schrodinger.application.bioluminate.antibody.scaffold_search module¶

Module containing classes for building antibody scaffolds, used by build_antibody.py

class schrodinger.application.bioluminate.antibody.scaffold_search.NumberingScheme(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)¶

Bases: enum.Enum

CHOTHIA = 'Chothia'¶

class schrodinger.application.bioluminate.antibody.scaffold_search.ScaffoldMatch(st: schrodinger.structure._structure.Structure, alignment: schrodinger.application.prime.packages.antibody.AntibodyAlignment, chain: str)¶

Bases: object

__init__(st: schrodinger.structure._structure.Structure, alignment: schrodinger.application.prime.packages.antibody.AntibodyAlignment, chain: str) → None¶

property pdbid: str¶

property score: float¶

st: schrodinger.structure._structure.Structure¶

alignment: schrodinger.application.prime.packages.antibody.AntibodyAlignment¶

chain: str¶

class schrodinger.application.bioluminate.antibody.scaffold_search.ScaffoldSearchInput(query_chain_sequence: str, numbering_params: Optional[dict] = None, databases: Optional[list] = None, maximum_identity: Optional[float] = None, num_scaffolds: int = 1, scheme: schrodinger.application.bioluminate.antibody.scaffold_search.NumberingScheme = <NumberingScheme.CHOTHIA: 'Chothia'>)¶

Bases: object

__init__(query_chain_sequence: str, numbering_params: Optional[dict] = None, databases: Optional[list] = None, maximum_identity: Optional[float] = None, num_scaffolds: int = 1, scheme: schrodinger.application.bioluminate.antibody.scaffold_search.NumberingScheme = NumberingScheme.CHOTHIA) → None¶

databases: Optional[list] = None¶

classmethod fromSeqDict(seq, options)¶

maximum_identity: Optional[float] = None¶

num_scaffolds: int = 1¶

numbering_params: Optional[dict] = None¶

scheme: schrodinger.application.bioluminate.antibody.scaffold_search.NumberingScheme = 'Chothia'¶

query_chain_sequence: str¶

class schrodinger.application.bioluminate.antibody.scaffold_search.ScaffoldSearchOutput(scaffolds: List[schrodinger.application.bioluminate.antibody.scaffold_search.ScaffoldMatch])¶

Bases: object

__init__(scaffolds: List[schrodinger.application.bioluminate.antibody.scaffold_search.ScaffoldMatch]) → None¶

scaffolds: List[schrodinger.application.bioluminate.antibody.scaffold_search.ScaffoldMatch]¶

schrodinger.application.bioluminate.antibody.scaffold_search.find_scaffolds(input: schrodinger.application.bioluminate.antibody.scaffold_search.ScaffoldSearchInput) → schrodinger.application.bioluminate.antibody.scaffold_search.ScaffoldSearchOutput¶: Perform antibody homology search with a single query sequence.

schrodinger.application.bioluminate.antibody.scaffold_search.process_homology_search_results(results: List, max_identity=None, num_scaffolds=1)¶: For each result from search_ab.antibody_homology_search(), create a ScaffoldMatch instance, and filter them by identity score.