gmol.base.data.mmcif.assembly#

Classes

Assembly(*, metadata, coords, ...], ...)

AssemblyAtom(atom_idx, residue_id, ...[, ...])

AssemblyConnection(src_idx, dst_idx, ...)

Branch(ptnr1, ptnr2, order)

BranchPartner(seq_id, atom_id, ...)

Chain(chain_id, auth_asym_id, entity_id, ...)

MolType(*values)

Residue(residue_id, chem_comp, atom_idxs)

ResidueId(chain_id, seq_id[, ins_code])

SequenceToResidue(comp_id, seq_id, res_id)

Transformation(matrix, vector)

Functions

expand_ops(operations, sym_ops)

load_one_assembly(file[, assembly_id])

mmcif_assemblies(data, ccd[, assembly_id])

mmcif_chain_types(metadata, ccd)

polymer_mol_type(seq_infos, chem_comps)

residue_mol_type(chem_comp)

class MolType(*values)#

Bases: IntEnum

Protein = 1#
RNA = 2#
DNA = 3#
Ligand = 4#
property is_polymer: bool#
property entity_poly_type: str#

Returns the mmCIF _entity_poly.type string for this MolType.

class ResidueId(chain_id: str, seq_id: int, ins_code: str = '')#
chain_id: str#
seq_id: int#
ins_code: str = ''#
classmethod from_scheme(scheme: Scheme)#
with_chain_suffix(suffix: str)#
class Residue(residue_id: gmol.base.data.mmcif.assembly.ResidueId, chem_comp: gmol.base.data.mmcif.parse.ChemComp, atom_idxs: list[int] = <factory>)#
residue_id: ResidueId#
chem_comp: ChemComp#
atom_idxs: list[int]#
new_residue(atom_idxs: list[int])#
with_updates(offset: int, chain_suffix: str)#
class SequenceToResidue(comp_id: str, seq_id: int, res_id: ResidueId | None)#
comp_id: str#
seq_id: int#
res_id: ResidueId | None#
classmethod from_scheme(scheme: Scheme)#
with_chain_suffix(suffix: str)#
class BranchPartner(seq_id: int, atom_id: str, leaving_atom_id: str, comp_id: str, res_id: ResidueId)#
seq_id: int#
atom_id: str#
leaving_atom_id: str#
comp_id: str#
res_id: ResidueId#
classmethod from_branch_scheme(scheme: Scheme, br_info: BranchLinkPartner)#
with_chain_suffix(suffix: str)#
to_scheme(entity_id: int) → Scheme#
class Branch(ptnr1: BranchPartner, ptnr2: BranchPartner, order: int)#
ptnr1: BranchPartner#
ptnr2: BranchPartner#
order: int#
with_chain_suffix(suffix: str)#
class Chain(chain_id: str, auth_asym_id: str, entity_id: int, type: gmol.base.data.mmcif.assembly.MolType, seqres: list[gmol.base.data.mmcif.assembly.SequenceToResidue] = <factory>, branches: list[gmol.base.data.mmcif.assembly.Branch] = <factory>, residue_ids: list[gmol.base.data.mmcif.assembly.ResidueId] = <factory>, atom_idxs: list[int] = <factory>)#
chain_id: str#
auth_asym_id: str#
entity_id: int#
type: MolType#
seqres: list[SequenceToResidue]#
branches: list[Branch]#
residue_ids: list[ResidueId]#
atom_idxs: list[int]#
property resseq: dict[ResidueId, int]#
new_chain(residue_ids: list[ResidueId], atom_idxs: list[int])#
with_updates(offset: int, suffix: str)#
sync_mappings()#
class AssemblyAtom(atom_idx: int, residue_id: ResidueId, type_symbol: str, atom_id: str, comp_id: str, occupancy: float, b_factor: float, label_alt_id: str | None = None, group_PDB: str = 'ATOM')#
atom_idx: int#
residue_id: ResidueId#
type_symbol: str#
atom_id: str#
comp_id: str#
occupancy: float#
b_factor: float#
label_alt_id: str | None = None#
group_PDB: str = 'ATOM'#
property chain_id: str#
new_atom(idx: int)#
with_updates(idx: int, chain_suffix: str)#
class AssemblyConnection(src_idx: int, dst_idx: int, conn_type: str, leaving_atom_count: int)#
src_idx: int#
dst_idx: int#
conn_type: str#
leaving_atom_count: int#
remap(idx_map: _IndexMapper)#
class Transformation(matrix: ndarray[tuple[Any, ...], dtype[float64]], vector: ndarray[tuple[Any, ...], dtype[float64]])#
ident: ClassVar[Transformation] = <gmol.base.data.mmcif.assembly.Transformation object>#
classmethod from_symop(op: SymOp)#
class Assembly(*, metadata: ~gmol.base.data.mmcif.parse.PdbMetadata, coords: ~numpy.ndarray[tuple[~typing.Any, ...], ~numpy.dtype[~numpy.float64]], atoms: list[~gmol.base.data.mmcif.assembly.AssemblyAtom], residues: dict[~gmol.base.data.mmcif.assembly.ResidueId, ~gmol.base.data.mmcif.assembly.Residue], chains: dict[str, ~gmol.base.data.mmcif.assembly.Chain], entities: dict[int, ~gmol.base.data.mmcif.parse.Entity], entity_poly: dict[int, ~gmol.base.data.mmcif.parse.EntityPoly] = <factory>, entity_poly_seq: dict[int, dict[int, ~gmol.base.data.mmcif.parse.EntityPolySeq]] = <factory>, connections: list[~gmol.base.data.mmcif.assembly.AssemblyConnection])#

Bases: LooseModel

metadata: PdbMetadata#
coords: ndarray[tuple[Any, ...], dtype[float64]]#
atoms: list[AssemblyAtom]#
residues: dict[ResidueId, Residue]#
chains: dict[str, Chain]#
entities: dict[int, Entity]#
entity_poly: dict[int, EntityPoly]#
entity_poly_seq: dict[int, dict[int, EntityPolySeq]]#
connections: list[AssemblyConnection]#
property comp_ids: ndarray[tuple[Any, ...], dtype[str_]]#
property chem_comps: dict[str, ChemComp]#
count_polymer_chains() → int#
chains_of_type(tp: MolType)#
has_chain_type(tp: MolType) → bool#
residues_of_chain(chain: Chain)#
atoms_of_chain(chain: Chain)#
atoms_of_residue(residue: Residue)#
filter(selected: ndarray[tuple[Any, ...], dtype[bool]]) → Assembly#
filter_chains(chain_ids: list[str])#
transform(xform: Transformation) → Assembly#
apply(operations: list[Transformation]) → Assembly#
classmethod join(assemblies: list[Assembly])#
to_mmcif(name: str, write_schemes: bool = True) → str#
to_pdb() → str#
to_fasta(name: str) → str#
residue_mol_type(chem_comp: ChemComp) → MolType#
polymer_mol_type(seq_infos: list[Scheme], chem_comps: dict[str, ChemComp]) → MolType#
mmcif_chain_types(metadata: Mmcif, ccd: dict[str, ChemComp]) → dict[str, MolType]#
expand_ops(operations: list[list[str]], sym_ops: dict[str, SymOp])#
mmcif_assemblies(data: Mmcif, ccd: dict[str, ChemComp], assembly_id: int | None = None) → list[Assembly]#
load_one_assembly(file: Path, assembly_id: int | None = None) → Assembly#
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