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Tactic MMIC for molecular docking using AutoDock Vina
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MolSSI/mmic_autodock_vina
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This is part of theMolSSI Molecular Mechanics Interoperable Components (MMIC) project. This package provides aprovides an engine component for running molecular docking withAutoDock Vina.
This is part of theMolSSI Molecular Mechanics Interoperable Components (MMIC) project. This package provides molecular docking compute viaAutoDock Vina program.
# Import MM molecule data modelfrommmelemental.models.moleculeimportMolecule# Construct MM moleculesreceptor=Molecule.from_file(pdb_file)ligand=Molecule.from_data(smiles_code,dtype="smiles")# Construct docking input data from MMSchema moleculesdock_input= {"mol": {"ligand":ligand,"receptor":receptor},"search_space": (xmin,xmax,ymin,ymax,zmin,zmax),"search_space_units":"angstrom",}
# Import docking simulation component for autodock vinafrommmic_autodock_vina.components.autodock_componentimportAutoDockComponent# Run autodock vinadock_output=AutoDockComponent.compute(dock_input)# Extract outputscores,ligands,flex=dock_output.scores,dock_output.poses.ligand,dock_output.poses.receptor
Copyright (c) 2021, MolSSI
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