This is part of the MolSSI Molecular Mechanics Interoperable Components (MMIC) project. This package provides a provides an engine component for running molecular docking with AutoDock Vina.

AutoDock Vina Component

This is part of the MolSSI Molecular Mechanics Interoperable Components (MMIC) project. This package provides molecular docking compute via AutoDock Vina program.

Preparing Input

# Import MM molecule data model
from mmelemental.models.molecule import Molecule

# Construct MM molecules
receptor = Molecule.from_file(pdb_file)
ligand   = Molecule.from_data(smiles_code, dtype="smiles")

# Construct docking input data from MMSchema molecules
dock_input = {
    "mol": {"ligand": ligand, "receptor": receptor},
    "search_space": (xmin, xmax, ymin, ymax, zmin, zmax),
    "search_space_units": "angstrom",
}

Running Docking with AutoDock Vina component

# Import docking simulation component for autodock vina
from mmic_autodock_vina.components.autodock_component import AutoDockComponent

# Run autodock vina
dock_output = AutoDockComponent.compute(dock_input)

# Extract output
scores, ligands, flex = dock_output.scores, dock_output.poses.ligand, dock_output.poses.receptor
    

Copyright

Copyright (c) 2021, MolSSI

Acknowledgements

Project based on the Computational Molecular Science Python Cookiecutter version 1.1.