gmol.base.data.mmcif.assembly#

Classes

`Assembly`(coords, atoms, residues, chains, ...)
`AssemblyAtom`(atom_idx, residue_id, ...)
`AssemblyConnection`(src_idx, dst_idx, ...)
`Branch`(ptnr1, ptnr2, order)
`BranchPartner`(seq_id, atom_id, ...)
`Chain`(chain_id, entity_id, type, seqres, ...)
`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)
`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#

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, 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#

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)#

atom_idx: int#

residue_id: ResidueId#

type_symbol: str#

atom_id: str#

comp_id: str#

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(coords: ndarray[tuple[Any, ...], dtype[float64]], atoms: list[AssemblyAtom], residues: dict[ResidueId, Residue], chains: dict[str, Chain], entities: dict[int, Entity], 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_mmcif_chain(name: str, cid: str, write_schemes: bool = True)#

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]#