schrodinger.application.bioluminate.classify module

schrodinger.application.bioluminate.classify.renumber_st_chain(chain: Structure, scheme: AntibodyCDRScheme = AntibodyCDRScheme.Kabat, resid_map: dict[str, str] = None) → dict[str, str]

Renumber the residues in a structure and the resids in a resid_map mapping the original residue ID to the current residue ID if provided.

Parameters:

  • chain – The structure chain to renumber

  • scheme – The numbering scheme to use

  • resid_map – Mapping original residue ID to current residue ID

Returns:

The updated resid_map

schrodinger.application.bioluminate.classify.update_resid_map(chain: Structure, resid_map: dict[str, str] = None) → dict[str, str]

Update the resid_map with the current residue IDs from the chain. If no resid_map is provided, a new one will be created.

Parameters:

  • chain – The structure chain to update

  • resid_map – A mapping from the original residue ID to the current residue ID; if not provided, a new mapping will be created

Returns:

The updated resid_map

schrodinger.application.bioluminate.classify.apply_numbering(chain: Structure, numbered_sequence: NumberedSequence, resid_map: dict[str, str] = None) → dict[str, str]

Apply the numbering to the chain residues and to the resid_map.

Parameters:

  • chain – The structure chain to renumber

  • numbered_sequence – The sequence numbering to apply

  • resid_map – A mapping from the original residue ID to the current residue ID; the mapping will be updated and returned

Returns:

The updated resid_map

schrodinger.application.bioluminate.classify.get_sequence_numbering(sequence, ab_scheme=AntibodyCDRScheme.Kabat, chain_name=None, classifiers=(<class 'schrodinger.application.bioluminate.anarci_classifier.AnarciClassifier'>, )) → NumberedSequence

Get the sequence numbering for a sequence.

schrodinger.application.bioluminate.classify.get_protein_family_data(sequence: str, ab_scheme=AntibodyCDRScheme.Kabat, chain_name: str = None, classifiers=(<class 'schrodinger.application.bioluminate.anarci_classifier.AnarciClassifier'>, )) → ProteinClass

Get the protein family data for a sequence.