gmol.base.data.mmcif.filter

Functions

filter_mmcif(assembly, chem_comp_dict[, ...])
filter_structure(assembly, exptl_method, ...)
ligand_atom_mask(assembly)
new_atom_mask(assembly)
remove_all_unknown_chains(assembly)
remove_clashing_chains(assembly[, ...])
remove_crystallization_aids(assembly, method)
remove_excluded_ligands(assembly)
remove_ions(assembly)
remove_large_ca_distance(assembly[, ...])
remove_leaving_atoms(assembly, chem_comp_dict)
remove_min_resolved_chains(assembly[, ...])
remove_non_ccd_atoms(assembly, chem_comp_dict)
remove_waters(assembly)

new_atom_mask(assembly: Assembly) → ndarray[tuple[Any, ...], dtype[bool]]

remove_min_resolved_chains(assembly: Assembly, min_resolved: int = 4)

remove_waters(assembly: Assembly) → ndarray[tuple[Any, ...], dtype[bool]]

remove_all_unknown_chains(assembly: Assembly)

remove_clashing_chains(assembly: Assembly, clash_threshold: float = 1.7, clash_cutoff: float = 0.3)

remove_non_ccd_atoms(assembly: Assembly, chem_comp_dict: dict[str, ChemComp])

remove_large_ca_distance(assembly: Assembly, max_distance: float = 10)

ligand_atom_mask(assembly: Assembly) → ndarray[tuple[Any, ...], dtype[bool]]

remove_crystallization_aids(assembly: Assembly, method: str)

remove_excluded_ligands(assembly: Assembly)

remove_ions(assembly: Assembly)

remove_leaving_atoms(assembly: Assembly, chem_comp_dict: dict[str, ChemComp])

filter_structure(assembly: Assembly, exptl_method: str, chem_comp_dict: dict[str, ChemComp], is_test: bool = False) → ndarray[tuple[Any, ...], dtype[bool]]

filter_mmcif(assembly: Assembly, chem_comp_dict: dict[str, ChemComp], cutoff_date: date = datetime.date(2021, 9, 30), max_resolution: float = 9.0, max_chains: int = 300, is_test: bool = False) → Assembly | None