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¶
- 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 ¶
- 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.