Structure class
Methods
- def add_conect(self, serial1: int, serial2: int, order: int) -> None
- def add_entity_types(self, overwrite: bool = False) -> None
- def add_model(self, model: Model, pos: int = -1) -> Model
- def assign_best_sequences(self, fasta_sequences: typing.List[str]) -> None
- def assign_label_seq_id(self, force: bool = False) -> None
- def assign_serial_numbers(self, numbered_ter: bool = False) -> None
- def assign_subchains(self, force: bool = False, fail_if_unknown: bool = True) -> None
- def calculate_box(self, margin: float = 0.0) -> PositionBox
- def calculate_fractional_box(self, margin: float = 0.0) -> FractionalBox
- def clear_conect(self, /) -> None
- def clear_sequences(self, /) -> None
- def clone(self, /) -> Structure
- def deduplicate_entities(self, /) -> None
- def ensure_entities(self, /) -> None
- def expand_ncs(self, how: HowToNameCopiedChain, merge_dist: float = 0.2) -> None
- def find_connection(self, partner1: AtomAddress, partner2: AtomAddress) -> Connection
- def find_connection_by_cra(self, cra1: CRA, cra2: CRA, ignore_segment: bool = False) -> Connection
- def find_or_add_model(self, name: str) -> Model
- def find_spacegroup(self, /) -> SpaceGroup
- def get_entity(self, subchain: str) -> Entity
- def get_entity_of(self, subchain: ResidueSpan) -> Entity
- def make_minimal_pdb(self, /) -> str
- def make_mmcif_block(self, groups: MmcifOutputGroups = MmcifOutputGroups(True)) -> cif.Block
- def make_mmcif_document(self, groups: MmcifOutputGroups = MmcifOutputGroups(True)) -> cif.Document
- def make_mmcif_headers(self, /) -> cif.Block
- def make_pdb_headers(self, /) -> str
- def make_pdb_string(self, options: PdbWriteOptions = PdbWriteOptions()) -> str
- def merge_chain_parts(self, min_sep: int = 0) -> None
- def remove_alternative_conformations(self, /) -> None
- def remove_empty_chains(self, /) -> None
- def remove_hydrogens(self, /) -> None
- def remove_ligands_and_waters(self, /) -> None
- def remove_waters(self, /) -> None
- def renumber_models(self, /) -> None
- def setup_cell_images(self, /) -> None
- def setup_entities(self, /) -> None
- def shorten_chain_names(self, /) -> None
- def standardize_crystal_frame(self, /) -> None
- def store_deuterium_as_fraction(self, arg0: bool, /) -> None
- def transform_to_assembly(self, assembly_name: str, how: HowToNameCopiedChain, keep_spacegroup: bool = False, merge_dist: float = 0.2) -> None
- def update_mmcif_block(self, block: cif.Block, groups: MmcifOutputGroups = MmcifOutputGroups(True)) -> None
- def write_minimal_pdb(self, path: str) -> None
- def write_pdb(self, arg0: str, arg1: PdbWriteOptions, /) -> None
- def write_pdb(self, path: str, **kwargs) -> None
Special methods
- def __delitem__(self, index: int) -> None
- def __delitem__(self, arg0: slice, /) -> None
- def __delitem__(self, name: str) -> None
- def __getitem__(self, index: int) -> Model
- def __getitem__(self, name: str) -> Model
- def __init__(self, /) -> None
- def __iter__(self, /) -> typing.Iterator
- def __len__(self, /) -> int
- def __repr__(self, /) -> str
- def __setitem__(self, arg0: int, arg1: Model, /) -> None
Properties
- assemblies: AssemblyList get set
- cell: UnitCell get set
- cispeps: typing.List[CisPep] get set
- connections: ConnectionList get set
- entities: EntityList get set
- has_d_fraction: bool get set
- has_origx: bool get set
- helices: HelixList get set
- info: InfoMap get set
- input_format: CoorFormat get set
- meta: Metadata get set
- mod_residues: typing.List[ModRes] get set
- name: str get set
- ncs: NcsOpList get set
- origx: Transform get
- raw_remarks: typing.List[str] get set
- resolution: float get set
- sheets: SheetList get set
- spacegroup_hm: str get set