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_with_gaps: 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.: sequence: ‘EVQ…’ type: Antibody VH region_bounds: {‘FR1’: (1, 26), ‘CDR1’: (27, 38), ‘FR2’: (39, 55), …} numbering_with_gaps: [ 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., the insertion code being ‘ ‘ is important; it cannot be ‘’. ]

type: str

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

numbering_with_gaps: schrodinger.application.bioluminate.classify.NumberedSequence

property 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, chain_name=None)

classmethod fromSequence(sequence, ab_scheme=AntibodyCDRScheme.Kabat, chain_name=None)

is_scfv()

adjustRegionBounds(region_adjustments: dict[str, [<class 'int'>, <class 'int'>]]) → schrodinger.application.bioluminate.classify.ProteinClass

Create a new ProteinClass with adjusted region bounds.

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

Get the sequence numbering for a sequence.

schrodinger.application.bioluminate.classify.unnumbered_tail_region_start(sequence: str, numbering: schrodinger.application.bioluminate.classify.NumberedSequence) → int

The numbering does not always start at the beginning of the sequence. This function finds the index in the sequence where the numbering ends so the rest of the sequence can be numbered.

Parameters

• sequence – The sequence to check.

• numbering – The numbering of the sequence.

schrodinger.application.bioluminate.classify.get_protein_family_data(sequence: str, ab_scheme=AntibodyCDRScheme.Kabat, chain_name: str = None) → 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.