pestifer.charmmff package¶
This package provides classes and methods for handling CHARMM force field files. It interfaces directly with the tarballed CHARMM force field in its freshly downloaded state, stored in the pestifer.resources subpackage. It includes functionality for handling atom types, residues, and patches. It also provides capabilities for generating PDB files for residues like lipids for use in membrane-packing using packmol.
Subpackages¶
- pestifer.charmmff.ligand_paramgen package
Submodules¶
- pestifer.charmmff.charmmffcontent module
CHARMMFFContentCHARMMFFContent.charmmff_pathCHARMMFFContent.tarfilenameCHARMMFFContent.filenamemapCHARMMFFContent.add_custom_directory()CHARMMFFContent.charmmff_filetype()CHARMMFFContent.checkout_pdb()CHARMMFFContent.clean_local_charmmff_files()CHARMMFFContent.copy_charmmfile_local()CHARMMFFContent.deprovision()CHARMMFFContent.find_resis_and_patches()CHARMMFFContent.get_filename()CHARMMFFContent.get_pres()CHARMMFFContent.get_resi()CHARMMFFContent.get_resnames_of_streamID()CHARMMFFContent.get_topfile_of_resname()CHARMMFFContent.provision()CHARMMFFContent.provision_pdbrepository()CHARMMFFContent.provision_residueobjects()
CHARMMFFResiTopCollectionCHARMMFFStreamIDcharmmff_version_key()extract_mass_lines()extract_resi_pres_blocks()parse_conditional_script()
- pestifer.charmmff.charmmffprm module
CharmmAngleParamCharmmBondParamCharmmCMAPParamCharmmDihedralParamCharmmImproperParamCharmmNBFixParamCharmmNonbondedParamCharmmParamFileCharmmParamFile.anglesCharmmParamFile.bondsCharmmParamFile.cmapsCharmmParamFile.dihedralsCharmmParamFile.extract_for_atomtypes()CharmmParamFile.from_file()CharmmParamFile.from_text()CharmmParamFile.impropersCharmmParamFile.merge()CharmmParamFile.nbfixCharmmParamFile.nonbondedCharmmParamFile.nonbonded_headerCharmmParamFile.summary()CharmmParamFile.write()
- pestifer.charmmff.charmmfftop module
CharmmAngleCharmmAngleListCharmmAtomCharmmAtomDictCharmmAtomListCharmmBondCharmmBondListCharmmDeleteCharmmDeleteListCharmmDihedralCharmmDihedralListCharmmICCharmmICListCharmmMassCharmmMassDictCharmmMassListCharmmResiCharmmResi.DeleteCharmmResi.ICsCharmmResi.atomdictCharmmResi.atomsCharmmResi.atoms_in_groupCharmmResi.blockstringCharmmResi.bondsCharmmResi.chargeCharmmResi.copy_ICs_from()CharmmResi.detergent_annotate()CharmmResi.error_codeCharmmResi.formula()CharmmResi.from_blockstring()CharmmResi.generic_lipid_annotate()CharmmResi.ispatchCharmmResi.keyCharmmResi.lipid_annotate()CharmmResi.massCharmmResi.metadataCharmmResi.model_annotate()CharmmResi.name_from_blockstring()CharmmResi.num_atoms()CharmmResi.resnameCharmmResi.set_mass()CharmmResi.show_error()CharmmResi.source_fileCharmmResi.sterol_annotate()CharmmResi.synonymCharmmResi.to_file()CharmmResi.to_graph()CharmmResi.to_psfgen()
CharmmResiDictCharmmResiList
- pestifer.charmmff.graphhelpers module
anchor_paths()carbon_component_from_neighbor()carbon_neighbors_outside_S()count_unsats_cc()cycle_atoms_heavy()elem()head_tail_pairs()heavy_degree()heavy_neighbors()heavy_only_nodes()is_C()is_H()is_N()is_O()is_P()is_S()label_lipid_chains_heavy_aware()leafs_in()mark_cc_doubles_by_degree()seed_set()
- pestifer.charmmff.make_pdb_collection module
- pestifer.charmmff.pdbrepository module