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: 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') 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