gmol.base.data.mmcif.input#

Classes

BondClass(*values)

BondOrder(*values)

ExtraBond(src, dst, bond_order, bond_class)

ExtraBondPartner(chain_id, res_idx, atom_id, ...)

Input(polymers, ligands, extra_bonds, ...)

NonPolymerLigand(entity_id, chain_id, ...)

PolymerChain(mol_type, entity_id, chain_id, ...)

PolymerConstants(restype_3_to_1, ...)

Functions

build_input(assembly, ccd[, split_modified, ...])

build_input_from_mmcif(mmcif_path, ccd_comp)

load_ccd_dict_json(file_path)

process_connections(assembly, modres_atom_map)

process_ligand_chain(assembly, chain)

process_polymer_chain(assembly, chain, ccd)

class PolymerConstants(restype_3_to_1: dict[str, str], restype_order_with_x: dict[str, int], backbone: set[str], modres_backbone_3: str, bb_src_atom: str, bb_src_leaving: list[str], bb_dst_atom: str, bb_dst_leaving: list[str], max_res_atoms: int, _modres_backbone_1: InitVar[str], _res_to_atom: InitVar[dict[str, list[str]]])#
restype_3_to_1: dict[str, str]#
restype_order_with_x: dict[str, int]#
backbone: set[str]#
modres_backbone_3: str#
bb_src_atom: str#
bb_src_leaving: list[str]#
bb_dst_atom: str#
bb_dst_leaving: list[str]#
max_res_atoms: int#
residue_atom_idxs: dict[str, dict[str, int]]#
restype_modres_backbone: int#
restype_x: int#
class BondOrder(*values)#

Bases: IntEnum

other = 0#
single = 1#
double = 2#
triple = 3#
quadruple = 4#
aromatic = 5#
classmethod from_rdkit_bond_type(bond_type: BondType)#
to_rdkit_bond_type()#
classmethod from_mmcif_value_order(value_order: int)#
class BondClass(*values)#

Bases: IntEnum

unknown = 0#
covalent = 1#
disulfide = 2#
hydrogen = 3#
metal_coordinate = 4#
classmethod from_mmcif_conn_type(conn_type: str)#
class PolymerChain(mol_type: MolType, entity_id: str, chain_id: str, auth_asym_id: str, restype: ndarray[tuple[Any, ...], dtype[int8]], chem_comp_raw: ndarray[tuple[Any, ...], dtype[str_]], atom_coords: ndarray[tuple[Any, ...], dtype[float64]], atom_b_factors: ndarray[tuple[Any, ...], dtype[float64]], residue_ids: list[ResidueId | None])#
mol_type: MolType#
entity_id: str#
chain_id: str#
auth_asym_id: str#

PDB auth_asym_id (author chain id); same as Assembly.Chain.auth_asym_id.

restype: ndarray[tuple[Any, ...], dtype[int8]]#
chem_comp_raw: ndarray[tuple[Any, ...], dtype[str_]]#
atom_coords: ndarray[tuple[Any, ...], dtype[float64]]#
atom_b_factors: ndarray[tuple[Any, ...], dtype[float64]]#
residue_ids: list[ResidueId | None]#
class NonPolymerLigand(entity_id: str, chain_id: str, auth_asym_id: str, smiles: str, atom_ids: ndarray[tuple[Any, ...], dtype[str_]], atom_coords: ndarray[tuple[Any, ...], dtype[float64]], atom_b_factors: ndarray[tuple[Any, ...], dtype[float64]])#
entity_id: str#
chain_id: str#
auth_asym_id: str#

PDB auth_asym_id (author chain id); same as Assembly.Chain.auth_asym_id.

smiles: str#
atom_ids: ndarray[tuple[Any, ...], dtype[str_]]#
atom_coords: ndarray[tuple[Any, ...], dtype[float64]]#
atom_b_factors: ndarray[tuple[Any, ...], dtype[float64]]#
class ExtraBondPartner(chain_id: str, res_idx: int, atom_id: str, leaving_atoms: list[str] = <factory>)#
chain_id: str#
res_idx: int#
atom_id: str#
leaving_atoms: list[str]#
class ExtraBond(src: ExtraBondPartner, dst: ExtraBondPartner, bond_order: BondOrder, bond_class: BondClass, bond_stereo_EZ: int = 0)#
src: ExtraBondPartner#
dst: ExtraBondPartner#
bond_order: BondOrder#
bond_class: BondClass#
bond_stereo_EZ: int = 0#
static stereo_from_mmcif(pdbx_stereo_config: str | None)#
class Input(polymers: list[PolymerChain], ligands: list[NonPolymerLigand], extra_bonds: list[ExtraBond], release_date: date, resolution: float, is_distillation: bool)#
polymers: list[PolymerChain]#
ligands: list[NonPolymerLigand]#
extra_bonds: list[ExtraBond]#
release_date: date#
resolution: float#
is_distillation: bool#
process_polymer_chain(assembly: Assembly, chain: Chain, ccd: dict[str, ChemComp], split_modified: bool = False, well_known_atoms: Set[str] = frozenset({'HXT', 'OXT'}))#
process_ligand_chain(assembly: Assembly, chain: Chain)#
process_connections(assembly: Assembly, modres_atom_map: dict[_ModresFrom, _ModresTo]) → list[ExtraBond]#
build_input(assembly: Assembly, ccd: dict[str, ChemComp], split_modified: bool = False, well_known_atoms: Set[str] = frozenset({'HXT', 'OXT'})) → Input#
build_input_from_mmcif(mmcif_path: str, ccd_comp: dict[str, ChemComp]) → Input | None#
load_ccd_dict_json(file_path: Path) → dict[str, ChemComp]#
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