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]¶
- start_index: int = 0¶
- classmethod from_domain_result(domain_result: schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciDomainResult)¶
Create an AnnotationResult from an AnarciDomainResult
- get_annotation_strings_with_gaps()¶
- get_annotation_strings()¶
- property annotation_strings_with_gaps¶
- property annotation_strings¶
- property ig_type_str¶
- __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[schrodinger.application.bioluminate.anarci.anarci_adapter.InputSequence]¶
- schrodinger.application.bioluminate.anarci.annotate.get_anarci_results_from_fasta(filename: str, **kwargs)¶
- schrodinger.application.bioluminate.anarci.annotate.split_numbers_by_region(scheme: str, anarci_type: schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciType, numbering: tuple[schrodinger.application.bioluminate.anarci.anarci_adapter.ResInfo], ignore_gaps=False) tuple[tuple[schrodinger.application.bioluminate.anarci.anarci_adapter.ResInfo], ...]¶
Split the numbering into tuples of ResInfo objects for each region
- Parameters
scheme – antibody numbering scheme to use for the region definitions
anarci_type – the type of antibody to get the region indices for
numbering – numbered residue info objects in sequential order
ignore_gaps – whether to skip ResInfo objects which represent gap characters in the sequence
- Returns
tuples of ResInfo objects for each region
- schrodinger.application.bioluminate.anarci.annotate.get_region_bounds(scheme: str, anarci_type: schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciType, numbering: tuple[schrodinger.application.bioluminate.anarci.anarci_adapter.ResInfo], ignore_gaps=False, start_index: int = 0) tuple[tuple[int, int], ...]¶
Get the start and end indices for each loop and non-loop region
- Parameters
scheme – antibody numbering scheme to use for the region definitions
anarci_type – the type of antibody to get the region indices for
numbering – numbered residue info objects in sequential order
ignore_gaps – whether to skip ResInfo objects which represent gap characters in the sequence
start_index – the starting index of the domain in the sequence
- Returns
a tuple of start and end indices for each region
- schrodinger.application.bioluminate.anarci.annotate.get_numbers_by_region_name(scheme: str, anarci_type: schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciType, numbering: tuple[schrodinger.application.bioluminate.anarci.anarci_adapter.ResInfo], ignore_gaps=False) dict[str, tuple[schrodinger.application.bioluminate.anarci.anarci_adapter.ResInfo]]¶
Get a dictionary of start and end indices for each loop and non-loop region for the given antibody type, keyed by the region name (e.g. “HFR1”, “L3”, etc.)
- Parameters
scheme – antibody numbering scheme to use for the region definitions
anarci_type – the type of antibody to get the region indices for
numbering – numbered residue info objects in sequential order
ignore_gaps – whether to skip ResInfo objects which represent gap characters in the sequence
scheme – antibody numbering scheme to use for the region definitions
anarci_type – the type of antibody to get the region indices for
numbering – numbered residue info objects in sequential order
ignore_gaps – whether to skip ResInfo objects which represent gap characters in the sequence
- Returns
tuples of ResInfo objects for each region, keyed by the region name
- schrodinger.application.bioluminate.anarci.annotate.get_region_lengths(scheme: str, anarci_type: schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciType, numbering: tuple[schrodinger.application.bioluminate.anarci.anarci_adapter.ResInfo], ignore_gaps=False) tuple[int, ...]¶
- Get the length of each loop and non-loop region for the given numbered
residues
- Parameters
scheme – antibody numbering scheme to use for the region definitions
numbering – numbered residue info objects in sequential order
- Returns
the lengths of the regions before, inside, and in between the supplied ranges
- schrodinger.application.bioluminate.anarci.annotate.get_annotations_from_results(results: schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciResults) list[schrodinger.application.bioluminate.anarci.annotate.AnnotationResult]¶
- schrodinger.application.bioluminate.anarci.annotate.get_annotations(sequences: list[schrodinger.application.bioluminate.anarci.anarci_adapter.InputSequence]) list[schrodinger.application.bioluminate.anarci.annotate.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[schrodinger.protein.sequence.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[schrodinger.application.bioluminate.anarci.annotate.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()¶