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.application.prime.packages.antibody.SeqType)¶
Bases:
schrodinger.application.bioluminate.antibody.sequence_indexer._AbstractAbSequenceIndexer
- 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.application.prime.packages.antibody.SeqType)¶
Bases:
schrodinger.application.bioluminate.antibody.sequence_indexer._AbstractAbSequenceIndexer
Detector for residues inside of any DVD chain.
- 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.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.
- 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 fromchain
. Cached due toSeqType
instantiation.
- schrodinger.application.bioluminate.antibody.sequence_indexer.get_sequence_indexer(chain: schrodinger.structure._structure._Chain, scheme='Kabat') schrodinger.application.bioluminate.antibody.sequence_indexer._AbstractAbSequenceIndexer ¶