schrodinger.application.bioluminate.anarci.annotate module¶

class schrodinger.application.bioluminate.anarci.annotate.AnnotationResult(anarci_type: Optional[AnarciType], sequence: ProteinSequence, start_index: int = 0)¶

Bases: object

anarci_type: Optional[schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciType]¶

sequence: schrodinger.protein.sequence.ProteinSequence¶

start_index: int = 0¶

classmethod from_domain_result(domain_result: schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciDomainResult)¶: Create an AnnotationResult from an AnarciDomainResult

property annotation_strings¶

property ig_type_str¶

get_ungapped_anno_strings()¶

__init__(anarci_type: Optional[schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciType], sequence: schrodinger.protein.sequence.ProteinSequence, start_index: int = 0) → None¶

schrodinger.application.bioluminate.anarci.annotate.read_fasta(filename: str) → list[InputSequence]¶

schrodinger.application.bioluminate.anarci.annotate.get_anarci_results_from_fasta(filename: str, **kwargs)¶

schrodinger.application.bioluminate.anarci.annotate.get_annotations_from_results(results: AnarciResults) → list[AnnotationResult]¶

schrodinger.application.bioluminate.anarci.annotate.get_annotations(sequences: list[InputSequence]) → list[AnnotationResult]¶

Get the MSV annotations for the given sequences

Parameters: sequences – the sequences to annotate
Returns: a tuple containing the type of immunoglobulin and a list of annotated sequences

schrodinger.application.bioluminate.anarci.annotate.show_msv_annotation(annotated_domains: list[ProteinSequence], ig_type_str: str)¶

Show an MSV window with the given annotated domains

Parameters

annotated_domains – the MSV-annotated domain objects to show
ig_type_str – the type of immunoglobulin to show (TCR or Antibody)

schrodinger.application.bioluminate.anarci.annotate.write_annotated_fasta(out_filename: str, dom_annotations: list[AnnotationResult])¶

schrodinger.application.bioluminate.anarci.annotate.get_out_filename(filename: str) → str¶: Get the output filename for the given input filename

schrodinger.application.bioluminate.anarci.annotate.parse_args(args)¶

schrodinger.application.bioluminate.anarci.annotate.main()¶