deepfold.data.pdbx_parsing

Protein Data Bank.

Functions

fetch_mmcif(rcsb_id)	Fetch mmCIF from RCSB.
get_assemblies(mmcif_object)
get_chain_features(mmcif_object, model_num, ...)	Get atom positions and mask from a list of Biopython Residues.
get_fasta(mmcif_object)
loop_to_dict(prefix, index, dic)
loop_to_list(prefix, dic)
print_amap(mmcif_object, auth_asym_id[, file])
print_chain_features(feats[, file])
read_mmcif(rcsb_id[, mmcif_path])	Fetch a mmCIF file from local directory or from the web.

Classes

AssemblyGenerator(assembly_id, asym_id_list, ...)
AtomSite(residue_name, author_chain_id, ...)
ModResidue(label_asym_id, label_comp_id, ...)
Monomer(entity_id, num, mon_id)
Op(op_id[, is_identity, rot, trans])	Op(op_id: str, is_identity: bool = True, rot: numpy.ndarray = array([[1., 0., 0.], [0., 1., 0.], [0., 0., 1.]]), trans: numpy.ndarray = array([0., 0., 0.]))
PDBxHeader(entry_id, deposition_date, method)
PDBxObject(header, structure, chain_ids, ...)
PDBxParser()	Parse a PDBx/mmCIF record.
ParsingResult(mmcif_object, errors)
ResidueAtPosition(position, name, ...[, ordinal])
ResiduePosition(label_asym_id, auth_asym_id, ...)

Exceptions

CategoryNotFoundError