schrodinger.application.bioluminate.anarci.annotate module¶

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

Bases: object

Basic information about a domain found by anarci. Includes the type of domain anarci found, the annotated sequence, and the index on the input sequence where the domain starts.

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

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: schrodinger.infra.util.AntibodyCDRScheme, anarci_type: schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciType, numbering: list[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: list[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: schrodinger.infra.util.AntibodyCDRScheme, anarci_type: schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciType, numbering: list[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_variable_region_names(anarci_type: schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciType)¶: Get the names of the variable regions for the given anarci type :param anarci_type: the type to get the region names for :return: a generator of the region names

schrodinger.application.bioluminate.anarci.annotate.get_region_lengths(scheme: schrodinger.infra.util.AntibodyCDRScheme, anarci_type: schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciType, numbering: list[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
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

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()¶

schrodinger.application.bioluminate.anarci.annotate.get_family_region_bounds(sequence: str, ab_scheme=AntibodyCDRScheme.Kabat, skip_constant=False) → dict[str, tuple[int, int]]¶: Get the region bounds for a sequence.

schrodinger.application.bioluminate.anarci.annotate.get_family_region_bounds_from_chain_result(chain_result)¶

schrodinger.application.bioluminate.anarci.annotate.get_const_ref_filename(chain_type: schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciType)¶

schrodinger.application.bioluminate.anarci.annotate.get_family_region_bounds_from_domain_result(result: schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciDomainResult) → dict[str, tuple[int, int]]¶: Get the region bounds for a domain result.

schrodinger.application.bioluminate.anarci.annotate.get_constant_domain_bounds(full_sequence, chain_type, subseq_bounds=None)¶