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.ScaffoldMatch(st: schrodinger.structure._structure.Structure, alignment: object, chain: str)¶

Bases: object

__init__(st: Structure, alignment: object, chain: str) → None¶

property pdbid: str¶

property score: float¶

st: Structure¶

alignment: object¶

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.infra.util.AntibodyCDRScheme = <AntibodyCDRScheme.Chothia: 1>)¶

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: AntibodyCDRScheme = AntibodyCDRScheme.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: AntibodyCDRScheme = 1¶

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[ScaffoldMatch]) → None¶

scaffolds: List[ScaffoldMatch]¶

schrodinger.application.bioluminate.antibody.scaffold_search.find_scaffolds(input: ScaffoldSearchInput) → 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.