schrodinger.application.bioluminate.protein_data module

class schrodinger.application.bioluminate.protein_data.ProteinClassifier

Bases: object

A classifier for a protein sequence.

PROTEIN_TYPES = ()

__init__()

class schrodinger.application.bioluminate.protein_data.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

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

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

Bases: list

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

class schrodinger.application.bioluminate.protein_data.ProteinClass(type: str = 'Unknown', region_bounds: dict[str, tuple[int, int]] = <factory>, numbering_with_gaps: ~schrodinger.application.bioluminate.protein_data.NumberedSequence = <factory>)

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 = 'Unknown'

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

numbering_with_gaps: NumberedSequence

property numbering: NumberedSequence

property numbering_strings: list[str]

property numbering_strings_with_chain_id: list[str]

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

adjustRegionBounds(region_adjustments: dict[str, [<class 'int'>, <class 'int'>]])

Create a new ProteinClass with adjusted region bounds.

__init__(type: str = 'Unknown', region_bounds: dict[str, tuple[int, int]] = <factory>, numbering_with_gaps: ~schrodinger.application.bioluminate.protein_data.NumberedSequence = <factory>) → None

schrodinger.application.bioluminate.protein_data.find_domains(sequence: str, scheme, chain_name: str, classifiers: tuple[ProteinClassifier, ...]) → list[ProteinClass]

Find domains in a protein sequence using the provided classifiers.

Parameters:

• sequence – The protein sequence to classify.

• scheme – The antibody CDR scheme to use for classification.

• chain_name – The name of the chain to classify.

• classifiers – A tuple of ProteinClassifier instances to use for classification.

Returns:

A list of ProteinClass instances representing the classified domains in the sequence.

schrodinger.application.bioluminate.protein_data.number_terminal_residues(numbering: NumberedSequence, start: int, end: int, full_sequence: str, skip_zero=True) → NumberedSequence

Number the terminal residues of a sequence based on the existing numbering. Each end of the sequence will be numbered sequentially. If skip_zero is True, the numbering will skip zero.

Parameters:

• numbering – The numbering of the sequence.

• start – The starting index where the sequence has already been numbered.

• end – The ending index where the sequence has already been numbered.

• full_sequence – The full sequence to number.

Returns:

The updated numbering with terminal residues numbered.

schrodinger.application.bioluminate.protein_data.validate_numbering(numbering: NumberedSequence, full_sequence: str)

Validate that the numbering matches the sequence, ignoring gaps.

Parameters:

• numbering – The numbered sequence to validate.

• full_sequence – The full sequence to validate against.