mmic_pdb

This is part of the MolSSI Molecular Mechanics Interoperable Components (MMIC) project. This package uses Peter Eastman's PDBFixer to extract, fix, and/or convert PDB files to MMSchema molecules.

Code snippet

from mmic_pdb.component import PdbFixerComponent

inp = {
    "pdbid": pdbid,
    "add_atoms": "all", # add all missing atoms
    "keep_hetero": "none", # remove all hetero atoms
    "std_residues": True, # convert non-std residues to the PDB std
}

# Execute component
outp = PdbFixerComponent.compute(inp)

# Extract log info and MMSchema molecule
log, mol = outp.log, outp.molecule

Copyright

Copyright (c) 2021, MolSSI

Acknowledgements

Project based on the Computational Molecular Science Python Cookiecutter version 1.5.