This is part of the MolSSI Molecular Mechanics Interoperable Components (MMIC) project. This package provides molecular docking compute via AutoDock Vina program.
# Import MM molecule data model
from mmelemental.models.molecule import Molecule
# Construct MM molecules
receptor_data = Molecule.from_file(pdb_file)
ligand_data = Molecule.from_data(smiles_code)
# Import docking data model compliant with MMSchema
from mmelemental.models.app.docking import DockInput
# Construct docking input data from MMSchema molecules
dock_input = DockInput(
ligand=ligand_data,
receptor=receptor_data,
searchSpace=(xmin, xmax, ymin, ymax, zmin, zmax),
)
# Import docking simulation component for autodock vina
from mmic_autodock.components.autodock_component import AutoDockComponent
# Run autodock vina
dock_output = AutoDockComponent.compute(dock_input)
# Extract output
affinity, ligands = dock_output.scores, dock_output.ligands
Copyright (c) 2021, MolSSI
Project based on the Computational Molecular Science Python Cookiecutter version 1.1.