schrodinger.application.bioluminate.antibody.sequence_indexer module

exception schrodinger.application.bioluminate.antibody.sequence_indexer.InvalidQueryLengthError

Bases: RuntimeError

Exception for query sequences that are longer than the reference sequences.

__init__()

exception schrodinger.application.bioluminate.antibody.sequence_indexer.InvalidAntibodySequenceError

Bases: RuntimeError

Exception for non-antibody sequences that try to be turned into a SeqType instance.

class schrodinger.application.bioluminate.antibody.sequence_indexer.ReferenceResidueInfo(idx: int, domain: models.VariableDomainType)

Bases: NamedTuple

Variables

• idx – The universal reference residue index.

• domain – The variable domain for this residue.

idx: int

Alias for field number 0

domain: schrodinger.application.bioluminate.antibody.models.VariableDomainType

Alias for field number 1

class schrodinger.application.bioluminate.antibody.sequence_indexer.SingleDomainAbSequenceIndexer(seq_type: <schrodinger.infra.unusable_module_importer.DummyModule object at 0x79ba4b42a5d0>)

Bases: schrodinger.application.bioluminate.antibody.sequence_indexer._AbstractAbSequenceIndexer

property domain: schrodinger.application.bioluminate.antibody.models.VariableDomainType

property ref_indices: List[int]

deriveReferenceResidueInfo(local_idx: int) → schrodinger.application.bioluminate.antibody.sequence_indexer.ReferenceResidueInfo

Return information about the reference residue that corresponds to the residue with index local_idx within the stored sequence.

class schrodinger.application.bioluminate.antibody.sequence_indexer.DVDSequenceIndexer(seq_type: <schrodinger.infra.unusable_module_importer.DummyModule object at 0x79ba4b42a5d0>)

Bases: schrodinger.application.bioluminate.antibody.sequence_indexer._AbstractAbSequenceIndexer

Detector for residues inside of any DVD chain.

property domain: schrodinger.application.bioluminate.antibody.models.VariableDomainType

deriveReferenceResidueInfo(local_idx: int) → schrodinger.application.bioluminate.antibody.sequence_indexer.ReferenceResidueInfo

Return information about the reference residue that corresponds to the residue with index local_idx within the stored sequence.

class schrodinger.application.bioluminate.antibody.sequence_indexer.SCFVSequenceIndexer(seq_type: <schrodinger.infra.unusable_module_importer.DummyModule object at 0x79ba4b42a5d0>)

Bases: schrodinger.application.bioluminate.antibody.sequence_indexer._AbstractAbSequenceIndexer

deriveReferenceResidueInfo(local_idx: int) → schrodinger.application.bioluminate.antibody.sequence_indexer.ReferenceResidueInfo

scFv-specific behavior: Unlike with other chain types, we don’t know ahead of time whether the residue in question is in the light or heavy domain. SeqType stores both domains of scFv chains into the expected lists of data (e.g. seq_type.refidx_vh and seq_type.refidx_vl). We must figure out which reference list our residue is in, which in turn tells us which domain (heavy or light) the residue is in as well.

schrodinger.application.bioluminate.antibody.sequence_indexer.seq_from_chain(chain: schrodinger.structure._structure._Chain) → str

schrodinger.application.bioluminate.antibody.sequence_indexer.seq_type_from_chain(chain: schrodinger.structure._structure._Chain, scheme: str = 'Kabat') → <schrodinger.infra.unusable_module_importer.DummyModule object at 0x79ba4b42a5d0>

Return a SeqType instance derived from chain. Cached due to SeqType instantiation.

schrodinger.application.bioluminate.antibody.sequence_indexer.get_sequence_indexer(chain: schrodinger.structure._structure._Chain, scheme='Kabat') → schrodinger.application.bioluminate.antibody.sequence_indexer._AbstractAbSequenceIndexer