pestifer.subcommands.make_ligand_mol2 module¶
The make-ligand-mol2 subcommand: generate CGenFF-ready mol2 files for every HETATM ligand in a PDB whose resname is not already defined in the loaded CHARMM force field.
The resulting mol2 files are intended as input either to a local
cgenff binary or to the CGenFF web tool (cgenff.com). The same
internals are reused by the build workflow when it encounters an
unknown ligand.
- class pestifer.subcommands.make_ligand_mol2.MakeLigandMol2Subcommand(name: 'str' = 'make-ligand-mol2', aliases: list = <factory>, log_file: str = 'pestifer_diagnostics.log', short_help: 'str' = 'generate CGenFF-ready mol2 files for unknown HETATM ligands in a PDB', long_help: 'str' = 'For each HETATM residue in the input PDB whose resname is not covered by the loaded CHARMM force-field topologies, fetch a SMILES from the RCSB Chemical Component Dictionary, protonate the ligand at the chosen pH (default 7.4) using RDKit + Dimorphite-DL, and write a Tripos mol2 ready to feed the CGenFF binary or web tool. SOURCE may be a 4-letter RCSB PDB code or a path to a local .pdb file.', func_returns_type: 'type' = <class 'dict'>, parser: argparse.ArgumentParser = None)[source]¶
Bases:
Subcommand- add_subparser(subparsers)[source]¶
Adds the subcommand parser to the given subparsers. Subclasses declare arguments here, after a super().add_subparser() call.
- static func(args: Namespace, **kwargs)[source]¶
the function that executes the subcommand. Subclasses must implement this method.
- long_help: str = 'For each HETATM residue in the input PDB whose resname is not covered by the loaded CHARMM force-field topologies, fetch a SMILES from the RCSB Chemical Component Dictionary, protonate the ligand at the chosen pH (default 7.4) using RDKit + Dimorphite-DL, and write a Tripos mol2 ready to feed the CGenFF binary or web tool. SOURCE may be a 4-letter RCSB PDB code or a path to a local .pdb file.'¶
description