Bugfix release

0.2.1

This release features various documentation fixes, minor bugfixes, and code cleanup.

See our installation instructions.

Please report bugs, request features, or ask questions through our issue tracker.

Please note that there may still be some changes to the API prior to a stable 1.0 release.

Bugfixes

• PR #267: Add neglected <ToolkitAM1BCC> tag to the SMIRNOFF 0.2 spec
• PR #258: General cleanup and removal of unused/inaccessible code.
• PR #244: Improvements and typo fixes for BRD4:inhibitor benchmark

Initial RDKit support

0.2.0

This version of the toolkit introduces RDKit support and many new features on the way to a stable 1.0 release.

See our installation instructions.

Please report bugs, request features, or ask questions through our issue tracker.

Please note that there may still be some changes to the API prior to a stable 1.0 release.

Major 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 ForceField implementation
• Implementation of modular ParameterHandler classes which process the topology to add all necessary forces to the system..
• Implementation of modular ParameterIOHandler classes for reading/writing different serialized SMIRNOFF forcefield representations
• Introduction of Molecule and Topology classes for representing molecules and biomolecular systems
• New ToolkitWrapper interface to RDKit, OpenEye, and AmberTools cheminformatics toolkits, managed by ToolkitRegistry
• API improvements to more closely follow PEP8 guidelines
• Improved documentation and examples

Version 0.1.0

This is an early preview release of the openforcefield 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

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.

Version 0.0.4

Most significantly, this release adds a small but nonzero set of LJ parameters to smirnoff99Frosst, as per (soon forthcoming) SMIRNOFF paper draft/discussion. Additional changes are:

• Minor fixes to cyclobutane parameters in smirnoff99Frosst
• Versioneer support
• Documentation via sphinx
• Rename .ffxml files to .offxml to avoid confusion with "normal" OpenMM .ffxml files, which are a totally different format
• Remove wildcard generics from smirnoff99Frosst; add a separate .offxml file with (improved) generics in case anyone wants to use these.

Version 0.0.3

This version:

• Fixes a compatibility issue with updated NetworkX
• Makes extensive updates to documentation
• Adds a considerable number of examples
• Makes OpenMM topologies generated preserve bond order
• Adds monovalent ion parameters
• Changes use of a SMIRKS decorator (R vs x) in smirnoff99Frosst for better consistency with non-OpenEye SMARTS/SMIRKS parsers
• Removes an extra application of OEAssignImplicitHydrogens which could in some cases result in openforcefield changing the protonation state of a molecule

Version 0.0.2

This version:

• Finishes migration of many tools from smarty to openforcefield
• Removes outdated examples and data
• Adds support for tip3p water and constraints, tests for the same; adds water monomers
• Extensively updates documentation
• Updates Jupyter notebooks
• Makes some fixes to chemical environments
• Fixes a bug where vdW parameters for mixtures consisting of multiple references molecules could get scrambled (and adds a test for this)
• Fixes a typo in descring the SMIRNOFF format (formerly SMIRFF) and finishes name change from SMIRFF to SMIRNOFF
• Adds an example of generating a mixed force field for a protein-ligand complex (AMBER protein force field, SMIRNOFF ligand)

0.0.1

Experimental initial release for testing conda build infrastructure.