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meekovina

python script easy to use Autodock Vina basic docking simulation

License

This package is distributed under the MIT License.

Tutorial

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

Requirements

  1. python >= 3.7
  2. pyyaml (https://pyyaml.org/)
  3. numpy (https://numpy.org/)
  4. scipy (https://scipy.org/)
  5. pandas (https://pandas.pydata.org/)
  6. rdkit (https://www.rdkit.org/)
  7. meeko >= 0.4.0 (https://github.com/forlilab/Meeko)
  8. AutoDock-Vina 1.2.3 binary (https://github.com/ccsb-scripps/AutoDock-Vina/releases/tag/v1.2.3 )

Optional

  1. vina 1.2.3 python API (https://github.com/ccsb-scripps/AutoDock-Vina )

Install

Install with pip

  • 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 .

Install with conda virtual environment

  • 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 .

Command usage

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)

Examples

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".

Exmaples of command line usage

  • 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

Exmaples of yaml input usage

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.

Author