us to export to whatever system we want. - # Check that the SMIRKS pattern matches the type it's supposed to - try: - chemenv = ChemicalEnvironment(self.smirks) - thistype = chemenv.getType() - if thistype != 'ProperTorsion': - raise Exception("Error: SMIRKS pattern %s (parameter %s) does not specify a %s torsion, but it is supposed to." % (self.smirks, self.pid, 'Proper')) - except SMIRKSParsingError: - print("Warning: Could not confirm whether smirks pattern %s is a valid %s torsion." % (self.smirks, self.torsiontype)) + # TODO: Should the Topology contain the default box vectors? Or should we require they be specified externally? + # TODO: How do we know if the system is periodic or not? + # TODO: Should we also accept a Molecule as an alternative to a Topology? - if 'fractional_bondorder' in parent.attrib: - self.fractional_bondorder = parent.attrib['fractional_bondorder'] - else: - self.fractional_bondorder = None - # Store parameters. - index = 1 - while 'phase%d'%index in node.attrib: - self.periodicity.append( int(_extractQuantity(node, parent, 'periodicity%d' % index)) ) - self.phase.append( _extractQuantity(node, parent, 'phase%d' % index, unit_name='phase_unit') ) - self.k.append( _extractQuantity(node, parent, 'k%d' % index, unit_name='k_unit') ) - # Optionally handle 'idivf', which divides the periodicity by the specified value - if ('idivf%d' % index) in node.attrib: - idivf = _extractQuantity(node, parent, 'idivf%d' % index) - self.k[-1] /= float(idivf) - index += 1 - # Check for errors, i.e. 'phase' instead of 'phase1' - if len(self.phase)==0: - raise Exception("Error: Torsion with id %s has no parseable phase entries." % self.pid) - - class ImproperTorsionType(object): - - """A SMIRNOFF torsion type for improper torsions.""" - def __init__(self, node, parent): - self.smirks = _validateSMIRKS(node.attrib['smirks'], node=node) - self.periodicity = list() - self.phase = list() - self.k = list() - self.pid = _extractQuantity(node, parent, 'id') - - if node.tag != 'Improper': - raise ValueError("Error: Attempting to process an invalid torsion type as an improper.") - - # Check that the SMIRKS pattern matches the type it's supposed to - try: - chemenv = ChemicalEnvironment(self.smirks) - thistype = chemenv.getType() - if thistype != 'ImproperTorsion': - raise Exception("Error: SMIRKS pattern %s (parameter %s) does not specify a %s torsion, but it is supposed to." % (self.smirks, self.pid, 'Improper')) - except SMIRKSParsingError: - print("Warning: Could not confirm whether smirks pattern %s is a valid %s torsion." % (self.smirks, self.torsiontype)) - if 'fractional_bondorder' in parent.attrib: - self.fractional_bondorder = parent.attrib['fractional_bondorder'] - else: - self.fractional_bondorder = None - # Store parameters. - index = 1 - while 'phase%d'%index in node.attrib: - self.periodicity.append( int(_extractQuantity(node, parent, 'periodicity%d' % index)) ) - self.phase.append( _extractQuantity(node, parent, 'phase%d' % index, unit_name='phase_unit') ) - self.k.append( _extractQuantity(node, parent, 'k%d' % index, unit_name='k_unit') ) - # Optionally handle 'idivf', which divides the periodicity by the specified value - if ('idivf%d' % index) in node.attrib: - idivf = _extractQuantity(node, parent, 'idivf%d' % index) - self.k[-1] /= float(idivf) - index += 1 - # SMIRNOFF applies trefoil (three-fold, because of right-hand rule) impropers unlike AMBER - # If it's an improper, divide by the factor of three internally - if node.tag=='Improper': - self.k[-1] /= 3. - # Check for errors, i.e. 'phase' instead of 'phase1' - if len(self.phase)==0: - raise Exception("Error: Torsion with id %s has no parseable phase entries." % self.pid) - - - def __init__(self, forcefield): - self.ff = forcefield - self._propertorsiontypes = list() - self._impropertorsiontypes = list() - - def registerProperTorsion(self, node, parent): - """Register a SMIRNOFF torsiontype definition for a proper.""" - torsion = PeriodicTorsionGenerator.ProperTorsionType(node, parent) - self._propertorsiontypes.append(torsion) - - def registerImproperTorsion(self, node, parent): - """Register a SMIRNOFF torsiontype definition for an improper.""" - torsion = PeriodicTorsionGenerator.ImproperTorsionType(node, parent) - self._impropertorsiontypes.append(torsion) - - @staticmethod - def parseElement(element, ff): - # Find existing force generator or create new one. - existing = [f for f in ff._forces if isinstance(f, PeriodicTorsionGenerator)] - if len(existing) == 0: - generator = PeriodicTorsionGenerator(ff) - ff.registerGenerator(generator) - else: - generator = existing[0] - - # Register all SMIRNOFF torsion definitions. - for torsion in element.findall('Proper'): - generator.registerProperTorsion(torsion, element) - for torsion in element.findall('Improper'): - generator.registerImproperTorsion(torsion, element) - - def createForce(self, system, topology, verbose=False, **kwargs): - # Find existing force or create new one. - existing = [system.getForce(i) for i in range(system.getNumForces())] - existing = [f for f in existing if type(f) == openmm.PeriodicTorsionForce] - if len(existing) == 0: - force = openmm.PeriodicTorsionForce() - system.addForce(force) - else: - force = existing[0] - - # Iterate over all defined torsion types, allowing later matches to override earlier ones. - torsions = ValenceDict() - for torsion in self._propertorsiontypes: - for atom_indices in topology.unrollSMIRKSMatches(torsion.smirks, aromaticity_model = self.ff._aromaticity_model): - torsions[atom_indices] = torsion - # Handle impropers in similar manner - impropers = ImproperDict() - for improper in self._impropertorsiontypes: - for atom_indices in topology.unrollSMIRKSMatches(improper.smirks, aromaticity_model = self.ff._aromaticity_model): - impropers[atom_indices] = improper - - - if verbose: - print('') - print('PeriodicTorsionGenerator Propers:') - print('') - for torsion in self._propertorsiontypes: - print('%64s : %8d matches' % (torsion.smirks, len(topology.unrollSMIRKSMatches(torsion.smirks, aromaticity_model = self.ff._aromaticity_model)))) - print('') - print('PeriodicTorsionGenerator Impropers:') - print('') - for improper in self._impropertorsiontypes: - print('%64s : %8d matches' % (improper.smirks, len(topology.unrollSMIRKSMatches(improper.smirks, aromaticity_model = self.ff._aromaticity_model)))) - print('') - - # Add all proper torsions to the system. - for (atom_indices, torsion) in torsions.items(): - # Ensure atoms are actually bonded correct pattern in Topology - assert topology._isBonded(atom_indices[0], atom_indices[1]), 'Atom indices %d and %d are not bonded in topology' % (atom_indices[0], atom_indices[1]) - assert topology._isBonded(atom_indices[1], atom_indices[2]), 'Atom indices %d and %d are not bonded in topology' % (atom_indices[1], atom_indices[2]) - assert topology._isBonded(atom_indices[2], atom_indices[3]), 'Atom indices %d and %d are not bonded in topology' % (atom_indices[2], atom_indices[3]) - - for (periodicity, phase, k) in zip(torsion.periodicity, torsion.phase, torsion.k): - force.addTorsion(atom_indices[0], atom_indices[1], atom_indices[2], atom_indices[3], periodicity, phase, k) - if verbose: print('%d torsions added' % (len(torsions))) - - # Check that no topological torsions are missing force parameters - _check_for_missing_valence_terms('PeriodicTorsionForce', topology, torsions.keys(), topology.torsions()) - - # Add all improper torsions to the system - for (atom_indices, improper) in impropers.items(): - # Ensure atoms are actually bonded correct pattern in Topology - # For impropers, central atom is atom 1 - assert topology._isBonded(atom_indices[0], atom_indices[1]), 'Atom indices %d and %d are not bonded in topology' % (atom_indices[0], atom_indices[1]) - assert topology._isBonded(atom_indices[1], atom_indices[2]), 'Atom indices %d and %d are not bonded in topology' % (atom_indices[1], atom_indices[2]) - assert topology._isBonded(atom_indices[1], atom_indices[3]), 'Atom indices %d and %d are not bonded in topology' % (atom_indices[1], atom_indices[3]) - - # Impropers are applied in three paths around the trefoil having the same handedness - for (periodicity, phase, k) in zip(improper.periodicity, improper.phase, improper.k): - force.addTorsion(atom_indices[1], atom_indices[0], atom_indices[2], atom_indices[3], periodicity, phase, k) - force.addTorsion(atom_indices[1], atom_indices[2], atom_indices[3], atom_indices[0], periodicity, phase, k) - force.addTorsion(atom_indices[1], atom_indices[3], atom_indices[0], atom_indices[2], periodicity, phase, k) - if verbose: print('%d impropers added, three per each smirks pattern' % (len(impropers)*3)) - - - - - def labelForce(self, oemol, verbose=False, **kwargs): - """Take a provided OEMol and parse PeriodicTorsionForce terms for this molecule. + def create_openmm_system(self, + topology, + **kwargs): + """Create an OpenMM System representing the interactions for the specified Topology with the current force field Parameters ---------- - oemol : OEChem OEMol object for molecule to be examined + topology : openforcefield.topology.Topology + The ``Topology`` corresponding to the system to be parameterized Returns - --------- - force_terms: list - Returns a list of tuples, [ ([atom id 1, ... atom id N], parameter id, smirks) , (....), ... ] for all forces of this type which would be applied. + ------- + system : simtk.openmm.System + The newly created OpenMM System corresponding to the specified ``topology`` + """ + # Make a deep copy of the topology so we don't accidentally modify it + topology = copy.deepcopy(topology) + # Set the topology aromaticity model to that used by the current forcefield + # TODO: See openforcefield issue #206 for proposed implementation of aromaticity + #topology.set_aromaticity_model(self._aromaticity_model) - # Iterate over all defined torsion types, allowing later matches to override earlier ones. - torsions = ValenceDict() - for torsion in self._propertorsiontypes: - for atom_indices in getSMIRKSMatches_OEMol(oemol, torsion.smirks, aromaticity_model = self.ff._aromaticity_model): - torsions[atom_indices] = torsion - # Handle impropers in similar manner - impropers = ImproperDict() - for improper in self._impropertorsiontypes: - for atom_indices in getSMIRKSMatches_OEMol(oemol, improper.smirks, aromaticity_model = self.ff._aromaticity_model): - impropers[atom_indices] = improper - - if verbose: - print('') - print('PeriodicTorsionGenerator:') - print('') - for torsion in self._propertorsiontypes: - print('%64s : %8d matches' % (torsion.smirks, len(getSMIRKSMatches_OEMol(oemol, torsion.smirks, aromaticity_model = self.ff._aromaticity_model)))) - print('') - print('PeriodicTorsionGenerator Impropers:') - print('') - for improper in self._impropertorsiontypes: - print('%64s : %8d matches' % (improper.smirks, len(getSMIRKSMatches_OEMol(oemol, improper.smirks, aromaticity_model = self.ff._aromaticity_model)))) - print('') - - # Add all torsions to the output list - force_terms = [] - for (atom_indices, torsion) in torsions.items(): - force_terms.append( ([atom_indices[0], atom_indices[1], atom_indices[2], atom_indices[3]], torsion.pid, torsion.smirks) ) - # Add all impropers to the output list - for (atom_indices, improper) in impropers.items(): - force_terms.append( ([atom_indices[1], atom_indices[0], atom_indices[2], atom_indices[3]], improper.pid, improper.smirks) ) - force_terms.append( ([atom_indices[1], atom_indices[2], atom_indices[3], atom_indices[0]], improper.pid, improper.smirks) ) - force_terms.append( ([atom_indices[1], atom_indices[3], atom_indices[0], atom_indices[2]], improper.pid, improper.smirks) ) - - return force_terms - -parsers["PeriodicTorsionForce"] = PeriodicTorsionGenerator.parseElement - -## @private -class NonbondedGenerator(object): - """A NonbondedGenerator constructs a NonbondedForce.""" - - SCALETOL = 1e-5 - - class LennardJonesType(object): - """A SMIRNOFF Lennard-Jones type.""" - def __init__(self, node, parent): - """Currently we support radius definition via 'sigma' or 'rmin_half'.""" - self.smirks = _validateSMIRKS(node.attrib['smirks'], node=node) - self.pid = _extractQuantity(node, parent, 'id') - if 'fractional_bondorder' in parent.attrib: - self.fractional_bondorder = parent.attrib['fractional_bondorder'] - else: - self.fractional_bondorder = None + # Create an empty OpenMM System + system = openmm.System() - # Make sure we don't have BOTH rmin_half AND sigma - try: - a = _extractQuantity(node, parent, 'sigma') - a = _extractQuantity(node, parent, 'rmin_half') - raise Exception("Error: BOTH sigma and rmin_half cannot be specified simultaneously in the .offxml file.") - except: - pass + # Set periodic boundary conditions if specified + if topology.box_vectors is not None: + system.setDefaultPeriodicBoxVectors(*topology.box_vectors) + + # Add particles (both atoms and virtual sites) with appropriate masses + for atom in topology.topology_particles: + system.addParticle(atom.atom.mass) + + # Determine the order in which to process ParameterHandler objects in order to satisfy dependencies + parameter_handlers = self._resolve_parameter_handler_order() + + # Check if any kwargs have been provided that aren't handled by force Handlers + # TODO: Delete this and kwargs from arguments above? + known_kwargs = set() + for parameter_handler in parameter_handlers: + known_kwargs.update(parameter_handler.known_kwargs) + unknown_kwargs = set(kwargs.keys()).difference(known_kwargs) + if len(unknown_kwargs) > 0: + msg = "The following keyword arguments to create_openmm_system() are not used by any registered force Handler: {}\n".format( + unknown_kwargs) + msg += "Known keyword arguments: {}".format(known_kwargs) + raise ValueError(msg) + + # Add forces and parameters to the System + for parameter_handler in parameter_handlers: + parameter_handler.create_force(system, topology, **kwargs) + + # Let force Handlers do postprocessing + for parameter_handler in parameter_handlers: + parameter_handler.postprocess_system(system, topology, **kwargs) - #Handle sigma - try: - self.sigma = _extractQuantity(node, parent, 'sigma') - #Handle rmin_half, AMBER-style - except: - rmin_half = _extractQuantity(node, parent, 'rmin_half', unit_name='sigma_unit') - self.sigma = 2.*rmin_half/(2.**(1./6.)) - self.epsilon = _extractQuantity(node, parent, 'epsilon') - - def __init__(self, forcefield, coulomb14scale, lj14scale): - self.ff = forcefield - self.coulomb14scale = coulomb14scale - self.lj14scale = lj14scale - self._ljtypes = list() - - def registerAtom(self, node, parent): - ljtype = NonbondedGenerator.LennardJonesType(node, parent) - self._ljtypes.append(ljtype) + return system - @staticmethod - def parseElement(element, ff): - existing = [f for f in ff._forces if isinstance(f, NonbondedGenerator)] - if len(existing) == 0: - generator = NonbondedGenerator(ff, float(element.attrib['coulomb14scale']), float(element.attrib['lj14scale'])) - ff.registerGenerator(generator) - else: - # Multiple tags were found, probably in different files. Simply add more types to the existing one. - generator = existing[0] - if abs(generator.coulomb14scale - float(element.attrib['coulomb14scale'])) > NonbondedGenerator.SCALETOL or \ - abs(generator.lj14scale - float(element.attrib['lj14scale'])) > NonbondedGenerator.SCALETOL: - raise ValueError('Found multiple NonbondedForce tags with different 1-4 scales') - for atom in element.findall('Atom'): - generator.registerAtom(atom, element) - - def createForce(self, system, topology, nonbondedMethod=NoCutoff, nonbondedCutoff=0.9, verbose=False, **args): - methodMap = {NoCutoff:openmm.NonbondedForce.NoCutoff, - CutoffNonPeriodic:openmm.NonbondedForce.CutoffNonPeriodic, - CutoffPeriodic:openmm.NonbondedForce.CutoffPeriodic, - Ewald:openmm.NonbondedForce.Ewald, - PME:openmm.NonbondedForce.PME} - if nonbondedMethod not in methodMap: - raise ValueError('Illegal nonbonded method for NonbondedForce; method given was %s' % nonbondedMethod) - force = openmm.NonbondedForce() - force.setNonbondedMethod(methodMap[nonbondedMethod]) - force.setCutoffDistance(nonbondedCutoff) - if 'ewaldErrorTolerance' in args: - force.setEwaldErrorTolerance(args['ewaldErrorTolerance']) - if 'useDispersionCorrection' in args: - force.setUseDispersionCorrection(bool(args['useDispersionCorrection'])) - system.addForce(force) - - # Iterate over all defined Lennard-Jones types, allowing later matches to override earlier ones. - atoms = ValenceDict() - for ljtype in self._ljtypes: - for atom_indices in topology.unrollSMIRKSMatches(ljtype.smirks, aromaticity_model = self.ff._aromaticity_model): - atoms[atom_indices] = ljtype - - if verbose: - print('') - print('NonbondedForceGenerator:') - print('') - for ljtype in self._ljtypes: - print('%64s : %8d matches' % (ljtype.smirks, len(topology.unrollSMIRKSMatches(ljtype.smirks, aromaticity_model = self.ff._aromaticity_model)))) - print('') - - # Add all Lennard-Jones terms to the system. - # Create all particles. - for atom in topology.atoms(): - force.addParticle(0.0, 1.0, 0.0) - # Set the particle Lennard-Jones terms. - for (atom_indices, ljtype) in atoms.items(): - force.setParticleParameters(atom_indices[0], 0.0, ljtype.sigma, ljtype.epsilon) - - # Check that no topological torsions are missing force parameters - _check_for_missing_valence_terms('NonbondedForce Lennard-Jones parameters', topology, atoms.keys(), topology.atoms()) - - # Set the partial charges based on reference molecules. - for reference_molecule in topology._reference_molecules: - atom_mappings = topology._reference_to_topology_atom_mappings[reference_molecule] - # Retrieve charges from reference molecule, stored by atom index - charge_by_atom = {} - for atom in reference_molecule.GetAtoms(): - charge_by_atom[atom.GetIdx()] = atom.GetPartialCharge() - - # Loop over mappings and copy NB parameters from reference molecule - # to other instances of the molecule - for atom_mapping in atom_mappings: - for (atom_index, map_atom_index) in atom_mapping.items(): - # Retrieve NB params for reference atom (charge not set yet) - charge, sigma, epsilon = force.getParticleParameters(map_atom_index) - # Look up the charge on the atom in the reference molecule - charge = charge_by_atom[atom_index]*unit.elementary_charge - - # Set parameters for equivalent atom in other instance of - # this molecule - force.setParticleParameters(map_atom_index, charge, sigma, epsilon) - # TODO: Should we check that there are no missing charges? - - def postprocessSystem(self, system, topology, verbose=False, **args): - atoms = [ atom for atom in topology.atoms() ] - natoms = len(atoms) - - # Create exceptions based on bonds. - bondIndices = [] - for (atom1, atom2) in topology.bonds(): - if (atom1.index < 0) or (atom2.index < 0) or (atom1.index >= natoms) or (atom2.index >= natoms): - raise Exception('atom indices out of bounds') - bondIndices.append((atom1.index, atom2.index)) - - # Create the exceptions. - nonbonded = [f for f in system.getForces() if isinstance(f, openmm.NonbondedForce)][0] - nonbonded.createExceptionsFromBonds(bondIndices, self.coulomb14scale, self.lj14scale) - - def labelForce(self, oemol, verbose=False, **kwargs): - """Take a provided OEMol and parse HarmonicBondForce terms for this molecule. + def create_parmed_structure(self, + topology, + positions, + **kwargs): + """Create a ParmEd Structure object representing the interactions for the specified Topology with the current force field + + This method creates a `ParmEd `_ ``Structure`` object containing a topology, positions, and parameters. Parameters ---------- - oemol : OEChem OEMol object for molecule to be examined + topology : openforcefield.topology.Topology + The ``Topology`` corresponding to the ``System`` object to be created. + positions : simtk.unit.Quantity of dimension (natoms,3) with units compatible with angstroms + The positions corresponding to the ``System`` object to be created Returns - --------- - force_terms: list - Returns a list of tuples, [ ([atom id 1, ... atom id N], parameter id, smirks) , (....), ... ] for all forces of this type which would be applied. - """ - - # Iterate over all defined Lennard-Jones types, allowing later matches to override earlier ones. - atoms = ValenceDict() - for ljtype in self._ljtypes: - for atom_indices in getSMIRKSMatches_OEMol(oemol, ljtype.smirks, aromaticity_model = self.ff._aromaticity_model): - atoms[atom_indices] = ljtype - - if verbose: - print('') - print('NonbondedForceGenerator:') - print('') - for ljtype in self._ljtypes: - print('%64s : %8d matches' % (ljtype.smirks, len(getSMIRKSMatches_OEMol(oemol, ljtype.smirks, aromaticity_model = self.ff._aromaticity_model)))) - print('') - - # Add all Lennard-Jones terms to the output list - force_terms = [] - for (atom_indices, ljtype) in atoms.items(): - force_terms.append( ([atom_indices[0]], ljtype.pid, ljtype.smirks) ) - - return force_terms - - -parsers["NonbondedForce"] = NonbondedGenerator.parseElement - -## @private -class BondChargeCorrectionGenerator(object): - """A BondChargeCorrectionGenerator handles .""" - - class BondChargeCorrectionType(object): - """A SMIRNOFF bond type.""" - def __init__(self, node, parent): - self.smirks = _validateSMIRKS(node.attrib['smirks'], node=node) - self.increment = _extractQuantity(node, parent, 'increment') - self.pid = _extractQuantity(node, parent, 'id') - # If no units are specified, assume elementary charge - if type(self.increment) == float: - self.increment *= unit.elementary_charge - - def __init__(self, forcefield, initialChargeMethod): - self.ff = forcefield - self._bondChargeCorrections = list() - self._initialChargeMethod = initialChargeMethod - self._oechargemethod = 'OECharges_' + initialChargeMethod - if not hasattr(oequacpac, self._oechargemethod): - raise Exception("BondChargeCorrectionGenerator: initialChargeMethod attribute was '%s', but '%s' was not found in oequacpac available methods." % (initialChargeMethod, self._oechargemethod)) - - def registerBondChargeCorrection(self, node, parent): - """Register a SMIRNOFF bondtype definition.""" - bond = BondChargeCorrectionGenerator.BondChargeCorrectionType(node, parent) - self._bondChargeCorrections.append(bond) - - @staticmethod - def parseElement(element, ff): - # Find existing force generator or create new one. - existing = [f for f in ff._forces if isinstance(f, BondChargeCorrectionGenerator)] - if len(existing) == 0: - generator = BondChargeCorrectionGenerator(ff, element.attrib['method']) - ff.registerGenerator(generator) - else: - # Check that new bond charge generator doesn't request a different method from existing one. - if element.attrib['method'] != existing[0]._initialChargeMethod: - raise Exception("Existing BondChargeCorrectionGenerator uses initial charging method '%s' while new BondChargeCorrectionGenerator requests '%s'" % (existing[0]._initialChargeMethod, element.attrib['method'])) - - generator = existing[0] - - # Register all SMIRNOFF bond definitions. - for bond in element.findall('BondChargeCorrection'): - generator.registerBondChargeCorrection(bond, element) + ------- + structure : parmed.Structure + The newly created ``parmed.Structure`` object - def createForce(self, system, topology, verbose=False, **args): - # No forces are created by this generator. - pass + """ + raise NotImplementedError + import parmed + # TODO: Automagically handle expansion of virtual sites? Or is Topology supposed to do that? - def labelForce(self, oemol, verbose=False, **kwargs): - """Take a provided OEMol and parse BondChargeCorrection terms for this molecule. + # Create OpenMM System + system = self.create_openmm_system( + topology, **kwargs) - Parameters: - ----------- - oemol : OEChem OEMol object for molecule to be examined + # Create a ParmEd Structure object + structure = parmed.openmm.topsystem.load_topology( + topology.to_openmm(), system, positions) - Returns - ------- - parameter_terms : list - Returns a list of tuples, [ ([atom id 1, atom id 2], parameter id, smirks), (...), ...] for all sets of atoms to which this parameter would be applied. - """ - bccs = {} - for bcc in self._bondChargeCorrections: - for atom_indices in getSMIRKSMatches_OEMol(oemol, bcc.smirks, aromaticity_model = self.ff._aromaticity_model): - bccs[atom_indices] = bcc - - if verbose: - print('') - print('BondChargeCorrectionGenerator:') - print('') - for bcc in self._bondChargeCorrections: - print('%64s : %8d matches' % (bcc.smirks, len(getSMIRKSMatches_OEMol(oemol, bcc.smirks, aromaticity_model = self.ff._aromaticity_model)))) - print('') - - # Add all BCCs to the output list - force_terms = [] - for (atom_indices, bcc) in bccs.items(): - force_terms.append( ([atom_indices[0], atom_indices[1]], bcc.pid, bcc.smirks) ) - - return force_terms - - def postprocessSystem(self, system, topology, verbose=False, chargeMethod=None, **args): - if chargeMethod != 'BCC': - # Only apply charge corrections if chargeMethod is 'BCC' - return - - # Iterate over all defined bond charge corrections, allowing later matches to override earlier ones. - bonds = ValenceDict() - for bond in self._bondChargeCorrections: - for atom_indices in topology.unrollSMIRKSMatches(bond.smirks, aromaticity_model = self.ff._aromaticity_model): - bonds[atom_indices] = bond - - if verbose: - print('') - print('Bond charge corrections:') - print('') - for bond in self._bondChargeCorrections: - print('%64s %12.6f : %8d matches' % (bond.smirks, bond.increment / unit.elementary_charge, len(topology.unrollSMIRKSMatches(bond.smirks, aromaticity_model = self.ff._aromaticity_model)))) - print('') - - # Apply bond charge increments - for force in system.getForces(): - if force.__class__.__name__ in ['NonbondedForce']: - for (atom_indices, bond) in bonds.items(): - # Retrieve parameters - [charge0, sigma0, epsilon0] = force.getParticleParameters(atom_indices[0]) - [charge1, sigma1, epsilon1] = force.getParticleParameters(atom_indices[1]) - # Apply bond charge increment - charge0 -= bond.increment - charge1 += bond.increment - # Update charges - force.setParticleParameters(atom_indices[0], charge0, sigma0, epsilon0) - force.setParticleParameters(atom_indices[1], charge1, sigma1, epsilon1) - -parsers["BondChargeCorrections"] = BondChargeCorrectionGenerator.parseElement - -## @private -class GBSAForceGenerator(object): - """A GBSAForceGenerator constructs GBSA forces.""" - # TODO: Differentiate between global and per-particle parameters for each model. - - # Global parameters for surface area (SA) component of model - SA_expected_parameters = { - 'ACE' : ['surface_area_penalty', 'solvent_radius'], - None : [], - } - - # Per-particle parameters for generalized Born (GB) model - GB_expected_parameters = { - 'HCT' : ['radius', 'scale'], - 'OBC1' : ['radius', 'scale'], - 'OBC2' : ['radius', 'scale'], - } - - class GBSAType(object): - """A SMIRNOFF GBSA type.""" - def __init__(self, node, parent): - """Create a GBSAType""" - self.smirks = _validateSMIRKS(node.attrib['smirks'], node=node) - - # Store model parameters. - gb_model = parent.attrib['gb_model'] - expected_parameters = GBSAForceGenerator.GB_expected_parameters[gb_model] - provided_parameters = list() - missing_parameters = list() - for name in expected_parameters: - if name in node.attrib: - provided_parameters.append(name) - value = _extractQuantity(node, parent, name) - setattr(self, name, value) - else: - missing_parameters.append(name) - if len(missing_parameters) > 0: - msg = 'GBSAForce: missing per-atom parameters for tag %s' % str(node) - msg += 'model "%s" requires specification of per-atom parameters %s\n' % (gb_model, str(expected_parameters)) - msg += 'provided parameters : %s\n' % str(provided_parameters) - msg += 'missing parameters: %s' % str(missing_parameters) - raise Exception(msg) - - def __init__(self, forcefield, element): - self.ff = forcefield - self._gbsa_types = list() - - # Initialize GB model - gb_model = element.attrib['gb_model'] - valid_GB_models = GBSAForceGenerator.GB_expected_parameters.keys() - if not gb_model in valid_GB_models: - raise Exception('Specified GBSAForce model "%s" not one of valid models: %s' % (gb_model, valid_GB_models)) - self.gb_model = gb_model - - # Initialize SA model - sa_model = element.attrib['sa_model'] - valid_SA_models = GBSAForceGenerator.SA_expected_parameters.keys() - if not sa_model in valid_SA_models: - raise Exception('Specified GBSAForce SA_model "%s" not one of valid models: %s' % (sa_model, valid_SA_models)) - self.sa_model = sa_model - - # Store parameters for GB and SA models - # TODO: Deep copy? - self.parameters = element.attrib - - def registerAtom(self, node, parent): - gbsa_type = GBSAForceGenerator.GBSAType(node, parent) - self._gbsa_types.append(gbsa_type) - - def checkCompatibility(self, generator): - """ - Check compatibility of this generator with another generators. - """ - generator = existing[0] - if (generator.gb_model != self.gb_model): - raise ValueError('Found multiple GBSAForce tags with different GB model specifications') - if (generator.sa_model != self.sa_model): - raise ValueError('Found multiple GBSAForce tags with different SA model specifications') - # TODO: Check other attributes (parameters of GB and SA models) automatically? + return structure - @staticmethod - def parseElement(element, ff): - existing = [f for f in ff._forces if isinstance(f, GBSAForceGenerator)] - generator = GBSAForceGenerator(ff, element) - if len(existing) > 0: - generator.checkCompatibility(existing[0]) - ff.registerGenerator(generator) - for atom in element.findall('Atom'): - generator.registerAtom(atom, element) - - def createForce(self, system, topology, verbose=False, **args): - from openforcefield.typing.engines.smirnoff import gbsaforces - force_class = getattr(gbsaforces, self.gb_model) - force = force_class(**self.parameters) - system.addForce(force) - - # Iterate over all defined GBSA types, allowing later matches to override earlier ones. - atoms = ValenceDict() - for gbsa_type in self._gbsa_types: - for atom_indices in topology.unrollSMIRKSMatches(gbsa_type.smirks, aromaticity_model = self.ff._aromaticity_model): - atoms[atom_indices] = gbsa_type - - if verbose: - print('') - print('GBSAForceGenerator:') - print('') - for gbsa_type in self._gbsa_types: - print('%64s : %8d matches' % (gbsa_type.smirks, len(topology.unrollSMIRKSMatches(gbsa_type.smirks, aromaticity_model = self.ff._aromaticity_model)))) - print('') - - # Add all GBSA terms to the system. - expected_parameters = GBSAForceGenerator.GB_expected_parameters[self.gb_model] - # Create all particle parmeters. - nparams = 1 + len(expected_parameters) # charge + GBSA parameters - params = [ 0.0 for i in range(nparams) ] - for atom in topology.atoms(): - force.addParticle(params) - # Set the particle Lennard-Jones terms. - natoms = sum([1 for atom in topology.atoms()]) - for (atom_indices, gbsa_type) in atoms.items(): - params = [0] + [ getattr(gbsa_type, name) for name in expected_parameters ] - force.setParticleParameters(atom_indices[0], params) - - # Set the partial charges based on reference molecules. - for reference_molecule in topology._reference_molecules: - atom_mappings = topology._reference_to_topology_atom_mappings[reference_molecule] - for atom_mapping in atom_mappings: - for (atom, atom_index) in zip(reference_molecule.GetAtoms(), atom_mapping): - params = force.getParticleParameters(atom_index) - params = list(params) - params[0] = atom.GetPartialCharge() * unit.elementary_charge - force.setParticleParameters(atom_index, params) - - def postprocessSystem(self, system, topology, verbose=False, **args): - pass - - def labelForce(self, oemol, verbose=False, **kwargs): - """Take a provided OEMol and parse HarmonicBondForce terms for this molecule. + def label_molecules(self, topology): + """Return labels for a list of molecules corresponding to parameters from this force field. + For each molecule, a dictionary of force types is returned, and for each force type, + each force term is provided with the atoms involved, the parameter id assigned, and the corresponding SMIRKS. Parameters ---------- - oemol : OEChem OEMol object for molecule to be examined + topology : openforcefield.topology.Topology + A Topology object containing one or more unique molecules to be labeled Returns - --------- - force_terms: list - Returns a list of tuples, [ ([atom id 1, ... atom id N], parameter id, smirks) , (....), ... ] for all forces of this type which would be applied. - """ - - # Iterate over all defined Lennard-Jones types, allowing later matches to override earlier ones. - atoms = ValenceDict() - for gbsa_type in self._ljtypes: - for atom_indices in getSMIRKSMatches_OEMol(oemol, gbsa_type.smirks, aromaticity_model = self.ff._aromaticity_model): - atoms[atom_indices] = gbsa_type - - if verbose: - print('') - print('GBSAForceGenerator:') - print('') - for ljtype in self._ljtypes: - print('%64s : %8d matches' % (gbsa_type.smirks, len(getSMIRKSMatches_OEMol(oemol, gbsa_type.smirks, aromaticity_model = self.ff._aromaticity_model)))) - print('') + ------- + molecule_labels : list + List of labels for unique molecules. Each entry in the list corresponds to + one unique molecule in the Topology and is a dictionary keyed by force type, + i.e., ``molecule_labels[0]['HarmonicBondForce']`` gives details for the harmonic + bond parameters for the first molecule. Each element is a list of the form: + ``[ ( [ atom1, ..., atomN], parameter_id, SMIRKS), ... ]`` - # Add all GBSA terms to the output list - force_terms = [] - for (atom_indices, gbsa_type) in atoms.items(): - force_terms.append( ([atom_indices[0]], gbsa_type.pid, gbsa_type.smirks) ) + .. todo :: - return force_terms + What is the most useful API for this method? + Should we instead accept :class:`Molecule` objects as input and individually return labels? + Should we attach the labels to the :class:`Molecule` object? + Or should we label all interactions in a :class:`Topology` instead of just labeling its ``unique_molecules``? -parsers["GBSAForce"] = GBSAForceGenerator.parseElement + """ + from openforcefield.topology import Topology + # Loop over molecules and label + molecule_labels = list() + for molecule_idx, molecule in enumerate(topology.reference_molecules): + top_mol = Topology.from_molecules([molecule]) + current_molecule_labels = dict() + for tag, parameter_handler in self._parameter_handlers.items(): + matches = parameter_handler.find_matches(top_mol) + current_molecule_labels[tag] = matches + + molecule_labels.append(current_molecule_labels) + return molecule_labels diff --git a/openforcefield/typing/engines/smirnoff/forcefield_utils.py b/openforcefield/typing/engines/smirnoff/forcefield_utils.py deleted file mode 100644 index 8f5f8c1e7..000000000 --- a/openforcefield/typing/engines/smirnoff/forcefield_utils.py +++ /dev/null @@ -1,473 +0,0 @@ -#!/bin/env python - -#============================================================================================= -# MODULE DOCSTRING -#============================================================================================= - -""" -forcefield_utils.py - -Utilities relating to OpenMM ForceField replacement using SMIRKS-based matching. - -AUTHORS - -David L. Mobley - -Based loosely on code from github.com/choderalab/openmoltools, and especially -parts from John Chodera and Kyle Beauchamp. -""" -#============================================================================================= -# GLOBAL IMPORTS -#============================================================================================= - -import os -from openforcefield.typing.engines.smirnoff import ForceField -from openforcefield.utils import get_data_filename -import simtk.openmm -from simtk.openmm import app -import simtk.openmm as mm -from simtk.openmm.app import element as elem -from simtk.openmm.app import Topology -import numpy as np -from openmoltools import system_checker -import copy - -import openeye.oechem -import openeye.oeomega -import openeye.oequacpac -from openeye import oechem - -from simtk import openmm, unit -import parmed - -#============================================================================= -# UTILITY FUNCTIONS -#============================================================================= - - -def create_system_from_amber( prmtop_filename, crd_filename, verbose = False ): - """Utility function. Create and return an OpenMM System given a prmtop and - crd, AMBER format files. - - Parameters - ---------- - prmtop_filename : str (filename) - Filename of input AMBER format prmtop file - crd_filename : str (filename) - Filename of input AMBER format crd file - - Returns - _______ - topology : OpenMM Topology - system : OpenMM System - positions : initial atomic positions (OpenMM) -""" - - # Create System object - prmtop = app.AmberPrmtopFile(prmtop_filename) - topology = prmtop.topology - system = prmtop.createSystem(nonbondedMethod = app.NoCutoff, constraints = None, implicitSolvent = None ) - - # Read coordinates - crd = app.AmberInpcrdFile( crd_filename ) - positions = crd.getPositions() - - return (topology, system, positions) - -def create_system_from_molecule(forcefield, mol, verbose=False): - """ - Generate a System from the given OEMol and SMIRNOFF forcefield, return the resulting System. - - Parameters - ---------- - forcefield : ForceField - SMIRNOFF forcefield - mol : oechem.OEMol - Molecule to test (must have coordinates) - - - Returns - ---------- - topology : OpenMM Topology - system : OpenMM System - positions : initial atomic positions (OpenMM) - """ - # Create system - from openforcefield.utils import generateTopologyFromOEMol - topology = generateTopologyFromOEMol(mol) - system = forcefield.createSystem(topology, [mol], verbose=verbose) - - # Get positions - coordinates = mol.GetCoords() - natoms = len(coordinates) - positions = np.zeros([natoms,3], np.float32) - for index in range(natoms): - (x,y,z) = coordinates[index] - positions[index,0] = x - positions[index,1] = y - positions[index,2] = z - positions = unit.Quantity(positions, unit.angstroms) - - return topology, system, positions - -def compare_system_energies( topology0, topology1, system0, system1, positions0, positions1=None, label0="AMBER system", label1 = "SMIRNOFF system", verbose = True, skip_assert = False, skip_improper = False ): - """ - Given two OpenMM systems, check that their energies and component-wise - energies are consistent, and return these. The same positions will be used - for both systems unless a second set of positions is provided. - - Parameters - ---------- - topology0 : OpenMM Topology - Topology of first system - topology1 : OpenMM Topology - Topology of second system - system0 : OpenMM System - First system for comparison (usually from AMBER) - system1 : OpenMM System - Second system for comparison (usually from SMIRNOFF) - positions0 : simtk.unit.Quantity wrapped - Positions to use for energy evaluation comparison - positions1 (optional) : simtk.unit.Quantity wrapped (optional) - Positions to use for second OpenMM system; original positions are used - if this is not provided - label0 (optional) : str - String labeling system0 for output. Default, "AMBER system" - label1 (optional) : str - String labeling system1 for output. Default, "SMIRNOFF system" - verbose (optional) : bool - Print out info on energies, True/False (default True) - skip_assert (optional) : bool - Skip assertion that energies must be equal within specified tolerance. Default False. - skip_improper (optional) : bool - Skip detailed checking of force terms on impropers (helpful here if comparing with AMBER force fields using different definitions of impropers.) Default False. - - Returns - ---------- - groups0 : dict - As returned by openmoltools.system_checker.check_energy_groups, - a dictionary with keys "bond", "angle", "nb", "torsion" and values - corresponding to the energies of these components for the first simulation object - groups1 : dict - As returned by openmoltools.system_checker.check_energy_groups, - a dictionary with keys "bond", "angle", "nb", "torsion" and values - corresponding to the energies of these components for the second simulation object - energy0 : simtk.unit.Quantity - Energy of first system - energy1 : simtk.unit.Quantity - Energy of second system - - TO DO: - Allow energy extraction/comparison of terms specified by particular - SMARTS queries i.e. for specific bond, angle, or torsional terms. - """ - - # Create integrator - timestep = 1.0 * unit.femtoseconds - integrator0 = simtk.openmm.VerletIntegrator( timestep ) - integrator1 = simtk.openmm.VerletIntegrator( timestep ) - - # Grab second positions - if positions1 == None: - positions1 = copy.deepcopy( positions0 ) - - # Create simulations - platform = simtk.openmm.Platform.getPlatformByName("Reference") - simulation0 = app.Simulation( topology0, system0, integrator0, platform = platform ) - simulation0.context.setPositions(positions0) - simulation1 = app.Simulation( topology1, system1, integrator1, platform = platform ) - simulation1.context.setPositions(positions1) - - # Print what torsions were found if verbose - if verbose: - # Build list of atoms for debugging info - atoms0 = [ atom for atom in simulation0.topology.atoms() ] - atoms1 = [ atom for atom in simulation1.topology.atoms() ] - # Loop over first system and print torsion info - for force in simulation0.system.getForces(): - if type(force) == mm.PeriodicTorsionForce: - print("Num (type) \t Num (type) \t Num (type) \t Num (type) \t per \t phase \t k0") - for k in range(force.getNumTorsions()): - i0, i1, i2, i3, per, phase, k0 = force.getTorsionParameters(k) - print("%3s (%3s)- %3s (%3s)- \t %s (%3s)- \t %3s (%3s)- \t %f \t %f \t %f " % (i0, atoms0[i0].name, i1, atoms0[i1].name, i2, atoms0[i2].name, i3, atoms0[i3].name, per, phase/unit.degree, k0/unit.kilojoule_per_mole) ) - for force in simulation1.system.getForces(): - if type(force) == mm.PeriodicTorsionForce: - print("Num (type) \t Num (type) \t Num (type) \t Num (type) \t per \t phase \t k0") - for k in range(force.getNumTorsions()): - i0, i1, i2, i3, per, phase, k0 = force.getTorsionParameters(k) - print("%3s (%3s)- %3s (%3s)- %3s (%3s)- %3s (%3s) - %f \t %f \t %f " % (i0, atoms1[i0].name, i1, atoms1[i1].name, i2, atoms1[i2].name, i3, atoms1[i3].name, per, phase/unit.degree, k0/unit.kilojoule_per_mole) ) - - - - - # Do energy comparison, print info if desired - syscheck = system_checker.SystemChecker( simulation0, simulation1 ) - if not skip_assert: - # Only check force terms if we want to make sure energies are identical - syscheck.check_force_parameters(skipImpropers = skip_improper) - groups0, groups1 = syscheck.check_energy_groups(skip_assert = skip_assert) - energy0, energy1 = syscheck.check_energies(skip_assert = skip_assert) - if verbose: - print("Energy of %s: " % label0, energy0 ) - print("Energy of %s: " % label1, energy1 ) - print("\nComponents of %s:" % label0 ) - for key in groups0.keys(): - print("%s: " % key, groups0[key] ) - print("\nComponents of %s:" % label1 ) - for key in groups1.keys(): - print("%s: " % key, groups1[key] ) - - # Return - return groups0, groups1, energy0, energy1 - - -def compare_molecule_energies( prmtop, crd, forcefield, mol, verbose = True, skip_assert=False, skip_improper = False): - """ - Compare energies for OpenMM Systems/topologies created from an AMBER prmtop - and crd versus from a SMIRNOFF forcefield file and OEMol which should - parameterize the same system with same parameters. - - - Parameters - ---------- - prmtop_filename : str (filename) - Filename of input AMBER format prmtop file - crd_filename : str (filename) - Filename of input AMBER format crd file - forcefield : ForceField - SMIRNOFF forcefield - mol : oechem.OEMol - Molecule to test - verbose (optional): Bool - Print out info. Default: True - skip_assert : bool - Skip assertion that energies must be equal within tolerance. Default, False. - skip_improper (optional) : bool - Skip detailed checking of force terms on impropers (helpful here if comparing with AMBER force fields using different definitions of impropers.) Default False. - - - Returns - -------- - groups0 : dict - As returned by openmoltools.system_checker.check_energy_groups, - a dictionary with keys "bond", "angle", "nb", "torsion" and values - corresponding to the energies of these components for the first simulation object - groups1 : dict - As returned by openmoltools.system_checker.check_energy_groups, - a dictionary with keys "bond", "angle", "nb", "torsion" and values - corresponding to the energies of these components for the second simulation object - energy0 : simtk.unit.Quantity - Energy of first system - energy1 : simtk.unit.Quantity - Energy of second system - """ - - ambertop, ambersys, amberpos = create_system_from_amber( prmtop, crd ) - smirfftop, smirffsys, smirffpos = create_system_from_molecule(forcefield, mol, verbose = verbose) - - groups0, groups1, energy0, energy1 = compare_system_energies( ambertop, - smirfftop, ambersys, smirffsys, amberpos, verbose = verbose, skip_assert = skip_assert, skip_improper = skip_improper ) - - return groups0, groups1, energy0, energy1 - - -def get_molecule_parameterIDs( oemols, ffxml): - """Process a list of oemols with a specified SMIRNOFF ffxml file and determine which parameters are used by which molecules, returning collated results. - - - Parameters - ---------- - oemols : list - List of OpenEye OEChem molecules to parse; must have explicit hydrogens. - - Returns - ------- - parameters_by_molecule : dict - Parameter IDs used in each molecule, keyed by isomeric SMILES - generated from provided OEMols. Each entry in the dict is a list - which does not necessarily have unique entries; i.e. parameter IDs - which are used more than once will occur multiple times. - - parameters_by_ID : dict - Molecules in which each parameter ID occur, keyed by parameter ID. - Each entry in the dict is a set of isomeric SMILES for molecules - in which that parameter occurs. No frequency information is stored. - - """ - - # Create storage - parameters_by_molecule = {} - parameters_by_ID = {} - - # Generate isomeric SMILES - isosmiles = list() - for mol in oemols: - smi = oechem.OECreateIsoSmiString(mol) - if not smi in isosmiles: - isosmiles.append(smi) - # If the molecule is already here, raise exception - else: - raise ValueError("Error: get_molecule_parameterIDs has been provided a list of oemols which contains the same molecule, having isomeric smiles %s, more than once." % smi ) - # Label molecules - ff = ForceField( ffxml ) - labels = ff.labelMolecules( oemols ) - - # Organize labels into output dictionary by looping over all molecules/smiles - for idx in range(len(isosmiles)): - # Pull smiles, initialize storage - smi = isosmiles[idx] - parameters_by_molecule[smi] = [] - - # Organize data for this molecule - data = labels[idx] - for force_type in data.keys(): - for (atom_indices, pid, smirks) in data[force_type]: - # Store pid to molecule - parameters_by_molecule[smi].append(pid) - - # Store which molecule this pid occurred in - if pid not in parameters_by_ID: - parameters_by_ID[pid] = set() - parameters_by_ID[pid].add(smi) - else: - parameters_by_ID[pid].add(smi) - - return parameters_by_molecule, parameters_by_ID - -def getMolParamIDToAtomIndex( oemol, ff): - """Take an OEMol and a SMIRNOFF forcefield object and return a dictionary, keyed by parameter ID, where each entry is a tuple of ( smirks, [[atom1, ... atomN], [atom1, ... atomN]) giving the SMIRKS corresponding to that parameter ID and a list of the atom groups in that molecule that parameter is applied to. - - Parameters - ---------- - oemol : OEMol - OpenEye OEMol with the molecule to investigate. - ff : ForceField - SMIRNOFF ForceField object (obtained from an ffxml via ForceField(ffxml)) containing FF of interest. - - Returns - ------- - param_usage : dictionary - Dictionary, keyed by parameter ID, where each entry is a tuple of ( smirks, [[atom1, ... atomN], [atom1, ... atomN]) giving the SMIRKS corresponding to that parameter ID and a list of the atom groups in that molecule that parameter is applied to. - - """ - - labels = ff.labelMolecules([oemol]) - param_usage = {} - for mol_entry in range(len(labels)): - for force in labels[mol_entry].keys(): - for (atom_indices, pid, smirks) in labels[mol_entry][force]: - if not pid in param_usage: - param_usage[pid] = (smirks, [atom_indices]) - else: - param_usage[pid][1].append( atom_indices ) - - return param_usage - -def merge_system( topology0, topology1, system0, system1, positions0, positions1, label0="AMBER system", label1 = "SMIRNOFF system", verbose = True): - """Merge two given OpenMM systems. Returns the merged OpenMM System. - - Parameters - ---------- - topology0 : OpenMM Topology - Topology of first system (i.e. a protein) - topology1 : OpenMM Topology - Topology of second system (i.e. a ligand) - system0 : OpenMM System - First system for merging (usually from AMBER) - system1 : OpenMM System - Second system for merging (usually from SMIRNOFF) - positions0 : simtk.unit.Quantity wrapped - Positions to use for energy evaluation comparison - positions1 (optional) : simtk.unit.Quantity wrapped (optional) - Positions to use for second OpenMM system - label0 (optional) : str - String labeling system0 for output. Default, "AMBER system" - label1 (optional) : str - String labeling system1 for output. Default, "SMIRNOFF system" - verbose (optional) : bool - Print out info on topologies, True/False (default True) - - Returns - ---------- - topology : OpenMM Topology - system : OpenMM System - positions: unit.Quantity position array - """ - - #Load OpenMM Systems to ParmEd Structures - structure0 = parmed.openmm.load_topology( topology0, system0 ) - structure1 = parmed.openmm.load_topology( topology1, system1 ) - - #Merge parameterized Structure - structure = structure0 + structure1 - topology = structure.topology - - #Concatenate positions arrays - positions_unit = unit.angstroms - positions0_dimensionless = np.array( positions0 / positions_unit ) - positions1_dimensionless = np.array( positions1 / positions_unit ) - - coordinates = np.vstack((positions0_dimensionless,positions1_dimensionless)) - natoms = len(coordinates) - positions = np.zeros([natoms,3], np.float32) - for index in range(natoms): - (x,y,z) = coordinates[index] - positions[index,0] = x - positions[index,1] = y - positions[index,2] = z - positions = unit.Quantity(positions, positions_unit) - - #Generate merged OpenMM system - system = structure.createSystem() - - if verbose: - print("Generating ParmEd Structures...\n \t{}: {}\n \t{}: {}\n".format(label0, structure0, label1, structure1)) - print("Merged ParmEd Structure: {}".format( structure )) - - return topology, system, positions - - -def save_system_to_amber( topology, system, positions, prmtop, crd ): - """Save an OpenMM System, with provided topology and positions, to AMBER prmtop and coordinate files. - - Parameters - ---------- - topology : OpenMM Topology - Topology of the system to be saved, perhaps as loaded from a PDB file or similar. - system : OpenMM System - Parameterized System to be saved, containing components represented by Topology - positions : unit.Quantity position array - Position array containing positions of atoms in topology/system - prmtop : filename - AMBER parameter file name to write - crd : filename - AMBER coordinate file name (ASCII crd format) to write - - """ - - structure = parmed.openmm.topsystem.load_topology( topology, system, positions ) - structure.save( prmtop, overwrite = True, format="amber" ) - structure.save( crd, format='rst7', overwrite = True) - - -def save_system_to_gromacs( topology, system, positions, top, gro ): - """Save an OpenMM System, with provided topology and positions, to AMBER prmtop and coordinate files. - - Parameters - ---------- - topology : OpenMM Topology - Topology of the system to be saved, perhaps as loaded from a PDB file or similar. - system : OpenMM System - Parameterized System to be saved, containing components represented by Topology - positions : unit.Quantity position array - Position array containing positions of atoms in topology/system - top : filename - GROMACS topology file name to write - gro : filename - GROMACS coordinate file name (.gro format) to write - - """ - - structure = parmed.openmm.topsystem.load_topology( topology, system, positions ) - structure.save( top, overwrite = True, format="gromacs") - structure.save( gro, overwrite = True, format="gro") diff --git a/openforcefield/typing/engines/smirnoff/io.py b/openforcefield/typing/engines/smirnoff/io.py new file mode 100644 index 000000000..953bae0dd --- /dev/null +++ b/openforcefield/typing/engines/smirnoff/io.py @@ -0,0 +1,336 @@ +#!/usr/bin/env python + +#============================================================================================= +# MODULE DOCSTRING +#============================================================================================= +""" +XML I/O parser for the SMIRNOFF (SMIRKS Native Open Force Field) format. + +.. codeauthor:: John D. Chodera +.. codeauthor:: David L. Mobley +.. codeauthor:: Peter K. Eastman + +""" + +#============================================================================================= +# GLOBAL IMPORTS +#============================================================================================= + +from collections import OrderedDict +import logging +import os +import sys + +import xmltodict + +from simtk import openmm, unit +from openforcefield.utils.utils import get_data_filename + + +#============================================================================================= +# CONFIGURE LOGGER +#============================================================================================= + +logger = logging.getLogger(__name__) + + +#============================================================================================= +# QUANTITY PARSING UTILITIES +#============================================================================================= + +def _ast_unit_eval(node): + """ + Performs a safe algebraic syntax tree evaluation of a unit. + + This will likely be replaced by the native implementation in Pint + if/when we'll switch over to Pint units. + """ + import ast + import operator as op + + operators = {ast.Add: op.add, ast.Sub: op.sub, ast.Mult: op.mul, + ast.Div: op.truediv, ast.Pow: op.pow, ast.BitXor: op.xor, + ast.USub: op.neg} + + if isinstance(node, ast.Num): # + return node.n + elif isinstance(node, ast.BinOp): # + return operators[type(node.op)](_ast_unit_eval(node.left), _ast_unit_eval(node.right)) + elif isinstance(node, ast.UnaryOp): # ( ) e.g., -1 + return operators[type(node.op)](_ast_unit_eval(node.operand)) + elif isinstance(node, ast.Name): + # Check if this is a simtk unit. + u = getattr(unit, node.id) + if not isinstance(u, unit.Unit): + raise ValueError('No unit named {} found in simtk.unit.'.format(node.id)) + return u + else: + raise TypeError(node) + + +#============================================================================================= +# Base ParameterIOHandler +#============================================================================================= + + +class ParameterIOHandler(object): + """ + Base class for handling serialization/deserialization of SMIRNOFF ForceField objects + """ + _FORMAT = None + + def __init__(self): + """ + Create a new ParameterIOHandler. + + """ + pass + #self._forcefield = forcefield + + def parse_file(self, filename): + """ + + Parameters + ---------- + filename + + Returns + ------- + + """ + pass + + def parse_string(self, data): + """ + Parse a SMIRNOFF force field definition in a seriaized format + + Parameters + ---------- + data + + Returns + ------- + + """ + pass + + def to_file(self, filename): + """ + Write the current forcefield parameter set to a file. + + Parameters + ---------- + filename : str + The filename to write to. + smirnoff_data : dict + A dictionary structured in compliance with the SMIRNOFF spec + + Returns + ------- + + """ + pass + + def to_string(self, smirnoff_data): + """ + Render the forcefield parameter set to a string + + Parameters + ---------- + smirnoff_data : dict + A dictionary structured in compliance with the SMIRNOFF spec + + Returns + ------- + str + """ + pass + + +#============================================================================================= +# XML I/O +#============================================================================================= + + + +class XMLParameterIOHandler(ParameterIOHandler): + """ + Handles serialization/deserialization of SMIRNOFF ForceField objects from OFFXML format. + """ + # TODO: Come up with a better keyword for format + _FORMAT = 'XML' + + + + # TODO: Fix this + def parse_file(self, source): + """Parse a SMIRNOFF force field definition in XML format, read from a file. + + A ``ParseError`` is raised if the XML cannot be processed. + + Parameters + ---------- + source : str or file-like obj + File path of file-like obj specifying a SMIRNOFF force field definition in `the SMIRNOFF XML format `_. + + .. notes :: + + * New SMIRNOFF sections are handled independently, as if they were specified in the same file. + * If a SMIRNOFF section that has already been read appears again, its definitions are appended to the end of the previously-read + definitions if the sections are configured with compatible attributes; otherwise, an ``IncompatibleTagException`` is raised. + """ + from pyexpat import ExpatError + from openforcefield.typing.engines.smirnoff.forcefield import ParseError + + # this handles open file-like objects (and strings) + try: + smirnoff_data = self.parse_string(source) + return smirnoff_data + except ParseError: + pass + + # This handles complete/local filenames + try: + # Check if the file exists in the data/forcefield directory + data = open(source).read() + smirnoff_data = xmltodict.parse(data, attr_prefix='') + return smirnoff_data + except ExpatError: + pass + except FileNotFoundError: + pass + + # This handles nonlocal filenames + try: + # Check if the file exists in the data/forcefield directory + temp_file = get_data_filename(os.path.join('forcefield', source)) + data = open(temp_file).read() + smirnoff_data = self.parse_string(data) + return smirnoff_data + + except Exception as e: + # Fail with an error message about which file could not be read. + # TODO: Also handle case where fallback to 'data' directory encounters problems, + # but this is much less worrisome because we control those files. + msg = str(e) + '\n' + if hasattr(source, 'name'): + filename = source.name + else: + filename = str(source) + msg += "ForceField.loadFile() encountered an error reading file '%s'\n" % filename + raise ParseError(msg) + + def parse_string(self, data): + """Parse a SMIRNOFF force field definition in XML format. + + A ``ParseError`` is raised if the XML cannot be processed. + + Parameters + ---------- + data : str + A SMIRNOFF force field definition in `the SMIRNOFF XML format `_. + + """ + from pyexpat import ExpatError + from openforcefield.typing.engines.smirnoff.forcefield import ParseError + + # Parse XML file + try: + smirnoff_data = xmltodict.parse(data, attr_prefix='') + return smirnoff_data + except ExpatError as e: + raise ParseError(e) + + def to_file(self, filename, smirnoff_data): + """Write the current forcefield parameter set to a file, autodetecting the type from the extension. + + Parameters + ---------- + filename : str + The name of the file to be written. + The `.offxml` file extension must be present. + smirnoff_data : dict + A dict structured in compliance with the SMIRNOFF data spec. + + """ + xml_string = self.to_string(smirnoff_data) + (basename, extension) = os.path.splitext(filename) + if extension == '.offxml': + with open(filename, 'wb') as of: + of.write(xml_string) + else: + msg = "Cannot export forcefield parameters to file '{}'\n".format( + filename) + msg += 'Export to extension {} not implemented yet.\n'.format( + extension) + msg += "Supported choices are: ['.offxml']" + raise NotImplementedError(msg) + + def to_string(self, smirnoff_data): + """ + Write the current forcefield parameter set to an XML string. + + Parameters + ---------- + smirnoff_data : dict + A dictionary structured in compliance with the SMIRNOFF spec + + Returns + ------- + serialized_forcefield : str + XML String representation of this forcefield. + + """ + def prepend_all_keys(d, char='@'): + """ + Modify a dictionary in-place, prepending a specified string to each key + that doesn't refer to a value that is list or dict. + + Parameters + ---------- + d : dict + Hierarchical dictionary to traverse and modify keys + char : string, optional. Default='@' + String to prepend onto each applicable dictionary key + + """ + if isinstance(d, dict): + for key in list(d.keys()): + if isinstance(d[key], list) or isinstance(d[key], dict): + prepend_all_keys(d[key]) + else: + new_key = char + key + d[new_key] = d[key] + del d[key] + prepend_all_keys(d[new_key]) + elif isinstance(d, list): + for item in d: + prepend_all_keys(item) + + prepend_all_keys(smirnoff_data['SMIRNOFF']) + print(smirnoff_data) + print() + return xmltodict.unparse(smirnoff_data, pretty=True) + + def to_xml(self, smirnoff_data): + """Render the forcefield parameter set to XML. + + Returns + ------- + smirnoff_data : dict + A dictionary structures in comliance with the SMIRNOFF data spec. + """ + return self.to_string(smirnoff_data) + + # # TODO: Do we need this? Should we use built-in dict-based serialization? + # def __getstate__(self): + # """Serialize to XML. + # """ + # return self.to_xml() + # + # # TODO: Do we need this? Should we use built-in dict-based serialization? + # def __setstate__(self, state): + # """Deserialize from XML. + # """ + # self._initialize() + # self.parse_xml(state) diff --git a/openforcefield/typing/engines/smirnoff/parameters.py b/openforcefield/typing/engines/smirnoff/parameters.py new file mode 100644 index 000000000..bc90a9e84 --- /dev/null +++ b/openforcefield/typing/engines/smirnoff/parameters.py @@ -0,0 +1,2420 @@ +#!/usr/bin/env python + +#============================================================================================= +# MODULE DOCSTRING +#============================================================================================= +""" +Parameter handlers for the SMIRNOFF force field engine + +This file contains standard parameter handlers for the SMIRNOFF force field engine. +These classes implement the object model for self-contained parameter assignment. +New pluggable handlers can be created by creating subclasses of :class:`ParameterHandler`. + +.. codeauthor:: John D. Chodera +.. codeauthor:: David L. Mobley +.. codeauthor:: Peter K. Eastman + +""" + +#============================================================================================= +# GLOBAL IMPORTS +#============================================================================================= + + +from enum import Enum +import logging + +from collections import OrderedDict + + +from simtk import openmm, unit + +from openforcefield.utils import detach_units, attach_units, unit_to_string, \ + extract_serialized_units_from_dict, ToolkitUnavailableException, MessageException +from openforcefield.topology import Topology, ValenceDict, ImproperDict +from openforcefield.typing.chemistry import ChemicalEnvironment + +#============================================================================================= +# CONFIGURE LOGGER +#============================================================================================= + +logger = logging.getLogger(__name__) + + +#====================================================================== +# CUSTOM EXCEPTIONS +#====================================================================== + +class SMIRNOFFSpecError(MessageException): + """ + Exception for when data is noncompliant with the SMIRNOFF data specification. + """ + pass + +class IncompatibleUnitError(MessageException): + """ + Exception for when a parameter is in the wrong units for a ParameterHandler's unit system + """ + pass + + +class IncompatibleParameterError(MessageException): + """ + Exception for when a set of parameters is scientifically/technically incompatible with another + """ + pass + + +class UnassignedValenceParameterException(Exception): + """Exception raised when there are valence terms for which a ParameterHandler can't find parameters.""" + pass + + +class UnassignedBondParameterException(UnassignedValenceParameterException): + """Exception raised when there are bond terms for which a ParameterHandler can't find parameters.""" + pass + + +class UnassignedAngleParameterException(UnassignedValenceParameterException): + """Exception raised when there are angle terms for which a ParameterHandler can't find parameters.""" + pass + + +class UnassignedProperTorsionParameterException(UnassignedValenceParameterException): + """Exception raised when there are proper torsion terms for which a ParameterHandler can't find parameters.""" + pass + +#====================================================================== +# UTILITY FUNCTIONS +#====================================================================== + + + + +#====================================================================== +# PARAMETER TYPE/LIST +#====================================================================== + +class NonbondedMethod(Enum): + """ + An enumeration of the nonbonded methods + """ + NoCutoff = 0 + CutoffPeriodic = 1 + CutoffNonPeriodic = 2 + Ewald = 3 + PME = 4 + + +# We can't actually make this derive from dict, because it's possible for the user to change SMIRKS +# of parameters already in the list, which would cause the ParameterType object's SMIRKS and +# the dictionary key's SMIRKS to be out of sync. +class ParameterList(list): + """ + Parameter list that also supports accessing items by SMARTS string. + + .. warning :: This API is experimental and subject to change. + + """ + + # TODO: Make this faster by caching SMARTS -> index lookup? + + # TODO: Override __del__ to make sure we don't remove root atom type + + # TODO: Allow retrieval by `id` as well + + def __init__(self, input_parameter_list=None): + """ + Initialize a new ParameterList, optionally providing a list of ParameterType objects + to initially populate it. + + Parameters + ---------- + input_parameter_list: list[ParameterType], default=None + A pre-existing list of ParameterType-based objects. If None, this ParameterList + will be initialized empty. + """ + super().__init__() + + input_parameter_list = input_parameter_list or [] + # TODO: Should a ParameterList only contain a single kind of ParameterType? + for input_parameter in input_parameter_list: + self.append(input_parameter) + + def append(self, parameter): + """ + Add a ParameterType object to the end of the ParameterList + + Parameters + ---------- + parameter : a ParameterType-derived object + + """ + # TODO: Ensure that newly added parameter is the same type as existing? + super().append(parameter) + + def extend(self, other): + """ + Add a ParameterList object to the end of the ParameterList + + Parameters + ---------- + other : a ParameterList + + """ + if not isinstance(other, ParameterList): + msg = 'ParameterList.extend(other) expected instance of ParameterList, ' \ + 'but received {} (type {}) instead'.format(other, type(other)) + raise TypeError(msg) + # TODO: Check if other ParameterList contains the same ParameterTypes? + super().extend(other) + + def index(self, item): + """ + Get the numerical index of a ParameterType object or SMIRKS in this ParameterList. Raises ValueError + if the item is not found. + + Parameters + ---------- + item : ParameterType-derived object or str + The parameter or SMIRKS to look up in this ParameterList + + Returns + ------- + index : int + The index of the found item + """ + if isinstance(item, ParameterType): + return super().index(item) + else: + for parameter in self: + if parameter.smirks == item: + return self.index(parameter) + raise IndexError('SMIRKS {item} not found in ParameterList'.format(item=item)) + + def insert(self, index, parameter): + """ + Add a ParameterType object as if this were a list + + Parameters + ---------- + index : int + The numerical position to insert the parameter at + parameter : a ParameterType-derived object + The parameter to insert + """ + # TODO: Ensure that newly added parameter is the same type as existing? + super().insert(index, parameter) + + def __delitem__(self, item): + """ + Delete item by index or SMIRKS. + + Parameters + ---------- + item : str or int + SMIRKS or numerical index of item in this ParameterList + """ + if type(item) is int: + index = item + else: + # Try to find by SMIRKS + index = self.index(item) + super().__delitem__(index) + + def __getitem__(self, item): + """ + Retrieve item by index or SMIRKS + + Parameters + ---------- + item : str or int + SMIRKS or numerical index of item in this ParameterList + """ + if type(item) is int: + index = item + elif type(item) is slice: + index = item + else: + index = self.index(item) + return super().__getitem__(index) + + + # TODO: Override __setitem__ and __del__ to ensure we can slice by SMIRKS as well + + def __contains__(self, item): + """Check to see if either Parameter or SMIRKS is contained in parameter list. + + + Parameters + ---------- + item : str + SMIRKS of item in this ParameterList + """ + if isinstance(item, str): + # Special case for SMIRKS strings + if item in [result.smirks for result in self]: + return True + # Fall back to traditional access + return list.__contains__(self, item) + + def to_list(self, return_cosmetic_attributes=False): + """ + Render this ParameterList to a normal list, serializing each ParameterType-derived object in it to dict. + + Parameters + ---------- + + return_cosmetic_attributes : bool, optional. default = False + Whether to return non-spec attributes of each ParameterType-derived object. + + Returns + ------- + parameter_list : List[dict] + A serialized representation of a ParameterList, with each ParameterType it contains converted to dict. + """ + parameter_list = list() + + for parameter in self: + parameter_dict = parameter.to_dict(return_cosmetic_attributes=return_cosmetic_attributes) + parameter_list.append(parameter_dict) + + return parameter_list + + + +# TODO: Rename to better reflect role as parameter base class? +class ParameterType(object): + """ + Base class for SMIRNOFF parameter types. + + .. warning :: This API is experimental and subject to change. + + """ + # These lists and dicts will be used for validating input and detecting cosmetic attributes. + _VALENCE_TYPE = None # ChemicalEnvironment valence type string expected by SMARTS string for this Handler + _ELEMENT_NAME = None # The string mapping to this ParameterType in a SMIRNOFF data source + _SMIRNOFF_ATTRIBS = ['smirks'] # Attributes expected per the SMIRNOFF spec. + _REQUIRE_UNITS = {} # A dict of attribs which will be checked for unit compatibility + _OPTIONAL_ATTRIBS = ['id', 'parent_id'] # Attributes in the SMIRNOFF spec that may + # be present but have no impact on performance + _INDEXED_ATTRIBS = [] # list of attribs that will have consecutive numerical suffixes starting at 1 + _ATTRIBS_TO_TYPE = {} # dict of attributes that need to be cast to a type (like int or float) to be interpreted + + # TODO: Can we provide some shared tools for returning settable/gettable attributes, and checking unit-bearing attributes? + + def __init__(self, smirks=None, permit_cosmetic_attributes=False, **kwargs): + """ + Create a ParameterType + + Parameters + ---------- + smirks : str + The SMIRKS match for the provided parameter type. + permit_cosmetic_attributes : bool optional. Default = False + Whether to store non-spec kwargs as "cosmetic attributes", which can be accessed and written out. + + """ + import openforcefield.utils.toolkits + + self._COSMETIC_ATTRIBS = [] # A list that may be populated to record the cosmetic + # attributes read from a SMIRNOFF data source + + if smirks is None: + raise ValueError("'smirks' must be specified") + + # TODO: Make better switch using toolkit registry + toolkit = None + if openforcefield.utils.toolkits.OPENEYE_AVAILABLE: + toolkit = 'openeye' + elif openforcefield.utils.toolkits.RDKIT_AVAILABLE: + toolkit = 'rdkit' + if toolkit is None: + raise ToolkitUnavailableException("Validating SMIRKS required either the OpenEye Toolkit or the RDKit." + " Unable to find either.") + ChemicalEnvironment.validate( + smirks, ensure_valence_type=self._VALENCE_TYPE, toolkit=toolkit) + + self._smirks = smirks + + def _assert_quantity_is_compatible(quantity_name, quantity, unit_to_check): + """ + Checks whether a simtk.unit.Quantity is compatible with another unit. + + Parameters + ---------- + quantity_name : string + quantity : A simtk.unit.Quantity + unit_to_check : A simtk.unit.Unit + + """ + + if not quantity.unit.is_compatible(unit_to_check): + msg = "{} constructor received kwarg {} with value {}, " \ + "which is incompatible with expected unit {}".format(self.__class__, + quantity_name, + val, + unit_to_check) + raise SMIRNOFFSpecError(msg) + + # First look for indexed attribs, removing them from kwargs as they're found + for unidx_key in self._INDEXED_ATTRIBS: + # Start by generating a string with the key + an index + index = 1 + idx_key = unidx_key+str(index) + + # If the indexed key is present in the kwargs, set the attrib data type to be a list + if idx_key in kwargs: + setattr(self, unidx_key, list()) + + # Iterate through increasing values on the index, appending them as they are found + while idx_key in kwargs: + val = kwargs[idx_key] + + # If the indexed keys require units, ensure they are compatible + if unidx_key in self._REQUIRE_UNITS: + _assert_quantity_is_compatible(idx_key, val, self._REQUIRE_UNITS[unidx_key]) + + # If the indexed keys need to be cast to a type, do that here + if unidx_key in self._ATTRIBS_TO_TYPE: + type_to_cast = self._ATTRIBS_TO_TYPE[unidx_key] + val = type_to_cast(val) + + # Finally, append this value to the attribute and remove the key from kwargs + getattr(self, unidx_key).append(val) + del kwargs[idx_key] + index += 1 + idx_key = unidx_key + str(index) + + + # Iterate through the remaining, non-indexed kwargs, + # doing validation and setting this ParameterType's attributes + for key, val in kwargs.items(): + if key in self._REQUIRE_UNITS: + # TODO: Add dynamic property-getter/setter for each thing in self._REQUIRE_UNITS + _assert_quantity_is_compatible(key, val, self._REQUIRE_UNITS[key]) + + + if key in self._ATTRIBS_TO_TYPE: + type_to_cast = self._ATTRIBS_TO_TYPE[key] + val = type_to_cast(val) + # Iterate through + # TODO: Decide on a scheme for prepending underscores to attributes + #attr_name = '_' + key + if key in self._SMIRNOFF_ATTRIBS: + setattr(self, key, val) + + # If it's an optional attrib, + elif key in self._OPTIONAL_ATTRIBS: + setattr(self, key, val) + + # Handle all unknown kwargs as cosmetic so we can write them back out + elif permit_cosmetic_attributes: + self._COSMETIC_ATTRIBS.append(key) + setattr(self, key, val) + else: + raise SMIRNOFFSpecError("Incompatible kwarg {} passed to {} constructor. If this is " + "a desired cosmetic attribute, consider setting " + "'permit_cosmetic_attributes=True'".format({key: val}, self.__class__)) + + @property + def smirks(self): + return self._smirks + + @smirks.setter + def smirks(self, smirks): + # Validate the SMIRKS string to ensure it matches the expected parameter type, + # raising an exception if it is invalid or doesn't tag a valid set of atoms + # TODO: Add check to make sure we can't make tree non-hierarchical + # This would require parameter type knows which ParameterList it belongs to + ChemicalEnvironment.validate( + smirks, ensure_valence_type=self._VALENCE_TYPE) + self._smirks = smirks + + def to_dict(self, return_cosmetic_attributes=False): + """ + Convert this ParameterType-derived object to dict. A unit-bearing attribute ('X') will be converted to two dict + entries, one (['X'] containing the unitless value, and another (['X_unit']) containing a string representation + of its unit. + + Parameters + ---------- + return_cosmetic_attributes : bool, optional. default = False + Whether to return non-spec attributes of this ParameterType + + + Returns + ------- + smirnoff_dict : dict + The SMIRNOFF-compliant dict representation of this ParameterType-derived object. + output_units : dict[str: simtk.unit.Unit] + A mapping from each simtk.unit.Quanitity-valued ParameterType attribute + to the unit it was converted to during serialization. + + """ + # Make a list of all attribs that should be included in the + # returned dict (call list() to make a copy) + attribs_to_return = list(self._SMIRNOFF_ATTRIBS) + attribs_to_return += [opt_attrib for opt_attrib in self._OPTIONAL_ATTRIBS if hasattr(self, opt_attrib)] + if return_cosmetic_attributes: + attribs_to_return += self._COSMETIC_ATTRIBS + + # Start populating a dict of the attribs + smirnoff_dict = OrderedDict() + # If attribs_to_return is ordered here, that will effectively be an informal output ordering + for attrib_name in attribs_to_return: + attrib_value = self.__getattribute__(attrib_name) + + if type(attrib_value) is list: + for idx, val in enumerate(attrib_value): + smirnoff_dict[attrib_name + str(idx+1)] = val + else: + smirnoff_dict[attrib_name] = attrib_value + + return smirnoff_dict + + def __repr__(self): + ret_str = '<{} with '.format(self.__class__.__name__) + for attr, val in self.to_dict().items(): + ret_str += f'{attr}: {val} ' + ret_str += '>' + return ret_str + + + + +#====================================================================== +# PARAMETER HANDLERS +# +# The following classes are Handlers that know how to create Force +# subclasses and add them to a System that is being created. Each Handler +# class must define three methods: +# 1) a constructor which takes as input hierarchical dictionaries of data +# conformant to the SMIRNOFF spec; +# 2) a create_force() method that constructs the Force object and adds it +# to the System; and +# 3) a labelForce() method that provides access to which terms are applied +# to which atoms in specified mols. +#====================================================================== + +# TODO: Should we have a parameter handler registry? + + +class ParameterHandler(object): + """Base class for parameter handlers. + + Parameter handlers are configured with some global parameters for a given section. They may also contain a + :class:`ParameterList` populated with :class:`ParameterType` objects if they are responsile for assigning + SMIRKS-based parameters. + + .. warning + + Parameter handler objects can only belong to a single :class:`ForceField` object. + If you need to create a copy to attach to a different :class:`ForceField` object, use ``create_copy()``. + + .. warning :: This API is experimental and subject to change. + + """ + + _TAGNAME = None # str of section type handled by this ParameterHandler (XML element name for SMIRNOFF XML representation) + _INFOTYPE = None # container class with type information that will be stored in self._parameters + _OPENMMTYPE = None # OpenMM Force class (or None if no equivalent) + _DEPENDENCIES = None # list of ParameterHandler classes that must precede this, or None + _REQUIRED_SPEC_ATTRIBS = [] # list of kwargs that must be present during handler initialization + _DEFAULT_SPEC_ATTRIBS = {} # dict of tag-level attributes and their default values + _OPTIONAL_SPEC_ATTRIBS = [] # list of non-required attributes that can be defined on initialization + _INDEXED_ATTRIBS = [] # list of parameter attribs that will have consecutive numerical suffixes starting at 1 + _REQUIRE_UNITS = {} # dict of {header attrib : unit } for input checking + _ATTRIBS_TO_TYPE = {} # dict of attribs that must be cast to a specific type to be interpreted correctly + _KWARGS = [] # Kwargs to catch when create_force is called + _SMIRNOFF_VERSION_INTRODUCED = 0.0 # the earliest version of SMIRNOFF spec that supports this ParameterHandler + _SMIRNOFF_VERSION_DEPRECATED = None # if deprecated, the first SMIRNOFF version number it is no longer used + + + def __init__(self, permit_cosmetic_attributes=False, **kwargs): + """ + Initialize a ParameterHandler, optionally with a list of parameters and other kwargs. + + Parameters + ---------- + permit_cosmetic_attributes : bool + Whether to accept non-spec kwargs + **kwargs : dict + The dict representation of the SMIRNOFF data source + + """ + + self._COSMETIC_ATTRIBS = [] # list of cosmetic header attributes to remember and optionally write out + + # Ensure that all required attribs are present + for reqd_attrib in self._REQUIRED_SPEC_ATTRIBS: + if not reqd_attrib in kwargs: + msg = "{} requires {} as a parameter during initialization, however this is not " \ + "provided. Defined kwargs are {}".format(self.__class__, + reqd_attrib, + list(kwargs.keys())) + raise SMIRNOFFSpecError(msg) + + # list of ParameterType objects (also behaves like an OrderedDict where keys are SMARTS) + self._parameters = ParameterList() + + # Handle all the unknown kwargs as cosmetic so we can write them back out + allowed_header_attribs = self._REQUIRED_SPEC_ATTRIBS + \ + list(self._DEFAULT_SPEC_ATTRIBS.keys()) + \ + self._OPTIONAL_SPEC_ATTRIBS + + # Check for attribs that need to be casted to specific types + for attrib, type_to_cast in self._ATTRIBS_TO_TYPE.items(): + if attrib in kwargs: + kwargs[attrib] = type_to_cast(kwargs[attrib]) + + # Check for indexed attribs + for attrib_basename in self._INDEXED_ATTRIBS: + attrib_unit_key = attrib_basename + '_unit' + + index = 1 + attrib_w_index = '{}{}'.format(attrib_basename, index) + while attrib_w_index in kwargs: + # As long as we keep finding higher-indexed entries for + # this attrib, add them to the expected arguments + allowed_header_attribs.append(attrib_w_index) + + # If there's a unit for this attrib, copy unit entries for each index instance + if attrib_unit_key in kwargs: + kwargs[attrib_w_index+'_unit'] = kwargs[attrib_unit_key] + + # Attach units to the handler kwargs, if applicable + unitless_kwargs, attached_units = extract_serialized_units_from_dict(kwargs) + smirnoff_data = attach_units(unitless_kwargs, attached_units) + + # Add default values to smirnoff_data if they're not already there + for default_key, default_val in self._DEFAULT_SPEC_ATTRIBS.items(): + if not (default_key in kwargs): + smirnoff_data[default_key] = default_val + + # Perform unit compatibility checks + for key, val in smirnoff_data.items(): + if key in self._REQUIRE_UNITS: + # TODO: Logic for indexed attributes + if not val.unit.is_compatible(self._REQUIRE_UNITS[key]): + msg = "{} constructor received kwarg {} with value {}, " \ + "which is incompatible with expected unit {}".format(self.__class__, + key, + val, + self._REQUIRE_UNITS[key]) + raise SMIRNOFFSpecError(msg) + + element_name = None + if self._INFOTYPE is not None: + element_name = self._INFOTYPE._ELEMENT_NAME + + for key, val in smirnoff_data.items(): + # If we're reading the parameter list, iterate through and attach units to + # each parameter_dict, then use it to initialize a ParameterType + if key == element_name: + # If there are multiple parameters, this will be a list. If there's just one, make it a list + if not(isinstance(val, list)): + val = [val] + for unitless_param_dict in val: + param_dict = attach_units(unitless_param_dict, attached_units) + new_parameter = self._INFOTYPE(**param_dict, + permit_cosmetic_attributes=permit_cosmetic_attributes) + self._parameters.append(new_parameter) + + elif key in allowed_header_attribs: + attr_name = '_' + key + # TODO: create @property.setter here if attrib requires unit + setattr(self, attr_name, val) + elif permit_cosmetic_attributes: + self._COSMETIC_ATTRIBS.append(key) + attr_name = '_' + key + setattr(self, attr_name, val) + + else: + raise SMIRNOFFSpecError("Incompatible kwarg {} passed to {} constructor. If this is " + "a desired cosmetic attribute, consider setting " + "'permit_cosmetic_attributes=True'".format(key, self.__class__)) + + + + @property + def parameters(self): + """The ParameterList that holds this ParameterHandler's parameter objects""" + return self._parameters + + # TODO: Do we need to return these, or can we handle this internally + @property + def known_kwargs(self): + """List of kwargs that can be parsed by the function. + """ + # TODO: Should we use introspection to inspect the function signature instead? + return set(self._KWARGS) + + + #@classmethod + def check_parameter_compatibility(self, parameter_kwargs): + """ + Check to make sure that the fields requiring defined units are compatible with the required units for the + Parameters handled by this ParameterHandler + + Parameters + ---------- + parameter_kwargs: dict + The dict that will be used to construct the ParameterType + + Raises + ------ + Raises a ValueError if the parameters are incompatible. + """ + for key in parameter_kwargs: + if key in self._REQUIRE_UNITS: + reqd_unit = self._REQUIRE_UNITS[key] + #if arg in cls._REQUIRE_UNITS: + # raise Exception(cls) + # reqd_unit = cls._REQUIRE_UNITS[arg] + val = parameter_kwargs[key] + if not (reqd_unit.is_compatible(val.unit)): + raise IncompatibleUnitError( + "Input unit {} is not compatible with ParameterHandler unit {}" + .format(val.unit, reqd_unit)) + + def check_handler_compatibility(self, handler_kwargs): + """ + Checks if a set of kwargs used to create a ParameterHandler are compatible with this ParameterHandler. This is + called if a second handler is attempted to be initialized for the same tag. + + Parameters + ---------- + handler_kwargs : dict + The kwargs that would be used to construct + + Raises + ------ + IncompatibleParameterError if handler_kwargs are incompatible with existing parameters. + """ + pass + + # TODO: Can we ensure SMIRKS and other parameters remain valid after manipulation? + def add_parameter(self, parameter_kwargs): + """Add a parameter to the forcefield, ensuring all parameters are valid. + + Parameters + ---------- + parameter_kwargs : dict + The kwargs to pass to the ParameterHandler.INFOTYPE (a ParameterType) constructor + """ + + # TODO: Do we need to check for incompatibility with existing parameters? + + # Perform unit compatibility checks + self.check_parameter_compatibility(parameter_kwargs) + # Check for correct SMIRKS valence + + new_parameter = self._INFOTYPE(**parameter_kwargs) + self._parameters.append(new_parameter) + + def get_parameter(self, parameter_attrs): + """ + Return the parameters in this ParameterHandler that match the parameter_attrs argument + + Parameters + ---------- + parameter_attrs : dict of {attr: value} + The attrs mapped to desired values (for example {"smirks": "[*:1]~[#16:2]=,:[#6:3]~[*:4]", "id": "t105"} ) + + Returns + ------- + list of ParameterType-derived objects + A list of matching ParameterType-derived objects + """ + # TODO: This is a necessary API point for Lee-Ping's ForceBalance + pass + + def find_matches(self, entity): + """Find the elements of the topology/molecule matched by a parameter type. + + Parameters + ---------- + entity : openforcefield.topology.Topology or openforcefield.topology.Molecule + Topology or molecule to search. + + Returns + --------- + matches : ValenceDict[Tuple[int], ParameterType] + ``matches[particle_indices]`` is the ``ParameterType`` object + matching the tuple of particle indices in ``entity``. + + """ + return self._find_matches(entity) + + def _find_matches(self, entity, transformed_dict_cls=ValenceDict): + """Implement find_matches() and allow using a difference valence dictionary.""" + from openforcefield.topology import FrozenMolecule + + logger.debug('Finding matches for {}'.format(self.__class__.__name__)) + + matches = transformed_dict_cls() + for parameter_type in self._parameters: + matches_for_this_type = {} + for atoms in entity.chemical_environment_matches(parameter_type.smirks): + # Collect the atom indices matching the entity. + if isinstance(entity, Topology): + atom_indices = tuple([atom.topology_particle_index for atom in atoms]) + elif isinstance(entity, FrozenMolecule): + atom_indices = tuple([atom.molecule_particle_index for atom in atoms]) + else: + raise ValueError('Unknown entity type {}'.format(entity.__class__)) + + # Update the matches for this parameter type. + matches_for_this_type[atom_indices] = parameter_type + + # Update matches of all parameter types. + matches.update(matches_for_this_type) + logger.debug('{:64} : {:8} matches'.format( + parameter_type.smirks, len(matches_for_this_type))) + + logger.debug('{} matches identified'.format(len(matches))) + return matches + + def assign_parameters(self, topology, system): + """Assign parameters for the given Topology to the specified System object. + + Parameters + ---------- + topology : openforcefield.topology.Topology + The Topology for which parameters are to be assigned. + Either a new Force will be created or parameters will be appended to an existing Force. + system : simtk.openmm.System + The OpenMM System object to add the Force (or append new parameters) to. + """ + pass + + def postprocess_system(self, topology, system, **kwargs): + """Allow the force to perform a a final post-processing pass on the System following parameter assignment, if needed. + + Parameters + ---------- + topology : openforcefield.topology.Topology + The Topology for which parameters are to be assigned. + Either a new Force will be created or parameters will be appended to an existing Force. + system : simtk.openmm.System + The OpenMM System object to add the Force (or append new parameters) to. + """ + pass + + def to_dict(self, output_units=None, return_cosmetic_attributes=False): + """ + Convert this ParameterHandler to an OrderedDict, compliant with the SMIRNOFF data spec. + + Parameters + ---------- + output_units : dict[str : simtk.unit.Unit], optional. Default = None + A mapping from the ParameterType attribute name to the output unit its value should be converted to. + return_cosmetic_attributes : bool, optional. Default = False. + Whether to return non-spec parameter and header attributes in this ParameterHandler. + + Returns + ------- + smirnoff_data : OrderedDict + SMIRNOFF-spec compliant representation of this ParameterHandler and its internal ParameterList. + """ + smirnoff_data = OrderedDict() + + # Set default output units to those from the last parameter added to the ParameterList + if (output_units is None): + output_units = dict() + # TODO: What if self._parameters is an empty list? + if len(self._parameters) > 0: + _, last_added_output_units = detach_units(self._parameters[-1].to_dict()) + # Overwrite key_value pairs in last_added_output_units with those specified by user in output_units + last_added_output_units.update(output_units) + output_units = last_added_output_units + + # Populate parameter list + parameter_list = self._parameters.to_list(return_cosmetic_attributes=return_cosmetic_attributes) + unitless_parameter_list = list() + + # Detach units into a separate dict. + for parameter_dict in parameter_list: + unitless_parameter_dict, attached_units = detach_units(parameter_dict, output_units=output_units) + unitless_parameter_list.append(unitless_parameter_dict) + output_units.update(attached_units) + + # Collapse down indexed attribute units + # (eg. {'k1_unit': angstrom, 'k2_unit': angstrom} --> {'k_unit': angstrom}) + for attrib_key in self._INDEXED_ATTRIBS: + index = 1 + # Store a variable that is 'k1_unit' + idxed_attrib_unit_key = attrib_key + str(index) + '_unit' + # See if 'k1_unit' is in output_units + if idxed_attrib_unit_key in output_units: + # If so, define 'k_unit' and add it to the output_units dict + attrib_unit_key = attrib_key + '_unit' + output_units[attrib_unit_key] = output_units[idxed_attrib_unit_key] + # Increment the 'kN_unit' value, checking that each is the same as the + # 'k1_unit' value, and deleting them from output_units + while idxed_attrib_unit_key in output_units: + # Ensure that no different units are defined for higher indexes of this attrib + assert output_units[attrib_unit_key] == output_units[idxed_attrib_unit_key] + del output_units[idxed_attrib_unit_key] + index += 1 + idxed_attrib_unit_key = attrib_key + str(index) + '_unit' + + + # NOTE: This assumes that a ParameterHandler will have just one homogenous ParameterList under it + if self._INFOTYPE is not None: + smirnoff_data[self._INFOTYPE._ELEMENT_NAME] = unitless_parameter_list + + + # Collect the names of handler attributes to return + header_attribs_to_return = self._REQUIRED_SPEC_ATTRIBS + list(self._DEFAULT_SPEC_ATTRIBS.keys()) + + # Check whether the optional attribs are defined, and add them if so + for key in self._OPTIONAL_SPEC_ATTRIBS: + attr_key = '_' + key + if hasattr(self, attr_key): + header_attribs_to_return.append(key) + # Add the cosmetic attributes if requested + if return_cosmetic_attributes: + header_attribs_to_return += self._COSMETIC_ATTRIBS + + + # Go through the attribs of this ParameterHandler and collect the appropriate values to return + header_attribute_dict = {} + for header_attribute in header_attribs_to_return: + value = getattr(self, '_' + header_attribute) + header_attribute_dict[header_attribute] = value + + # Detach all units from the header attribs + unitless_header_attribute_dict, attached_header_units = detach_units(header_attribute_dict) + + # Convert all header attrib units (eg. {'length_unit': simtk.unit.angstrom}) to strings (eg. + # {'length_unit': 'angstrom'}) and add them to the header attribute dict + # TODO: Should we check for collisions between parameter "_unit" keys and header "_unit" keys? + output_units.update(attached_header_units) + for key, value in output_units.items(): + value_str = unit_to_string(value) + # Made a note to add this to the smirnoff spec + output_units[key] = value_str + + # Reattach the attached units here + smirnoff_data.update(unitless_header_attribute_dict) + smirnoff_data.update(output_units) + return smirnoff_data + + # ------------------------------- + # Utilities for children classes. + # ------------------------------- + + @classmethod + def _check_all_valence_terms_assigned(cls, assigned_terms, valence_terms, + exception_cls=UnassignedValenceParameterException): + """Check that all valence terms have been assigned and print a user-friendly error message. + + Parameters + ---------- + assigned_terms : ValenceDict + Atom index tuples defining added valence terms. + valence_terms : Iterable[TopologyAtom] or Iterable[Iterable[TopologyAtom]] + Atom or atom tuples defining topological valence terms. + exception_cls : UnassignedValenceParameterException + A specific exception class to raise to allow catching only specific + types of errors. + + """ + # Convert the valence term to a valence dictionary to make sure + # the order of atom indices doesn't matter for comparison. + valence_terms_dict = assigned_terms.__class__() + for atoms in valence_terms: + try: + # valence_terms is a list of TopologyAtom tuples. + atom_indices = (a.topology_particle_index for a in atoms) + except TypeError: + # valence_terms is a list of TopologyAtom. + atom_indices = (atoms.topology_particle_index,) + valence_terms_dict[atom_indices] = atoms + + # Check that both valence dictionaries have the same keys (i.e. terms). + assigned_terms_set = set(assigned_terms.keys()) + valence_terms_set = set(valence_terms_dict.keys()) + unassigned_terms = valence_terms_set.difference(assigned_terms_set) + not_found_terms = assigned_terms_set.difference(valence_terms_set) + + # Raise an error if there are unassigned terms. + err_msg = "" + + if len(unassigned_terms) > 0: + unassigned_str = '\n- '.join([str(x) for x in unassigned_terms]) + err_msg += ("{parameter_handler} was not able to find parameters for the following valence terms:\n" + "- {unassigned_str}").format(parameter_handler=cls.__name__, + unassigned_str=unassigned_str) + if len(not_found_terms) > 0: + if err_msg != "": + err_msg += '\n' + not_found_str = '\n- '.join([str(x) for x in not_found_terms]) + err_msg += ("{parameter_handler} assigned terms that were not found in the topology:\n" + "- {not_found_str}").format(parameter_handler=cls.__name__, + not_found_str=not_found_str) + if err_msg != "": + err_msg += '\n' + raise exception_cls(err_msg) + + +#============================================================================================= + + +class ConstraintHandler(ParameterHandler): + """Handle SMIRNOFF ```` tags + + ``ConstraintHandler`` must be applied before ``BondHandler`` and ``AngleHandler``, + since those classes add constraints for which equilibrium geometries are needed from those tags. + + .. warning :: This API is experimental and subject to change. + """ + + class ConstraintType(ParameterType): + """A SMIRNOFF constraint type + + .. warning :: This API is experimental and subject to change. + """ + _VALENCE_TYPE = 'Bond' + _ELEMENT_NAME = 'Constraint' + _SMIRNOFF_ATTRIBS = ['smirks'] # Attributes expected per the SMIRNOFF spec. + _OPTIONAL_ATTRIBS = ['distance', 'id', 'parent_id'] + _REQUIRE_UNITS = {'distance': unit.angstrom} + def __init__(self, **kwargs): + super().__init__(**kwargs) + # TODO: Re-implement ability to set 'distance = True' + # if 'distance' in node.attrib: + # self.distance = _extract_quantity_from_xml_element( + # node, parent, 'distance' + # ) # Constraint with specified distance will be added by ConstraintHandler + # else: + # self.distance = True # Constraint to equilibrium bond length will be added by HarmonicBondHandler + + _TAGNAME = 'Constraints' + _INFOTYPE = ConstraintType + _OPENMMTYPE = None # don't create a corresponding OpenMM Force class + + + def __init__(self, **kwargs): + super().__init__(**kwargs) + + def create_force(self, system, topology, **kwargs): + constraints = self.find_matches(topology) + for (atoms, constraint) in constraints.items(): + # Update constrained atom pairs in topology + #topology.add_constraint(*atoms, constraint.distance) + # If a distance is specified (constraint.distance != True), add the constraint here. + # Otherwise, the equilibrium bond length will be used to constrain the atoms in HarmonicBondHandler + if hasattr(constraint, 'distance'):# is not True: + system.addConstraint(*atoms, constraint.distance) + topology.add_constraint(*atoms, constraint.distance) + else: + topology.add_constraint(*atoms, True) + + +#============================================================================================= + + +class BondHandler(ParameterHandler): + """Handle SMIRNOFF ```` tags + + .. warning :: This API is experimental and subject to change. + """ + + + class BondType(ParameterType): + """A SMIRNOFF bond type + + .. warning :: This API is experimental and subject to change. + """ + _VALENCE_TYPE = 'Bond' # ChemicalEnvironment valence type string expected by SMARTS string for this Handler + _ELEMENT_NAME = 'Bond' + _SMIRNOFF_ATTRIBS = ['smirks', 'length', 'k'] # Attributes expected per the SMIRNOFF spec. + _REQUIRE_UNITS = {'length' : unit.angstrom, + 'k' : unit.kilocalorie_per_mole / unit.angstrom**2} + _INDEXED_ATTRIBS = ['length', 'k'] # May be indexed (by integer bond order) if fractional bond orders are used + + def __init__(self, **kwargs): + super().__init__(**kwargs) # Base class handles ``smirks`` and ``id`` fields + + + _TAGNAME = 'Bonds' # SMIRNOFF tag name to process + _INFOTYPE = BondType # class to hold force type info + _OPENMMTYPE = openmm.HarmonicBondForce # OpenMM force class to create + _DEPENDENCIES = [ConstraintHandler] # ConstraintHandler must be executed first + _DEFAULT_SPEC_ATTRIBS = {'potential': 'harmonic', + 'fractional_bondorder_method': None, + 'fractional_bondorder_interpolation': 'linear'} + _INDEXED_ATTRIBS = ['k'] # May be indexed (by integer bond order) if fractional bond orders are used + + def __init__(self, **kwargs): + # TODO: Do we want a docstring here? If not, check that docstring get inherited from ParameterHandler. + super().__init__(**kwargs) + + def create_force(self, system, topology, **kwargs): + # Create or retrieve existing OpenMM Force object + # TODO: The commented line below should replace the system.getForce search + #force = super(BondHandler, self).create_force(system, topology, **kwargs) + existing = [system.getForce(i) for i in range(system.getNumForces())] + existing = [f for f in existing if type(f) == self._OPENMMTYPE] + if len(existing) == 0: + force = self._OPENMMTYPE() + system.addForce(force) + else: + force = existing[0] + + # Add all bonds to the system. + bonds = self.find_matches(topology) + skipped_constrained_bonds = 0 # keep track of how many bonds were constrained (and hence skipped) + for (atoms, bond_params) in bonds.items(): + # Get corresponding particle indices in Topology + #particle_indices = tuple([ atom.particle_index for atom in atoms ]) + + # Ensure atoms are actually bonded correct pattern in Topology + topology.assert_bonded(atoms[0], atoms[1]) + + # Compute equilibrium bond length and spring constant. + topology_bond = topology.get_bond_between(atoms[0], atoms[1]) + if topology_bond.bond.fractional_bond_order is None: + [k, length] = [bond_params.k, bond_params.length] + else: + # Interpolate using fractional bond orders + # TODO: Do we really want to allow per-bond specification of interpolation schemes? + order = topology_bond.bond.fractional_bond_order + if self.fractional_bondorder_interpolation == 'interpolate-linear': + k = bond_params.k[0] + (bond_params.k[1] - bond_params.k[0]) * (order - 1.) + length = bond_params.length[0] + ( + bond_params.length[1] - bond_params.length[0]) * (order - 1.) + else: + raise Exception( + "Partial bondorder treatment {} is not implemented.". + format(self.fractional_bondorder_method)) + + # Handle constraints. + if topology.is_constrained(*atoms): + # Atom pair is constrained; we don't need to add a bond term. + skipped_constrained_bonds += 1 + # Check if we need to add the constraint here to the equilibrium bond length. + if topology.is_constrained(*atoms) is True: + # Mark that we have now assigned a specific constraint distance to this constraint. + topology.add_constraint(*atoms, length) + # Add the constraint to the System. + system.addConstraint(*atoms, length) + #system.addConstraint(*particle_indices, length) + continue + + # Add harmonic bond to HarmonicBondForce + force.addBond(*atoms, length, k) + + logger.info('{} bonds added ({} skipped due to constraints)'.format( + len(bonds) - skipped_constrained_bonds, skipped_constrained_bonds)) + + # Check that no topological bonds are missing force parameters. + valence_terms = [list(b.atoms) for b in topology.topology_bonds] + self._check_all_valence_terms_assigned(assigned_terms=bonds, valence_terms=valence_terms, + exception_cls=UnassignedBondParameterException) + + +#============================================================================================= + + +class AngleHandler(ParameterHandler): + """Handle SMIRNOFF ```` tags + + .. warning :: This API is experimental and subject to change. + """ + + class AngleType(ParameterType): + """A SMIRNOFF angle type. + + .. warning :: This API is experimental and subject to change. + """ + _VALENCE_TYPE = 'Angle' # ChemicalEnvironment valence type string expected by SMARTS string for this Handler + _ELEMENT_NAME = 'Angle' + _SMIRNOFF_ATTRIBS = ['smirks', 'angle', 'k'] # Attributes expected per the SMIRNOFF spec. + _REQUIRE_UNITS = {'angle': unit.degree, + 'k': unit.kilocalorie_per_mole / unit.degree**2} + + + def __init__(self, **kwargs): + super().__init__(**kwargs) # base class handles ``smirks`` and ``id`` fields + + + _TAGNAME = 'Angles' # SMIRNOFF tag name to process + _INFOTYPE = AngleType # class to hold force type info + _OPENMMTYPE = openmm.HarmonicAngleForce # OpenMM force class to create + _DEFAULT_SPEC_ATTRIBS = {'potential': 'harmonic'} + + def __init__(self, **kwargs): + super().__init__(**kwargs) + + def create_force(self, system, topology, **kwargs): + #force = super(AngleHandler, self).create_force(system, topology, **kwargs) + existing = [system.getForce(i) for i in range(system.getNumForces())] + existing = [f for f in existing if type(f) == self._OPENMMTYPE] + if len(existing) == 0: + force = self._OPENMMTYPE() + system.addForce(force) + else: + force = existing[0] + + # Add all angles to the system. + angles = self.find_matches(topology) + skipped_constrained_angles = 0 # keep track of how many angles were constrained (and hence skipped) + for (atoms, angle) in angles.items(): + # Ensure atoms are actually bonded correct pattern in Topology + for (i, j) in [(0, 1), (1, 2)]: + topology.assert_bonded(atoms[i], atoms[j]) + + if topology.is_constrained( + atoms[0], atoms[1]) and topology.is_constrained( + atoms[1], atoms[2]) and topology.is_constrained( + atoms[0], atoms[2]): + # Angle is constrained; we don't need to add an angle term. + skipped_constrained_angles += 1 + continue + + force.addAngle(*atoms, angle.angle, angle.k) + + logger.info('{} angles added ({} skipped due to constraints)'.format( + len(angles) - skipped_constrained_angles, + skipped_constrained_angles)) + + # Check that no topological angles are missing force parameters + self._check_all_valence_terms_assigned(assigned_terms=angles, + valence_terms=list(topology.angles), + exception_cls=UnassignedAngleParameterException) + + +#============================================================================================= + + +class ProperTorsionHandler(ParameterHandler): + """Handle SMIRNOFF ```` tags + + .. warning :: This API is experimental and subject to change. + """ + + class ProperTorsionType(ParameterType): + """A SMIRNOFF torsion type for proper torsions. + + .. warning :: This API is experimental and subject to change. + """ + + _VALENCE_TYPE = 'ProperTorsion' + _ELEMENT_NAME = 'Proper' + _SMIRNOFF_ATTRIBS = ['smirks', 'periodicity', 'phase', 'k'] # Attributes expected per the SMIRNOFF spec. + _REQUIRE_UNITS = {'k': unit.kilocalorie_per_mole, + 'phase': unit.degree} + _OPTIONAL_ATTRIBS = ['id', 'parent_id', 'idivf'] + _INDEXED_ATTRIBS = ['k', 'phase', 'periodicity', 'idivf'] + _ATTRIBS_TO_TYPE = {'periodicity': int, + 'idivf': float} + + def __init__(self, **kwargs): + super().__init__(**kwargs) # base class handles ``smirks`` and ``id`` fields + + + _TAGNAME = 'ProperTorsions' # SMIRNOFF tag name to process + _INFOTYPE = ProperTorsionType # info type to store + _OPENMMTYPE = openmm.PeriodicTorsionForce # OpenMM force class to create + _DEFAULT_SPEC_ATTRIBS = {'potential': 'charmm', + 'default_idivf': 'auto'} + _INDEXED_ATTRIBS = ['k', 'phase', 'periodicity', 'idivf'] + + def __init__(self, **kwargs): + + # NOTE: We do not want to overwrite idivf values here! If they're missing from the ParameterType + # dictionary, that means they should be set to defualt _AT SYSTEM CREATION TIME_. The user may + # change that default to a different value than it is now. The solution here will be to leave + # those idivfX values uninitialized and deal with it during system creation + + super().__init__(**kwargs) + + + def create_force(self, system, topology, **kwargs): + #force = super(ProperTorsionHandler, self).create_force(system, topology, **kwargs) + existing = [system.getForce(i) for i in range(system.getNumForces())] + existing = [f for f in existing if type(f) == self._OPENMMTYPE] + if len(existing) == 0: + force = self._OPENMMTYPE() + system.addForce(force) + else: + force = existing[0] + # Add all proper torsions to the system. + torsions = self.find_matches(topology) + for (atom_indices, torsion) in torsions.items(): + # Ensure atoms are actually bonded correct pattern in Topology + for (i, j) in [(0, 1), (1, 2), (2, 3)]: + topology.assert_bonded(atom_indices[i], atom_indices[j]) + + + for (periodicity, phase, k, idivf) in zip(torsion.periodicity, + torsion.phase, torsion.k, torsion.idivf): + if idivf == 'auto': + # TODO: Implement correct "auto" behavior + raise NotImplementedError("The OpenForceField toolkit hasn't implemented " + "support for the torsion `idivf` value of 'auto'") + + force.addTorsion(atom_indices[0], atom_indices[1], + atom_indices[2], atom_indices[3], periodicity, + phase, k/idivf) + + logger.info('{} torsions added'.format(len(torsions))) + + # Check that no topological torsions are missing force parameters + self._check_all_valence_terms_assigned(assigned_terms=torsions, + valence_terms=list(topology.propers), + exception_cls=UnassignedProperTorsionParameterException) + + +class ImproperTorsionHandler(ParameterHandler): + """Handle SMIRNOFF ```` tags + + .. warning :: This API is experimental and subject to change. + """ + + class ImproperTorsionType(ParameterType): + """A SMIRNOFF torsion type for improper torsions. + + .. warning :: This API is experimental and subject to change. + """ + _VALENCE_TYPE = 'ImproperTorsion' + _ELEMENT_NAME = 'Improper' + _SMIRNOFF_ATTRIBS = ['smirks', 'periodicity', 'phase', 'k'] # Attributes expected per the SMIRNOFF spec. + _REQUIRE_UNITS = {'k': unit.kilocalorie_per_mole, + 'phase': unit.degree} + _OPTIONAL_ATTRIBS = ['id', 'parent_id', 'idivf'] + _INDEXED_ATTRIBS = ['k', 'phase', 'periodicity', 'idivf'] + _ATTRIBS_TO_TYPE = {'periodicity': int, + 'idivf': float} + + def __init__(self, **kwargs): + super().__init__( **kwargs) + + + _TAGNAME = 'ImproperTorsions' # SMIRNOFF tag name to process + _INFOTYPE = ImproperTorsionType # info type to store + _OPENMMTYPE = openmm.PeriodicTorsionForce # OpenMM force class to create + _OPTIONAL_SPEC_ATTRIBS = ['potential', 'default_idivf'] + _HANDLER_DEFAULTS = {'potential': 'charmm', + 'default_idivf': 'auto'} + _INDEXED_ATTRIBS = ['k', 'phase', 'periodicity', 'idivf'] + + def __init__(self, **kwargs): + super().__init__(**kwargs) + + def find_matches(self, entity): + """Find the improper torsions in the topology/molecule matched by a parameter type. + + Parameters + ---------- + entity : openforcefield.topology.Topology or openforcefield.topology.Molecule + Topology or molecule to search. + + Returns + --------- + matches : ImproperDict[Tuple[int], ParameterType] + ``matches[atom_indices]`` is the ``ParameterType`` object + matching the 4-tuple of atom indices in ``entity``. + + """ + return self._find_matches(entity, transformed_dict_cls=ImproperDict) + + def create_force(self, system, topology, **kwargs): + #force = super(ImproperTorsionHandler, self).create_force(system, topology, **kwargs) + #force = super().create_force(system, topology, **kwargs) + existing = [system.getForce(i) for i in range(system.getNumForces())] + existing = [ + f for f in existing if type(f) == openmm.PeriodicTorsionForce + ] + if len(existing) == 0: + force = openmm.PeriodicTorsionForce() + system.addForce(force) + else: + force = existing[0] + + # Add all improper torsions to the system + impropers = self.find_matches(topology) + for (atom_indices, improper) in impropers.items(): + # Ensure atoms are actually bonded correct pattern in Topology + # For impropers, central atom is atom 1 + for (i, j) in [(0, 1), (1, 2), (1, 3)]: + topology.assert_bonded(atom_indices[i], atom_indices[j]) + + # TODO: This is a lazy hack. idivf should be set according to the ParameterHandler's default_idivf attrib + if not hasattr(improper, 'idivf'): + improper.idivf = [3 for item in improper.k] + # Impropers are applied in three paths around the trefoil having the same handedness + for (improper_periodicity, improper_phase, improper_k, improper_idivf) in zip(improper.periodicity, + improper.phase, improper.k, improper.idivf): + # TODO: Implement correct "auto" behavior + if improper_idivf == 'auto': + improper_idivf = 3 + logger.warning("The OpenForceField toolkit hasn't implemented " + "support for the torsion `idivf` value of 'auto'." + "Currently assuming a value of '3' for impropers.") + # Permute non-central atoms + others = [atom_indices[0], atom_indices[2], atom_indices[3]] + # ((0, 1, 2), (1, 2, 0), and (2, 0, 1)) are the three paths around the trefoil + for p in [(others[i], others[j], others[k]) for (i, j, k) in [(0, 1, 2), (1, 2, 0), (2, 0, 1)]]: + # The torsion force gets added three times, since the k is divided by three + force.addTorsion(atom_indices[1], p[0], p[1], p[2], + improper_periodicity, improper_phase, improper_k/improper_idivf) + logger.info( + '{} impropers added, each applied in a six-fold trefoil'.format( + len(impropers))) + + +class vdWHandler(ParameterHandler): + """Handle SMIRNOFF ```` tags + + .. warning :: This API is experimental and subject to change. + """ + + class vdWType(ParameterType): + """A SMIRNOFF vdWForce type. + + .. warning :: This API is experimental and subject to change. + """ + _VALENCE_TYPE = 'Atom' # ChemicalEnvironment valence type expected for SMARTS + _ELEMENT_NAME = 'Atom' + _SMIRNOFF_ATTRIBS = ['smirks', 'epsilon'] # Attributes expected per the SMIRNOFF spec. + _OPTIONAL_ATTRIBS = ['id', 'parent_id', 'sigma', 'rmin_half'] + _REQUIRE_UNITS = { + 'epsilon': unit.kilocalorie_per_mole, + 'sigma': unit.angstrom, + 'rmin_half': unit.angstrom + } + + def __init__(self, **kwargs): + sigma = kwargs.get('sigma', None) + rmin_half = kwargs.get('rmin_half', None) + if (sigma is None) and (rmin_half is None): + raise SMIRNOFFSpecError("Either sigma or rmin_half must be specified.") + if (sigma is not None) and (rmin_half is not None): + raise SMIRNOFFSpecError( + "BOTH sigma and rmin_half cannot be specified simultaneously." + ) + + # TODO: Is it necessary to force everything to be sigma? We could handle having either when create_force runs + if (rmin_half is not None): + kwargs['sigma'] = 2. * rmin_half / (2.**(1. / 6.)) + del kwargs['rmin_half'] + + super().__init__(**kwargs) + + + # @property + # def attrib(self): + # """Return all storable attributes as a dict. + # """ + # names = ['smirks', 'sigma', 'epsilon'] + # return { + # name: getattr(self, name) + # for name in names if hasattr(self, name) + # } + + _TAGNAME = 'vdW' # SMIRNOFF tag name to process + _INFOTYPE = vdWType # info type to store + _OPENMMTYPE = openmm.NonbondedForce # OpenMM force class to create + # _KWARGS = ['ewaldErrorTolerance', + # 'useDispersionCorrection', + # 'usePbc'] # Kwargs to catch when create_force is called + _REQUIRE_UNITS = {'switch_width': unit.angstrom, + 'cutoff': unit.angstrom} + _DEFAULT_SPEC_ATTRIBS = { + 'potential': 'Lennard-Jones-12-6', + 'combining_rules': 'Lorentz-Berthelot', + 'scale12': 0.0, + 'scale13': 0.0, + 'scale14': 0.5, + 'scale15': 1.0, + #'pme_tolerance': 1.e-5, + 'switch_width': 1.0 * unit.angstroms, + 'cutoff': 9.0 * unit.angstroms, + 'method': 'cutoff', + } + + _ATTRIBS_TO_TYPE = {'scale12': float, + 'scale13': float, + 'scale14': float, + 'scale15': float + } + + # TODO: Is this necessary? It's used in check_compatibility but could be hard-coded. + _SCALETOL = 1e-5 + + + def __init__(self, **kwargs): + + super().__init__(**kwargs) + self._validate_parameters() + + # TODO: These properties are a fast hack and should be replaced by something better + @property + def potential(self): + """The potential used to model van der Waals interactions""" + return self._potential + + @potential.setter + def potential(self, other): + """The potential used to model van der Waals interactions""" + valid_potentials = ['Lennard-Jones-12-6'] + if other not in valid_potentials: + raise IncompatibleParameterError(f"Attempted to set vdW potential to {other}. Expected " + f"one of {valid_potentials}") + self._potential = other + + @property + def combining_rules(self): + """The combining_rules used to model van der Waals interactions""" + return self._combining_rules + + @combining_rules.setter + def combining_rules(self, other): + """The combining_rules used to model van der Waals interactions""" + valid_combining_ruless = ['Lorentz-Berthelot'] + if other not in valid_combining_ruless: + raise IncompatibleParameterError(f"Attempted to set vdW combining_rules to {other}. Expected " + f"one of {valid_combining_ruless}") + self._method = other + + @property + def method(self): + """The method used to handle long-range van der Waals interactions""" + return self._method + + @method.setter + def method(self, other): + """The method used to handle long-range van der Waals interactions""" + valid_methods = ['cutoff', 'PME'] + if other not in valid_methods: + raise IncompatibleParameterError(f"Attempted to set vdW method to {other}. Expected " + f"one of {valid_methods}") + self._method = other + + @property + def cutoff(self): + """The cutoff used for long-range van der Waals interactions""" + return self._cutoff + + @cutoff.setter + def cutoff(self, other): + """The cutoff used for long-range van der Waals interactions""" + unit_to_check = self._REQUIRE_UNITS['cutoff'] + if not unit_to_check.unit_is_compatible(other.unit): + raise IncompatibleParameterError( + f"Attempted to set vdW cutoff to {other}, which is not compatible with " + f"expected unit {unit_to_check}") + self._cutoff = other + + @property + def switch_width(self): + """The switching width used for long-range van der Waals interactions""" + return self._switch_width + + @switch_width.setter + def switch_width(self, other): + """The switching width used for long-range van der Waals interactions""" + unit_to_check = self._REQUIRE_UNITS['switch_width'] + if not unit_to_check.unit_is_compatible(other.unit): + raise IncompatibleParameterError( + f"Attempted to set vdW switch_width to {other}, which is not compatible with " + f"expected unit {unit_to_check}") + self._switch_width = other + + def _validate_parameters(self): + """ + Checks internal attributes, raising an exception if they are configured in an invalid way. + """ + if self._scale12 != 0.0: + raise SMIRNOFFSpecError("Current OFF toolkit is unable to handle scale12 values other than 0.0. " + "Specified 1-2 scaling was {}".format(self._scale12)) + if self._scale13 != 0.0: + raise SMIRNOFFSpecError("Current OFF toolkit is unable to handle scale13 values other than 0.0. " + "Specified 1-3 scaling was {}".format(self._scale13)) + if self._scale15 != 1.0: + raise SMIRNOFFSpecError("Current OFF toolkit is unable to handle scale15 values other than 1.0. " + "Specified 1-5 scaling was {}".format(self._scale15)) + + + supported_methods = ['cutoff', 'PME'] + if self._method not in supported_methods: + raise SMIRNOFFSpecError("The Open Force Field toolkit currently only supports vdW method " + "values of {}. Received unsupported value " + "{}".format(supported_methods, self._method)) + + elif self._method == 'cutoff': + if self._cutoff is None: + raise SMIRNOFFSpecError("If vdW method is cutoff, a cutoff distance " + "must be provided") + + elif self._method == 'PME': + if self._cutoff is None: + raise SMIRNOFFSpecError("If vdW method is PME, a cutoff distance " + "must be provided") + + # if self._pme_tolerance is None: + # raise SMIRNOFFSpecError("If PME vdW method is selected, a pme_tolerance value must " + # "be specified.") + + if self._potential != "Lennard-Jones-12-6": + raise SMIRNOFFSpecError("vdW potential set to {}. Only 'Lennard-Jones-12-6' is currently " + "supported".format(self._potential)) + + + if self._combining_rules != "Lorentz-Berthelot": + raise SMIRNOFFSpecError("vdW combining_rules set to {}. Only 'Lorentz-Berthelot' is currently " + "supported".format(self._combining_rules)) + # TODO: Find a better way to set defaults + # TODO: Validate these values against the supported output types (openMM force kwargs?) + # TODO: Add conditional logic to assign NonbondedMethod and check compatibility + + + + + def check_handler_compatibility(self, + handler_kwargs, + assume_missing_is_default=True): + """ + Checks if a set of kwargs used to create a ParameterHandler are compatible with this ParameterHandler. This is + called if a second handler is attempted to be initialized for the same tag. If no value is given for a field, it + will be assumed to expect the ParameterHandler class default. + + Parameters + ---------- + handler_kwargs : dict + The kwargs that would be used to construct a ParameterHandler + assume_missing_is_default : bool + If True, will assume that parameters not specified in handler_kwargs would have been set to the default. + Therefore, an exception is raised if the ParameterHandler is incompatible with the default value for a + unspecified field. + + Raises + ------ + IncompatibleParameterError if handler_kwargs are incompatible with existing parameters. + """ + compare_attr_to_kwargs = { + self._scale12: 'scale12', + self._scale13: 'scale13', + self._scale14: 'scale14', + self._scale15: 'scale15' + } + for attr, kwarg_key in compare_attr_to_kwargs.items(): + kwarg_val = handler_kwargs.get(kwarg_key, + self._DEFAULT_SPEC_ATTRIBS[kwarg_key]) + if abs(kwarg_val - attr) > self._SCALETOL: + raise IncompatibleParameterError( + "Difference between '{}' values is beyond allowed tolerance {}. " + "(handler value: {}, incompatible valie: {}".format( + kwarg_key, self._SCALETOL, attr, kwarg_val)) + + # TODO: Test for other possible incompatibilities here -- Probably just check for string equality for now, + # detailed check will require some openMM/MD expertise) + #self._potential: 'potential', + #self._combining_rules: 'combining_rules', + #self._switch: 'switch', + #self._cutoff: 'cutoff', + #self._method:'method' + #} + + def create_force(self, system, topology, **kwargs): + + self._validate_parameters() + + force = openmm.NonbondedForce() + + + # If we're using PME, then the only possible openMM Nonbonded type is LJPME + if self._method == 'PME': + # If we're given a nonperiodic box, we always set NoCutoff. Later we'll add support for CutoffNonPeriodic + if (topology.box_vectors is None): + force.setNonbondedMethod(openmm.NonbondedForce.NoCutoff) + # if (topology.box_vectors is None): + # raise SMIRNOFFSpecError("If vdW method is PME, a periodic Topology " + # "must be provided") + else: + force.setNonbondedMethod(openmm.NonbondedForce.LJPME) + force.setCutoffDistance(9. * unit.angstrom) + force.setEwaldErrorTolerance(1.e-4) + + # If method is cutoff, then we currently support openMM's PME for periodic system and NoCutoff for nonperiodic + elif self._method == 'cutoff': + # If we're given a nonperiodic box, we always set NoCutoff. Later we'll add support for CutoffNonPeriodic + if (topology.box_vectors is None): + force.setNonbondedMethod(openmm.NonbondedForce.NoCutoff) + else: + force.setNonbondedMethod(openmm.NonbondedForce.PME) + force.setUseDispersionCorrection(True) + force.setCutoffDistance(self._cutoff) + + system.addForce(force) + + # Iterate over all defined Lennard-Jones types, allowing later matches to override earlier ones. + atoms = self.find_matches(topology) + + # Create all particles. + for particle in topology.topology_particles: + force.addParticle(0.0, 1.0, 0.0) + + # Set the particle Lennard-Jones terms. + for atom_key, ljtype in atoms.items(): + atom_idx = atom_key[0] + force.setParticleParameters(atom_idx, 0.0, ljtype.sigma, + ljtype.epsilon) + + # Check that no atoms (n.b. not particles) are missing force parameters. + self._check_all_valence_terms_assigned(assigned_terms=atoms, + valence_terms=topology.topology_atoms) + + # TODO: Can we express separate constraints for postprocessing and normal processing? + def postprocess_system(self, system, topology, **kwargs): + # Create exceptions based on bonds. + # TODO: This postprocessing must occur after the ChargeIncrementModelHandler + # QUESTION: Will we want to do this for *all* cases, or would we ever want flexibility here? + bond_particle_indices = [] + for bond in topology.topology_bonds: + topology_atoms = [atom for atom in bond.atoms] + bond_particle_indices.append( + (topology_atoms[0].topology_particle_index, + topology_atoms[1].topology_particle_index)) + for force in system.getForces(): + # TODO: Should we just store which `Force` object we are adding to and use that instead, + # to prevent interference with other kinds of forces in the future? + # TODO: Can we generalize this to allow for `CustomNonbondedForce` implementations too? + if isinstance(force, openmm.NonbondedForce): + #nonbonded.createExceptionsFromBonds(bond_particle_indices, self.coulomb14scale, self.lj14scale) + + # TODO: Don't mess with electrostatic scaling here. Have a separate electrostatics handler. + force.createExceptionsFromBonds(bond_particle_indices, 0.83333, + self._scale14) + #force.createExceptionsFromBonds(bond_particle_indices, self.coulomb14scale, self._scale14) + + +class ElectrostaticsHandler(ParameterHandler): + """Handles SMIRNOFF ```` tags. + + .. warning :: This API is experimental and subject to change. + """ + _TAGNAME = 'Electrostatics' + _OPENMMTYPE = openmm.NonbondedForce + _DEPENDENCIES = [vdWHandler] + _DEFAULT_SPEC_ATTRIBS = { + 'method': 'PME', + 'scale12': 0.0, + 'scale13': 0.0, + 'scale14': 0.833333, + 'scale15': 1.0, + #'pme_tolerance': 1.e-5, + #'switch_width': 8.0 * unit.angstrom, # OpenMM can't support an electrostatics switch + 'switch_width': 0.0 * unit.angstrom, + 'cutoff': 9.0 * unit.angstrom + } + _ATTRIBS_TO_TYPE = {'scale12': float, + 'scale13': float, + 'scale14': float, + 'scale15': float + } + + _OPTIONAL_SPEC_ATTRIBS = ['cutoff', 'switch_width'] + + def __init__(self, **kwargs): + + super().__init__(**kwargs) + self._validate_parameters() + + + @property + def method(self): + """The method used to model long-range electrostatic interactions""" + return self._method + + @method.setter + def method(self, other): + """The method used to model long-range electrostatic interactions""" + valid_methods = ['PME', 'Coulomb', 'reaction-field'] + if other not in valid_methods: + raise IncompatibleParameterError(f"Attempted to set electrostatics method to {other}. Expected " + f"one of {valid_methods}") + self._method = other + + + @property + def cutoff(self): + """The cutoff used for long-range van der Waals interactions""" + return self._cutoff + + @cutoff.setter + def cutoff(self, other): + """The cutoff used for long-range van der Waals interactions""" + unit_to_check = self._REQUIRE_UNITS['cutoff'] + if not unit_to_check.unit_is_compatible(other.unit): + raise IncompatibleParameterError( + f"Attempted to set vdW cutoff to {other}, which is not compatible with " + f"expected unit {unit_to_check}") + self._cutoff = other + + @property + def switch_width(self): + """The switching width used for long-range electrostatics interactions""" + return self._switch_width + + @switch_width.setter + def switch_width(self, other): + """The switching width used for long-range van der Waals interactions""" + unit_to_check = self._REQUIRE_UNITS['switch_width'] + if not unit_to_check.unit_is_compatible(other.unit): + raise IncompatibleParameterError( + f"Attempted to set vdW switch_width to {other}, which is not compatible with " + f"expected unit {unit_to_check}") + self._switch_width = other + + + def _validate_parameters(self): + """ + Checks internal attributes, raising an exception if they are configured in an invalid way. + """ + if self._scale12 != 0.0: + raise IncompatibleParameterError("Current OFF toolkit is unable to handle scale12 values other than 0.0. " + "Specified 1-2 scaling was {}".format(self._scale12)) + if self._scale13 != 0.0: + raise IncompatibleParameterError("Current OFF toolkit is unable to handle scale13 values other than 0.0. " + "Specified 1-3 scaling was {}".format(self._scale13)) + if self._scale15 != 1.0: + raise IncompatibleParameterError("Current OFF toolkit is unable to handle scale15 values other than 1.0. " + "Specified 1-5 scaling was {}".format(self._scale15)) + + supported_methods = ['PME', 'Coulomb'] # 'reaction-field' + if self._method == 'reaction-field': + raise IncompatibleParameterError('The Open Force Field toolkit does not currently support reaction-field ' + 'electrostatics.') + + if not self._method in supported_methods: + raise IncompatibleParameterError("'method' parameter in Electrostatics tag {} is not a supported " + "option. Valid methods are {}".format(self._method, supported_methods)) + + if self._method == 'reaction-field' or self._method == 'PME': + if self._cutoff is None: + raise SMIRNOFFSpecError("If Electrostatics method is 'reaction-field' or 'PME', then 'cutoff' must " + "also be specified") + + if self._switch_width != 0.0 * unit.angstrom: + raise IncompatibleParameterError("The current implementation of the Open Force Field toolkit can not " + "support an electrostatic switching width. Currently only `0.0 angstroms` " + "is supported (SMIRNOFF data specified {})".format(self._switch_width)) + + def create_force(self, system, topology, **kwargs): + existing = [system.getForce(i) for i in range(system.getNumForces())] + existing = [ + f for f in existing if type(f) == openmm.NonbondedForce + ] + force = existing[0] + + # Among other sanity checks, this ensures that the switch value is 0. + self._validate_parameters() + + + # Set the nonbonded method + settings_matched = False + current_nb_method = force.getNonbondedMethod() + + + # First, check whether the vdWHandler set the nonbonded method to LJPME, because that means + # that electrostatics also has to be PME + if (current_nb_method == openmm.NonbondedForce.LJPME) and (self._method != 'PME'): + raise IncompatibleParameterError("In current Open Force Field toolkit implementation, if vdW " + "treatment is set to LJPME, electrostatics must also be PME " + "(electrostatics treatment currently set to {}".format(self._method)) + + + + + + + # Then, set nonbonded methods based on method keyword + if self._method == 'PME': + # Check whether the topology is nonperiodic, in which case we always switch to NoCutoff + # (vdWHandler will have already set this to NoCutoff) + # TODO: This is an assumption right now, and a bad one. See issue #219 + if topology.box_vectors is None: + assert current_nb_method == openmm.NonbondedForce.NoCutoff + settings_matched = True + # raise IncompatibleParameterError("Electrostatics handler received PME method keyword, but a nonperiodic" + # " topology. Use of PME electrostatics requires a periodic topology.") + else: + if current_nb_method == openmm.NonbondedForce.LJPME: + pass + # There's no need to check for matching cutoff/tolerance here since both are hard-coded defaults + else: + force.setNonbondedMethod(openmm.NonbondedForce.PME) + force.setCutoffDistance(9. * unit.angstrom) + force.setEwaldErrorTolerance(1.e-4) + + settings_matched = True + + # If vdWHandler set the nonbonded method to NoCutoff, then we don't need to change anything + elif self._method == 'Coulomb': + if topology.box_vectors is None: + # (vdWHandler will have already set this to NoCutoff) + assert current_nb_method == openmm.NonbondedForce.NoCutoff + settings_matched = True + else: + raise IncompatibleParameterError("Electrostatics method set to Coulomb, and topology is periodic. " + "In the future, this will lead to use of OpenMM's CutoffPeriodic " + "Nonbonded force method, however this is not supported in the " + "current Open Force Field toolkit.") + + # If the vdWHandler set the nonbonded method to PME, then ensure that it has the same cutoff + elif self._method == 'reaction-field': + if topology.box_vectors is None: + # (vdWHandler will have already set this to NoCutoff) + assert current_nb_method == openmm.NonbondedForce.NoCutoff + settings_matched = True + else: + raise IncompatibleParameterError("Electrostatics method set to reaction-field. In the future, " + "this will lead to use of OpenMM's CutoffPeriodic or CutoffNonPeriodic" + " Nonbonded force method, however this is not supported in the " + "current Open Force Field toolkit") + + if not settings_matched: + raise IncompatibleParameterError("Unable to support provided vdW method, electrostatics " + "method ({}), and topology periodicity ({}) selections. Additional " + "options for nonbonded treatment may be added in future versions " + "of the Open Force Field toolkit.".format(self._method, + topology.box_vectors is not None)) + + +class ToolkitAM1BCCHandler(ParameterHandler): + """Handle SMIRNOFF ```` tags + + .. warning :: This API is experimental and subject to change. + """ + + _TAGNAME = 'ToolkitAM1BCC' # SMIRNOFF tag name to process + _OPENMMTYPE = openmm.NonbondedForce # OpenMM force class to create or utilize + _DEPENDENCIES = [vdWHandler] # vdWHandler must first run NonBondedForce.addParticle for each particle in the topology + _KWARGS = ['charge_from_molecules', 'toolkit_registry'] # Kwargs to catch when create_force is called + + + + def __init__(self, **kwargs): + super().__init__(**kwargs) + + + + def check_handler_compatibility(self, handler_kwargs, assume_missing_is_default=True): + """ + Checks if a set of kwargs used to create a ParameterHandler are compatible with this ParameterHandler. This is + called if a second handler is attempted to be initialized for the same tag. If no value is given for a field, it + will be assumed to expect the ParameterHandler class default. + + Parameters + ---------- + handler_kwargs : dict + The kwargs that would be used to construct a ParameterHandler + assume_missing_is_default : bool + If True, will assume that parameters not specified in handler_kwargs would have been set to the default. + Therefore, an exception is raised if the ParameterHandler is incompatible with the default value for a + unspecified field. + + Raises + ------ + IncompatibleParameterError if handler_kwargs are incompatible with existing parameters. + """ + pass + + def assign_charge_from_molecules(self, molecule, charge_mols): + """ + Given an input molecule, checks against a list of molecules for an isomorphic match. If found, assigns + partial charges from the match to the input molecule. + + Parameters + ---------- + molecule : an openforcefield.topology.FrozenMolecule + The molecule to have partial charges assigned if a match is found. + charge_mols : list of [openforcefield.topology.FrozenMolecule] + A list of molecules with charges already assigned. + + Returns + ------- + match_found : bool + Whether a match was found. If True, the input molecule will have been modified in-place. + """ + + from networkx.algorithms.isomorphism import GraphMatcher + import simtk.unit + # Define the node/edge attributes that we will use to match the atoms/bonds during molecule comparison + node_match_func = lambda x, y: ((x['atomic_number'] == y['atomic_number']) and + (x['stereochemistry'] == y['stereochemistry']) and + (x['is_aromatic'] == y['is_aromatic']) + ) + edge_match_func = lambda x, y: ((x['bond_order'] == y['bond_order']) and + (x['stereochemistry'] == y['stereochemistry']) and + (x['is_aromatic'] == y['is_aromatic']) + ) + # Check each charge_mol for whether it's isomorphic to the input molecule + for charge_mol in charge_mols: + if molecule.is_isomorphic(charge_mol): + # Take the first valid atom indexing map + ref_mol_G = molecule.to_networkx() + charge_mol_G = charge_mol.to_networkx() + GM = GraphMatcher( + charge_mol_G, + ref_mol_G, + node_match=node_match_func, + edge_match=edge_match_func) + for mapping in GM.isomorphisms_iter(): + topology_atom_map = mapping + break + # Set the partial charges + + # Get the partial charges + # Make a copy of the charge molecule's charges array (this way it's the right shape) + temp_mol_charges = simtk.unit.Quantity(charge_mol.partial_charges) + for charge_idx, ref_idx in topology_atom_map.items(): + temp_mol_charges[ref_idx] = charge_mol.partial_charges[charge_idx] + molecule.partial_charges = temp_mol_charges + return True + + # If no match was found, return False + return False + + def create_force(self, system, topology, **kwargs): + + from openforcefield.utils.toolkits import GLOBAL_TOOLKIT_REGISTRY + from openforcefield.topology import FrozenMolecule, TopologyAtom, TopologyVirtualSite + + existing = [system.getForce(i) for i in range(system.getNumForces())] + existing = [f for f in existing if type(f) == self._OPENMMTYPE] + if len(existing) == 0: + force = self._OPENMMTYPE() + system.addForce(force) + else: + force = existing[0] + + for ref_mol in topology.reference_molecules: + + # Make a temporary copy of ref_mol to assign charges from charge_mol + temp_mol = FrozenMolecule(ref_mol) + + # First, check whether any of the reference molecules in the topology are in the charge_from_mol list + charges_from_charge_mol = False + if 'charge_from_molecules' in kwargs: + charges_from_charge_mol = self.assign_charge_from_molecules(temp_mol, kwargs['charge_from_molecules']) + + # If the molecule wasn't assigned parameters from a manually-input charge_mol, calculate them here + if not(charges_from_charge_mol): + toolkit_registry = kwargs.get('toolkit_registry', GLOBAL_TOOLKIT_REGISTRY) + temp_mol.generate_conformers(num_conformers=10, toolkit_registry=toolkit_registry) + #temp_mol.compute_partial_charges(quantum_chemical_method=self._quantum_chemical_method, + # partial_charge_method=self._partial_charge_method) + temp_mol.compute_partial_charges_am1bcc(toolkit_registry=toolkit_registry) + # Assign charges to relevant atoms + for topology_molecule in topology._reference_molecule_to_topology_molecules[ref_mol]: + for topology_particle in topology_molecule.particles: + topology_particle_index = topology_particle.topology_particle_index + if type(topology_particle) is TopologyAtom: + ref_mol_particle_index = topology_particle.atom.molecule_particle_index + if type(topology_particle) is TopologyVirtualSite: + ref_mol_particle_index = topology_particle.virtual_site.molecule_particle_index + particle_charge = temp_mol._partial_charges[ref_mol_particle_index] + + # Retrieve nonbonded parameters for reference atom (charge not set yet) + _, sigma, epsilon = force.getParticleParameters(topology_particle_index) + # Set the nonbonded force with the partial charge + force.setParticleParameters(topology_particle_index, + particle_charge, sigma, + epsilon) + + + + # TODO: Move chargeModel and library residue charges to SMIRNOFF spec + def postprocess_system(self, system, topology, **kwargs): + bonds = self.find_matches(topology) + + # Apply bond charge increments to all appropriate force groups + # QUESTION: Should we instead apply this to the Topology in a preprocessing step, prior to spreading out charge onto virtual sites? + for force in system.getForces(): + if force.__class__.__name__ in [ + 'NonbondedForce' + ]: # TODO: We need to apply this to all Force types that involve charges, such as (Custom)GBSA forces and CustomNonbondedForce + for (atoms, bond) in bonds.items(): + # Get corresponding particle indices in Topology + particle_indices = tuple( + [atom.particle_index for atom in atoms]) + # Retrieve parameters + [charge0, sigma0, epsilon0] = force.getParticleParameters( + particle_indices[0]) + [charge1, sigma1, epsilon1] = force.getParticleParameters( + particle_indices[1]) + # Apply bond charge increment + charge0 -= bond.increment + charge1 += bond.increment + # Update charges + force.setParticleParameters(particle_indices[0], charge0, + sigma0, epsilon0) + force.setParticleParameters(particle_indices[1], charge1, + sigma1, epsilon1) + # TODO: Calculate exceptions + + +class ChargeIncrementModelHandler(ParameterHandler): + """Handle SMIRNOFF ```` tags + + .. warning :: This API is experimental and subject to change. + """ + + class ChargeIncrementType(ParameterType): + """A SMIRNOFF bond charge correction type. + + .. warning :: This API is experimental and subject to change. + """ + _VALENCE_TYPE = 'Bond' # ChemicalEnvironment valence type expected for SMARTS + _ELEMENT_NAME = 'ChargeIncrement' + _SMIRNOFF_ATTRIBS = ['smirks', 'chargeIncrement'] + _REQUIRE_UNITS = { + 'chargeIncrement': unit.elementary_charge + } + _INDEXED_ATTRIBS = ['chargeIncrement'] + + def __init__(self, node, parent): + super().__init__(**kwargs) + + _TAGNAME = 'ChargeIncrementModel' # SMIRNOFF tag name to process + _INFOTYPE = ChargeIncrementType # info type to store + _OPENMMTYPE = openmm.NonbondedForce # OpenMM force class to create or utilize + # TODO: The structure of this is still undecided + _KWARGS = ['charge_from_molecules'] + _DEFAULTS = {'number_of_conformers': 10, + 'quantum_chemical_method': 'AM1', + 'partial_charge_method': 'CM2'} + _ALLOWED_VALUES = {'quantum_chemical_method': ['AM1'], + 'partial_charge_method': ['CM2']} + + + + def __init__(self, **kwargs): + raise NotImplementedError("ChangeIncrementHandler is not yet implemented, pending finalization of the " + "SMIRNOFF spec") + super().__init__(**kwargs) + + if number_of_conformers is None: + self._number_of_conformers = self._DEFAULTS['number_of_conformers'] + elif type(number_of_conformers) is str: + self._number_of_conformers = int(number_of_conformers) + else: + self._number_of_conformers = number_of_conformers + + if quantum_chemical_method is None: + self._quantum_chemical_method = self._DEFAULTS['quantum_chemical_method'] + elif number_of_conformers in self._ALLOWED_VALUES['quantum_chemical_method']: + self._number_of_conformers = number_of_conformers + + if partial_charge_method is None: + self._partial_charge_method = self._DEFAULTS['partial_charge_method'] + elif partial_charge_method in self._ALLOWED_VALUES['partial_charge_method']: + self._partial_charge_method = partial_charge_method + + + + def check_handler_compatibility(self, handler_kwargs, assume_missing_is_default=True): + """ + Checks if a set of kwargs used to create a ParameterHandler are compatible with this ParameterHandler. This is + called if a second handler is attempted to be initialized for the same tag. If no value is given for a field, it + will be assumed to expect the ParameterHandler class default. + + Parameters + ---------- + handler_kwargs : dict + The kwargs that would be used to construct a ParameterHandler + assume_missing_is_default : bool + If True, will assume that parameters not specified in handler_kwargs would have been set to the default. + Therefore, an exception is raised if the ParameterHandler is incompatible with the default value for a + unspecified field. + + Raises + ------ + IncompatibleParameterError if handler_kwargs are incompatible with existing parameters. + """ + compare_kwarg_to_attr = { + 'number_of_conformers': self._number_of_conformers, + 'quantum_chemical_method': self._quantum_chemical_method, + 'partial_charge_method': self._partial_charge_method, + } + + for kwarg_key, attr in compare_kwarg_to_attr.items(): + # Skip this comparison if the kwarg isn't in handler_kwargs and we're not comparing against defaults + if not(assume_missing_is_default) and not(kwarg_key in handler_kwargs): + continue + + kwarg_val = handler_kwargs.get(kwarg_key, self._DEFAULTS[kwarg_key]) + if kwarg_val != attr: + raise IncompatibleParameterError( + "Incompatible '{}' values found during handler compatibility check." + "(existing handler value: {}, new existing value: {}".format(kwarg_key, attr, kwarg_val)) + + def assign_charge_from_molecules(self, molecule, charge_mols): + """ + Given an input molecule, checks against a list of molecules for an isomorphic match. If found, assigns + partial charges from the match to the input molecule. + + Parameters + ---------- + molecule : an openforcefield.topology.FrozenMolecule + The molecule to have partial charges assigned if a match is found. + charge_mols : list of [openforcefield.topology.FrozenMolecule] + A list of molecules with charges already assigned. + + Returns + ------- + match_found : bool + Whether a match was found. If True, the input molecule will have been modified in-place. + """ + + from networkx.algorithms.isomorphism import GraphMatcher + # Define the node/edge attributes that we will use to match the atoms/bonds during molecule comparison + node_match_func = lambda x, y: ((x['atomic_number'] == y['atomic_number']) and + (x['stereochemistry'] == y['stereochemistry']) and + (x['is_aromatic'] == y['is_aromatic']) + ) + edge_match_func = lambda x, y: ((x['order'] == y['order']) and + (x['stereochemistry'] == y['stereochemistry']) and + (x['is_aromatic'] == y['is_aromatic']) + ) + # Check each charge_mol for whether it's isomorphic to the input molecule + for charge_mol in charge_mols: + if molecule.is_isomorphic(charge_mol): + # Take the first valid atom indexing map + ref_mol_G = molecule.to_networkx() + charge_mol_G = charge_mol.to_networkX() + GM = GraphMatcher( + charge_mol_G, + ref_mol_G, + node_match=node_match_func, + edge_match=edge_match_func) + for mapping in GM.isomorphisms_iter(): + topology_atom_map = mapping + break + # Set the partial charges + charge_mol_charges = charge_mol.get_partial_charges() + temp_mol_charges = charge_mol_charges.copy() + for charge_idx, ref_idx in topology_atom_map: + temp_mol_charges[ref_idx] = charge_mol_charges[charge_idx] + molecule.set_partial_charges(temp_mol_charges) + return True + + # If no match was found, return False + return False + + def create_force(self, system, topology, **kwargs): + + + from openforcefield.topology import FrozenMolecule, TopologyAtom, TopologyVirtualSite + + existing = [system.getForce(i) for i in range(system.getNumForces())] + existing = [f for f in existing if type(f) == self._OPENMMTYPE] + if len(existing) == 0: + force = self._OPENMMTYPE() + system.addForce(force) + else: + force = existing[0] + + for ref_mol in topology.reference_molecules: + + # Make a temporary copy of ref_mol to assign charges from charge_mol + temp_mol = FrozenMolecule(ref_mol) + + # First, check whether any of the reference molecules in the topology are in the charge_from_mol list + charges_from_charge_mol = False + if 'charge_from_mol' in kwargs: + charges_from_charge_mol = self.assign_charge_from_molecules(temp_mol, kwargs['charge_from_mol']) + + # If the molecule wasn't assigned parameters from a manually-input charge_mol, calculate them here + if not(charges_from_charge_mol): + temp_mol.generate_conformers(num_conformers=10) + temp_mol.compute_partial_charges(quantum_chemical_method=self._quantum_chemical_method, + partial_charge_method=self._partial_charge_method) + + # Assign charges to relevant atoms + for topology_molecule in topology._reference_molecule_to_topology_molecules[ref_mol]: + for topology_particle in topology_molecule.particles: + topology_particle_index = topology_particle.topology_particle_index + if type(topology_particle) is TopologyAtom: + ref_mol_particle_index = topology_particle.atom.molecule_particle_index + if type(topology_particle) is TopologyVirtualSite: + ref_mol_particle_index = topology_particle.virtual_site.molecule_particle_index + particle_charge = temp_mol._partial_charges[ref_mol_particle_index] + + # Retrieve nonbonded parameters for reference atom (charge not set yet) + _, sigma, epsilon = force.getParticleParameters(topology_particle_index) + # Set the nonbonded force with the partial charge + force.setParticleParameters(topology_particle_index, + particle_charge, sigma, + epsilon) + + + + # TODO: Move chargeModel and library residue charges to SMIRNOFF spec + def postprocess_system(self, system, topology, **kwargs): + bonds = self.find_matches(topology) + + # Apply bond charge increments to all appropriate force groups + # QUESTION: Should we instead apply this to the Topology in a preprocessing step, prior to spreading out charge onto virtual sites? + for force in system.getForces(): + if force.__class__.__name__ in [ + 'NonbondedForce' + ]: # TODO: We need to apply this to all Force types that involve charges, such as (Custom)GBSA forces and CustomNonbondedForce + for (atoms, bond) in bonds.items(): + # Get corresponding particle indices in Topology + particle_indices = tuple( + [atom.particle_index for atom in atoms]) + # Retrieve parameters + [charge0, sigma0, epsilon0] = force.getParticleParameters( + particle_indices[0]) + [charge1, sigma1, epsilon1] = force.getParticleParameters( + particle_indices[1]) + # Apply bond charge increment + charge0 -= bond.increment + charge1 += bond.increment + # Update charges + force.setParticleParameters(particle_indices[0], charge0, + sigma0, epsilon0) + force.setParticleParameters(particle_indices[1], charge1, + sigma1, epsilon1) + # TODO: Calculate exceptions + + +class GBSAParameterHandler(ParameterHandler): + """Handle SMIRNOFF ```` tags + + .. warning :: This API is experimental and subject to change. + """ + # TODO: Differentiate between global and per-particle parameters for each model. + + # Global parameters for surface area (SA) component of model + SA_expected_parameters = { + 'ACE': ['surface_area_penalty', 'solvent_radius'], + None: [], + } + + # Per-particle parameters for generalized Born (GB) model + GB_expected_parameters = { + 'HCT': ['radius', 'scale'], + 'OBC1': ['radius', 'scale'], + 'OBC2': ['radius', 'scale'], + } + + class GBSAType(ParameterType): + """A SMIRNOFF GBSA type. + + .. warning :: This API is experimental and subject to change. + """ + _VALENCE_TYPE = 'Atom' + _ELEMENT_NAME = 'Atom' # TODO: This isn't actually in the spec + _SMIRNOFF_ATTRIBS = ['smirks', 'radius', 'scale'] + _REQUIRE_UNITS = {'radius': unit.angstrom} + _ATTRIBS_TO_TYPE = {'scale': float} + + def __init__(self, **kwargs): + super().__init__(**kwargs) + + # # Store model parameters. + # gb_model = parent.attrib['gb_model'] + # expected_parameters = GBSAParameterHandler.GB_expected_parameters[ + # gb_model] + # provided_parameters = list() + # missing_parameters = list() + # for name in expected_parameters: + # if name in node.attrib: + # provided_parameters.append(name) + # value = _extract_quantity_from_xml_element( + # node, parent, name) + # setattr(self, name, value) + # else: + # missing_parameters.append(name) + # if len(missing_parameters) > 0: + # msg = 'GBSAForce: missing per-atom parameters for tag %s' % str( + # node) + # msg += 'model "%s" requires specification of per-atom parameters %s\n' % ( + # gb_model, str(expected_parameters)) + # msg += 'provided parameters : %s\n' % str(provided_parameters) + # msg += 'missing parameters: %s' % str(missing_parameters) + # raise Exception(msg) + + # TODO: Finish this + _TAGNAME = 'GBSA' + _INFOTYPE = GBSAType + #_OPENMMTYPE = + + def __init__(self, **kwargs): + + super().__init__(**kwargs) + + # TODO: Fix this + def parseElement(self): + # Initialize GB model + gb_model = element.attrib['gb_model'] + valid_GB_models = GBSAParameterHandler.GB_expected_parameters.keys() + if not gb_model in valid_GB_models: + raise Exception( + 'Specified GBSAForce model "%s" not one of valid models: %s' % + (gb_model, valid_GB_models)) + self.gb_model = gb_model + + # Initialize SA model + sa_model = element.attrib['sa_model'] + valid_SA_models = GBSAParameterHandler.SA_expected_parameters.keys() + if not sa_model in valid_SA_models: + raise Exception( + 'Specified GBSAForce SA_model "%s" not one of valid models: %s' + % (sa_model, valid_SA_models)) + self.sa_model = sa_model + + # Store parameters for GB and SA models + # TODO: Deep copy? + self.parameters = element.attrib + + # TODO: Generalize this to allow forces to know when their OpenMM Force objects can be combined + def checkCompatibility(self, Handler): + """ + Check compatibility of this Handler with another Handlers. + """ + Handler = existing[0] + if (Handler.gb_model != self.gb_model): + raise ValueError( + 'Found multiple GBSAForce tags with different GB model specifications' + ) + if (Handler.sa_model != self.sa_model): + raise ValueError( + 'Found multiple GBSAForce tags with different SA model specifications' + ) + # TODO: Check other attributes (parameters of GB and SA models) automatically? + + def create_force(self, system, topology, **args): + # TODO: Rework this + from openforcefield.typing.engines.smirnoff import gbsaforces + force_class = getattr(gbsaforces, self.gb_model) + force = force_class(**self.parameters) + system.addForce(force) + + # Add all GBSA terms to the system. + expected_parameters = GBSAParameterHandler.GB_expected_parameters[ + self.gb_model] + + # Create all particles with parameters set to zero + atoms = self.getMatches(topology) + nparams = 1 + len(expected_parameters) # charge + GBSA parameters + params = [0.0 for i in range(nparams)] + for particle in topology.topology_particles(): + force.addParticle(params) + # Set the GBSA parameters (keeping charges at zero for now) + for (atoms, gbsa_type) in atoms.items(): + atom = atoms[0] + # Set per-particle parameters for assigned parameters + params = [atom.charge] + [ + getattr(gbsa_type, name) for name in expected_parameters + ] + force.setParticleParameters(atom.particle_index, params) diff --git a/openforcefield/utils/__init__.py b/openforcefield/utils/__init__.py index b7f15e9ec..df9d7f10c 100644 --- a/openforcefield/utils/__init__.py +++ b/openforcefield/utils/__init__.py @@ -1,3 +1,7 @@ # General utilities for forcefields from openforcefield.utils.utils import * +from openforcefield.utils.toolkits import * + + + diff --git a/openforcefield/utils/serialization.py b/openforcefield/utils/serialization.py new file mode 100644 index 000000000..7d8b6ebb4 --- /dev/null +++ b/openforcefield/utils/serialization.py @@ -0,0 +1,435 @@ +#!/usr/bin/env python +""" +Serialization mix-in + +.. todo :: + + Currently, the ``openforcefield`` toolkit package requires a number of dependencies to support all of these serialization protocols. + Instead, should we not include these by default, and instead raise a helpful exception with installation instructions if one of the serialization schemes is called but the requisite library is not installed? + +""" + +#============================================================================================= +# GLOBAL IMPORTS +#============================================================================================= + +import abc + + +#============================================================================================= +# SERIALIZATION MIX-IN +#============================================================================================= + + +class Serializable(abc.ABC): + """Mix-in to add serialization and deserialization support via JSON, YAML, BSON, TOML, MessagePack, and XML. + + For more information on these formats, see: `JSON `_, `BSON `_, `YAML `_, `TOML `_, `MessagePack `_, and `XML `_. + + To use this mix-in, the class inheriting from this class must have implemented ``to_dict()`` and ``from_dict()`` methods + that utilize dictionaries containing only serialiable Python objects. + + .. warning :: + + The serialization/deserialiation schemes used here place some strict constraints on what kinds of ``dict`` objects + can be serialized. No effort is made to add further protection to ensure serialization is possible. Use with caution. + + Examples + -------- + + Example class using :class:`Serializable` mix-in: + + >>> from openforcefield.utils.serialization import Serializable + >>> class Thing(Serializable): + ... def __init__(self, description): + ... self.description = description + ... + ... def to_dict(self): + ... return { 'description' : self.description } + ... + ... @classmethod + ... def from_dict(cls, d): + ... return cls(d['description']) + ... + >>> # Create an example object + >>> thing = Thing('blorb') + + Get `JSON `_ representation: + + >>> json_thing = thing.to_json() + + Reconstruct an object from its `JSON `_ representation: + + >>> thing_from_json = Thing.from_json(json_thing) + + Get `BSON `_ representation: + + >>> bson_thing = thing.to_bson() + + Reconstruct an object from its `BSON `_ representation: + + >>> thing_from_bson = Thing.from_bson(bson_thing) + + Get `YAML `_ representation: + + >>> yaml_thing = thing.to_yaml() + + Reconstruct an object from its `YAML `_ representation: + + >>> thing_from_yaml = Thing.from_yaml(yaml_thing) + + Get `MessagePack `_ representation: + + >>> messagepack_thing = thing.to_messagepack() + + Reconstruct an object from its `MessagePack `_ representation: + + >>> thing_from_messagepack = Thing.from_messagepack(messagepack_thing) + + Get `XML `_ representation: + + >>> xml_thing = thing.to_xml() + + """ + + @abc.abstractmethod + def to_dict(self): + pass + + @classmethod + @abc.abstractmethod + def from_dict(cls, d): + pass + + def to_json(self, indent=None): + """ + Return a JSON serialized representation. + + Specification: https://www.json.org/ + + Parameters + ---------- + indent : int, optional, default=None + If not None, will pretty-print with specified number of spaces for indentation + + Returns + ------- + serialized : str + A JSON serialized representation of the object + + """ + import json + d = self.to_dict() + return json.dumps(d, indent=indent) + + @classmethod + def from_json(cls, serialized): + """ + Instantiate an object from a JSON serialized representation. + + Specification: https://www.json.org/ + + Parameters + ---------- + serialized : str + A JSON serialized representation of the object + + Returns + ------- + instance : cls + An instantiated object + + """ + import json + d = json.loads(serialized) + return cls.from_dict(d) + + def to_bson(self): + """ + Return a BSON serialized representation. + + Specification: http://bsonspec.org/ + + Returns + ------- + serialized : bytes + A BSON serialized representation of the objecft + + """ + import bson + d = self.to_dict() + return bson.dumps(d) + + @classmethod + def from_bson(cls, serialized): + """ + Instantiate an object from a BSON serialized representation. + + Specification: http://bsonspec.org/ + + Parameters + ---------- + serialized : bytes + A BSON serialized representation of the object + + Returns + ------- + instance : cls + An instantiated object + + """ + import bson + d = bson.loads(serialized) + return cls.from_dict(d) + + def to_toml(self): + """ + Return a TOML serialized representation. + + Specification: https://github.com/toml-lang/toml + + Returns + ------- + serialized : str + A TOML serialized representation of the object + + """ + raise NotImplementedError() + # TODO: This implementation currently discards dict keys associated to the None value. + # See test_utils_serialization::TestUtilsSMIRNOFFSerialization::test_toml. + import toml + d = self.to_dict() + return toml.dumps(d) + + @classmethod + def from_toml(cls, serialized): + """ + Instantiate an object from a TOML serialized representation. + + Specification: https://github.com/toml-lang/toml + + Parameters + ---------- + serlialized : str + A TOML serialized representation of the object + + Returns + ------- + instance : cls + An instantiated object + + """ + import toml + d = toml.loads(serialized) + return cls.from_dict(d) + + @staticmethod + def _represent_odict(dump, tag, mapping, flow_style=None): + """Like BaseRepresenter.represent_mapping, but does not issue the sort(). + """ + import yaml + value = [] + node = yaml.MappingNode(tag, value, flow_style=flow_style) + if dump.alias_key is not None: + dump.represented_objects[dump.alias_key] = node + best_style = True + if hasattr(mapping, 'items'): + mapping = mapping.items() + for item_key, item_value in mapping: + node_key = dump.represent_data(item_key) + node_value = dump.represent_data(item_value) + if not (isinstance(node_key, yaml.ScalarNode) + and not node_key.style): + best_style = False + if not (isinstance(node_value, yaml.ScalarNode) + and not node_value.style): + best_style = False + value.append((node_key, node_value)) + if flow_style is None: + if dump.default_flow_style is not None: + node.flow_style = dump.default_flow_style + else: + node.flow_style = best_style + return node + + def to_yaml(self): + """ + Return a YAML serialized representation. + + Specification: http://yaml.org/ + + Returns + ------- + serialized : str + A YAML serialized representation of the object + + """ + import yaml + from collections import OrderedDict + yaml.SafeDumper.add_representer(OrderedDict, + lambda dumper, value: self._represent_odict(dumper, u'tag:yaml.org,2002:map', value)) + d = self.to_dict() + return yaml.safe_dump(d, width=180) + + @classmethod + def from_yaml(cls, serialized): + """ + Instantiate from a YAML serialized representation. + + Specification: http://yaml.org/ + + Parameters + ---------- + serialized : str + A YAML serialized representation of the object + + Returns + ------- + instance : cls + Instantiated object + + """ + import yaml + from collections import OrderedDict + yaml.SafeDumper.add_representer(OrderedDict, + lambda dumper, value: self._represent_odict(dumper, u'tag:yaml.org,2002:map', value)) + d = yaml.safe_load(serialized) + return cls.from_dict(d) + + def to_messagepack(self): + """ + Return a MessagePack representation. + + Specification: https://msgpack.org/index.html + + Returns + ------- + serialized : bytes + A MessagePack-encoded bytes serialized representation of the object + + """ + import msgpack + d = self.to_dict() + return msgpack.dumps(d, use_bin_type=True) + + @classmethod + def from_messagepack(cls, serialized): + """ + Instantiate an object from a MessagePack serialized representation. + + Specification: https://msgpack.org/index.html + + Parameters + ---------- + serialized : bytes + A MessagePack-encoded bytes serialized representation + + Returns + ------- + instance : cls + Instantiated object. + + """ + import msgpack + d = msgpack.loads(serialized, raw=False) + return cls.from_dict(d) + + def to_xml(self, indent=2): + """ + Return an XML representation. + + Specification: https://www.w3.org/XML/ + + Parameters + ---------- + indent : int, optional, default=2 + If not None, will pretty-print with specified number of spaces for indentation + + Returns + ------- + serialized : bytes + A MessagePack-encoded bytes serialized representation. + + """ + import xmltodict + # An XML document requires one and only one root node. + root_name = self.__class__.__name__ + d = {root_name: self.to_dict()} + # Configure indentation level. + if indent is not None: + pretty = True + indent = ' ' * indent + else: + pretty = False + # Convert data from dictionary to XML format. + return xmltodict.unparse(d, pretty=pretty, indent=indent) + + @classmethod + def from_xml(cls, serialized): + """ + Instantiate an object from an XML serialized representation. + + Specification: https://www.w3.org/XML/ + + Parameters + ---------- + serialized : bytes + An XML serialized representation + + Returns + ------- + instance : cls + Instantiated object. + + """ + raise NotImplementedError() + # TODO: This implementation currently loads numbers as strings. + # See test_utils_serialization::TestUtilsSerialization::test_xml. + import xmltodict + d = xmltodict.parse(serialized) + root_name = cls.__name__ + return cls.from_dict(d[root_name]) + + def to_pickle(self): + """ + Return a pickle serialized representation. + + .. warning :: + + This is not recommended for safe, stable storage since the pickle specification + may change between Python versions. + + Returns + ------- + serialized : str + A pickled representation of the object + + """ + import pickle + d = self.to_dict() + return pickle.dumps(d) + + @classmethod + def from_pickle(cls, serialized): + """ + Instantiate an object from a pickle serialized representation. + + .. warning :: + + This is not recommended for safe, stable storage since the pickle specification + may change between Python versions. + + Parameters + ---------- + serialized : str + A pickled representation of the object + + Returns + ------- + instance : cls + An instantiated object + + """ + import pickle + d = pickle.loads(serialized) + return cls.from_dict(d) diff --git a/openforcefield/utils/structure.py b/openforcefield/utils/structure.py new file mode 100644 index 000000000..209ebe445 --- /dev/null +++ b/openforcefield/utils/structure.py @@ -0,0 +1,737 @@ +#!/usr/bin/env python + +""" +Utility subroutines for manipulating parmed Structure objects + +""" +#============================================================================================= +# GLOBAL IMPORTS +#============================================================================================= + +import os +import time + +import numpy as np + +from simtk import openmm, unit + +#============================================================================================= +# PARMED UTILITIES +#============================================================================================= + +# TODO: Can we get rid of this, or convert it to use Molecule instead? +def generateSMIRNOFFStructure(oemol): + """ + Given an OpenEye molecule (oechem.OEMol), create an OpenMM System and use to + generate a ParmEd structure using the SMIRNOFF forcefield parameters. + + Parameters + ---------- + oemol : openeye.oechem.OEMol + OpenEye molecule + + Returns + ------- + molecule_structure : parmed.Structure + The resulting Structure + + """ + from openforcefield.topology import Molecule, Topology + from openforcefield.typing.engines.smirnoff import ForceField + + off_mol = Molecule.from_openeye(oemol) + off_top = Topology.from_molecules([off_mol]) + mol_ff = ForceField('smirnoff99Frosst.offxml') + + # Create OpenMM System and Topology. + omm_top = generateTopologyFromOEMol(oemol) + + # If it's a nonperiodic box, then we can't use default (PME) settings + if omm_top.getPeriodicBoxVectors() is None: + mol_ff.get_handler("Electrostatics", {})._method = 'Coulomb' + + system = mol_ff.create_openmm_system(off_top) + + # Convert to ParmEd structure. + import parmed + xyz = extractPositionsFromOEMol(oemol) + molecule_structure = parmed.openmm.load_topology(omm_top, system, xyz=xyz) + + return molecule_structure + +def generateProteinStructure(proteinpdb, protein_forcefield='amber99sbildn.xml', solvent_forcefield='tip3p.xml'): + """ + Given an OpenMM PDBFile, create the OpenMM System of the protein using OpenMM's ForceField and then generate the parametrized ParmEd Structure of the protein. + + Parameters + ---------- + proteinpdb : simtk.openmm.app.PDBFile object, + Loaded PDBFile object of the protein. + protein_forcefield : xml file, default='amber99sbildn.xml' + Forcefield parameters for protein + solvent_forcefield : xml file, default='tip3p.xml' + Forcefield parameters for solvent + + Returns + ------- + solv_structure : parmed.structure.Structure + The parameterized Structure of the protein with solvent molecules. (No ligand). + + """ + # Generate protein Structure object using OpenMM ForceField + from simtk.openmm import app + import parmed + forcefield = openmm.app.ForceField(protein_forcefield, solvent_forcefield) + protein_system = forcefield.createSystem( proteinpdb.topology ) + protein_structure = parmed.openmm.load_topology(proteinpdb.topology, + protein_system, + xyz=proteinpdb.positions) + return protein_structure + +def combinePositions(proteinPositions, molPositions): + """ + Loops through the positions from the ParmEd structures of the protein and ligand, + divides by unit.angstroms which will ensure both positions arrays are in the same units. + + Parameters + ---------- + proteinPositions : list of 3-element Quantity tuples. + Positions list taken directly from the protein Structure. + molPositions : list of 3-element Quantity tuples. + Positions list taken directly from the molecule Structure. + + Returns + ------- + positions : list of 3-element Quantity tuples. + ex. unit.Quantity(positions, positions_unit) + Combined positions of the protein and molecule Structures. + """ + + positions_unit = unit.angstroms + positions0_dimensionless = np.array(proteinPositions / positions_unit) + positions1_dimensionless = np.array(molPositions / positions_unit) + coordinates = np.vstack( + (positions0_dimensionless, positions1_dimensionless)) + natoms = len(coordinates) + positions = np.zeros([natoms, 3], np.float32) + for index in range(natoms): + (x, y, z) = coordinates[index] + positions[index, 0] = x + positions[index, 1] = y + positions[index, 2] = z + positions = unit.Quantity(positions, positions_unit) + return positions + +def mergeStructure(proteinStructure, molStructure): + """ + Combines the parametrized ParmEd structures of the protein and ligand to + create the Structure for the protein:ligand complex, while retaining the SMIRNOFF + parameters on the ligand. Preserves positions and box vectors. + (Not as easily achieved using native OpenMM tools). + + Parameters + ---------- + proteinStructure : parmed.structure.Structure + The parametrized structure of the protein. + moleculeStructure : parmed.structure.Structure + The parametrized structure of the ligand. + + Returns + ------- + structure : parmed.structure.Structure + The parametrized structure of the protein:ligand complex. + """ + structure = proteinStructure + molStructure + positions = combinePostions(proteinStructure.positions, molStructure.positions) + # Concatenate positions arrays (ensures same units) + structure.positions = positions + # Restore original box vectors + structure.box = proteinStructure.box + return structure + +# TODO: Migrate into Molecule +def generateTopologyFromOEMol(molecule): + """ + Generate an OpenMM Topology object from an OEMol molecule. + + Parameters + ---------- + molecule : openeye.oechem.OEMol + The molecule from which a Topology object is to be generated. + + Returns + ------- + topology : simtk.openmm.app.Topology + The Topology object generated from `molecule`. + + """ + from openeye import oechem + + # Avoid manipulating the molecule + mol = oechem.OEMol(molecule) + + # Create a Topology object with one Chain and one Residue. + from simtk.openmm.app import Topology + topology = Topology() + chain = topology.addChain() + resname = mol.GetTitle() + residue = topology.addResidue(resname, chain) + + # Make sure the atoms have names, otherwise bonds won't be created properly below + if any([atom.GetName() =='' for atom in mol.GetAtoms()]): + oechem.OETriposAtomNames(mol) + # Check names are unique; non-unique names will also cause a problem + atomnames = [ atom.GetName() for atom in mol.GetAtoms() ] + if any( atomnames.count(atom.GetName())>1 for atom in mol.GetAtoms()): + raise Exception("Error: Reference molecule must have unique atom names in order to create a Topology.") + + # Create atoms in the residue. + for atom in mol.GetAtoms(): + name = atom.GetName() + element = openmm.app.element.Element.getByAtomicNumber(atom.GetAtomicNum()) + openmm_atom = topology.addAtom(name, element, residue) + + # Create bonds. + atoms = { atom.name : atom for atom in topology.atoms() } + for bond in mol.GetBonds(): + aromatic = None + if bond.IsAromatic(): aromatic = 'Aromatic' + # Add bond, preserving order assessed by OEChem + topology.addBond(atoms[bond.GetBgn().GetName()], atoms[bond.GetEnd().GetName()], type=aromatic, order=bond.GetOrder()) + + return topology + +def get_testdata_filename(relative_path): + """Get the full path to one of the reference files in testsystems. + + In the source distribution, these files are in ``openforcefield/data/``, + but on installation, they're moved to somewhere in the user's python + site-packages directory. + + Parameters + ---------- + name : str + Name of the file to load (with respect to the repex folder). + + """ + + from pkg_resources import resource_filename + fn = resource_filename('openforcefield', os.path.join('data', relative_path)) + + if not os.path.exists(fn): + raise ValueError("Sorry! %s does not exist. If you just added it, you'll have to re-install" % fn) + + return fn + +# TODO: Do we need this? +def normalize_molecules(molecules): + """ + Normalize all molecules in specified set. + + ARGUMENTS + + molecules (list of OEMol) - molecules to be normalized (in place) + + """ + from openeye import oechem + + # Add explicit hydrogens. + for molecule in molecules: + oechem.OEAddExplicitHydrogens(molecule) + + # Build a conformation for all molecules with Omega. + print("Building conformations for all molecules...") + from openeye import oeomega + omega = oeomega.OEOmega() + omega.SetMaxConfs(1) + omega.SetFromCT(True) + for molecule in molecules: + #omega.SetFixMol(molecule) + omega(molecule) + end_time = time.time() + elapsed_time = end_time - start_time + print("%.3f s elapsed" % elapsed_time) + + # Regularize all molecules through writing as mol2. + print("Regularizing all molecules...") + ligand_mol2_dirname = os.path.dirname(mcmcDbName) + '/mol2' + if( not os.path.exists( ligand_mol2_dirname ) ): + os.makedirs(ligand_mol2_dirname) + ligand_mol2_filename = ligand_mol2_dirname + '/temp' + os.path.basename(mcmcDbName) + '.mol2' + start_time = time.time() + omolstream = oechem.oemolostream(ligand_mol2_filename) + for molecule in molecules: + # Write molecule as mol2, changing molecule through normalization. + oechem.OEWriteMolecule(omolstream, molecule) + omolstream.close() + end_time = time.time() + elapsed_time = end_time - start_time + print("%.3f s elapsed" % elapsed_time) + + # Assign AM1-BCC charges. + print("Assigning AM1-BCC charges...") + start_time = time.time() + for molecule in molecules: + # Assign AM1-BCC charges. + if molecule.NumAtoms() == 1: + # Use formal charges for ions. + OEFormalPartialCharges(molecule) + else: + # Assign AM1-BCC charges for multiatom molecules. + OEAssignPartialCharges(molecule, OECharges_AM1BCC, False) # use explicit hydrogens + # Check to make sure we ended up with partial charges. + if OEHasPartialCharges(molecule) == False: + print("No charges on molecule: '%s'" % molecule.GetTitle()) + print("IUPAC name: %s" % OECreateIUPACName(molecule)) + # TODO: Write molecule out + # Delete themolecule. + molecules.remove(molecule) + + end_time = time.time() + elapsed_time = end_time - start_time + print("%.3f s elapsed" % elapsed_time) + print("%d molecules remaining" % len(molecules)) + + return + +# TODO: Migrate into Molecule +def read_molecules(filename, verbose=True): + """ + Read molecules from an OpenEye-supported file. + + Parameters + ---------- + filename : str + Filename from which molecules are to be read (e.g. mol2, sdf) + + Returns + ------- + molecules : list of OEMol + List of molecules read from file + + """ + from openeye import oechem + + if not os.path.exists(filename): + built_in = get_testdata_filename('molecules/%s' % filename) + if not os.path.exists(built_in): + raise Exception("File '%s' not found." % filename) + filename = built_in + + if verbose: print("Loading molecules from '%s'..." % filename) + start_time = time.time() + molecules = list() + input_molstream = oechem.oemolistream(filename) + + flavor = oechem.OEIFlavor_Generic_Default | oechem.OEIFlavor_MOL2_Default | oechem.OEIFlavor_MOL2_Forcefield + input_molstream.SetFlavor(oechem.OEFormat_MOL2, flavor) + + molecule = oechem.OECreateOEGraphMol() + while oechem.OEReadMolecule(input_molstream, molecule): + # If molecule has no title, try getting SD 'name' tag + if molecule.GetTitle() == '': + name = oechem.OEGetSDData(molecule, 'name').strip() + molecule.SetTitle(name) + # Append to list. + molecule_copy = oechem.OEMol(molecule) + molecules.append(molecule_copy) + input_molstream.close() + if verbose: print("%d molecules read" % len(molecules)) + end_time = time.time() + elapsed_time = end_time - start_time + if verbose: print("%.3f s elapsed" % elapsed_time) + + return molecules + +# TODO: Migrate into Molecule +def setPositionsInOEMol(oemol, positions): + """Set the positions in an OEMol using a position array with units from simtk.unit, i.e. from OpenMM. Atoms must have same order. + + Arguments: + --------- + oemol : OEMol + OpenEye molecule + positions : Nx3 array + Unit-bearing via simtk.unit Nx3 array of coordinates + """ + from openeye import oechem + + if oemol.NumAtoms() != len(positions): raise ValueError("Number of atoms in molecule does not match length of position array.") + pos_unitless = positions/unit.angstroms + + coordlist = [] + for idx in range(len(pos_unitless)): + for j in range(3): + coordlist.append(pos_unitless[idx][j]) + oemol.SetCoords(oechem.OEFloatArray(coordlist)) + +# TODO: Migrate into Molecule +def extractPositionsFromOEMol(oemol): + """Get the positions from an OEMol and return in a position array with units via simtk.unit, i.e. foramtted for OpenMM. + Adapted from choderalab/openmoltools test function extractPositionsFromOEMOL + + Arguments: + ---------- + oemol : OEMol + OpenEye molecule + + Returns: + -------- + positions : Nx3 array + Unit-bearing via simtk.unit Nx3 array of coordinates + """ + positions = unit.Quantity(np.zeros([oemol.NumAtoms(), 3], np.float32), unit.angstroms) + coords = oemol.GetCoords() + for index in range(oemol.NumAtoms()): + positions[index,:] = unit.Quantity(coords[index], unit.angstroms) + return positions + +def read_typelist(filename): + """ + Read a parameter type or decorator list from a file. + Lines in these files have the format + "SMARTS/SMIRKS shorthand" + lines beginning with '%' are ignored + + Parameters + ---------- + filename : str + Path and name of file to be read + Could be file in openforcefield/data/ + + Returns + ------- + typelist : list of tuples + Typelist[i] is element i of the typelist in format (smarts, shorthand) + """ + if filename is None: + return None + + if not os.path.exists(filename): + built_in = get_testdata_filename(filename) + if not os.path.exists(built_in): + raise Exception("File '%s' not found." % filename) + filename = built_in + + typelist = list() + ifs = open(filename) + lines = ifs.readlines() + used_typenames = list() + + for line in lines: + # Strip trailing comments + index = line.find('%') + if index != -1: + line = line[0:index] + + # Split into tokens. + tokens = line.split() + # Process if we have enough tokens + if len(tokens) >= 2: + smarts = tokens[0] + typename = ' '.join(tokens[1:]) + if typename not in used_typenames: + typelist.append([smarts,typename]) + used_typenames.append(typename) + else: + raise Exception("Error in file '%s' -- each entry must " + "have a unique name." % filename ) + + ifs.close() + + return typelist + +# TODO: This only works with the OpenEye toolkit installed; replace with Molecule API +def positions_from_oemol(mol): + """ + Extract OpenMM positions from OEMol. + + Parameters + ---------- + mol : oechem.openeye.OEMol + OpenEye molecule from which to extract coordinates. + + Returns + ------- + positions : simtk.unit.Quantity of dimension (nparticles,3) + + """ + from openeye import oechem, oeomega + if mol.GetDimension() != 3: + # Assign coordinates + omega = oeomega.OEOmega() + omega.SetMaxConfs(1) + omega.SetIncludeInput(False) + omega.SetCanonOrder(False) + omega.SetSampleHydrogens(True) # Word to the wise: skipping this step can lead to significantly different charges! + status = omega(mol) # generate conformation + + coordinates = mol.GetCoords() + natoms = len(coordinates) + positions = np.zeros([natoms,3], np.float32) + for index in range(natoms): + (x,y,z) = coordinates[index] + positions[index,0] = x + positions[index,1] = y + positions[index,2] = z + positions = unit.Quantity(positions, unit.angstroms) + return positions + +def check_energy_is_finite(system, positions): + """ + Check the potential energy is not NaN. + + Parameters + ---------- + system : simtk.openmm.System + The system to check + positions : simtk.unit.Quantity of dimension (natoms,3) with units of length + The positions to use + + """ + integrator = openmm.VerletIntegrator(1.0 * unit.femtoseconds) + context = openmm.Context(system, integrator) + context.setPositions(positions) + state = context.getState(getEnergy=True) + energy = state.getPotentialEnergy() / unit.kilocalories_per_mole + if np.isnan(energy): + raise Exception('Potential energy is NaN') + +def get_energy(system, positions): + """ + Return the potential energy. + + Parameters + ---------- + system : simtk.openmm.System + The system to check + positions : simtk.unit.Quantity of dimension (natoms,3) with units of length + The positions to use + Returns + --------- + energy + """ + + integrator = openmm.VerletIntegrator(1.0 * unit.femtoseconds) + context = openmm.Context(system, integrator) + context.setPositions(positions) + state = context.getState(getEnergy=True) + energy = state.getPotentialEnergy() / unit.kilocalories_per_mole + return energy + +#============================================================================= +# OPENMM MERGING AND EXPORTING UTILITY FUNCTIONS +#============================================================================= + +# TODO: Reorganize this file, moving exporters to openforcefield.exporters + +def get_molecule_parameterIDs(molecules, forcefield): + """Process a list of molecules with a specified SMIRNOFF ffxml file and determine which parameters are used by + which molecules, returning collated results. + + Parameters + ---------- + molecules : list of openforcefield.topology.Molecule + List of molecules (with explicit hydrogens) to parse + forcefield : openforcefield.typing.engines.smirnoff.ForceField + The ForceField to apply + + Returns + ------- + parameters_by_molecule : dict + Parameter IDs used in each molecule, keyed by isomeric SMILES + generated from provided OEMols. Each entry in the dict is a list + which does not necessarily have unique entries; i.e. parameter IDs + which are used more than once will occur multiple times. + + parameters_by_ID : dict + Molecules in which each parameter ID occur, keyed by parameter ID. + Each entry in the dict is a set of isomeric SMILES for molecules + in which that parameter occurs. No frequency information is stored. + + """ + from openforcefield.topology import Topology + # Create storage + parameters_by_molecule = dict() + parameters_by_ID = dict() + + # Generate isomeric SMILES for each molecule, ensuring all molecules are unique + isosmiles = [ molecule.to_smiles() for molecule in molecules ] + already_seen = set() + duplicates = set(smiles for smiles in isosmiles if smiles in already_seen or already_seen.add(smiles)) + if len(duplicates) > 0: + raise ValueError("Error: get_molecule_parameterIDs has been provided a list of oemols which contains some duplicates: {}".format(duplicates)) + + # Assemble molecules into a Topology + topology = Topology() + for molecule in molecules: + topology.add_molecule(molecule) + + # Label molecules + labels = forcefield.label_molecules(topology) + + # Organize labels into output dictionary by looping over all molecules/smiles + for idx in range(len(isosmiles)): + # Pull smiles, initialize storage + smi = isosmiles[idx] + parameters_by_molecule[smi] = [] + + # Organize data for this molecule + data = labels[idx] + for force_type in data.keys(): + for atom_indices, parameter_type in data[force_type].items(): + + pid = parameter_type.id + # Store pid to molecule + parameters_by_molecule[smi].append(pid) + + # Store which molecule this pid occurred in + if pid not in parameters_by_ID: + parameters_by_ID[pid] = set() + parameters_by_ID[pid].add(smi) + else: + parameters_by_ID[pid].add(smi) + + return parameters_by_molecule, parameters_by_ID + +def getMolParamIDToAtomIndex(molecule, forcefield): + """Take a Molecule and a SMIRNOFF forcefield object and return a dictionary, keyed by parameter ID, where each entry is a tuple of ( smirks, [[atom1, ... atomN], [atom1, ... atomN]) giving the SMIRKS corresponding to that parameter ID and a list of the atom groups in that molecule that parameter is applied to. + + Parameters + ---------- + molecule : openforcefield.topology.Molecule + Molecule to investigate + forcefield : ForceField + SMIRNOFF ForceField object (obtained from an ffxml via ForceField(ffxml)) containing FF of interest. + + Returns + ------- + param_usage : dictionary + Dictionary, keyed by parameter ID, where each entry is a tuple of ( smirks, [[atom1, ... atomN], [atom1, ... atomN]) giving the SMIRKS corresponding to that parameter ID and a list of the atom groups in that molecule that parameter is applied to. + + """ + + topology = Topology() + topology.add_molecule(molecule) + labels = ff.labal_molecules(topology) + + param_usage = {} + for mol_entry in range(len(labels)): + for force in labels[mol_entry].keys(): + for (atom_indices, pid, smirks) in labels[mol_entry][force]: + if not pid in param_usage: + param_usage[pid] = (smirks, [atom_indices]) + else: + param_usage[pid][1].append( atom_indices ) + + return param_usage + +def merge_system(topology0, topology1, system0, system1, positions0, positions1, label0="AMBER system", label1="SMIRNOFF system", verbose=True): + """Merge two given OpenMM systems. Returns the merged OpenMM System. + + Parameters + ---------- + topology0 : OpenMM Topology + Topology of first system (i.e. a protein) + topology1 : OpenMM Topology + Topology of second system (i.e. a ligand) + system0 : OpenMM System + First system for merging (usually from AMBER) + system1 : OpenMM System + Second system for merging (usually from SMIRNOFF) + positions0 : simtk.unit.Quantity wrapped + Positions to use for energy evaluation comparison + positions1 (optional) : simtk.unit.Quantity wrapped (optional) + Positions to use for second OpenMM system + label0 (optional) : str + String labeling system0 for output. Default, "AMBER system" + label1 (optional) : str + String labeling system1 for output. Default, "SMIRNOFF system" + verbose (optional) : bool + Print out info on topologies, True/False (default True) + + Returns + ---------- + topology : OpenMM Topology + system : OpenMM System + positions: unit.Quantity position array + """ + + #Load OpenMM Systems to ParmEd Structures + import parmed + structure0 = parmed.openmm.load_topology( topology0, system0 ) + structure1 = parmed.openmm.load_topology( topology1, system1 ) + + #Merge parameterized Structure + structure = structure0 + structure1 + topology = structure.topology + + #Concatenate positions arrays + positions_unit = unit.angstroms + positions0_dimensionless = np.array( positions0 / positions_unit ) + positions1_dimensionless = np.array( positions1 / positions_unit ) + + coordinates = np.vstack((positions0_dimensionless,positions1_dimensionless)) + natoms = len(coordinates) + positions = np.zeros([natoms,3], np.float32) + for index in range(natoms): + (x,y,z) = coordinates[index] + positions[index,0] = x + positions[index,1] = y + positions[index,2] = z + positions = unit.Quantity(positions, positions_unit) + + #Generate merged OpenMM system + system = structure.createSystem() + + if verbose: + print("Generating ParmEd Structures...\n \t{}: {}\n \t{}: {}\n".format(label0, structure0, label1, structure1)) + print("Merged ParmEd Structure: {}".format( structure )) + + return topology, system, positions + +def save_system_to_amber(openmm_topology, system, positions, prmtop, inpcrd): + """Save an OpenMM System, with provided topology and positions, to AMBER prmtop and coordinate files. + + Parameters + ---------- + openmm_topology : OpenMM Topology + Topology of the system to be saved, perhaps as loaded from a PDB file or similar. + system : OpenMM System + Parameterized System to be saved, containing components represented by Topology + positions : unit.Quantity position array + Position array containing positions of atoms in topology/system + prmtop : filename + AMBER parameter file name to write + inpcrd : filename + AMBER coordinate file name (ASCII crd format) to write + + """ + + import parmed + structure = parmed.openmm.topsystem.load_topology(openmm_topology, system, positions) + structure.save(prmtop, overwrite = True, format="amber") + structure.save(inpcrd, format='rst7', overwrite = True) + +def save_system_to_gromacs(openmm_topology, system, positions, top, gro): + """Save an OpenMM System, with provided topology and positions, to AMBER prmtop and coordinate files. + + Parameters + ---------- + openmm_topology : OpenMM Topology + Topology of the system to be saved, perhaps as loaded from a PDB file or similar. + system : OpenMM System + Parameterized System to be saved, containing components represented by Topology + positions : unit.Quantity position array + Position array containing positions of atoms in topology/system + top : filename + GROMACS topology file name to write + gro : filename + GROMACS coordinate file name (.gro format) to write + + """ + + import parmed + structure = parmed.openmm.topsystem.load_topology(openmm_topology, system, positions ) + structure.save(top, overwrite = True, format="gromacs") + structure.save(gro, overwrite = True, format="gro") diff --git a/openforcefield/utils/toolkits.py b/openforcefield/utils/toolkits.py new file mode 100644 index 000000000..a7f4918ce --- /dev/null +++ b/openforcefield/utils/toolkits.py @@ -0,0 +1,3039 @@ +#!/usr/bin/env python +""" +Wrapper classes for providing a minimal consistent interface to cheminformatics toolkits + +Currently supported toolkits: + +* The `OpenEye Toolkit `_ +* The `RDKit `_ +* `AmberTools `_ + +.. todo:: + + * Add checks at the beginning of each toolkit method call to make sure toolkit is licened + * Switch toolkit methods to object methods instead of static methods + * Should this be under ``openforcefield.utils.toolkits`` or ``openforcefield.toolkits``? + * Add singleton global toolkit registry that registers all available toolkits by default when this file is imported + * Add description fields for each toolkit wrapper + * Eliminate global variables in favor of a singleton pattern + * Change global variables from _INSTALLED to _AVAILABLE + +""" +#============================================================================================= +# GLOBAL IMPORTS +#============================================================================================= + +import copy +from distutils.spawn import find_executable +from functools import wraps +import importlib +import logging + +from simtk import unit +import numpy as np + +from openforcefield.utils import all_subclasses, MessageException, inherit_docstrings + + +#============================================================================================= +# CONFIGURE LOGGER +#============================================================================================= + +logger = logging.getLogger(__name__) + +#============================================================================================= +# SUPPORTED MODELS +# +# TODO: We may no longer need these since we now require SMIRNOFF to specify these models explicitly. +#============================================================================================= + +DEFAULT_AROMATICITY_MODEL = 'OEAroModel_MDL' # TODO: Is there a more specific name and reference for the aromaticity model? +ALLOWED_AROMATICITY_MODELS = ['OEAroModel_MDL'] + +DEFAULT_FRACTIONAL_BOND_ORDER_MODEL = 'Wiberg' # TODO: Is there a more specific name and reference for the fractional bond order models? +ALLOWED_FRACTIONAL_BOND_ORDER_MODELS = ['Wiberg'] + +DEFAULT_CHARGE_MODEL = 'AM1-BCC' # TODO: Should this be `AM1-BCC`, or should we encode BCCs explicitly via AM1-CM2 preprocessing? +ALLOWED_CHARGE_MODELS = ['AM1-BCC' + ] # TODO: Which models do we want to support? + + +#============================================================================================= +# Exceptions +#============================================================================================= + +class LicenseError(Exception): + """This function requires a license that cannot be found.""" + pass + + +class MissingPackageError(MessageException): + """This function requires a package that is not installed.""" + pass + + +class ToolkitUnavailableException(MessageException): + """The requested toolkit is unavailable.""" + # TODO: Allow toolkit to be specified and used in formatting/printing exception. + pass + + +class InvalidToolkitError(MessageException): + """A non-toolkit object was received when a toolkit object was expected""" + + + +class UndefinedStereochemistryError(MessageException): + """A molecule was attempted to be loaded with undefined stereochemistry""" + pass + + +class GAFFAtomTypeWarning(RuntimeWarning): + """A warning raised if a loaded mol2 file possibly uses GAFF atom types.""" + pass + + +#============================================================================================= +# TOOLKIT UTILITY DECORATORS +#============================================================================================= + +#============================================================================================= +# UTILITY FUNCTIONS +#============================================================================================= + +#============================================================================================= +# CHEMINFORMATICS TOOLKIT WRAPPERS +#============================================================================================= + +class ToolkitWrapper(object): + """ + Toolkit wrapper base class. + + .. warning :: This API is experimental and subject to change. + """ + _is_available = None # True if toolkit is available + _toolkit_name = None # Name of the toolkit + _toolkit_installation_instructions = None # Installation instructions for the toolkit + _toolkit_file_read_formats = None # The file types that this toolkit can read + _toolkit_file_write_formats = None # The file types that this toolkit can write + + #@staticmethod + # TODO: Right now, to access the class definition, I have to make this a classmethod + # and thereby call it with () on the outermost decorator. Is this wasting time? Are we caching + # the is_available results? + @classmethod + def requires_toolkit(cls): #remember cls is a ToolkitWrapper subclass here + def decorator(func): + @wraps(func) + def wrapped_function(*args, **kwargs): + if not cls.toolkit_is_available(): + msg = 'This function requires the {} toolkit'.format( + cls._toolkit_name) + raise LicenseError(msg) + value = func(*args, **kwargs) + return value + + return wrapped_function + + return decorator + + @property + #@classmethod + def toolkit_name(self): + """ + The name of the toolkit wrapped by this class. + """ + return self.__class__._toolkit_name + + @property + @classmethod + def toolkit_installation_instructions(cls): + """ + Instructions on how to install the wrapped toolkit. + """ + return cls._toolkit_installation_instructions + + #@classmethod + @property + def toolkit_file_read_formats(self): + """ + List of file formats that this toolkit can read. + """ + return self._toolkit_file_read_formats + + #@classmethod + @property + def toolkit_file_write_formats(self): + """ + List of file formats that this toolkit can write. + """ + return self._toolkit_file_write_formats + + @staticmethod + def toolkit_is_available(): + """ + Check whether the corresponding toolkit can be imported + + .. note :: This method call may be expensive. + + Returns + ------- + is_installed : bool + True if corresponding toolkit is installed, False otherwise. + + """ + return NotImplementedError + + @classmethod + def is_available(cls): + """ + Check whether this toolkit wrapper is available for use because the underlying toolkit can be found. + + .. note :: This method caches the result of any costly checks for file paths or module imports. + + Parameters + ---------- + is_available : bool + True if toolkit is available for use, False otherwise + + """ + return NotImplementedError + + def from_file(self, + filename, + file_format, + allow_undefined_stereo=False): + """ + Return an openforcefield.topology.Molecule from a file using this toolkit. + + Parameters + ---------- + filename : str + The file to read the molecule from + file_format : str + Format specifier, usually file suffix (eg. 'MOL2', 'SMI') + Note that not all toolkits support all formats. Check ToolkitWrapper.toolkit_file_read_formats for details. + allow_undefined_stereo : bool, default=False + If false, raises an exception if any molecules contain undefined stereochemistry. + Returns + ------- + molecules : Molecule or list of Molecules + a list of Molecule objects is returned. + + """ + return NotImplementedError + + def from_file_obj(self, + file_obj, + file_format, + allow_undefined_stereo=False): + """ + Return an openforcefield.topology.Molecule from a file-like object (an object with a ".read()" method using this + toolkit. + + Parameters + ---------- + file_obj : file-like object + The file-like object to read the molecule from + file_format : str + Format specifier, usually file suffix (eg. 'MOL2', 'SMI') + Note that not all toolkits support all formats. Check ToolkitWrapper.toolkit_file_read_formats for details. + allow_undefined_stereo : bool, default=False + If false, raises an exception if any molecules contain undefined stereochemistry. If false, the function + skips loading the molecule. + + Returns + ------- + molecules : Molecule or list of Molecules + a list of Molecule objects is returned. + """ + return NotImplementedError + + +@inherit_docstrings +class OpenEyeToolkitWrapper(ToolkitWrapper): + """ + OpenEye toolkit wrapper + + .. warning :: This API is experimental and subject to change. + """ + _toolkit_name = 'OpenEye Toolkit' + _toolkit_installation_instructions = 'The OpenEye toolkit requires a (free for academics) license, and can be ' \ + 'found at: ' \ + 'https://docs.eyesopen.com/toolkits/python/quickstart-python/install.html' + _toolkit_file_read_formats = [ + 'CAN', 'CDX', 'CSV', 'FASTA', 'INCHI', 'INCHIKEY', 'ISM', 'MDL', 'MF', + 'MMOD', 'MOL2', 'MOL2H', 'MOPAC', 'OEB', 'PDB', 'RDF', 'SDF', 'SKC', + 'SLN', 'SMI', 'USM', 'XYC' + ] + _toolkit_file_write_formats = [ + 'CAN', 'CDX', 'CSV', 'FASTA', 'INCHI', 'INCHIKEY', 'ISM', 'MDL', 'MF', + 'MMOD', 'MOL2', 'MOL2H', 'MOPAC', 'OEB', 'PDB', 'RDF', 'SDF', 'SKC', + 'SLN', 'SMI', 'USM', 'XYC' + ] + + # TODO: AR - Do we need both toolkit_is_available() and is_available()? + @staticmethod + def toolkit_is_available( + oetools=('oechem', 'oequacpac', 'oeiupac', 'oeomega')): + """ + Check if the given OpenEye toolkit components are available. + + If the OpenEye toolkit is not installed or no license is found + for at least one the given toolkits , ``False`` is returned. + + Parameters + ---------- + oetools : str or iterable of strings, optional, default=('oechem', 'oequacpac', 'oeiupac', 'oeomega') + Set of tools to check by their Python module name. Defaults + to the complete set of tools supported by this function. + Also accepts a single tool to check as a string instead of + an iterable of length 1. + + Returns + ------- + all_installed : bool + ``True`` if all tools in ``oetools`` are installed and licensed, + ``False`` otherwise + + """ + # Complete list of module -> license function to check. + license_function_names = { + 'oechem': 'OEChemIsLicensed', + 'oequacpac': 'OEQuacPacIsLicensed', + 'oeiupac': 'OEIUPACIsLicensed', + 'oeomega': 'OEOmegaIsLicensed' + } + supported_tools = set(license_function_names.keys()) + + # Make sure oetools is a set. + if isinstance(oetools, str): + oetools = {oetools} + else: + oetools = set(oetools) + + # Check for unkown tools. + unknown_tools = oetools.difference(supported_tools) + if len(unknown_tools) > 0: + raise ValueError("Found unkown OpenEye tools: {}. Supported values are: {}".format( + sorted(unknown_tools), sorted(supported_tools))) + + # Check license of all tools. + all_licensed = True + for tool in oetools: + try: + module = importlib.import_module('openeye.' + tool) + except (ImportError, ModuleNotFoundError): + return False + else: + all_licensed &= getattr(module, license_function_names[tool])() + return all_licensed + + @classmethod + def is_available(cls): + """ + Check whether this toolkit wrapper is available for use because the underlying toolkit can be found. + + .. note :: This method caches the result of any costly checks for file paths or module imports. + + Parameters + ---------- + is_available : bool + True if toolkit wrapper is available for use, False otherwise + + """ + if cls._is_available is None: + cls._is_available = cls.toolkit_is_available() + #oetools=('oechem', 'oequacpac') + return cls._is_available + + def from_object(self, object): + """ + If given an OEMol (or OEMol-derived object), this function will load it into an openforcefield.topology.molecule + Otherwise, it will return False. + + Parameters + ---------- + object : A molecule-like object + An object to by type-checked. + + Returns + ------- + Molecule + An openforcefield.topology.molecule Molecule. + + Raises + ------ + NotImplementedError + If the object could not be converted into a Molecule. + """ + # TODO: Add tests for the from_object functions + from openeye import oechem + if isinstance(object, oechem.OEMolBase): + return self.from_openeye(object) + raise NotImplementedError('Cannot create Molecule from {} object'.format(type(object))) + + def from_file(self, + filename, + file_format, + allow_undefined_stereo=False): + """ + Return an openforcefield.topology.Molecule from a file using this toolkit. + + Parameters + ---------- + filename : str + The file to read the molecule from + file_format : str + Format specifier, usually file suffix (eg. 'MOL2', 'SMI') + Note that not all toolkits support all formats. Check ToolkitWrapper.toolkit_file_read_formats for details. + allow_undefined_stereo : bool, default=False + If false, raises an exception if oemol contains undefined stereochemistry. + + Returns + ------- + molecules : list of Molecules + a list of Molecule objects is returned. + + Raises + ------ + GAFFAtomTypeWarning + If the loaded mol2 file possibly uses GAFF atom types, which + are not supported. + + """ + from openforcefield.topology import Molecule + from openeye import oechem + + # With mol2 files, we raise a warning if we detect OS or HO types + # that OpenEye interprets as Osmium and Holmium. + is_mol2 = file_format.lower() == 'mol2' + + mols = list() + oemol = oechem.OEMol() + ifs = oechem.oemolistream(filename) + while oechem.OEReadMolecule(ifs, oemol): + oechem.OEPerceiveChiral(oemol) + oechem.OEAssignAromaticFlags(oemol, oechem.OEAroModel_MDL) + oechem.OE3DToInternalStereo(oemol) + mol = Molecule.from_openeye( + oemol, + allow_undefined_stereo=allow_undefined_stereo) + + mols.append(mol) + + # Check if this file may be using GAFF atom types. + if is_mol2 and not(mol is None): + self._check_mol2_gaff_atom_type(mol, filename) + + return mols + + def from_file_obj(self, + file_obj, + file_format, + allow_undefined_stereo=False): + """ + Return an openforcefield.topology.Molecule from a file-like object (an object with a ".read()" method using + this toolkit. + + Parameters + ---------- + file_obj : file-like object + The file-like object to read the molecule from + file_format : str + Format specifier, usually file suffix (eg. 'MOL2', 'SMI') + Note that not all toolkits support all formats. Check ToolkitWrapper.toolkit_file_read_formats for details. + allow_undefined_stereo : bool, default=False + If false, raises an exception if oemol contains undefined stereochemistry. + + Returns + ------- + molecules : Molecule or list of Molecules + a list of Molecule objects is + + """ + from openforcefield.topology import Molecule + from openeye import oechem + mols = list() + oemol = oechem.OEMol() + file_data = file_obj.read() + ifs = oechem.oemolistream() + ifs.openstring(file_data) + oeformat = getattr(oechem, 'OEFormat_' + file_format) + ifs.SetFormat(oeformat) + while oechem.OEReadMolecule(ifs, oemol): + oechem.OEPerceiveChiral(oemol) + oechem.OEAssignAromaticFlags(oemol, oechem.OEAroModel_MDL) + oechem.OE3DToInternalStereo(oemol) + mol = Molecule.from_openeye( + oemol, + allow_undefined_stereo=allow_undefined_stereo) + mols.append(mol) + return mols + + def to_file_obj(self, molecule, file_obj, outfile_format): + """ + Writes an OpenFF Molecule to a file-like object + + Parameters + ---------- + molecule : an OpenFF Molecule + The molecule to write + file_obj + The file-like object to write to + outfile_format + The format for writing the molecule data + + """ + from openeye import oechem + from openforcefield.utils import temporary_directory, temporary_cd + + oemol = self.to_openeye(molecule) + + # TODO: This is inefficiently implemented. Is there any way to attach a file-like object to an oemolstream? + with temporary_directory() as tmpdir: + with temporary_cd(tmpdir): + outfile = 'temp_molecule.' + outfile_format + ofs = oechem.oemolostream(outfile) + openeye_format = getattr(oechem, 'OEFormat_' + outfile_format) + ofs.SetFormat(outfile_format) + oechem.OEWriteMolecule(ofs, oemol) + ofs.close() + file_data = open(outfile).read() + file_obj.write(file_data) + + def to_file(self, molecule, outfile, outfile_format): + """ + Writes an OpenFF Molecule to a file-like object + + Parameters + ---------- + molecule : an OpenFF Molecule + The molecule to write + outfile + The filename to write to + outfile_format + The format for writing the molecule data + + """ + from openeye import oechem + oemol = self.to_openeye(molecule) + ofs = oechem.oemolostream(outfile) + openeye_format = getattr(oechem, 'OEFormat_' + outfile_format) + ofs.SetFormat(openeye_format) + oechem.OEWriteMolecule(ofs, oemol) + ofs.close() + + @staticmethod + def _check_mol2_gaff_atom_type(molecule, file_path): + """Attempts to detect the presence of GAFF atom types in a molecule loaded from a mol2 file. + + For now, this raises a ``GAFFAtomTypeWarning`` if the molecule + include Osmium and Holmium atoms, which have GAFF types OS and + HO respectively. + + Parameters + ---------- + molecule : openforcefield.topology.molecule.Molecule + The loaded molecule. + file_path : str + The path to the mol2 file. This is used exclusively to make + the error message more meaningful. + + """ + # atomic_number: (GAFF_type, element_name) + warning_atomic_numbers = { + 76: ('OS', 'Osmium'), + 67: ('HO', 'Holmium') + } + + for atom in molecule.atoms: + try: + atom_type, element_name = warning_atomic_numbers[atom.atomic_number] + except KeyError: + pass + else: + import warnings + warn_msg = ('OpenEye interpreted the type "{atom_type}" in {file_path}:{mol_name}' + ' as {element_name}. Does your mol2 file uses Tripos SYBYL atom types?' + ' Other atom types such as GAFF are not supported.').format( + atom_type=atom_type, mol_name=molecule.name, + file_path=file_path, element_name=element_name) + warnings.warn(warn_msg, GAFFAtomTypeWarning) + + @staticmethod + def _openeye_cip_atom_stereochemistry(oemol, oeatom): + """ + Determine CIP stereochemistry (R/S) for the specified atom + + Parameters + ---------- + oemol : openeye.oechem.OEMolBase + The molecule of interest + oeatom : openeye.oechem.OEAtomBase + The atom whose stereochemistry is to be computed + + Returns + ------- + stereochemistry : str + 'R', 'S', or None if no stereochemistry is specified or the atom is not a stereocenter + """ + from openeye import oechem + + if not oeatom.HasStereoSpecified(): + # No stereochemical information has been stored, so this could be unknown stereochemistry + # TODO: Should we raise an exception? + return None + + cip = oechem.OEPerceiveCIPStereo(oemol, oeatom) + + if cip == oechem.OECIPAtomStereo_S: + return 'S' + elif cip == oechem.OECIPAtomStereo_R: + return 'R' + elif cip == oechem.OECIPAtomStereo_NotStereo: + # Not a stereocenter + # TODO: Should this be a different case from ``None``? + return None + + @staticmethod + def _openeye_cip_bond_stereochemistry(oemol, oebond): + """ + Determine CIP stereochemistry (E/Z) for the specified bond + + Parameters + ---------- + oemol : openeye.oechem.OEMolBase + The molecule of interest + oebond : openeye.oechem.OEBondBase + The bond whose stereochemistry is to be computed + + Returns + ------- + stereochemistry : str + 'E', 'Z', or None if stereochemistry is unspecified or the bond is not a stereo bond + + """ + from openeye import oechem + + if not oebond.HasStereoSpecified(): + # No stereochemical information has been stored, so this could be unknown stereochemistry + # TODO: Should we raise an exception? + return None + + cip = oechem.OEPerceiveCIPStereo(oemol, oebond) + + if cip == oechem.OECIPBondStereo_E: + return 'E' + elif cip == oechem.OECIPBondStereo_Z: + return 'Z' + elif cip == oechem.OECIPBondStereo_NotStereo: + return None + + @staticmethod + def from_openeye(oemol, allow_undefined_stereo=False): + """ + Create a Molecule from an OpenEye molecule. + + .. warning :: This API is experimental and subject to change. + + Parameters + ---------- + oemol : openeye.oechem.OEMol + An OpenEye molecule + allow_undefined_stereo : bool, default=False + If false, raises an exception if oemol contains undefined stereochemistry. + + Returns + ------- + molecule : openforcefield.topology.Molecule + An openforcefield molecule + + Examples + -------- + + Create a Molecule from an OpenEye OEMol + + >>> from openeye import oechem + >>> from openforcefield.tests.utils import get_data_filename + >>> ifs = oechem.oemolistream(get_data_filename('systems/monomers/ethanol.mol2')) + >>> oemols = list(ifs.GetOEGraphMols()) + + >>> toolkit_wrapper = OpenEyeToolkitWrapper() + >>> molecule = toolkit_wrapper.from_openeye(oemols[0]) + + """ + from openeye import oechem + from openforcefield.topology.molecule import Molecule + + # TODO: Is there any risk to perceiving aromaticity here instead of later? + oechem.OEAssignAromaticFlags(oemol, oechem.OEAroModel_MDL) + + oechem.OEPerceiveChiral(oemol) + + # Check that all stereo is specified + # Potentially better OE stereo check: OEFlipper — Toolkits - - Python + # https: // docs.eyesopen.com / toolkits / python / omegatk / OEConfGenFunctions / OEFlipper.html + + unspec_chiral = False + unspec_db = False + problematic_atoms = list() + problematic_bonds = list() + + for oeatom in oemol.GetAtoms(): + if oeatom.IsChiral(): + if not (oeatom.HasStereoSpecified()): + unspec_chiral = True + problematic_atoms.append(oeatom) + for oebond in oemol.GetBonds(): + if oebond.IsChiral(): + if not (oebond.HasStereoSpecified()): + unspec_db = True + problematic_bonds.append(oebond) + if (unspec_chiral or unspec_db): + + def oeatom_to_str(oeatom): + return 'atomic num: {}, name: {}, idx: {}, aromatic: {}, chiral: {}'.format( + oeatom.GetAtomicNum(), oeatom.GetName(), oeatom.GetIdx(), + oeatom.IsAromatic(), oeatom.IsChiral()) + + def oebond_to_str(oebond): + return "order: {}, chiral: {}".format(oebond.GetOrder(), + oebond.IsChiral()) + + def describe_oeatom(oeatom): + description = "Atom {} with bonds:".format( + oeatom_to_str(oeatom)) + for oebond in oeatom.GetBonds(): + description += "\nbond {} to atom {}".format( + oebond_to_str(oebond), + oeatom_to_str(oebond.GetNbr(oeatom))) + return description + + msg = "Unable to make OFFMol from OEMol: OEMol has unspecified stereochemistry. " \ + "oemol.GetTitle(): {}\n".format(oemol.GetTitle()) + if len(problematic_atoms) != 0: + msg += "Problematic atoms are:\n" + for problematic_atom in problematic_atoms: + msg += describe_oeatom(problematic_atom) + '\n' + if len(problematic_bonds) != 0: + msg += "Problematic bonds are: {}\n".format(problematic_bonds) + if allow_undefined_stereo: + logger.warning(msg) + else: + raise UndefinedStereochemistryError(msg) + + # TODO: What other information should we preserve besides name? + # TODO: How should we preserve the name? + + molecule = Molecule() + molecule.name = oemol.GetTitle() + + # Copy any attached SD tag information + # TODO: Should we use an API for this? + molecule._properties = dict() + for dp in oechem.OEGetSDDataPairs(oemol): + molecule._properties[dp.GetTag()] = dp.GetValue() + + map_atoms = dict() # {oemol_idx: molecule_idx} + for oeatom in oemol.GetAtoms(): + oe_idx = oeatom.GetIdx() + atomic_number = oeatom.GetAtomicNum() + formal_charge = oeatom.GetFormalCharge() + is_aromatic = oeatom.IsAromatic() + stereochemistry = OpenEyeToolkitWrapper._openeye_cip_atom_stereochemistry( + oemol, oeatom) + #stereochemistry = self._openeye_cip_atom_stereochemistry(oemol, oeatom) + name = '' + if oeatom.HasData('name'): + name = oeatom.GetData('name') + atom_index = molecule.add_atom( + atomic_number, + formal_charge, + is_aromatic, + stereochemistry=stereochemistry, + name=name) + map_atoms[ + oe_idx] = atom_index # store for mapping oeatom to molecule atom indices below + + for oebond in oemol.GetBonds(): + atom1_index = map_atoms[oebond.GetBgnIdx()] + atom2_index = map_atoms[oebond.GetEndIdx()] + bond_order = oebond.GetOrder() + is_aromatic = oebond.IsAromatic() + stereochemistry = OpenEyeToolkitWrapper._openeye_cip_bond_stereochemistry( + oemol, oebond) + if oebond.HasData('fractional_bond_order'): + fractional_bond_order = oebond.GetData('fractional_bond_order') + else: + fractional_bond_order = None + + molecule.add_bond( + atom1_index, + atom2_index, + bond_order, + is_aromatic=is_aromatic, + stereochemistry=stereochemistry, + fractional_bond_order=fractional_bond_order) + + # TODO: Copy conformations, if present + # TODO: Come up with some scheme to know when to import coordinates + # From SMILES: no + # From MOL2: maybe + # From other: maybe + if hasattr(oemol, 'GetConfs'): + for conf in oemol.GetConfs(): + n_atoms = molecule.n_atoms + positions = unit.Quantity( + np.zeros([n_atoms, 3], np.float), unit.angstrom) + for oe_id in conf.GetCoords().keys(): + off_atom_coords = unit.Quantity(conf.GetCoords()[oe_id], + unit.angstrom) + off_atom_index = map_atoms[oe_id] + positions[off_atom_index, :] = off_atom_coords + if (positions == 0 * unit.angstrom).all(): + continue + molecule.add_conformer(positions) + + # Copy partial charges, if present + partial_charges = unit.Quantity( + np.zeros(molecule.n_atoms, dtype=np.float), + unit=unit.elementary_charge) + for oe_idx, oe_atom in enumerate(oemol.GetAtoms()): + off_idx = map_atoms[oe_idx] + charge = oe_atom.GetPartialCharge() * unit.elementary_charge + partial_charges[off_idx] = charge + + molecule.partial_charges = partial_charges + + return molecule + + @staticmethod + def to_openeye(molecule, aromaticity_model=DEFAULT_AROMATICITY_MODEL): + """ + Create an OpenEye molecule using the specified aromaticity model + + .. todo :: + + * Should the aromaticity model be specified in some other way? + + .. warning :: This API is experimental and subject to change. + + Parameters + ---------- + molecule : openforcefield.topology.molecule.Molecule object + The molecule to convert to an OEMol + aromaticity_model : str, optional, default=DEFAULT_AROMATICITY_MODEL + The aromaticity model to use + + Returns + ------- + oemol : openeye.oechem.OEMol + An OpenEye molecule + + Examples + -------- + + Create an OpenEye molecule from a Molecule + + >>> from openforcefield.topology import Molecule + >>> toolkit_wrapper = OpenEyeToolkitWrapper() + >>> molecule = Molecule.from_smiles('CC') + >>> oemol = toolkit_wrapper.to_openeye(molecule) + + """ + from openeye import oechem + + oemol = oechem.OEMol() + #if not(molecule.name is None): + oemol.SetTitle(molecule.name) + map_atoms = {} # {off_idx : oe_idx} + # Add atoms + oemol_atoms = list() # list of corresponding oemol atoms + for atom in molecule.atoms: + oeatom = oemol.NewAtom(atom.atomic_number) + oeatom.SetFormalCharge(atom.formal_charge) + oeatom.SetAromatic(atom.is_aromatic) + oeatom.SetData('name', atom.name) + oemol_atoms.append(oeatom) + map_atoms[atom.molecule_atom_index] = oeatom.GetIdx() + + # Add bonds + oemol_bonds = list() # list of corresponding oemol bonds + for bond in molecule.bonds: + #atom1_index = molecule.atoms.index(bond.atom1) + #atom2_index = molecule.atoms.index(bond.atom2) + atom1_index = bond.atom1_index + atom2_index = bond.atom2_index + oebond = oemol.NewBond(oemol_atoms[atom1_index], + oemol_atoms[atom2_index]) + oebond.SetOrder(bond.bond_order) + oebond.SetAromatic(bond.is_aromatic) + if not (bond.fractional_bond_order is None): + oebond.SetData('fractional_bond_order', + bond.fractional_bond_order) + oemol_bonds.append(oebond) + + # Set atom stereochemistry now that all connectivity is in place + for atom, oeatom in zip(molecule.atoms, oemol_atoms): + if not atom.stereochemistry: + continue + + # Set arbitrary initial stereochemistry + neighs = [n for n in oeatom.GetAtoms()] + oeatom.SetStereo(neighs, oechem.OEAtomStereo_Tetra, + oechem.OEAtomStereo_Right) + + # Flip chirality if stereochemistry isincorrect + oeatom_stereochemistry = OpenEyeToolkitWrapper._openeye_cip_atom_stereochemistry( + oemol, oeatom) + if oeatom_stereochemistry != atom.stereochemistry: + # Flip the stereochemistry + oeatom.SetStereo(neighs, oechem.OEAtomStereo_Tetra, + oechem.OEAtomStereo_Left) + # Verify it matches now as a sanity check + oeatom_stereochemistry = OpenEyeToolkitWrapper._openeye_cip_atom_stereochemistry( + oemol, oeatom) + if oeatom_stereochemistry != atom.stereochemistry: + raise Exception( + 'Programming error: OpenEye atom stereochemistry assumptions failed.' + ) + + # Set bond stereochemistry + for bond, oebond in zip(molecule.bonds, oemol_bonds): + if not bond.stereochemistry: + continue + + atom1_index = bond.molecule.atoms.index(bond.atom1) + atom2_index = bond.molecule.atoms.index(bond.atom2) + # Set arbitrary initial stereochemistry + oeatom1, oeatom2 = oemol_atoms[atom1_index], oemol_atoms[ + atom2_index] + oeatom1_neighbor = [ + n for n in oeatom1.GetAtoms() if not n == oeatom2 + ][0] + oeatom2_neighbor = [ + n for n in oeatom2.GetAtoms() if not n == oeatom1 + ][0] + #oebond.SetStereo([oeatom1, oeatom2], oechem.OEBondStereo_CisTrans, oechem.OEBondStereo_Cis) + oebond.SetStereo([oeatom1_neighbor, oeatom2_neighbor], + oechem.OEBondStereo_CisTrans, + oechem.OEBondStereo_Cis) + + # Flip stereochemistry if incorrect + oebond_stereochemistry = OpenEyeToolkitWrapper._openeye_cip_bond_stereochemistry( + oemol, oebond) + #print('AAAA', oebond_stereochemistry, bond.stereochemistry) + if oebond_stereochemistry != bond.stereochemistry: + # Flip the stereochemistry + #oebond.SetStereo([oeatom1, oeatom2], oechem.OEBondStereo_CisTrans, oechem.OEBondStereo_Trans) + oebond.SetStereo([oeatom1_neighbor, oeatom2_neighbor], + oechem.OEBondStereo_CisTrans, + oechem.OEBondStereo_Trans) + # Verify it matches now as a sanity check + oebond_stereochemistry = OpenEyeToolkitWrapper._openeye_cip_bond_stereochemistry( + oemol, oebond) + if oebond_stereochemistry != bond.stereochemistry: + raise Exception( + 'Programming error: OpenEye bond stereochemistry assumptions failed.' + ) + + # Retain conformations, if present + if molecule.n_conformers != 0: + oemol.DeleteConfs() + for conf in molecule._conformers: + # OE needs a 1 x (3*n_Atoms) double array as input + flat_coords = np.zeros((oemol.NumAtoms() * 3), + dtype=np.float32) + for index, oe_idx in map_atoms.items(): + (x, y, z) = conf[index, :] / unit.angstrom + flat_coords[(3 * oe_idx)] = x + flat_coords[(3 * oe_idx) + 1] = y + flat_coords[(3 * oe_idx) + 2] = z + + # TODO: Do we need to do these internal unit checks? + # TODO: Is there any risk that the atom indexing systems will change? + #flat_coords = (conf.in_units_of(unit.angstrom) / unit.angstrom).flatten() + oecoords = oechem.OEFloatArray(flat_coords) + oemol.NewConf(oecoords) + + # Retain charges, if present + if not (molecule._partial_charges is None): + # for off_atom, oe_atom in zip(molecule.atoms, oemol_atoms): + # charge_unitless = molecule._partial_charges + + oe_indexed_charges = np.zeros((molecule.n_atoms), dtype=np.float) + for off_idx, charge in enumerate(molecule._partial_charges): + oe_idx = map_atoms[off_idx] + charge_unitless = charge / unit.elementary_charge + oe_indexed_charges[oe_idx] = charge_unitless + for oe_idx, oe_atom in enumerate(oemol.GetAtoms()): + oe_atom.SetPartialCharge(oe_indexed_charges[oe_idx]) + + # TODO: Retain properties, if present + # Clean Up phase + # The only feature of a molecule that wasn't perceived above seemed to be ring connectivity, better to run it + # here then for someone to inquire about ring sizes and get 0 when it shouldn't be + oechem.OEFindRingAtomsAndBonds(oemol) + + return oemol + + @staticmethod + def to_smiles(molecule): + """ + Uses the OpenEye toolkit to convert a Molecule into a SMILES string. + + Parameters + ---------- + molecule : An openforcefield.topology.Molecule + The molecule to convert into a SMILES. + + Returns + ------- + smiles : str + The SMILES of the input molecule. + """ + from openeye import oechem + oemol = OpenEyeToolkitWrapper.to_openeye(molecule) + smiles = oechem.OECreateSmiString( + oemol, oechem.OESMILESFlag_DEFAULT | oechem.OESMILESFlag_Hydrogens + | oechem.OESMILESFlag_Isotopes | oechem.OESMILESFlag_BondStereo + | oechem.OESMILESFlag_AtomStereo) + return smiles + + def from_smiles(self, smiles, hydrogens_are_explicit=False): + """ + Create a Molecule from a SMILES string using the OpenEye toolkit. + + .. warning :: This API is experimental and subject to change. + + Parameters + ---------- + smiles : str + The SMILES string to turn into a molecule + hydrogens_are_explicit : bool, default = False + If False, OE will perform hydrogen addition using OEAddExplicitHydrogens + + Returns + ------- + molecule : openforcefield.topology.Molecule + An openforcefield-style molecule. + """ + + from openeye import oechem + oemol = oechem.OEGraphMol() + oechem.OESmilesToMol(oemol, smiles) + if not (hydrogens_are_explicit): + result = oechem.OEAddExplicitHydrogens(oemol) + if result == False: + raise Exception( + "Addition of explicit hydrogens failed in from_openeye") + # TODO: Add allow_undefined_stereo to this function, and pass to from_openeye? + molecule = self.from_openeye(oemol) + return molecule + + def generate_conformers(self, molecule, num_conformers=1, clear_existing=True): + """ + Generate molecule conformers using OpenEye Omega. + + .. warning :: This API is experimental and subject to change. + + .. todo :: + + * which parameters should we expose? (or can we implement a general system with **kwargs?) + * will the coordinates be returned in the OpenFF Molecule's own indexing system? Or is there a chance that + they'll get reindexed when we convert the input into an OEmol? + + Parameters + --------- + molecule : a :class:`Molecule` + The molecule to generate conformers for. + num_conformers : int, default=1 + The maximum number of conformers to generate. + clear_existing : bool, default=True + Whether to overwrite existing conformers for the molecule + + """ + from openeye import oeomega + oemol = self.to_openeye(molecule) + omega = oeomega.OEOmega() + omega.SetMaxConfs(num_conformers) + omega.SetCanonOrder(False) + omega.SetSampleHydrogens(True) + omega.SetEnergyWindow(15.0) #unit? + omega.SetRMSThreshold(1.0) + #Don't generate random stereoisomer if not specified + omega.SetStrictStereo(True) + status = omega(oemol) + + if status is False: + raise Exception("OpenEye Omega conformer generation failed") + + molecule2 = self.from_openeye(oemol) + + if clear_existing: + molecule._conformers = list() + + for conformer in molecule2._conformers: + molecule._add_conformer(conformer) + + def compute_partial_charges(self, molecule, quantum_chemical_method="AM1-BCC", partial_charge_method='None'): + #charge_model="am1bcc"): + """ + Compute partial charges with OpenEye quacpac + + .. warning :: This API is experimental and subject to change. + + .. todo :: + + * Should the default be ELF? + * Can we expose more charge models? + + + Parameters + ---------- + molecule : Molecule + Molecule for which partial charges are to be computed + charge_model : str, optional, default=None + The charge model to use. One of ['noop', 'mmff', 'mmff94', 'am1bcc', 'am1bccnosymspt', 'amber', + 'amberff94', 'am1bccelf10'] + If None, 'am1bcc' will be used. + + Returns + ------- + charges : numpy.array of shape (natoms) of type float + The partial charges + + """ + raise NotImplementedError + # TODO: Implement this in a way that's compliant with SMIRNOFF's tag when the spec gets finalized + + from openeye import oequacpac + import numpy as np + + if molecule.n_conformers == 0: + raise Exception( + "No conformers present in molecule submitted for partial charge calculation. Consider " + "loading the molecule from a file with geometry already present or running " + "molecule.generate_conformers() before calling molecule.compute_partial_charges" + ) + oemol = molecule.to_openeye() + + ## This seems like a big decision. Implemented a simple solution here. Not to be considered final. + ## Some discussion at https://github.com/openforcefield/openforcefield/pull/86#issuecomment-350111236 + + if charge_model is None: + charge_model = "am1bcc" + + if charge_model == "noop": + result = oequacpac.OEAssignCharges(oemol, + oequacpac.OEChargeEngineNoOp()) + elif charge_model == "mmff" or charge_model == "mmff94": + result = oequacpac.OEAssignCharges(oemol, + oequacpac.OEMMFF94Charges()) + elif charge_model == "am1bcc": + result = oequacpac.OEAssignCharges(oemol, + oequacpac.OEAM1BCCCharges()) + elif charge_model == "am1bccnosymspt": + optimize = True + symmetrize = True + result = oequacpac.OEAssignCharges( + oemol, oequacpac.OEAM1BCCCharges(not optimize, not symmetrize)) + elif charge_model == "amber" or charge_model == "amberff94": + result = oequacpac.OEAssignCharges(oemol, + oequacpac.OEAmberFF94Charges()) + elif charge_model == "am1bccelf10": + result = oequacpac.OEAssignCharges( + oemol, oequacpac.OEAM1BCCELF10Charges()) + else: + raise ValueError('charge_model {} unknown'.format(charge_model)) + + if result is False: + raise Exception('Unable to assign charges') + + # Extract and return charges + ## TODO: Behavior when given multiple conformations? + ## TODO: Make sure atom mapping remains constant + + charges = unit.Quantity( + np.zeros([oemol.NumAtoms()], np.float64), unit.elementary_charge) + for index, atom in enumerate(oemol.GetAtoms()): + charge = atom.GetPartialCharge() + charge = charge * unit.elementary_charge + charges[index] = charge + + if ((charges / unit.elementary_charge) == 0. + ).all() and not (charge_model == 'noop'): + # TODO: These will be 0 if the charging failed. What behavior do we want in that case? + raise Exception( + "Partial charge calculation failed. Charges from compute_partial_charges() are all 0." + ) + molecule.set_partial_charges(charges) + + + + def compute_partial_charges_am1bcc(self, molecule): + """ + Compute AM1BCC partial charges with OpenEye quacpac + + .. warning :: This API is experimental and subject to change. + + .. todo :: + + * Should the default be ELF? + * Can we expose more charge models? + + + Parameters + ---------- + molecule : Molecule + Molecule for which partial charges are to be computed + + Returns + ------- + charges : numpy.array of shape (natoms) of type float + The partial charges + + """ + from openeye import oequacpac + import numpy as np + + if molecule.n_conformers == 0: + raise Exception( + "No conformers present in molecule submitted for partial charge calculation. Consider " + "loading the molecule from a file with geometry already present or running " + "molecule.generate_conformers() before calling molecule.compute_partial_charges" + ) + oemol = molecule.to_openeye() + + result = oequacpac.OEAssignCharges(oemol, oequacpac.OEAM1BCCELF10Charges()) + + if result is False: + raise Exception('Unable to assign charges') + + # Extract and return charges + ## TODO: Make sure atom mapping remains constant + + charges = unit.Quantity( + np.zeros([oemol.NumAtoms()], np.float64), unit.elementary_charge) + for index, atom in enumerate(oemol.GetAtoms()): + charge = atom.GetPartialCharge() + charge = charge * unit.elementary_charge + charges[index] = charge + + if ((charges / unit.elementary_charge) == 0.).all(): + # TODO: These will be 0 if the charging failed. What behavior do we want in that case? + raise Exception( + "Partial charge calculation failed. Charges from compute_partial_charges() are all 0." + ) + return charges + + def compute_wiberg_bond_orders(self, molecule, charge_model=None): + """ + Update and store list of bond orders this molecule. Can be used for initialization of bondorders list, or + for updating bond orders in the list. + + .. warning :: This API is experimental and subject to change. + + Parameters + ---------- + molecule : openforcefield.topology.molecule Molecule + The molecule to assign wiberg bond orders to + charge_model : str, optional, default=None + The charge model to use. One of ['am1', 'pm3']. If None, 'am1' will be used. + + """ + # TODO: Cache charged molecule so we don't have to redo the computation (Can we do this given the different + # AM1 interfaces?) + + from openeye import oequacpac + + oemol = self.to_openeye(molecule) + if molecule.n_conformers == 0: + raise Exception( + "No conformers present in molecule submitted for wiberg bond order calculation. Consider " + "loading the molecule from a file with geometry already present or running " + "molecule.generate_conformers() before calling molecule.compute_wiberg_bond_orders()" + ) + + if charge_model is None: + charge_model = 'am1' + + # Based on example at https://docs.eyesopen.com/toolkits/python/quacpactk/examples_summary_wibergbondorders.html + am1 = oequacpac.OEAM1() + am1results = oequacpac.OEAM1Results() + am1options = am1.GetOptions() + if charge_model == "am1": + am1options.SetSemiMethod(oequacpac.OEMethodType_AM1) + elif charge_model == "pm3": + # TODO: Make sure that modifying am1options actually works + am1options.SetSemiMethod(oequacpac.OEMethodType_PM3) + else: + raise ValueError('charge_model {} unknown'.format(charge_model)) + + #for conf in oemol.GetConfs(): + #TODO: How to handle multiple confs here? + status = am1.CalcAM1(am1results, oemol) + + if status is False: + raise Exception( + 'Unable to assign charges (in the process of calculating Wiberg bond orders)' + ) + + # TODO: Will bonds always map back to the same index? Consider doing a topology mapping. + # Loop over bonds + for idx, bond in enumerate(oemol.GetBonds()): + # Get bond order + order = am1results.GetBondOrder(bond.GetBgnIdx(), bond.GetEndIdx()) + mol_bond = molecule._bonds[idx] + mol_bond.fractional_bond_order = order + + @staticmethod + def _find_smarts_matches(oemol, smarts, aromaticity_model=None): + """Find all sets of atoms in the provided OpenEye molecule that match the provided SMARTS string. + + Parameters + ---------- + oemol : openeye.oechem.OEMol or similar + oemol to process with the SMIRKS in order to find matches + smarts : str + SMARTS string with any number of sequentially tagged atoms. + If there are N tagged atoms numbered 1..N, the resulting matches will be N-tuples of atoms that match the corresponding tagged atoms. + aromaticity_model : str, optional, default=None + OpenEye aromaticity model designation as a string, such as ``OEAroModel_MDL``. + If ``None``, molecule is processed exactly as provided; otherwise it is prepared with this aromaticity model prior to querying. + + Returns + ------- + matches : list of tuples of atoms indices within the ``oemol`` + matches[index] is an N-tuple of atom numbers from the ``oemol`` + Matches are returned in no guaranteed order. + # TODO: What is returned if no matches are found? An empty list, or None? + # TODO: Ensure that SMARTS numbers 1, 2, 3... are rendered into order of returnd matches indexed by 0, 1, 2... + + .. notes :: + + * Raises ``LicenseError`` if valid OpenEye tools license is not found, rather than causing program to terminate + * Raises ``ValueError`` if ``smarts`` query is malformed + + """ + from openeye import oechem + # Make a copy of molecule so we don't influence original (probably safer than deepcopy per C Bayly) + mol = oechem.OEMol(oemol) + + # Set up query + qmol = oechem.OEQMol() + if not oechem.OEParseSmarts(qmol, smarts): + raise ValueError("Error parsing SMARTS '%s'" % smarts) + + # Determine aromaticity model + if aromaticity_model: + if type(aromaticity_model) == str: + # Check if the user has provided a manually-specified aromaticity_model + if hasattr(oechem, aromaticity_model): + oearomodel = getattr(oechem, + 'OEAroModel_' + aromaticity_model) + else: + raise ValueError( + "Error: provided aromaticity model not recognized by oechem." + ) + else: + raise ValueError( + "Error: provided aromaticity model must be a string.") + + # If aromaticity model was provided, prepare molecule + oechem.OEClearAromaticFlags(mol) + oechem.OEAssignAromaticFlags(mol, oearomodel) + # Avoid running OEPrepareSearch or we lose desired aromaticity, so instead: + oechem.OEAssignHybridization(mol) + + # Build list of matches + # TODO: The MoleculeImage mapping should preserve ordering of template molecule for equivalent atoms + # and speed matching for larger molecules. + unique = False # We require all matches, not just one of each kind + substructure_search = oechem.OESubSearch(qmol) + matches = list() + for match in substructure_search.Match(mol, unique): + # Compile list of atom indices that match the pattern tags + atom_indices = dict() + for matched_atom in match.GetAtoms(): + if matched_atom.pattern.GetMapIdx() != 0: + atom_indices[matched_atom.pattern.GetMapIdx() - + 1] = matched_atom.target.GetIdx() + # Compress into list + atom_indices = [ + atom_indices[index] for index in range(len(atom_indices)) + ] + # Convert to tuple + matches.append(tuple(atom_indices)) + return matches + + def find_smarts_matches(self, + molecule, + smarts, + aromaticity_model='OEAroModel_MDL'): + """ + Find all SMARTS matches for the specified molecule, using the specified aromaticity model. + + .. warning :: This API is experimental and subject to change. + + Parameters + ---------- + molecule : openforcefield.topology.Molecule + The molecule for which all specified SMARTS matches are to be located + smarts : str + SMARTS string with optional SMIRKS-style atom tagging + aromaticity_model : str, optional, default='OEAroModel_MDL' + Aromaticity model to use during matching + + .. note :: Currently, the only supported ``aromaticity_model`` is ``OEAroModel_MDL`` + + """ + oemol = molecule.to_openeye() + return self._find_smarts_matches(oemol, smarts) + + +class RDKitToolkitWrapper(ToolkitWrapper): + """ + RDKit toolkit wrapper + + .. warning :: This API is experimental and subject to change. + """ + _toolkit_name = 'The RDKit' + _toolkit_installation_instructions = 'A conda-installable version of the free and open source RDKit cheminformatics ' \ + 'toolkit can be found at: https://anaconda.org/rdkit/rdkit' + _toolkit_file_read_formats = ['SDF', 'MOL', 'SMI'] #TODO: Add TDT support + _toolkit_file_write_formats = ['SDF', 'MOL', 'SMI', 'PDB'] + + @staticmethod + def toolkit_is_available(): + """ + Check whether the RDKit toolkit can be imported + + Returns + ------- + is_installed : bool + True if RDKit is installed, False otherwise. + + """ + try: + module = importlib.import_module('rdkit', 'Chem') + return True + except ImportError: + return False + + @classmethod + def is_available(cls): + """ + Check whether toolkit is available for use. + + Parameters + ---------- + is_available : bool + True if toolkit is available for use, False otherwise + + """ + if cls._is_available is None: + cls._is_available = cls.toolkit_is_available() + return cls._is_available + + def from_object(self, object): + """ + If given an rdchem.Mol (or rdchem.Mol-derived object), this function will load it into an + openforcefield.topology.molecule. Otherwise, it will return False. + + Parameters + ---------- + object : A rdchem.Mol-derived object + An object to be type-checked and converted into a Molecule, if possible. + + Returns + ------- + Molecule or False + An openforcefield.topology.molecule Molecule. + + Raises + ------ + NotImplementedError + If the object could not be converted into a Molecule. + """ + # TODO: Add tests for the from_object functions + from rdkit import Chem + if isinstance(object, Chem.rdchem.Mol): + return self.from_rdkit(object) + raise NotImplementedError('Cannot create Molecule from {} object'.format(type(object))) + + def from_file(self, + filename, + file_format, + allow_undefined_stereo=False): + """ + Create an openforcefield.topology.Molecule from a file using this toolkit. + + + + Parameters + ---------- + filename : str + The file to read the molecule from + file_format : str + Format specifier, usually file suffix (eg. 'MOL2', 'SMI') + Note that not all toolkits support all formats. Check ToolkitWrapper.toolkit_file_read_formats for details. + allow_undefined_stereo : bool, default=False + If false, raises an exception if oemol contains undefined stereochemistry. + + Returns + ------- + molecules : iterable of Molecules + a list of Molecule objects is returned. + + """ + from openforcefield.topology import Molecule + from rdkit import Chem + mols = list() + if (file_format == 'MOL') or (file_format == 'SDF'): + for rdmol in Chem.SupplierFromFilename(filename, removeHs=False, sanitize=False, strictParsing=True): + if rdmol is None: + continue + + # Sanitize the molecules (fails on nitro groups) + try: + Chem.SanitizeMol(rdmol, Chem.SANITIZE_ALL ^ Chem.SANITIZE_SETAROMATICITY ^ Chem.SANITIZE_ADJUSTHS) + Chem.AssignStereochemistryFrom3D(rdmol) + except ValueError as e: + print(rdmol.GetProp('_Name'), e) + continue + Chem.SetAromaticity(rdmol, Chem.AromaticityModel.AROMATICITY_MDL) + mol = Molecule.from_rdkit( + rdmol, + allow_undefined_stereo=allow_undefined_stereo + ) + + mols.append(mol) + elif (file_format == 'SMI'): + # TODO: We have to do some special stuff when we import SMILES (currently + # just adding H's, but could get fancier in the future). It might be + # worthwhile to parse the SMILES file ourselves and pass each SMILES + # through the from_smiles function instead + for rdmol in Chem.SmilesMolSupplier(filename): + rdmol = Chem.AddHs(rdmol) + mol = Molecule.from_rdkit(rdmol) + mols.append(mol) + + elif (file_format == 'PDB'): + raise Exception( + "RDKit can not safely read PDBs on their own. Information about bond order and aromaticity " + "is likely to be lost.") + # TODO: See if we can implement PDB+mol/smi combinations to get complete bond information. + # https://github.com/openforcefield/openforcefield/issues/121 + rdmol = Chem.MolFromPDBFile(filename, removeHs=False) + mol = Molecule.from_rdkit(rdmol) + mols.append(mol) + # TODO: Add SMI, TDT(?) support + + return mols + + def from_file_obj(self, + file_obj, + file_format, + allow_undefined_stereo=False): + """ + Return an openforcefield.topology.Molecule from a file-like object (an object with a ".read()" method using + this toolkit. + + .. warning :: This API is experimental and subject to change. + + Parameters + ---------- + file_obj : file-like object + The file-like object to read the molecule from + file_format : str + Format specifier, usually file suffix (eg. 'MOL2', 'SMI') + Note that not all toolkits support all formats. Check ToolkitWrapper.toolkit_file_read_formats for details. + allow_undefined_stereo : bool, default=False + If false, raises an exception if oemol contains undefined stereochemistry. + + Returns + ------- + molecules : Molecule or list of Molecules + a list of Molecule objects is returned. + + """ + from openforcefield.topology import Molecule + from rdkit import Chem + if (file_format == "MOL") or (file_format == "SDF"): + # TODO: Iterate over all mols in file_data + for rdmol in Chem.ForwardSDMolSupplier(file_obj): + mol = Molecule.from_rdkit(rdmol) + mols.append(mol) + + if (file_format == 'SMI'): + # TODO: Find a cleaner way to parse SMILES lines + file_data = file_obj.read() + lines = [line.strip() for line in file_data.split('\n')] + # remove blank lines + lines.remove('') + for line in lines: + mol = self.from_smiles(line) + mols.append(mol) + + elif file_format == 'PDB': + raise Exception( + "RDKit can not safely read PDBs on their own. Information about bond order and aromaticity " + "is likely to be lost.") + # TODO: See if we can implement PDB+mol/smi combinations to get complete bond information. + # https://github.com/openforcefield/openforcefield/issues/121 + rdmol = Chem.MolFromPDBBlock(file_data) + mol = Molecule.from_rdkit(rdmol) + mols.append(mol) + # TODO: TDT file support + return mols + + def to_file_obj(self, molecule, file_obj, outfile_format): + """ + Writes an OpenFF Molecule to a file-like object + + Parameters + ---------- + molecule : an OpenFF Molecule + The molecule to write + file_obj + The file-like object to write to + outfile_format + The format for writing the molecule data + + Returns + ------- + + """ + from rdkit import Chem + outfile_format = outfile_format.upper() + rdmol = self.to_rdkit(molecule) + rdkit_writers = { + 'SDF': Chem.SDWriter, + 'PDB': Chem.PDBWriter, + 'SMI': Chem.SmilesWriter, + 'TDT': Chem.TDTWriter + } + writer = rdkit_writers[outfile_format](file_obj) + writer.write(rdmol) + writer.close() + + def to_file(self, molecule, outfile, outfile_format): + """ + Writes an OpenFF Molecule to a file-like object + + Parameters + ---------- + molecule : an OpenFF Molecule + The molecule to write + outfile + The filename to write to + outfile_format + The format for writing the molecule data + + Returns + ------ + + """ + from rdkit import Chem + outfile_format = outfile_format.upper() + with open(outfile, 'w') as file_obj: + rdmol = self.to_rdkit(molecule) + rdkit_writers = { + 'SDF': Chem.SDWriter, + 'PDB': Chem.PDBWriter, + 'SMI': Chem.SmilesWriter, + 'TDT': Chem.TDTWriter + } + writer = rdkit_writers[outfile_format](file_obj) + writer.write(rdmol) + writer.close() + + @classmethod + def to_smiles(cls, molecule): + """ + Uses the RDKit toolkit to convert a Molecule into a SMILES string. + + Parameters + ---------- + molecule : An openforcefield.topology.Molecule + The molecule to convert into a SMILES. + + Returns + ------- + smiles : str + The SMILES of the input molecule. + """ + from rdkit import Chem + rdmol = cls.to_rdkit(molecule) + return Chem.MolToSmiles(rdmol, isomericSmiles=True, allHsExplicit=True) + + def from_smiles(self, smiles, hydrogens_are_explicit=False): + """ + Create a Molecule from a SMILES string using the RDKit toolkit. + + .. warning :: This API is experimental and subject to change. + + Parameters + ---------- + smiles : str + The SMILES string to turn into a molecule + hydrogens_are_explicit : bool, default=False + If False, RDKit will perform hydrogen addition using Chem.AddHs + + Returns + ------- + molecule : openforcefield.topology.Molecule + An openforcefield-style molecule. + """ + from openforcefield.topology.molecule import Molecule + from rdkit import Chem + + rdmol = Chem.MolFromSmiles(smiles, sanitize=False) + # TODO: I think UpdatePropertyCache(strict=True) is called anyway in Chem.SanitizeMol(). + rdmol.UpdatePropertyCache(strict=False) + Chem.SanitizeMol(rdmol, Chem.SANITIZE_ALL ^ Chem.SANITIZE_ADJUSTHS ^ Chem.SANITIZE_SETAROMATICITY) + Chem.SetAromaticity(rdmol, Chem.AromaticityModel.AROMATICITY_MDL) + + # Chem.MolFromSmiles adds bond directions (i.e. ENDDOWNRIGHT/ENDUPRIGHT), but + # doesn't set bond.GetStereo(). We need to call AssignStereochemistry for that. + Chem.AssignStereochemistry(rdmol) + + # Throw an exception/warning if there is unspecified stereochemistry. + self._detect_undefined_stereo(rdmol, err_msg_prefix='Unable to make OFFMol from SMILES: ') + + # Add explicit hydrogens if they aren't there already + if not hydrogens_are_explicit: + rdmol = Chem.AddHs(rdmol) + + # TODO: Add allow_undefined_stereo to this function, and pass to from_rdkit? + molecule = Molecule.from_rdkit(rdmol) + + return molecule + + def generate_conformers(self, molecule, num_conformers=1, clear_existing=True): + """ + Generate molecule conformers using RDKit. + + .. warning :: This API is experimental and subject to change. + + .. todo :: + + * which parameters should we expose? (or can we implement a general system with **kwargs?) + * will the coordinates be returned in the OpenFF Molecule's own indexing system? Or is there a chance that they'll get reindexed when we convert the input into an RDMol? + + Parameters + --------- + molecule : a :class:`Molecule` + The molecule to generate conformers for. + num_conformers : int, default=1 + Maximum number of conformers to generate. + clear_existing : bool, default=True + Whether to overwrite existing conformers for the molecule. + + + """ + from rdkit.Chem import AllChem + rdmol = self.to_rdkit(molecule) + # TODO: This generates way more conformations than omega, given the same nConfs and RMS threshold. Is there some way to set an energy cutoff as well? + AllChem.EmbedMultipleConfs( + rdmol, + numConfs=num_conformers, + pruneRmsThresh=1.0, + randomSeed=1, + #params=AllChem.ETKDG() + ) + molecule2 = self.from_rdkit(rdmol) + + if clear_existing: + molecule._conformers = list() + + for conformer in molecule2._conformers: + molecule._add_conformer(conformer) + + def from_rdkit(self, rdmol, allow_undefined_stereo=False): + """ + Create a Molecule from an RDKit molecule. + + Requires the RDKit to be installed. + + .. warning :: This API is experimental and subject to change. + + Parameters + ---------- + rdmol : rkit.RDMol + An RDKit molecule + allow_undefined_stereo : bool, default=False + If false, raises an exception if rdmol contains undefined stereochemistry. + + Returns + ------- + molecule : openforcefield.Molecule + An openforcefield molecule + + Examples + -------- + + Create a molecule from an RDKit molecule + + >>> from rdkit import Chem + >>> from openforcefield.tests.utils import get_data_filename + >>> rdmol = Chem.MolFromMolFile(get_data_filename('systems/monomers/ethanol.sdf')) + + >>> toolkit_wrapper = RDKitToolkitWrapper() + >>> molecule = toolkit_wrapper.from_rdkit(rdmol) + + """ + from rdkit import Chem + from openforcefield.topology.molecule import Molecule + + # Make a copy of the RDKit Mol as we'll need to change it (e.g. assign stereo). + rdmol = Chem.Mol(rdmol) + + # Sanitize the molecule. We handle aromaticity and chirality manually. + Chem.SanitizeMol(rdmol, (Chem.SANITIZE_ALL ^ Chem.SANITIZE_SETAROMATICITY ^ + Chem.SANITIZE_ADJUSTHS ^ Chem.SANITIZE_CLEANUPCHIRALITY)) + Chem.SetAromaticity(rdmol, Chem.AromaticityModel.AROMATICITY_MDL) + # Make sure the bond stereo tags are set before checking for + # undefined stereo. RDKit can figure out bond stereo from other + # information in the Mol object like bond direction properties. + # Do not overwrite eventual chiral tags provided by the user. + Chem.AssignStereochemistry(rdmol, cleanIt=False) + + # Check for undefined stereochemistry. + self._detect_undefined_stereo(rdmol, raise_warning=allow_undefined_stereo, + err_msg_prefix="Unable to make OFFMol from RDMol: ") + + # Create a new openforcefield Molecule + offmol = Molecule() + + # If RDMol has a title save it + if rdmol.HasProp("_Name"): + #raise Exception('{}'.format(rdmol.GetProp('name'))) + offmol.name = rdmol.GetProp("_Name") + else: + offmol.name = "" + + # Store all properties + # TODO: Should there be an API point for storing properties? + properties = rdmol.GetPropsAsDict() + offmol._properties = properties + + # setting chirality in openeye requires using neighbor atoms + # therefore we can't do it until after the atoms and bonds are all added + chiral_atoms = dict() # {rd_idx: openeye chirality} + map_atoms = {} + map_bonds = {} + for rda in rdmol.GetAtoms(): + rd_idx = rda.GetIdx() + + # create a new atom + #atomic_number = oemol.NewAtom(rda.GetAtomicNum()) + atomic_number = rda.GetAtomicNum() + formal_charge = rda.GetFormalCharge() + is_aromatic = rda.GetIsAromatic() + if rda.HasProp('_Name'): + name = rda.GetProp('_Name') + else: + name = '' + + # If chiral, store the chirality to be set later + stereochemistry = None + #tag = rda.GetChiralTag() + if rda.HasProp('_CIPCode'): + stereo_code = rda.GetProp('_CIPCode') + #if tag == Chem.CHI_TETRAHEDRAL_CCW: + if stereo_code == 'R': + stereochemistry = 'R' + #if tag == Chem.CHI_TETRAHEDRAL_CW: + elif stereo_code == 'S': + stereochemistry = 'S' + else: + raise UndefinedStereochemistryError("In from_rdkit: Expected atom stereochemistry of R or S. " + "Got {} instead.".format(stereo_code)) + + atom_index = offmol.add_atom( + atomic_number, + formal_charge, + is_aromatic, + name=name, + stereochemistry=stereochemistry) + map_atoms[rd_idx] = atom_index + + # Similar to chirality, stereochemistry of bonds in OE is set relative to their neighbors + stereo_bonds = list() + # stereo_bonds stores tuples in the form (oe_bond, rd_idx1, rd_idx2, OE stereo specification) + # where rd_idx1 and 2 are the atoms on the outside of the bond + # i.e. Cl and F in the example above + aro_bond = 0 + for rdb in rdmol.GetBonds(): + rdb_idx = rdb.GetIdx() + a1 = rdb.GetBeginAtomIdx() + a2 = rdb.GetEndAtomIdx() + + # Determine bond aromaticity and Kekulized bond order + is_aromatic = False + order = rdb.GetBondTypeAsDouble() + if order == 1.5: + # get the bond order for this bond in the kekulized molecule + order = rdmol.GetBondWithIdx( + rdb.GetIdx()).GetBondTypeAsDouble() + is_aromatic = True + # Convert floating-point bond order to integral bond order + order = int(order) + + # create a new bond + bond_index = offmol.add_bond(map_atoms[a1], map_atoms[a2], order, + is_aromatic) + map_bonds[rdb_idx] = bond_index + + # Now fill in the cached (structure-dependent) properties. We have to have the 2D structure of the molecule + # in place first, because each call to add_atom and add_bond invalidates all cached properties + for rdb in rdmol.GetBonds(): + rdb_idx = rdb.GetIdx() + offb_idx = map_bonds[rdb_idx] + offb = offmol.bonds[offb_idx] + # determine if stereochemistry is needed + stereochemistry = None + tag = rdb.GetStereo() + if tag == Chem.BondStereo.STEREOZ: + stereochemistry = 'Z' + elif tag == Chem.BondStereo.STEREOE: + stereochemistry = 'E' + elif tag == Chem.BondStereo.STEREOTRANS or tag == Chem.BondStereo.STEREOCIS: + raise ValueError( + "Expected RDKit bond stereochemistry of E or Z, got {} instead" + .format(tag)) + offb._stereochemistry = stereochemistry + fractional_bond_order = None + if rdb.HasProp("fractional_bond_order"): + fractional_bond_order = rdb.GetDoubleProp( + 'fractional_bond_order') + offb.fractional_bond_order = fractional_bond_order + + # TODO: Save conformer(s), if present + # If the rdmol has a conformer, store its coordinates + if len(rdmol.GetConformers()) != 0: + for conf in rdmol.GetConformers(): + n_atoms = offmol.n_atoms + # TODO: Will this always be angstrom when loading from RDKit? + positions = unit.Quantity( + np.zeros((n_atoms, 3)), unit.angstrom) + for rd_idx, off_idx in map_atoms.items(): + atom_coords = conf.GetPositions()[rd_idx, :] * unit.angstrom + positions[off_idx, :] = atom_coords + offmol.add_conformer(positions) + + partial_charges = unit.Quantity( + np.zeros(offmol.n_atoms, dtype=np.float), unit=unit.elementary_charge) + + any_atom_has_partial_charge = False + for rd_idx, rd_atom in enumerate(rdmol.GetAtoms()): + off_idx = map_atoms[rd_idx] + if rd_atom.HasProp("partial_charge"): + charge = rd_atom.GetDoubleProp( + "partial_charge") * unit.elementary_charge + partial_charges[off_idx] = charge + any_atom_has_partial_charge = True + else: + # If some other atoms had partial charges but this one doesn't, raise an Exception + if any_atom_has_partial_charge: + raise Exception( + "Some atoms in rdmol have partial charges, but others do not." + ) + + offmol.partial_charges = partial_charges + return offmol + + @classmethod + def to_rdkit(cls, molecule, aromaticity_model=DEFAULT_AROMATICITY_MODEL): + """ + Create an RDKit molecule + + Requires the RDKit to be installed. + + .. warning :: This API is experimental and subject to change. + + Parameters + ---------- + aromaticity_model : str, optional, default=DEFAULT_AROMATICITY_MODEL + The aromaticity model to use + + Returns + ------- + rdmol : rkit.RDMol + An RDKit molecule + + Examples + -------- + + Convert a molecule to RDKit + + >>> from openforcefield.topology import Molecule + >>> ethanol = Molecule.from_smiles('CCO') + >>> rdmol = ethanol.to_rdkit() + + """ + from rdkit import Chem, Geometry + + # Create an editable RDKit molecule + rdmol = Chem.RWMol() + + # Set name + # TODO: What is the best practice for how this should be named? + if not (molecule.name is None): + rdmol.SetProp('_Name', molecule.name) + + # TODO: Set other properties + for name, value in molecule.properties.items(): + if type(value) == str: + rdmol.SetProp(name, value) + elif type(value) == int: + rdmol.SetIntProp(name, value) + elif type(value) == float: + rdmol.SetDoubleProp(name, value) + elif type(value) == bool: + rdmol.SetBoolProp(name, value) + else: + # Shove everything else into a string + rdmol.SetProp(name, str(value)) + + _bondtypes = { + 1: Chem.BondType.SINGLE, + 1.5: Chem.BondType.AROMATIC, + 2: Chem.BondType.DOUBLE, + 3: Chem.BondType.TRIPLE, + 4: Chem.BondType.QUADRUPLE, + 5: Chem.BondType.QUINTUPLE, + 6: Chem.BondType.HEXTUPLE, + 7: Chem.BondType.ONEANDAHALF, + } + + for index, atom in enumerate(molecule.atoms): + rdatom = Chem.Atom(atom.atomic_number) + rdatom.SetFormalCharge(atom.formal_charge) + rdatom.SetIsAromatic(atom.is_aromatic) + rdatom.SetProp('_Name', atom.name) + + ## Stereo handling code moved to after bonds are added + if atom.stereochemistry == 'S': + rdatom.SetChiralTag(Chem.CHI_TETRAHEDRAL_CW) + elif atom.stereochemistry == 'R': + rdatom.SetChiralTag(Chem.CHI_TETRAHEDRAL_CCW) + + rd_index = rdmol.AddAtom(rdatom) + + # Let's make sure al the atom indices in the two molecules + # are the same, otherwise we need to create an atom map. + assert index == atom.molecule_atom_index + assert index == rd_index + + for bond in molecule.bonds: + atom_indices = (bond.atom1.molecule_atom_index, bond.atom2.molecule_atom_index) + rdmol.AddBond(*atom_indices) + rdbond = rdmol.GetBondBetweenAtoms(*atom_indices) + if not (bond.fractional_bond_order is None): + rdbond.SetDoubleProp("fractional_bond_order", + bond.fractional_bond_order) + # Assign bond type, which is based on order unless it is aromatic + if bond.is_aromatic: + rdbond.SetBondType(_bondtypes[1.5]) + rdbond.SetIsAromatic(True) + else: + rdbond.SetBondType(_bondtypes[bond.bond_order]) + rdbond.SetIsAromatic(False) + + Chem.SanitizeMol(rdmol, Chem.SANITIZE_ALL ^ Chem.SANITIZE_ADJUSTHS ^ Chem.SANITIZE_SETAROMATICITY) + + # Assign atom stereochemsitry and collect atoms for which RDKit + # can't figure out chirality. The _CIPCode property of these atoms + # will be forcefully set to the stereo we want (see #196). + undefined_stereo_atoms = {} + for index, atom in enumerate(molecule.atoms): + rdatom = rdmol.GetAtomWithIdx(index) + + # Skip non-chiral atoms. + if atom.stereochemistry is None: + continue + + # Let's randomly assign this atom's (local) stereo to CW + # and check if this causes the (global) stereo to be set + # to the desired one (S or R). + rdatom.SetChiralTag(Chem.CHI_TETRAHEDRAL_CW) + # We need to do force and cleanIt to recalculate CIP stereo. + Chem.AssignStereochemistry(rdmol, force=True, cleanIt=True) + # If our random initial assignment worked, then we're set. + if rdatom.HasProp('_CIPCode') and rdatom.GetProp("_CIPCode") == atom.stereochemistry: + continue + + # Otherwise, set it to CCW. + rdatom.SetChiralTag(Chem.CHI_TETRAHEDRAL_CCW) + # We need to do force and cleanIt to recalculate CIP stereo. + Chem.AssignStereochemistry(rdmol, force=True, cleanIt=True) + # Hopefully this worked, otherwise something's wrong + if rdatom.HasProp('_CIPCode') and rdatom.GetProp("_CIPCode") == atom.stereochemistry: + continue + + # Keep track of undefined stereo atoms. We'll force stereochemistry + # at the end to avoid the next AssignStereochemistry to overwrite. + if not rdatom.HasProp('_CIPCode'): + undefined_stereo_atoms[rdatom] = atom.stereochemistry + continue + + # Something is wrong. + err_msg = ("Unknown atom stereochemistry encountered in to_rdkit. " + "Desired stereochemistry: {}. Set stereochemistry {}".format( + atom.stereochemistry, rdatom.GetProp("_CIPCode"))) + raise RuntimeError(err_msg) + + # Copy bond stereo info from molecule to rdmol. + cls._assign_rdmol_bonds_stereo(molecule, rdmol) + + # Set coordinates if we have them + if molecule._conformers: + for conformer in molecule._conformers: + rdmol_conformer = Chem.Conformer() + for atom_idx in range(molecule.n_atoms): + x, y, z = conformer[atom_idx, :].value_in_unit(unit.angstrom) + rdmol_conformer.SetAtomPosition(atom_idx, + Geometry.Point3D(x, y, z)) + rdmol.AddConformer(rdmol_conformer) + + # Retain charges, if present + if not (molecule._partial_charges is None): + + rdk_indexed_charges = np.zeros((molecule.n_atoms), dtype=np.float) + for atom_idx, charge in enumerate(molecule._partial_charges): + charge_unitless = charge.value_in_unit(unit.elementary_charge) + rdk_indexed_charges[atom_idx] = charge_unitless + for atom_idx, rdk_atom in enumerate(rdmol.GetAtoms()): + rdk_atom.SetDoubleProp('partial_charge', + rdk_indexed_charges[atom_idx]) + + # Cleanup the rdmol + rdmol.UpdatePropertyCache(strict=False) + Chem.GetSSSR(rdmol) + + # Forcefully assign stereo information on the atoms that RDKit + # can't figure out. This must be done last as calling AssignStereochemistry + # again will delete these properties (see #196). + for rdatom, stereochemistry in undefined_stereo_atoms.items(): + rdatom.SetProp('_CIPCode', stereochemistry) + + # Return non-editable version + return Chem.Mol(rdmol) + + @staticmethod + def _find_smarts_matches(rdmol, smirks, + aromaticity_model='OEAroModel_MDL'): + """Find all sets of atoms in the provided RDKit molecule that match the provided SMARTS string. + + Parameters + ---------- + rdmol : rdkit.Chem.Mol + rdmol to process with the SMIRKS in order to find matches + smarts : str + SMARTS string with any number of sequentially tagged atoms. + If there are N tagged atoms numbered 1..N, the resulting matches will be N-tuples of atoms that match the corresponding tagged atoms. + aromaticity_model : str, optional, default='OEAroModel_MDL' + OpenEye aromaticity model designation as a string, such as ``OEAroModel_MDL``. + If ``None``, molecule is processed exactly as provided; otherwise it is prepared with this aromaticity model prior to querying. + + Returns + ------- + matches : list of tuples of atoms indices within the ``rdmol`` + matches[index] is an N-tuple of atom numbers from the ``rdmol`` + Matches are returned in no guaranteed order. + # TODO: What is returned if no matches are found? An empty list, or None? + # TODO: Ensure that SMARTS numbers 1, 2, 3... are rendered into order of returnd matches indexed by 0, 1, 2... + + .. notes :: + + * Raises ``ValueError`` if ``smarts`` query is malformed + + """ + from rdkit import Chem + + # Make a copy of the molecule + rdmol = Chem.Mol(rdmol) + # Use designated aromaticity model + if aromaticity_model == 'OEAroModel_MDL': + Chem.SanitizeMol(rdmol, + Chem.SANITIZE_ALL ^ Chem.SANITIZE_SETAROMATICITY) + Chem.SetAromaticity(rdmol, Chem.AromaticityModel.AROMATICITY_MDL) + else: + # Only the OEAroModel_MDL is supported for now + raise ValueError( + 'Unknown aromaticity model: {}'.aromaticity_models) + + # Set up query. + qmol = Chem.MolFromSmarts(smirks) #cannot catch the error + if qmol is None: + raise ValueError( + 'RDKit could not parse the SMIRKS string "{}"'.format(smirks)) + + # Create atom mapping for query molecule + idx_map = dict() + for atom in qmol.GetAtoms(): + smirks_index = atom.GetAtomMapNum() + if smirks_index != 0: + idx_map[smirks_index - 1] = atom.GetIdx() + map_list = [idx_map[x] for x in sorted(idx_map)] + + # Perform matching + matches = list() + for match in rdmol.GetSubstructMatches(qmol, uniquify=False): + mas = [match[x] for x in map_list] + matches.append(tuple(mas)) + + return matches + + def find_smarts_matches(self, + molecule, + smarts, + aromaticity_model='OEAroModel_MDL'): + """ + Find all SMARTS matches for the specified molecule, using the specified aromaticity model. + + .. warning :: This API is experimental and subject to change. + + Parameters + ---------- + molecule : openforcefield.topology.Molecule + The molecule for which all specified SMARTS matches are to be located + smarts : str + SMARTS string with optional SMIRKS-style atom tagging + aromaticity_model : str, optional, default='OEAroModel_MDL' + Aromaticity model to use during matching + + .. note :: Currently, the only supported ``aromaticity_model`` is ``OEAroModel_MDL`` + + """ + rdmol = self.to_rdkit(molecule, aromaticity_model=aromaticity_model) + return self._find_smarts_matches( + rdmol, smarts, aromaticity_model='OEAroModel_MDL') + + # -------------------------------- + # Stereochemistry RDKit utilities. + # -------------------------------- + + @staticmethod + def _find_undefined_stereo_atoms(rdmol, assign_stereo=False): + """Find the chiral atoms with undefined stereochemsitry in the RDMol. + + Parameters + ---------- + rdmol : rdkit.RDMol + The RDKit molecule. + assign_stereo : bool, optional, default=False + As a side effect, this function calls ``Chem.AssignStereochemistry()`` + so by default we work on a molecule copy. Set this to ``True`` to avoid + making a copy and assigning the stereochemistry to the Mol object. + + Returns + ------- + undefined_atom_indices : List[int] + A list of atom indices that are chiral centers with undefined + stereochemistry. + + See Also + -------- + rdkit.Chem.FindMolChiralCenters + + """ + from rdkit import Chem + + if not assign_stereo: + # Avoid modifying the original molecule. + rdmol = copy.deepcopy(rdmol) + + # Flag possible chiral centers with the "_ChiralityPossible". + Chem.AssignStereochemistry(rdmol, force=True, flagPossibleStereoCenters=True) + + # Find all atoms with undefined stereo. + undefined_atom_indices = [] + for atom_idx, atom in enumerate(rdmol.GetAtoms()): + if (atom.GetChiralTag() == Chem.ChiralType.CHI_UNSPECIFIED and + atom.HasProp('_ChiralityPossible')): + undefined_atom_indices.append(atom_idx) + return undefined_atom_indices + + @staticmethod + def _find_undefined_stereo_bonds(rdmol): + """Find the chiral atoms with undefined stereochemsitry in the RDMol. + + Parameters + ---------- + rdmol : rdkit.RDMol + The RDKit molecule. + + Returns + ------- + undefined_bond_indices : List[int] + A list of bond indices with undefined stereochemistry. + + See Also + -------- + Chem.EnumerateStereoisomers._getFlippers + + Links + ----- + https://github.com/rdkit/rdkit/blob/master/Code/GraphMol/Chirality.cpp#L1509-L1515 + This comment in FindPotentialStereoBonds mention that the method + ignores ring bonds. + https://github.com/DrrDom/rdk/blob/master/gen_stereo_rdkit3.py + The function get_unspec_double_bonds() in this module looks like + may solve the problem with the rings. + + """ + from rdkit import Chem + + # Copy the molecule to avoid side effects. Chem.FindPotentialStereoBonds + # assign Bond.STEREOANY to unspecific bond, which make subsequent calls + # of Chem.AssignStereochemistry ignore the bond even if there are + # ENDDOWNRIGHT/ENDUPRIGHT bond direction indications. + rdmol = copy.deepcopy(rdmol) + + # This function assigns Bond.GetStereo() == Bond.STEREOANY to bonds with + # undefined stereochemistry. + Chem.FindPotentialStereoBonds(rdmol) + + undefined_bond_indices = [] + for bond_idx, bond in enumerate(rdmol.GetBonds()): + if bond.GetStereo() == Chem.BondStereo.STEREOANY: + undefined_bond_indices.append(bond_idx) + return undefined_bond_indices + + @classmethod + def _detect_undefined_stereo(cls, rdmol, err_msg_prefix='', raise_warning=False): + """Raise UndefinedStereochemistryError if the RDMol has undefined stereochemistry. + + Parameters + ---------- + rdmol : rdkit.Chem.Mol + The RDKit molecule. + err_msg_prefix : str, optional + A string to prepend to the error/warning message. + raise_warning : bool, optional, default=False + If True, a warning is issued instead of an exception. + + Raises + ------ + UndefinedStereochemistryError + If the RDMol has undefined atom or bond stereochemistry. + + """ + # Find undefined atom/bond stereochemistry. + undefined_atom_indices = cls._find_undefined_stereo_atoms(rdmol) + undefined_bond_indices = cls._find_undefined_stereo_bonds(rdmol) + + # Build error message. + if len(undefined_atom_indices) == 0 and len(undefined_bond_indices) == 0: + msg = None + else: + msg = err_msg_prefix + "RDMol has unspecified stereochemistry. " + # The "_Name" property is not always assigned. + if rdmol.HasProp("_Name"): + msg += "RDMol name: " + rdmol.GetProp("_Name") + + # Details about undefined atoms. + if len(undefined_atom_indices) > 0: + msg += "Undefined chiral centers are:\n" + for undefined_atom_idx in undefined_atom_indices: + msg += ' - Atom {symbol} (index {index})\n'.format( + symbol=rdmol.GetAtomWithIdx(undefined_atom_idx).GetSymbol(), + index=undefined_atom_idx) + + # Details about undefined bond. + if len(undefined_bond_indices) > 0: + msg += "Bonds with undefined stereochemistry are:\n" + for undefined_bond_idx in undefined_bond_indices: + bond = rdmol.GetBondWithIdx(undefined_bond_idx) + atom1, atom2 = bond.GetBeginAtom(), bond.GetEndAtom() + msg += ' - Bond {bindex} (atoms {aindex1}-{aindex2} of element ({symbol1}-{symbol2})\n'.format( + bindex=undefined_bond_idx, + aindex1=atom1.GetIdx(), aindex2=atom2.GetIdx(), + symbol1=atom1.GetSymbol(), symbol2=atom2.GetSymbol()) + + if msg is not None: + if raise_warning: + logger.warning(msg) + else: + raise UndefinedStereochemistryError(msg) + + @staticmethod + def _flip_rdbond_direction(rdbond, paired_rdbonds): + """Flip the rdbond and all those paired to it. + + Parameters + ---------- + rdbond : rdkit.Chem.Bond + The Bond whose direction needs to be flipped. + paired_rdbonds : Dict[Tuple[int], List[rdkit.Chem.Bond]] + Maps bond atom indices that are assigned a bond direction to + the bonds on the other side of the double bond. + """ + from rdkit import Chem + + # The function assumes that all bonds are either up or down. + supported_directions = {Chem.BondDir.ENDUPRIGHT, Chem.BondDir.ENDDOWNRIGHT} + + def _flip(b, paired, flipped, ignored): + # The function assumes that all bonds are either up or down. + assert b.GetBondDir() in supported_directions + bond_atom_indices = (b.GetBeginAtomIdx(), b.GetEndAtomIdx()) + + # Check that we haven't flipped this bond already. + if bond_atom_indices in flipped: + # This should never happen. + raise RuntimeError('Cannot flip the bond direction consistently.') + + # Flip the bond. + if b.GetBondDir() == Chem.BondDir.ENDUPRIGHT: + b.SetBondDir(Chem.BondDir.ENDDOWNRIGHT) + else: + b.SetBondDir(Chem.BondDir.ENDUPRIGHT) + flipped.add(bond_atom_indices) + + # Flip all the paired bonds as well (if there are any). + if bond_atom_indices in paired: + for paired_rdbond in paired[bond_atom_indices]: + # Don't flip the bond that was flipped in the upper-level recursion. + if (paired_rdbond.GetBeginAtomIdx(), paired_rdbond.GetEndAtomIdx()) != ignored: + # Don't flip this bond in the next recursion. + _flip(paired_rdbond, paired, flipped, ignored=bond_atom_indices) + + _flip(rdbond, paired_rdbonds, flipped=set(), ignored=None) + + @classmethod + def _assign_rdmol_bonds_stereo(cls, offmol, rdmol): + """Copy the info about bonds stereochemistry from the OFF Molecule to RDKit Mol.""" + from rdkit import Chem + + # Map the bonds indices that are assigned bond direction + # to the bond on the other side of the double bond. + # (atom_index1, atom_index2) -> List[rdkit.Chem.Bond] + paired_bonds = {} + + for bond in offmol.bonds: + # No need to do anything with bonds without stereochemistry. + if not bond.stereochemistry: + continue + + # Isolate stereo RDKit bond object. + rdbond_atom_indices = (bond.atom1.molecule_atom_index, + bond.atom2.molecule_atom_index) + stereo_rdbond = rdmol.GetBondBetweenAtoms(*rdbond_atom_indices) + + # Collect all neighboring rdbonds of atom1 and atom2. + neighbor_rdbonds1 = [rdmol.GetBondBetweenAtoms(n.molecule_atom_index, + bond.atom1.molecule_atom_index) + for n in bond.atom1.bonded_atoms if n != bond.atom2] + neighbor_rdbonds2 = [rdmol.GetBondBetweenAtoms(bond.atom2.molecule_atom_index, + n.molecule_atom_index) + for n in bond.atom2.bonded_atoms if n != bond.atom1] + + # Select only 1 neighbor bond per atom out of the two. + neighbor_rdbonds = [] + for i, rdbonds in enumerate([neighbor_rdbonds1, neighbor_rdbonds2]): + # If there are no neighbors for which we have already + # assigned the bond direction, just pick the first one. + neighbor_rdbonds.append(rdbonds[0]) + # Otherwise, pick neighbor that was already assigned to + # avoid inconsistencies and keep the tree non-cyclic. + for rdb in rdbonds: + if (rdb.GetBeginAtomIdx(), rdb.GetBeginAtomIdx()) in paired_bonds: + neighbor_rdbonds[i] = rdb + break + + # Assign a random direction to the bonds that were not already assigned + # keeping track of which bond would be best to flip later (i.e. does that + # are not already determining the stereochemistry of another double bond). + flipped_rdbond = neighbor_rdbonds[0] + for rdb in neighbor_rdbonds: + if (rdb.GetBeginAtomIdx(), rdb.GetEndAtomIdx()) not in paired_bonds: + rdb.SetBondDir(Chem.BondDir.ENDUPRIGHT) + # Set this bond as a possible bond to flip. + flipped_rdbond = rdb + + Chem.AssignStereochemistry(rdmol, cleanIt=True, force=True) + + # Verify that the current directions give us the desired stereochemistries. + assert bond.stereochemistry in {'E', 'Z'} + if bond.stereochemistry == 'E': + desired_rdk_stereo_code = Chem.rdchem.BondStereo.STEREOE + else: + desired_rdk_stereo_code = Chem.rdchem.BondStereo.STEREOZ + + # If that doesn't work, flip the direction of one bond preferring + # those that are not already determining the stereo of another bond. + if stereo_rdbond.GetStereo() != desired_rdk_stereo_code: + cls._flip_rdbond_direction(flipped_rdbond, paired_bonds) + Chem.AssignStereochemistry(rdmol, cleanIt=True, force=True) + + # The stereo should be set correctly here. + assert stereo_rdbond.GetStereo() == desired_rdk_stereo_code + + # Update paired bonds map. + neighbor_bond_indices = [(rdb.GetBeginAtomIdx(), rdb.GetEndAtomIdx()) for rdb in neighbor_rdbonds] + for i, bond_indices in enumerate(neighbor_bond_indices): + try: + paired_bonds[bond_indices].append(neighbor_rdbonds[1-i]) + except KeyError: + paired_bonds[bond_indices] = [neighbor_rdbonds[1-i]] + + +class AmberToolsToolkitWrapper(ToolkitWrapper): + """ + AmberTools toolkit wrapper + + .. warning :: This API is experimental and subject to change. + """ + _toolkit_name = 'AmberTools' + _toolkit_installation_instructions = 'The AmberTools toolkit (free and open source) can be found at ' \ + 'https://anaconda.org/omnia/ambertools' + _toolkit_file_read_formats = [] + _toolkit_file_write_formats = [] + + @staticmethod + def toolkit_is_available(): + """ + Check whether the AmberTools toolkit is installed + + Returns + ------- + is_installed : bool + True if AmberTools is installed, False otherwise. + + """ + # TODO: Check all tools needed + # TODO: How should we implement find_executable? + ANTECHAMBER_PATH = find_executable("antechamber") + if ANTECHAMBER_PATH is None: + return False + else: + return True + + @classmethod + def is_available(cls): + """ + Check whether this toolkit wrapper is available for use because the underlying toolkit can be found. + + .. note :: This method caches the result of any costly checks for file paths or module imports. + + Parameters + ---------- + is_available : bool + True if toolkit wrapper is available for use, False otherwise + + """ + if cls._is_available is None: + cls._is_available = cls.toolkit_is_available() + return cls._is_available + + def __init__(self): + # TODO: Find AMBERHOME or executable home, checking miniconda if needed + # Store an instance of an RDKitToolkitWrapper for file I/O + self._rdkit_toolkit_wrapper = RDKitToolkitWrapper() + + def compute_partial_charges(self, molecule, charge_model=None): + """ + Compute partial charges with AmberTools using antechamber/sqm + + .. warning :: This API experimental and subject to change. + + .. todo :: + + * Do we want to also allow ESP/RESP charges? + + Parameters + ---------- + molecule : Molecule + Molecule for which partial charges are to be computed + charge_model : str, optional, default=None + The charge model to use. One of ['gas', 'mul', 'bcc']. If None, 'bcc' will be used. + + + Raises + ------ + ValueError if the requested charge method could not be handled + + Notes + ----- + Currently only sdf file supported as input and mol2 as output + https://github.com/choderalab/openmoltools/blob/master/openmoltools/packmol.py + + """ + raise NotImplementedError + # TODO: Implement this in a way that's compliant with SMIRNOFF's tag when the spec gets finalized + + import os + from simtk import unit + + if charge_model is None: + charge_model = 'bcc' + + # Check that the requested charge method is supported + # Needs to be fixed: 'cm1', 'cm2', + SUPPORTED_ANTECHAMBER_CHARGE_MODELS = ['gas', 'mul', 'bcc'] + if charge_model not in SUPPORTED_ANTECHAMBER_CHARGE_MODELS: + raise ValueError( + 'Requested charge method {} not among supported charge ' + 'methods {}'.format(charge_model, + SUPPORTED_ANTECHAMBER_CHARGE_MODELS)) + + # Find the path to antechamber + # TODO: How should we implement find_executable? + ANTECHAMBER_PATH = find_executable("antechamber") + if ANTECHAMBER_PATH is None: + raise (IOError("Antechamber not found, cannot run charge_mol()")) + + if len(molecule._conformers) == 0: + raise Exception( + "No conformers present in molecule submitted for partial charge calculation. Consider " + "loading the molecule from a file with geometry already present or running " + "molecule.generate_conformers() before calling molecule.compute_partial_charges" + ) + + + # Compute charges + from openforcefield.utils import temporary_directory, temporary_cd + with temporary_directory() as tmpdir: + with temporary_cd(tmpdir): + net_charge = molecule.total_charge + # Write out molecule in SDF format + ## TODO: How should we handle multiple conformers? + self._rdkit_toolkit_wrapper.to_file( + molecule, 'molecule.sdf', outfile_format='sdf') + #os.system('ls') + #os.system('cat molecule.sdf') + # Compute desired charges + # TODO: Add error handling if antechamber chokes + # TODO: Add something cleaner than os.system + os.system( + "antechamber -i molecule.sdf -fi sdf -o charged.mol2 -fo mol2 -pf " + "yes -c {} -nc {}".format(charge_model, net_charge)) + #os.system('cat charged.mol2') + + # Write out just charges + os.system( + "antechamber -i charged.mol2 -fi mol2 -o charges2.mol2 -fo mol2 -c wc " + "-cf charges.txt -pf yes") + #os.system('cat charges.txt') + # Check to ensure charges were actually produced + if not os.path.exists('charges.txt'): + # TODO: copy files into local directory to aid debugging? + raise Exception( + "Antechamber/sqm partial charge calculation failed on " + "molecule {} (SMILES {})".format( + molecule.name, molecule.to_smiles())) + # Read the charges + with open('charges.txt', 'r') as infile: + contents = infile.read() + text_charges = contents.split() + charges = np.zeros([molecule.n_atoms], np.float64) + for index, token in enumerate(text_charges): + charges[index] = float(token) + # TODO: Ensure that the atoms in charged.mol2 are in the same order as in molecule.sdf + + charges = unit.Quantity(charges, unit.elementary_charge) + + molecule.set_partial_charges(charges) + + def compute_partial_charges_am1bcc(self, molecule): + """ + Compute partial charges with AmberTools using antechamber/sqm. This will calculate AM1-BCC charges on the first + conformer only. + + .. warning :: This API experimental and subject to change. + + Parameters + ---------- + molecule : Molecule + Molecule for which partial charges are to be computed + + + Raises + ------ + ValueError if the requested charge method could not be handled + + """ + + import os + from simtk import unit + + + # Find the path to antechamber + # TODO: How should we implement find_executable? + ANTECHAMBER_PATH = find_executable("antechamber") + if ANTECHAMBER_PATH is None: + raise (IOError("Antechamber not found, cannot run " + "AmberToolsToolkitWrapper.compute_partial_charges_am1bcc()")) + + if len(molecule._conformers) == 0: + raise ValueError( + "No conformers present in molecule submitted for partial charge calculation. Consider " + "loading the molecule from a file with geometry already present or running " + "molecule.generate_conformers() before calling molecule.compute_partial_charges" + ) + if len(molecule._conformers) > 1: + logger.warning("In AmberToolsToolkitwrapper.computer_partial_charges_am1bcc: " + "Molecule '{}' has more than one conformer, but this function " + "will only generate charges for the first one.".format(molecule.name)) + + + # Compute charges + from openforcefield.utils import temporary_directory, temporary_cd + with temporary_directory() as tmpdir: + with temporary_cd(tmpdir): + net_charge = molecule.total_charge + # Write out molecule in SDF format + ## TODO: How should we handle multiple conformers? + self._rdkit_toolkit_wrapper.to_file( + molecule, 'molecule.sdf', outfile_format='sdf') + #os.system('ls') + #os.system('cat molecule.sdf') + # Compute desired charges + # TODO: Add error handling if antechamber chokes + # TODO: Add something cleaner than os.system + os.system( + "antechamber -i molecule.sdf -fi sdf -o charged.mol2 -fo mol2 -pf " + "yes -c bcc -nc {}".format(net_charge)) + #os.system('cat charged.mol2') + + # Write out just charges + os.system( + "antechamber -i charged.mol2 -fi mol2 -o charges2.mol2 -fo mol2 -c wc " + "-cf charges.txt -pf yes") + #os.system('cat charges.txt') + # Check to ensure charges were actually produced + if not os.path.exists('charges.txt'): + # TODO: copy files into local directory to aid debugging? + raise Exception( + "Antechamber/sqm partial charge calculation failed on " + "molecule {} (SMILES {})".format( + molecule.name, molecule.to_smiles())) + # Read the charges + with open('charges.txt', 'r') as infile: + contents = infile.read() + text_charges = contents.split() + charges = np.zeros([molecule.n_atoms], np.float64) + for index, token in enumerate(text_charges): + charges[index] = float(token) + # TODO: Ensure that the atoms in charged.mol2 are in the same order as in molecule.sdf + + charges = unit.Quantity(charges, unit.elementary_charge) + return charges + + +#============================================================================================= +# Toolkit registry +#============================================================================================= + + +class ToolkitRegistry(object): + """ + Registry for ToolkitWrapper objects + + Examples + -------- + + Register toolkits in a specified order, skipping if unavailable + + >>> from openforcefield.utils.toolkits import ToolkitRegistry + >>> toolkit_registry = ToolkitRegistry() + >>> toolkit_precedence = [OpenEyeToolkitWrapper, RDKitToolkitWrapper, AmberToolsToolkitWrapper] + >>> for toolkit in toolkit_precedence: + ... if toolkit.is_available(): + ... toolkit_registry.register_toolkit(toolkit) + + Register specified toolkits, raising an exception if one is unavailable + + >>> toolkit_registry = ToolkitRegistry() + >>> toolkits = [OpenEyeToolkitWrapper, AmberToolsToolkitWrapper] + >>> for toolkit in toolkits: + ... toolkit_registry.register_toolkit(toolkit) + + Register all available toolkits in arbitrary order + + >>> from openforcefield.utils import all_subclasses + >>> toolkits = all_subclasses(ToolkitWrapper) + >>> for toolkit in toolkit_precedence: + ... if toolkit.is_available(): + ... toolkit_registry.register_toolkit(toolkit) + + Retrieve the global singleton toolkit registry, which is created when this module is imported from all available + toolkits: + + >>> from openforcefield.utils.toolkits import GLOBAL_TOOLKIT_REGISTRY as toolkit_registry + >>> available_toolkits = toolkit_registry.registered_toolkits + + .. warning :: This API is experimental and subject to change. + """ + + def __init__(self, + register_imported_toolkit_wrappers=False, + toolkit_precedence=None, + exception_if_unavailable=True): + """ + Create an empty toolkit registry. + + Parameters + ---------- + register_imported_toolkit_wrappers : bool, optional, default=False + If True, will attempt to register all imported ToolkitWrapper subclasses that can be found, in no particular + order. + toolkit_precedence : list, optional, default=None + List of toolkit wrapper classes, in order of desired precedence when performing molecule operations. If + None, defaults to [OpenEyeToolkitWrapper, RDKitToolkitWrapper, AmberToolsToolkitWrapper]. + exception_if_unavailable : bool, optional, default=True + If True, an exception will be raised if the toolkit is unavailable + + """ + + self._toolkits = list() + + if toolkit_precedence == None: + toolkit_precedence = [ + OpenEyeToolkitWrapper, RDKitToolkitWrapper, + AmberToolsToolkitWrapper + ] + + if register_imported_toolkit_wrappers: + # TODO: The precedence ordering of any non-specified remaining wrappers will be arbitrary. + # How do we fix this? + # Note: The precedence of non-specifid wrappers may be determined by the order in which + # they were defined + all_importable_toolkit_wrappers = all_subclasses(ToolkitWrapper) + for toolkit in all_importable_toolkit_wrappers: + if toolkit in toolkit_precedence: + continue + toolkit_precedence.append(toolkit) + + for toolkit in toolkit_precedence: + self.register_toolkit(toolkit, exception_if_unavailable=exception_if_unavailable) + + @property + def registered_toolkits(self): + """ + List registered toolkits. + + .. warning :: This API is experimental and subject to change. + + .. todo :: Should this return a generator? Deep copies? Classes? Toolkit names? + + Returns + ------- + toolkits : iterable of toolkit objects + """ + return list(self._toolkits) + + def register_toolkit(self, + toolkit_wrapper, + exception_if_unavailable=True): + """ + Register the provided toolkit wrapper class, instantiating an object of it. + + .. warning :: This API is experimental and subject to change. + + .. todo :: + + This method should raise an exception if the toolkit is unavailable, unless an optional argument + is specified that silently avoids registration of toolkits that are unavailable. + + Parameters + ---------- + toolkit_wrapper : instance or subclass of ToolkitWrapper + The toolkit wrapper to register or its class. + exception_if_unavailable : bool, optional, default=True + If True, an exception will be raised if the toolkit is unavailable + + """ + # Instantiate class if class, or just add if already instantiated. + if isinstance(toolkit_wrapper, type): + toolkit_wrapper = toolkit_wrapper() + + # Raise exception if not available. + if not toolkit_wrapper.is_available(): + msg = "Unable to load toolkit {}.".format(toolkit_wrapper) + if exception_if_unavailable: + raise ToolkitUnavailableException(msg) + else: + logger.warning(msg) + return + + # Add toolkit to the registry. + self._toolkits.append(toolkit_wrapper) + + def add_toolkit(self, toolkit_wrapper): + """ + Append a ToolkitWrapper onto the list of toolkits in this ToolkitRegistry + + .. warning :: This API is experimental and subject to change. + + Parameters + ---------- + toolkit_wrapper : openforcefield.utils.ToolkitWrapper + The ToolkitWrapper object to add to the list of registered toolkits + + """ + if not isinstance(toolkit_wrapper, ToolkitWrapper): + msg = "Something other than a ToolkitWrapper object was passed to ToolkitRegistry.add_toolkit()\n" + msg += "Given object {} of type {}".format(toolkit_wrapper, + type(toolkit_wrapper)) + raise Exception(msg) + self._toolkits.append(toolkit_wrapper) + + # TODO: Can we automatically resolve calls to methods that are not explicitly defined using some Python magic? + + def resolve(self, method_name): + """ + Resolve the requested method name by checking all registered toolkits in order of precedence for one that provides the requested method. + + Parameters + ---------- + method_name : str + The name of the method to resolve + + Returns + ------- + method + The method of the first registered toolkit that provides the requested method name + + Raises + ------ + NotImplementedError if the requested method cannot be found among the registered toolkits + + Examples + -------- + + Create a molecule, and call the toolkit ``to_smiles()`` method directly + + >>> from openforcefield.topology import Molecule + >>> molecule = Molecule.from_smiles('Cc1ccccc1') + >>> toolkit_registry = ToolkitRegistry(register_imported_toolkit_wrappers=True) + >>> method = toolkit_registry.resolve('to_smiles') + >>> smiles = method(molecule) + + .. todo :: Is there a better way to figure out which toolkits implement given methods by introspection? + + """ + for toolkit in self._toolkits: + if hasattr(toolkit, method_name): + method = getattr(toolkit, method_name) + try: + return method + except NotImplementedError as e: + pass + + # No toolkit was found to provide the requested capability + # TODO: Can we help developers by providing a check for typos in expected method names? + msg = 'No registered toolkits can provide the capability "{}".\n'.format( + method_name) + msg += 'Available toolkits are: {}\n'.format(self.registered_toolkits) + raise NotImplementedError(msg) + + # TODO: Can we instead register available methods directly with `ToolkitRegistry`, so we can just use `ToolkitRegistry.method()`? + def call(self, method_name, *args, **kwargs): + """ + Execute the requested method by attempting to use all registered toolkits in order of precedence. + + ``*args`` and ``**kwargs`` are passed to the desired method, and return values of the method are returned + + This is a convenient shorthand for ``toolkit_registry.resolve_method(method_name)(*args, **kwargs)`` + + Parameters + ---------- + method_name : str + The name of the method to execute + + Raises + ------ + NotImplementedError if the requested method cannot be found among the registered toolkits + + Examples + -------- + + Create a molecule, and call the toolkit ``to_smiles()`` method directly + + >>> from openforcefield.topology import Molecule + >>> molecule = Molecule.from_smiles('Cc1ccccc1') + >>> toolkit_registry = ToolkitRegistry(register_imported_toolkit_wrappers=True) + >>> smiles = toolkit_registry.call('to_smiles', molecule) + + """ + # TODO: catch ValueError and compile list of methods that exist but rejected the specific parameters because they did not implement the requested methods + + value_errors = list() + for toolkit in self._toolkits: + if hasattr(toolkit, method_name): + method = getattr(toolkit, method_name) + try: + return method(*args, **kwargs) + except NotImplementedError: + pass + except ValueError as value_error: + value_errors.append((toolkit, value_error)) + + # No toolkit was found to provide the requested capability + # TODO: Can we help developers by providing a check for typos in expected method names? + msg = 'No registered toolkits can provide the capability "{}".\n'.format( + method_name) + msg += 'Available toolkits are: {}\n'.format(self.registered_toolkits) + # Append information about toolkits that implemented the method, but could not handle the provided parameters + for toolkit, value_error in value_errors: + msg += ' {} : {}\n'.format(toolkit, value_error) + raise NotImplementedError(msg) + + +#============================================================================================= +# GLOBAL TOOLKIT REGISTRY +#============================================================================================= + +# Create global toolkit registry, where all available toolkits are registered + +GLOBAL_TOOLKIT_REGISTRY = ToolkitRegistry( + register_imported_toolkit_wrappers=True, + exception_if_unavailable=False) + +#============================================================================================= +# SET GLOBAL TOOLKIT-AVAIABLE VARIABLES +#============================================================================================= + +OPENEYE_AVAILABLE = False +RDKIT_AVAILABLE = False +AMBERTOOLS_AVAILABLE = False + +# Only available toolkits will have made it into the GLOBAL_TOOLKIT_REGISTRY +for toolkit in GLOBAL_TOOLKIT_REGISTRY.registered_toolkits: + if type(toolkit) is OpenEyeToolkitWrapper: + OPENEYE_AVAILABLE = True + elif type(toolkit) is RDKitToolkitWrapper: + RDKIT_AVAILABLE = True + elif type(toolkit) is AmberToolsToolkitWrapper: + AMBERTOOLS_AVAILABLE = True + +#============================================================================================= +# WARN IF INSUFFICIENT TOOLKITS INSTALLED +#============================================================================================= + +# Define basic toolkits that handle essential file I/O + +BASIC_CHEMINFORMATICS_TOOLKITS = [RDKitToolkitWrapper, OpenEyeToolkitWrapper] + +# Ensure we have at least one basic toolkit +if sum([ + tk.toolkit_is_available() + for tk in GLOBAL_TOOLKIT_REGISTRY.registered_toolkits + if type(tk) in BASIC_CHEMINFORMATICS_TOOLKITS +]) == 0: + msg = 'WARNING: No basic cheminformatics toolkits are available.\n' + msg += 'At least one basic toolkit is required to handle SMARTS matching and file I/O. \n' + msg += 'Please install at least one of the following basic toolkits:\n' + for wrapper in all_subclasses(ToolkitWrapper): + if wrapper.toolkit_name is not None: + msg += '{} : {}\n'.format( + wrapper._toolkit_name, + wrapper._toolkit_installation_instructions) + print(msg) diff --git a/openforcefield/utils/utils.py b/openforcefield/utils/utils.py index db6f75092..695ac7997 100644 --- a/openforcefield/utils/utils.py +++ b/openforcefield/utils/utils.py @@ -1,438 +1,459 @@ #!/usr/bin/env python - """ -Utility subroutines for open forcefield tools +Utility subroutines """ #============================================================================================= # GLOBAL IMPORTS #============================================================================================= -import sys -import string +import contextlib +from simtk import unit -from optparse import OptionParser # For parsing of command line arguments -import os -import math -import copy -import re -import numpy -import random -import parmed -import openeye.oechem -import openeye.oeomega -import openeye.oequacpac +#============================================================================================= +# COMMON EXCEPTION TYPES +#============================================================================================= -from openeye.oechem import * -from openeye.oeomega import * -from openeye.oequacpac import * -from simtk.openmm import app -from simtk.openmm.app import element as elem -from simtk.openmm.app import Topology +class MessageException(Exception): + """A base class for exceptions that print out a string given in their constructor""" + def __init__(self, msg): + super().__init__(self, msg) + self.msg = msg -import time -from simtk import unit +# ============================================================================================= +# UTILITY SUBROUTINES +# ============================================================================================= -#============================================================================================= -# UTILITY ROUTINES -#============================================================================================= -def checkCharges(molecule): - # Check that molecule is charged. - #is_charged = False - for atom in molecule.GetAtoms(): - if atom.GetPartialCharge() != 0.0: - return True - else: - print('WARNING: Molecule %s has no charges; input molecules must be charged.' % molecule.GetTitle()) - return False -def generateSMIRNOFFStructure(molecule): +def inherit_docstrings(cls): + """Inherit docstrings from parent class""" + from inspect import getmembers, isfunction + for name, func in getmembers(cls, isfunction): + if func.__doc__: continue + for parent in cls.__mro__[1:]: + if hasattr(parent, name): + func.__doc__ = getattr(parent, name).__doc__ + return cls + + +def all_subclasses(cls): + """Recursively retrieve all subclasses of the specified class""" + return cls.__subclasses__() + [ + g for s in cls.__subclasses__() for g in all_subclasses(s) + ] + + +@contextlib.contextmanager +def temporary_cd(dir_path): + """Context to temporary change the working directory. + + Parameters + ---------- + dir_path : str + The directory path to enter within the context + + Examples + -------- + >>> dir_path = '/tmp' + >>> with temporary_cd(dir_path): + ... pass # do something in dir_path + """ - Given an OpenEye molecule (oechem.OEMol), create an OpenMM System and use to - generate a ParmEd structure using the SMIRNOFF forcefield parameters. + import os + prev_dir = os.getcwd() + os.chdir(os.path.abspath(dir_path)) + try: + yield + finally: + os.chdir(prev_dir) + + +@contextlib.contextmanager +def temporary_directory(): + """Context for safe creation of temporary directories.""" + + import tempfile + tmp_dir = tempfile.mkdtemp() + try: + yield tmp_dir + finally: + import shutil + shutil.rmtree(tmp_dir) + + +def get_data_filename(relative_path): + """Get the full path to one of the reference files in testsystems. + In the source distribution, these files are in ``openforcefield/data/``, + but on installation, they're moved to somewhere in the user's python + site-packages directory. + Parameters + ---------- + name : str + Name of the file to load (with respect to the repex folder). """ - from openforcefield.typing.engines.smirnoff import ForceField - from openforcefield.typing.engines.smirnoff.forcefield_utils import create_system_from_molecule - ff = get_data_filename('forcefield/smirnoff99Frosst.offxml') - with open(ff) as ffxml: - mol_ff = ForceField(ffxml) + from pkg_resources import resource_filename + import os + fn = resource_filename('openforcefield', os.path.join( + 'data', relative_path)) - if not checkCharges(molecule): - from openmoltools.openeye import get_charges - print("Assigning charges to molecule.") - charged_molecule = get_charges(molecule) - else: - charged_molecule = molecule - mol_top, mol_sys, mol_pos = create_system_from_molecule(mol_ff, charged_molecule) - molecule_structure = parmed.openmm.load_topology(mol_top, mol_sys, xyz=mol_pos) + if not os.path.exists(fn): + raise ValueError( + "Sorry! %s does not exist. If you just added it, you'll have to re-install" + % fn) + + return fn - return molecule_structure -def generateProteinStructure(proteinpdb, protein_forcefield='amber99sbildn.xml', solvent_forcefield='tip3p.xml'): +def unit_to_string(input_unit): """ - Given an OpenMM PDBFile, create the OpenMM System of the protein and - then generate the parametrized ParmEd Structure of the protein. + Serialize a simtk.unit.Unit and return it as a string. + Parameters ---------- - proteinpdb : openmm.app.PDBFile object, - Loaded PDBFile object of the protein. - protein_forcefield : xml file, default='amber99sbildn.xml' - Forcefield parameters for protein - solvent_forcefield : xml file, default='tip3p.xml' - Forcefield parameters for solvent + input_unit : A simtk.unit + The unit to serialize + Returns ------- - solv_structure : parmed.structure.Structure - The parameterized Structure of the protein with solvent molecules. (No ligand). + unit_string : str + The serialized unit. """ - #Generate protein Structure object - forcefield = app.ForceField(protein_forcefield, solvent_forcefield) - protein_system = forcefield.createSystem( proteinpdb.topology ) - protein_structure = parmed.openmm.load_topology(proteinpdb.topology, - protein_system, - xyz=proteinpdb.positions) - return protein_structure - -def combinePostions(proteinPositions, molPositions): + + + # Decompose output_unit into a tuples of (base_dimension_unit, exponent) + unit_string = None + + for unit_component in input_unit.iter_base_or_scaled_units(): + unit_component_name = unit_component[0].name + # Convert, for example "elementary charge" --> "elementary_charge" + unit_component_name = unit_component_name.replace(' ', '_') + if unit_component[1] == 1: + contribution = '{}'.format(unit_component_name) + else: + contribution = '{}**{}'.format(unit_component_name, int(unit_component[1])) + if unit_string is None: + unit_string = contribution + else: + unit_string += ' * {}'.format(contribution) + + return unit_string + +def quantity_to_string(input_quantity): """ - Loops through the positions from the ParmEd structures of the protein and ligand, - divides by unit.angstroms which will ensure both positions arrays are in the same units. + Serialize a simtk.unit.Quantity to a string. + Parameters ---------- - proteinPositions : list of 3-element Quantity tuples. - Positions list taken directly from the protein Structure. - molPositions : list of 3-element Quantity tuples. - Positions list taken directly from the molecule Structure. + input_quantity : simtk.unit.Quantity + The quantity to serialize + Returns ------- - positions : list of 3-element Quantity tuples. - ex. unit.Quantity(positions, positions_unit) - Combined positions of the protein and molecule Structures. + output_string : str + The serialized quantity + """ - positions_unit = unit.angstroms - positions0_dimensionless = numpy.array(proteinPositions / positions_unit) - positions1_dimensionless = numpy.array(molPositions / positions_unit) - coordinates = numpy.vstack( - (positions0_dimensionless, positions1_dimensionless)) - natoms = len(coordinates) - positions = numpy.zeros([natoms, 3], numpy.float32) - for index in range(natoms): - (x, y, z) = coordinates[index] - positions[index, 0] = x - positions[index, 1] = y - positions[index, 2] = z - positions = unit.Quantity(positions, positions_unit) - return positions - -def mergeStructure(proteinStructure, molStructure): + import numpy as np + if input_quantity is None: + return None + unitless_value = input_quantity.value_in_unit(input_quantity.unit) + # The string representaiton of a numpy array doesn't have commas and breaks the + # parser, thus we convert any arrays to list here + if isinstance(unitless_value, np.ndarray): + unitless_value = list(unitless_value) + unit_string = unit_to_string(input_quantity.unit) + print(input_quantity, type(unitless_value)) + output_string = '{} * {}'.format(unitless_value, unit_string) + return output_string + +def _ast_eval(node): """ - Combines the parametrized ParmEd structures of the protein and ligand to - create the Structure for the protein:ligand complex, while retaining the SMIRNOFF - parameters on the ligand. Preserves positions and box vectors. - (Not as easily achieved using native OpenMM tools). + Performs an algebraic syntax tree evaluation of a unit. + Parameters ---------- - proteinStructure : parmed.structure.Structure - The parametrized structure of the protein. - moleculeStructure : parmed.structure.Structure - The parametrized structure of the ligand. - Returns - ------- - structure : parmed.structure.Structure - The parametrized structure of the protein:ligand complex. + node : An ast parsing tree node """ - structure = proteinStructure + molStructure - positions = combinePostions(proteinStructure.positions, molStructure.positions) - # Concatenate positions arrays (ensures same units) - structure.positions = positions - # Restore original box vectors - structure.box = proteinStructure.box - return structure + import ast + import operator as op + + operators = {ast.Add: op.add, ast.Sub: op.sub, ast.Mult: op.mul, + ast.Div: op.truediv, ast.Pow: op.pow, ast.BitXor: op.xor, + ast.USub: op.neg} + + if isinstance(node, ast.Num): # + return node.n + elif isinstance(node, ast.BinOp): # + return operators[type(node.op)](_ast_eval(node.left), _ast_eval(node.right)) + elif isinstance(node, ast.UnaryOp): # e.g., -1 + return operators[type(node.op)](_ast_eval(node.operand)) + elif isinstance(node, ast.Name): + # see if this is a simtk unit + b = getattr(unit, node.id) + return b + # TODO: This was a quick hack that surprisingly worked. We should validate this further. + elif isinstance(node, ast.List): + return ast.literal_eval(node) + else: + raise TypeError(node) -def generateTopologyFromOEMol(molecule): +def string_to_unit(unit_string): """ - Generate an OpenMM Topology object from an OEMol molecule. + Deserializes a simtk.unit.Quantity from a string representation, for + example: "kilocalories_per_mole / angstrom ** 2" + Parameters ---------- - molecule : openeye.oechem.OEMol - The molecule from which a Topology object is to be generated. + unit_string : dict + Serialized representation of a simtk.unit.Quantity. Returns ------- - topology : simtk.openmm.app.Topology - The Topology object generated from `molecule`. - + output_unit: simtk.unit.Quantity + The deserialized unit from the string """ - # Avoid manipulating the molecule - mol = OEMol(molecule) - - # Create a Topology object with one Chain and one Residue. - from simtk.openmm.app import Topology - topology = Topology() - chain = topology.addChain() - resname = mol.GetTitle() - residue = topology.addResidue(resname, chain) - - # Make sure the atoms have names, otherwise bonds won't be created properly below - if any([atom.GetName() =='' for atom in mol.GetAtoms()]): - oechem.OETriposAtomNames(mol) - # Check names are unique; non-unique names will also cause a problem - atomnames = [ atom.GetName() for atom in mol.GetAtoms() ] - if any( atomnames.count(atom.GetName())>1 for atom in mol.GetAtoms()): - raise Exception("Error: Reference molecule must have unique atom names in order to create a Topology.") - - # Create atoms in the residue. - for atom in mol.GetAtoms(): - name = atom.GetName() - element = elem.Element.getByAtomicNumber(atom.GetAtomicNum()) - openmm_atom = topology.addAtom(name, element, residue) - - # Create bonds. - atoms = { atom.name : atom for atom in topology.atoms() } - for bond in mol.GetBonds(): - aromatic = None - if bond.IsAromatic(): aromatic = 'Aromatic' - # Add bond, preserving order assessed by OEChem - topology.addBond(atoms[bond.GetBgn().GetName()], atoms[bond.GetEnd().GetName()], type=aromatic, order=bond.GetOrder()) - - return topology - -def get_data_filename(relative_path): - """Get the full path to one of the reference files in testsystems. - - In the source distribution, these files are in ``openforcefield/data/``, - but on installation, they're moved to somewhere in the user's python - site-packages directory. + import ast + output_unit = _ast_eval(ast.parse(unit_string, mode='eval').body) + return output_unit + + #if (serialized['unitless_value'] is None) and (serialized['unit'] is None): + # return None + 3#quantity_unit = None + #for unit_name, power in serialized['unit']: + # unit_name = unit_name.replace( + # ' ', '_') # Convert eg. 'elementary charge' to 'elementary_charge' + # if quantity_unit is None: + # quantity_unit = (getattr(unit, unit_name)**power) + # else: + # quantity_unit *= (getattr(unit, unit_name)**power) + #quantity = unit.Quantity(serialized['unitless_value'], quantity_unit) + #return quantity + +def string_to_quantity(quantity_string): + """ + Takes a string representation of a quantity and returns a simtk.unit.Quantity Parameters ---------- - name : str - Name of the file to load (with respect to the repex folder). + quantity_string : str + The quantity to deserialize + Returns + ------- + output_quantity : simtk.unit.Quantity + The deserialized quantity """ + if quantity_string is None: + return None + # This can be the exact same as string_to_unit + import ast + output_quantity = _ast_eval(ast.parse(quantity_string, mode='eval').body) + return output_quantity - from pkg_resources import resource_filename - fn = resource_filename('openforcefield', os.path.join('data', relative_path)) - - if not os.path.exists(fn): - raise ValueError("Sorry! %s does not exist. If you just added it, you'll have to re-install" % fn) - - return fn -def normalize_molecules(molecules): +def extract_serialized_units_from_dict(input_dict): """ - Normalize all molecules in specified set. + Create a mapping of (potentially unit-bearing) quantities from a dictionary, where some keys exist in pairs like + {'length': 8, 'length_unit':'angstrom'}. - ARGUMENTS + Parameters + ---------- + input_dict : dict + Dictionary where some keys are paired like {'X': 1.0, 'X_unit': angstrom}. - molecules (list of OEMol) - molecules to be normalized (in place) + Returns + ------- + unitless_dict : dict + input_dict, but with keys ending in ``_unit`` removed. + attached_units : dict str : simtk.unit.Unit + ``attached_units[parameter_name]`` is the simtk.unit.Unit combination that should be attached to corresponding + parameter ``parameter_name``. For example ``attached_units['X'] = simtk.unit.angstrom. """ - # Add explicit hydrogens. - for molecule in molecules: - openeye.oechem.OEAddExplicitHydrogens(molecule) - - # Build a conformation for all molecules with Omega. - print("Building conformations for all molecules...") - import openeye.oeomega - omega = openeye.oeomega.OEOmega() - omega.SetMaxConfs(1) - omega.SetFromCT(True) - for molecule in molecules: - #omega.SetFixMol(molecule) - omega(molecule) - end_time = time.time() - elapsed_time = end_time - start_time - print("%.3f s elapsed" % elapsed_time) - - # Regularize all molecules through writing as mol2. - print("Regularizing all molecules...") - ligand_mol2_dirname = os.path.dirname(mcmcDbName) + '/mol2' - if( not os.path.exists( ligand_mol2_dirname ) ): - os.makedirs(ligand_mol2_dirname) - ligand_mol2_filename = ligand_mol2_dirname + '/temp' + os.path.basename(mcmcDbName) + '.mol2' - start_time = time.time() - omolstream = openeye.oechem.oemolostream(ligand_mol2_filename) - for molecule in molecules: - # Write molecule as mol2, changing molecule through normalization. - openeye.oechem.OEWriteMolecule(omolstream, molecule) - omolstream.close() - end_time = time.time() - elapsed_time = end_time - start_time - print("%.3f s elapsed" % elapsed_time) - - # Assign AM1-BCC charges. - print("Assigning AM1-BCC charges...") - start_time = time.time() - for molecule in molecules: - # Assign AM1-BCC charges. - if molecule.NumAtoms() == 1: - # Use formal charges for ions. - OEFormalPartialCharges(molecule) - else: - # Assign AM1-BCC charges for multiatom molecules. - OEAssignPartialCharges(molecule, OECharges_AM1BCC, False) # use explicit hydrogens - # Check to make sure we ended up with partial charges. - if OEHasPartialCharges(molecule) == False: - print("No charges on molecule: '%s'" % molecule.GetTitle()) - print("IUPAC name: %s" % OECreateIUPACName(molecule)) - # TODO: Write molecule out - # Delete themolecule. - molecules.remove(molecule) - - end_time = time.time() - elapsed_time = end_time - start_time - print("%.3f s elapsed" % elapsed_time) - print("%d molecules remaining" % len(molecules)) - - return - -def read_molecules(filename, verbose=True): + # TODO: Should this scheme also convert "1" to int(1) and "8.0" to float(8.0)? + from collections import OrderedDict + attached_units = OrderedDict() + unitless_dict = input_dict.copy() + keys_to_delete = [] + for key in input_dict.keys(): + if key.endswith('_unit'): + parameter_name = key[:-5] + parameter_units_string = input_dict[key] + try: + parameter_units = string_to_unit(parameter_units_string) + except Exception as e: + e.msg = "Could not parse units {}\n".format( + parameter_units_string) + e.msg + raise e + attached_units[parameter_name] = parameter_units + # Remember this key and delete it later (we break the dict if we delete a key in the loop) + keys_to_delete.append(key) + # Clean out the '*_unit' keys that we processed + for key in keys_to_delete: + del unitless_dict[key] + + return unitless_dict, attached_units + + +def attach_units(unitless_dict, attached_units): """ - Read molecules from an OpenEye-supported file. + Attach units to dict entries for which units are specified. Parameters ---------- - filename : str - Filename from which molecules are to be read (e.g. mol2, sdf) + unitless_dict : dict + Dictionary, where some items are to have units applied. + attached_units : dict [str : simtk.unit.Unit] + ``attached_units[parameter_name]`` is the simtk.unit.Unit combination that should be attached to corresponding + parameter ``parameter_name`` Returns ------- - molecules : list of OEMol - List of molecules read from file + unit_bearing_dict : dict + Updated dict with simtk.unit.Unit units attached to values for which units were specified for their keys """ + temp_dict = unitless_dict.copy() + for parameter_name, units_to_attach in attached_units.items(): + if parameter_name in temp_dict.keys(): + parameter_attrib_string = temp_dict[parameter_name] + try: + temp_dict[parameter_name] = float(parameter_attrib_string) * units_to_attach + except ValueError as e: + e.msg = ( + "Expected numeric value for parameter '{}'," + "instead found '{}' when trying to attach units '{}'\n" + ).format(parameter_name, parameter_attrib_string, units_to_attach) + raise e + + # Now check for matches like "phase1", "phase2" + c = 1 + while (parameter_name + str(c)) in temp_dict.keys(): + indexed_parameter_name = parameter_name + str(c) + parameter_attrib_string = temp_dict[indexed_parameter_name] + try: + temp_dict[indexed_parameter_name] = float( + parameter_attrib_string) * units_to_attach + except ValueError as e: + e.msg = "Expected numeric value for parameter '{}', instead found '{}' when trying to attach units '{}'\n".format( + indexed_parameter_name, parameter_attrib_string, + units_to_attach) + raise e + c += 1 + return temp_dict + + + +def detach_units(unit_bearing_dict, output_units=None): + """ + Given a dict which may contain some simtk.unit.Quantity objects, return the same dict with the Quantities + replaced with unitless values, and a new dict containing entries with the suffix "_unit" added, containing + the units. - if not os.path.exists(filename): - built_in = get_data_filename('molecules/%s' % filename) - if not os.path.exists(built_in): - raise Exception("File '%s' not found." % filename) - filename = built_in - - if verbose: print("Loading molecules from '%s'..." % filename) - start_time = time.time() - molecules = list() - input_molstream = oemolistream(filename) - - from openeye import oechem - flavor = oechem.OEIFlavor_Generic_Default | oechem.OEIFlavor_MOL2_Default | oechem.OEIFlavor_MOL2_Forcefield - input_molstream.SetFlavor(oechem.OEFormat_MOL2, flavor) - - molecule = OECreateOEGraphMol() - while OEReadMolecule(input_molstream, molecule): - # If molecule has no title, try getting SD 'name' tag - if molecule.GetTitle() == '': - name = OEGetSDData(molecule, 'name').strip() - molecule.SetTitle(name) - # Append to list. - molecule_copy = OEMol(molecule) - molecules.append(molecule_copy) - input_molstream.close() - if verbose: print("%d molecules read" % len(molecules)) - end_time = time.time() - elapsed_time = end_time - start_time - if verbose: print("%.3f s elapsed" % elapsed_time) - - return molecules - -def setPositionsInOEMol(molecule, positions): - """Set the positions in an OEMol using a position array with units from simtk.unit, i.e. from OpenMM. Atoms must have same order. - - Arguments: - --------- - molecule : OEMol - OpenEye molecule - positions : Nx3 array - Unit-bearing via simtk.unit Nx3 array of coordinates + Parameters + ---------- + unit_bearing_dict : dict + A dictionary potentially containing simtk.unit.Quantity objects as values. + output_units : dict[str : simtk.unit.Unit], optional. Default = None + A mapping from parameter fields to the output unit its value should be converted to. + For example, {'length_unit': unit.angstrom}. If no output_unit is defined for a key:value pair in which + the value is a simtk.unit.Quantity, the output unit will be the Quantity's unit, and this information + will be included in the unit_dict return value. + + Returns + ------- + unitless_dict : dict + The input smirnoff_dict object, with all simtk.unit.Quantity values converted to unitless values. + unit_dict : dict + A dictionary in which keys are keys of simtk.unit.Quantity values in unit_bearing_dict, + but suffixed with "_unit". Values are simtk.unit.Unit . """ - if molecule.NumAtoms() != len(positions): raise ValueError("Number of atoms in molecule does not match length of position array.") - pos_unitless = positions/unit.angstroms + from simtk import unit + + if output_units is None: + output_units = {} + + # initialize dictionaries for outputs + unit_dict = {} + unitless_dict = unit_bearing_dict.copy() + + for key, value in unit_bearing_dict.items(): + # If no conversion is needed, skip this item + if not isinstance(value, unit.Quantity): + continue + + # If conversion is needed, see if the user has requested an output unit + unit_key = key + '_unit' + + if unit_key in output_units: + output_unit = output_units[unit_key] + else: + output_unit = value.unit + if not (output_unit.is_compatible(value.unit)): + raise ValueError("Requested output unit {} is not compatible with " + "quantity unit {} .".format(output_unit, value.unit)) + unitless_dict[key] = value.value_in_unit(output_unit) + unit_dict[unit_key] = output_unit - coordlist = [] - for idx in range(len(pos_unitless)): - for j in range(3): - coordlist.append( pos_unitless[idx][j]) - molecule.SetCoords(OEFloatArray(coordlist)) + return unitless_dict, unit_dict -def extractPositionsFromOEMol(molecule): - """Get the positions from an OEMol and return in a position array with units via simtk.unit, i.e. foramtted for OpenMM. - Adapted from choderalab/openmoltools test function extractPositionsFromOEMOL - Arguments: + + +def serialize_numpy(np_array): + """ + Serializes a numpy array into a JSON-compatible string. Leverages the numpy.save function, + thereby preserving the shape of the input array + + from https://stackoverflow.com/questions/30698004/how-can-i-serialize-a-numpy-array-while-preserving-matrix-dimensions#30699208 + + Parameters ---------- - molecule : OEMol - OpenEye molecule + np_array : A numpy array + Input numpy array - Returns: - -------- - positions : Nx3 array - Unit-bearing via simtk.unit Nx3 array of coordinates + Returns + ------- + serialized : str + A serialized representation of the numpy array. + shape : tuple of ints + The shape of the serialized array """ - positions = unit.Quantity(numpy.zeros([molecule.NumAtoms(), 3], numpy.float32), unit.angstroms) - coords = molecule.GetCoords() - for index in range(molecule.NumAtoms()): - positions[index,:] = unit.Quantity(coords[index], unit.angstroms) - return positions + bigendian_array = np_array.newbyteorder('>') + serialized = bigendian_array.tobytes() + shape = np_array.shape + return serialized, shape + -def read_typelist(filename): +def deserialize_numpy(serialized_np, shape): """ - Read a parameter type or decorator list from a file. - Lines in these files have the format - "SMARTS/SMIRKS shorthand" - lines beginning with '%' are ignored + Deserializes a numpy array from a JSON-compatible string. + + from https://stackoverflow.com/questions/30698004/how-can-i-serialize-a-numpy-array-while-preserving-matrix-dimensions#30699208 Parameters ---------- - filename : str - Path and name of file to be read - Could be file in openforcefield/data/ - + serialized_np : str + A serialized numpy array + shape : tuple of ints + The shape of the serialized array Returns ------- - typelist : list of tuples - Typelist[i] is element i of the typelist in format (smarts, shorthand) + np_array : numpy.ndarray + The deserialized numpy array """ - if filename is None: - return None - if not os.path.exists(filename): - built_in = get_data_filename(filename) - if not os.path.exists(built_in): - raise Exception("File '%s' not found." % filename) - filename = built_in - - typelist = list() - ifs = open(filename) - lines = ifs.readlines() - used_typenames = list() - - for line in lines: - # Strip trailing comments - index = line.find('%') - if index != -1: - line = line[0:index] - - # Split into tokens. - tokens = line.split() - # Process if we have enough tokens - if len(tokens) >= 2: - smarts = tokens[0] - typename = ' '.join(tokens[1:]) - if typename not in used_typenames: - typelist.append([smarts,typename]) - used_typenames.append(typename) - else: - raise Exception("Error in file '%s' -- each entry must " - "have a unique name." % filename ) - - ifs.close() - - return typelist + import numpy as np + dt = np.dtype('float') + dt.newbyteorder('>') # set to big-endian + np_array = np.frombuffer(serialized_np, dtype=dt) + np_array = np_array.reshape(shape) + return np_array diff --git a/readthedocs.yml b/readthedocs.yml new file mode 100644 index 000000000..73ca3fef7 --- /dev/null +++ b/readthedocs.yml @@ -0,0 +1,15 @@ +# .readthedocs.yml + +build: + image: latest + +python: + version: 3.6 + setup_py_install: true + +# Build PDF in addition to default HTML and JSON +formats: + - pdf + +conda: + file: docs/environment.yml diff --git a/setup.cfg b/setup.cfg index e0f23ccc0..529f82cf6 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,7 +1,29 @@ +# Helper file to handle all configs + +[coverage:run] +# .coveragerc to control coverage.py and pytest-cov +omit = + # Omit the tests + */tests/* + # Omit generated versioneer + openforcefield/_version.py + +[yapf] +# YAPF, in .style.yapf files this shows up as "[style]" header +COLUMN_LIMIT = 119 +INDENT_WIDTH = 4 +USE_TABS = False + +[flake8] +# Flake8, PyFlakes, etc +max-line-length = 119 + [versioneer] +# Automatic version numbering scheme VCS = git style = pep440 versionfile_source = openforcefield/_version.py versionfile_build = openforcefield/_version.py -tag_prefix = +tag_prefix = '' +# TODO: parentdir_prefix is left empty in the cookiecutter setup.cfg. parentdir_prefix = openforcefield- diff --git a/setup.py b/setup.py index 6faa59bdb..c9fa86db4 100644 --- a/setup.py +++ b/setup.py @@ -25,6 +25,7 @@ def find_package_data(data_root, package_root): 'openforcefield', 'openforcefield/tests', 'openforcefield/data', + 'openforcefield/topology', 'openforcefield/typing', 'openforcefield/typing/chemistry', 'openforcefield/typing/engines', diff --git a/utilities/convert_frosst/check_different_smirnoffs.ipynb b/utilities/convert_frosst/check_different_smirnoffs.ipynb index aef35f7f5..6d11177a0 100755 --- a/utilities/convert_frosst/check_different_smirnoffs.ipynb +++ b/utilities/convert_frosst/check_different_smirnoffs.ipynb @@ -190,7 +190,7 @@ "# Input and output info\n", "#infile = 'example.frcmod' # smirnoffish frcmod file to convert\n", "infile = 'smirnoffishFrcmod.parm99Frosst.txt' # smirnoffish frcmod file to convert\n", - "ffxmlFile = 'smirnoff99Frosst.offxml'\n", + "ffxmlFile = 'smirnoff99FrosstFrcmod.offxml'\n", "template = 'template.offxml' # Template FFXML file without parameters (but with remainder of contents)" ] }, @@ -236,8 +236,7 @@ }, "outputs": [], "source": [ - "current_smirnoff = \"forcefield/smirnoff99Frosst.offxml\"\n", - "ref_ff = ForceField(current_smirnoff)" + "ref_ff = ForceField('smirnoff99Frosst.offxml')" ] }, { diff --git a/utilities/convert_frosst/parameter_usage.ipynb b/utilities/convert_frosst/parameter_usage.ipynb index 2fa81f97f..2bd9aaf28 100755 --- a/utilities/convert_frosst/parameter_usage.ipynb +++ b/utilities/convert_frosst/parameter_usage.ipynb @@ -295,7 +295,7 @@ "# Input and output info\n", "#infile = 'example.frcmod' # smirnoffish frcmod file to convert\n", "infile = 'smirnoffishFrcmod.parm99Frosst.txt' # smirnoffish frcmod file to convert\n", - "ffxmlFile = 'smirnoff99Frosst.offxml'\n", + "ffxmlFile = 'smirnoff99FrosstFrcmod.offxml'\n", "template = 'template.offxml' # Template FFXML file without parameters (but with remainder of contents)" ] }, @@ -684,13 +684,13 @@ { "ename": "NameError", "evalue": "name 'mols_with_param' is not defined", - "output_type": "error", "traceback": [ "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", "\u001b[0;31mNameError\u001b[0m Traceback (most recent call last)", "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m()\u001b[0m\n\u001b[1;32m 8\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 9\u001b[0m \u001b[0;31m# Correct with list of molecules is less than upper limit\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 10\u001b[0;31m \u001b[0;32mif\u001b[0m \u001b[0mlen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmols_with_param\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m<\u001b[0m \u001b[0mupperlimit\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 11\u001b[0m \u001b[0mupperlimit\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mlen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmols_with_param\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 12\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n", "\u001b[0;31mNameError\u001b[0m: name 'mols_with_param' is not defined" - ] + ], + "output_type": "error" } ], "source": [