schrodinger.application.bioluminate.classify module¶
- class schrodinger.application.bioluminate.classify.NumberedResidue(residue: str, chain_id: str, number: int, insertion_code: str)¶
Bases:
object
A residue with a sequence number.
- residue: str¶
- chain_id: str¶
- number: int¶
- insertion_code: str¶
- property number_with_ins_code: str¶
- property number_with_ins_code_and_chain_id: str¶
- classmethod from_anarci_resinfo(resinfo: schrodinger.application.bioluminate.anarci.anarci_adapter.ResInfo, chain_id='') schrodinger.application.bioluminate.classify.NumberedResidue ¶
- __init__(residue: str, chain_id: str, number: int, insertion_code: str) None ¶
- class schrodinger.application.bioluminate.classify.NumberedSequence(*args, scheme=None, **kwargs)¶
Bases:
list
- __init__(*args, scheme=None, **kwargs)¶
- class schrodinger.application.bioluminate.classify.ProteinClass(type: str, region_bounds: dict[str, tuple[int, int]], numbering: schrodinger.application.bioluminate.classify.NumberedSequence)¶
Bases:
object
The basic information about a protein class - its type, the bounds of its regions, and its re-numbered sequence.
e.g.: type: Antibody VH region_bounds: {‘FR1’: (1, 26), ‘CDR1’: (27, 38), ‘FR2’: (39, 55), …} numbering: [ NumberedResidue(residue=’E’, chain_id=’H’, number=1, insertion_code=’’), NumberedResidue(residue=’V’, chain_id=’H’, number=2, insertion_code=’’), NumberedResidue(residue=’Q’, chain_id=’H’, number=3, insertion_code=’’), …, # etc. ]
- type: str¶
- region_bounds: dict[str, tuple[int, int]]¶
- property numbering_strings: list[str]¶
- property numbering_strings_with_chain_id: list[str]¶
- classmethod fromAnarciDomainResult(domain_result)¶
- classmethod fromAnarciChainResultAndSeq(full_sequence, chain_result)¶
- classmethod fromSequence(sequence, ab_scheme=AntibodyCDRScheme.Kabat)¶
- __init__(type: str, region_bounds: dict[str, tuple[int, int]], numbering: schrodinger.application.bioluminate.classify.NumberedSequence) None ¶
- schrodinger.application.bioluminate.classify.renumber_st_chain(st_chain, ab_scheme=AntibodyCDRScheme.Kabat)¶
Renumber the residues in a structure chain.
- schrodinger.application.bioluminate.classify.get_sequence_numbering(sequence, ab_scheme=AntibodyCDRScheme.Kabat, chain_id='') schrodinger.application.bioluminate.classify.NumberedSequence ¶
Get the sequence numbering for a sequence.
- schrodinger.application.bioluminate.classify.get_protein_family_data(sequence: str, ab_scheme=AntibodyCDRScheme.Kabat) schrodinger.application.bioluminate.classify.ProteinClass ¶
Get the protein family data for a sequence.
- schrodinger.application.bioluminate.classify.get_protein_family(sequence: str) str ¶
Get the protein family for a sequence.