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)

Bases: enum.Enum

An enumeration.

CHOTHIA = 'Chothia'

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

Bases: object

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

property pdbid: str

property score: float

st: schrodinger.structure._structure.Structure

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

class schrodinger.application.bioluminate.antibody.scaffold_search.ScaffoldSearchInput(query_chain_sequence: str, numbering_params: Union[dict, NoneType] = None, databases: Union[list, NoneType] = None, maximum_identity: Union[float, NoneType] = 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

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.