schrodinger.application.bioluminate.classify module¶

class schrodinger.application.bioluminate.classify.NumberedResidue(residue: str, chain_id: str, number: int, insertion_code: str)¶

Bases: object

A residue with a sequence number.

residue: str¶

chain_id: str¶

number: int¶

insertion_code: str¶

property number_with_ins_code: str¶

property number_with_ins_code_and_chain_id: str¶

classmethod from_anarci_resinfo(resinfo: schrodinger.application.bioluminate.anarci.anarci_adapter.ResInfo, chain_id='') → schrodinger.application.bioluminate.classify.NumberedResidue¶

__init__(residue: str, chain_id: str, number: int, insertion_code: str) → None¶

class schrodinger.application.bioluminate.classify.NumberedSequence(*args, scheme=None, **kwargs)¶

Bases: list

__init__(*args, scheme=None, **kwargs)¶

class schrodinger.application.bioluminate.classify.ProteinClass(type: str, region_bounds: dict[str, tuple[int, int]], numbering: schrodinger.application.bioluminate.classify.NumberedSequence)¶

Bases: object

The basic information about a protein class - its type, the bounds of its regions, and its re-numbered sequence.

e.g.: type: Antibody VH region_bounds: {‘FR1’: (1, 26), ‘CDR1’: (27, 38), ‘FR2’: (39, 55), …} numbering: [ NumberedResidue(residue=’E’, chain_id=’H’, number=1, insertion_code=’’), NumberedResidue(residue=’V’, chain_id=’H’, number=2, insertion_code=’’), NumberedResidue(residue=’Q’, chain_id=’H’, number=3, insertion_code=’’), …, # etc. ]

type: str¶

region_bounds: dict[str, tuple[int, int]]¶

numbering: schrodinger.application.bioluminate.classify.NumberedSequence¶

property numbering_strings: list[str]¶

property numbering_strings_with_chain_id: list[str]¶

classmethod fromAnarciDomainResult(domain_result)¶

classmethod fromAnarciChainResultAndSeq(full_sequence, chain_result)¶

classmethod fromSequence(sequence, ab_scheme=AntibodyCDRScheme.Kabat)¶

__init__(type: str, region_bounds: dict[str, tuple[int, int]], numbering: schrodinger.application.bioluminate.classify.NumberedSequence) → None¶

schrodinger.application.bioluminate.classify.renumber_st_chain(st_chain, ab_scheme=AntibodyCDRScheme.Kabat)¶: Renumber the residues in a structure chain.

schrodinger.application.bioluminate.classify.get_sequence_numbering(sequence, ab_scheme=AntibodyCDRScheme.Kabat, chain_id='') → schrodinger.application.bioluminate.classify.NumberedSequence¶: Get the sequence numbering for a sequence.

schrodinger.application.bioluminate.classify.get_protein_family_data(sequence: str, ab_scheme=AntibodyCDRScheme.Kabat) → schrodinger.application.bioluminate.classify.ProteinClass¶: Get the protein family data for a sequence.

schrodinger.application.bioluminate.classify.get_protein_family(sequence: str) → str¶: Get the protein family for a sequence.