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__()¶

args¶

with_traceback()¶: Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

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

Bases: RuntimeError

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

__init__(*args, **kwargs)¶

args¶

with_traceback()¶: Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

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

Bases: tuple

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

__contains__(key, /)¶: Return key in self.

__len__()¶: Return len(self).

count(value, /)¶: Return number of occurrences of value.

index(value, start=0, stop=9223372036854775807, /)¶

Return first index of value.

Raises ValueError if the value is not present.

class schrodinger.application.bioluminate.antibody.sequence_indexer.SingleDomainAbSequenceIndexer(seq_type: schrodinger.application.prime.packages.antibody.SeqType)¶

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.

__init__(seq_type: schrodinger.application.prime.packages.antibody.SeqType) → None¶

seq_type: schrodinger.application.prime.packages.antibody.SeqType¶

class schrodinger.application.bioluminate.antibody.sequence_indexer.DVDSequenceIndexer(seq_type: schrodinger.application.prime.packages.antibody.SeqType)¶

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.

__init__(seq_type: schrodinger.application.prime.packages.antibody.SeqType) → None¶

seq_type: schrodinger.application.prime.packages.antibody.SeqType¶

class schrodinger.application.bioluminate.antibody.sequence_indexer.SCFVSequenceIndexer(seq_type: schrodinger.application.prime.packages.antibody.SeqType)¶

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.

__init__(seq_type: schrodinger.application.prime.packages.antibody.SeqType) → None¶

seq_type: schrodinger.application.prime.packages.antibody.SeqType¶

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.application.prime.packages.antibody.SeqType¶: 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¶