pestifer.subcommands.make_pdbcollection module

The make-pdb-collection subcommand. This allows a user to generate their own collection of sample PDB files for residues defined in the CHARMM force field (or in files that have CHARMM-format RESI blocks). These sample PDB’s are specifically used as inputs to packmol.

class pestifer.subcommands.make_pdbcollection.MakePDBCollectionSubcommand(name: str = 'make-pdb-collection', aliases: list = <factory>, log_file: str = 'pestifer_diagnostics.log', short_help: str = 'create a PDB collection from a set of input files', long_help: str = 'Generate a PDB collection from a list of PDB files or IDs.', func_returns_type: type = <class 'bool'>, parser: argparse.ArgumentParser = None)

Bases: Subcommand

add_subparser(subparsers)

Adds the subcommand parser to the given subparsers. Subclasses declare arguments here, after a super().add_subparser() call.

static func(args: Namespace, **kwargs)

Create a PDB collection from a set of input files.

long_help: str = 'Generate a PDB collection from a list of PDB files or IDs.'

description

name: str = 'make-pdb-collection'

subcommand name

short_help: str = 'create a PDB collection from a set of input files'

help string