python script easy to use Autodock Vina basic docking simulation
This package is distributed under the MIT License.
You can try tutorial of meekovina to know how to install and run:
https://colab.research.google.com/github/mkatouda/meekovina/blob/main/meekovina_tutorial_jp.ipynb
- python >= 3.7
- pyyaml (https://pyyaml.org/)
- numpy (https://numpy.org/)
- scipy (https://scipy.org/)
- pandas (https://pandas.pydata.org/)
- rdkit (https://www.rdkit.org/)
- meeko >= 0.4.0 (https://github.com/forlilab/Meeko)
- AutoDock-Vina 1.2.3 binary (https://github.com/ccsb-scripps/AutoDock-Vina/releases/tag/v1.2.3 )
- vina 1.2.3 python API (https://github.com/ccsb-scripps/AutoDock-Vina )
- Install AutoDock Vina binary
wget https://github.com/ccsb-scripps/AutoDock-Vina/releases/download/v1.2.3/vina_1.2.3_linux_x86_64
mkdir ~/bin
mv ./vina_1.2.3_linux_x86_64 ~/bin/vina
chmod 755 ~/bin/vina
export PATH=~/bin/vina:$PATH
- Install from github
pip install git+https://github.com/mkatouda/meekovina.git- Local install
git clone https://github.com/mkatouda/meekovina.git
cd meekovina
pip install .- Create conda virtual environment
conda create -n py310-meekovina python=3.10
conda activate py310-meekovina
- Run the following command to install required conda packages
conda install -c conda-forge rdkit vina
- Install from github
pip install git+https://github.com/mkatouda/meekovina.git- Local install
git clone https://github.com/mkatouda/meekovina.git
cd meekovina
pip install .usage: meekovina [-h] [-i INP] [-l LIGAND] [--input_smiles INPUT_SMILES]
[-r RECEPTOR] [-lr REFLIGAND] [-o OUT] [-od OUTDIR]
[-cx CENTER_X] [-cy CENTER_Y] [-cz CENTER_Z]
[-sx SIZE_X] [-sy SIZE_Y] [-sz SIZE_Z]
[-c CPU] [--scoring SCORING] [--seed SEED]
[--exhaustiveness EXHAUSTIVENESS] [--max_evals MAX_EVALS]
[--num_modes NUM_MODES] [--min_rmsd MIN_RMSD]
[--energy_range ENERGY_RANGE] [--spacing SPACING]
[--verbosity VERBOSITY] [--score_only] [--local_only]
[--exec EXEC] [--bin_path BIN_PATH] [--boxauto]
[--gybox_ratio GYBOX_RATIO] [-v]
optional arguments:
-h, --help show this help message and exit
-i INP, --inp INP yaml style input file, overwriting argument values (default: None)
-l LIGAND, --ligand LIGAND
ligand (PDBQT, MOL, SDF, MOL2, PDB) (default: None)
--input_smiles INPUT_SMILES
SMILES string (Need to put the atom you want to extend at the end of the string) (default: None)
-r RECEPTOR, --receptor RECEPTOR
rigid part of the receptor (PDBQT) (default: None)
-lr REFLIGAND, --refligand REFLIGAND
reference ligand (PDBQT, MOL, SDF, MOL2, PDB) to determine the box center (default: None)
-o OUT, --out OUT output models (PDBQT), the default is chosen based on the ligand file name (default: None)
-od OUTDIR, --outdir OUTDIR
make output directry if argument is specified (default: None)
-cx CENTER_X, --center_x CENTER_X
X coordinate of the center (default: None)
-cy CENTER_Y, --center_y CENTER_Y
Y coordinate of the center (default: None)
-cz CENTER_Z, --center_z CENTER_Z
Z coordinate of the center (default: None)
-sx SIZE_X, --size_x SIZE_X
size in the X dimension (Angstroms) (default: 22.5)
-sy SIZE_Y, --size_y SIZE_Y
size in the Y dimension (Angstroms) (default: 22.5)
-sz SIZE_Z, --size_z SIZE_Z
size in the Z dimension (Angstroms) (default: 22.5)
-c CPU, --cpu CPU the number of CPUs to use (the default is to try todetect the number of CPUs or, failing that, use 1) (default: 4)
--scoring SCORING force field name: vina(default), ad4, vinardo (default: vina)
--seed SEED explicit random seed (default: 0)
--exhaustiveness EXHAUSTIVENESS
exhaustiveness of the global search(roughly proportional to time): 1+ (default: 8)
--max_evals MAX_EVALS
number of evaluations in each MC run (if zero,which is the default, the number of MC steps isbased on heuristics) (default: 0)
--num_modes NUM_MODES
maximum number of binding modes to generate (default: 9)
--min_rmsd MIN_RMSD minimum RMSD between output poses (default: 1)
--energy_range ENERGY_RANGE
maximum energy difference between the best bindingmode and the worst one displayed (kcal/mol) (default: 3)
--spacing SPACING grid spacing (Angstrom) (default: 0.375)
--verbosity VERBOSITY
verbosity (0=no output, 1=normal, 2=verbose) (default: 1)
--score_only evaluate the energy of the current pose or poses without strucutre optimization (default: False)
--local_only evaluate the energy of the current pose or poses with local structure optimization (default: False)
--exec EXEC select AutoDock-Vina executer (default: bin)
--bin_path BIN_PATH AutoDock-Vina binary path (default: vina)
--boxauto enable automatic box determination algorithm (default: False)
--gybox_ratio GYBOX_RATIO
scaling factor of radius of gyration to determine of docking box with automatic box determination algorithm (default: 2.5)
-v, --verbose verbose mode (default: False)
Input files of example jobs are loated at "meekovina/example/input". You can example jobs using job script files "meekovina_com.sh" and "meekovina_yml.sh" located at "meekovina/example".
- Ligand input from file
meekovina -l LIGAND -r RECEPTOR -o OUTPUT -cx CENTER_X -cy CENTER_Y -cz CENTER_Z
- Ligand input from SMILES
meekovina --input_smiles INPUT_SMILES -r RECEPTOR -o OUTPUT -cx CENTER_X -cy CENTER_Y -cz CENTER_Z
Prepare input yaml file input.yml:
ligand: './inputs/1iep_ligand.mol'
refligand: './inputs/1iep_ligand.mol'
receptor: './inputs/1iep_receptorH.pdbqt'
out: '1iep_ligand'
outdir: 'outputs'
size_x: 20.0
size_y: 20.0
size_z: 20.0
cpu: 2
exhaustiveness: 3
num_modes: 9
seed: 1234
Then, run meekivina in command line:
meekovina -i input.yml
Keywards of yaml file are the same in the name of command line options.
See above explanation of command line options.
- Michio Katouda ([email protected])