schrodinger.application.bioluminate.antibody.annotate module¶

class schrodinger.application.bioluminate.antibody.annotate.Properties(value)¶

Bases: enum.Enum

Class to store custom property names associated with antibody annotation.

PROTEIN_CATEGORY = 'i_bioluminate_protein_category'¶

VERNIER_RES = 'b_bioluminate_vernier_residue'¶

CANONICAL_STRUCTURAL_RES = 'b_bioluminate_canonical_structural_residue'¶

INTERFACE_RES = 'b_bioluminate_interface_residue'¶

class schrodinger.application.bioluminate.antibody.annotate.SpecialResidueTypes(value)¶

Bases: enum.Enum

An enumeration.

VERNIER = 1¶

CANONICAL_STRUCTURAL = 2¶

INTERFACE = 3¶

class schrodinger.application.bioluminate.antibody.annotate.SpecialResidueZone(res_type: schrodinger.application.bioluminate.antibody.annotate.SpecialResidueTypes)¶

Bases: object

Class to store mappings of universal (scheme-independent) alignment residue indices to their corresponding Kabat-numbered residue IDs for both heavy and light chains.

res_type: schrodinger.application.bioluminate.antibody.annotate.SpecialResidueTypes¶

res_ids_by_idx_l: Dict[int, str]¶

res_ids_by_idx_h: Dict[int, str]¶

getResidueIdsByIndex(domain: schrodinger.application.bioluminate.antibody.models.VariableDomainType) → Dict[int, str]¶

residueIsInZone(univ_idx: int, domain: schrodinger.application.bioluminate.antibody.models.VariableDomainType) → bool¶

__init__(res_type: schrodinger.application.bioluminate.antibody.annotate.SpecialResidueTypes) → None¶

schrodinger.application.bioluminate.antibody.annotate.get_res_zones_by_res_type() → Dict[schrodinger.application.bioluminate.antibody.annotate.SpecialResidueTypes, schrodinger.application.bioluminate.antibody.annotate.SpecialResidueZone]¶: Return a mapping of special residue type to its corresponding SpecialResidueZone instance.

schrodinger.application.bioluminate.antibody.annotate.reslist_between_schemes(reslist1, scheme1, scheme2)¶

Given a list of residue IDs in scheme1, return the corresponding residue ID list in scheme2

Param: a list of residue IDs, must have H or L as chain name, e.g. [L:21, H:35B]
Param: one of the supported numbering schemes
Param: one of the supported numbering schemes
Return type: reslist2
Returns: a list of new residue IDs

schrodinger.application.bioluminate.antibody.annotate.is_special_residue(ref_info: schrodinger.application.bioluminate.antibody.sequence_indexer.ReferenceResidueInfo, res_type: schrodinger.application.bioluminate.antibody.annotate.SpecialResidueTypes) → bool¶

schrodinger.application.bioluminate.antibody.annotate.annotate_ab_regions(st, scheme='Chothia')¶

Annotate the given structure using atom-level properties to mark antibody regions.

This is done by marking atoms by their minimum indivisible region classification. Lineage is standard and as described here and by the ‘REGION_CHILDREN’ and ‘REGION_DESCENDENTS’ module level variables.

Children of VL and VH regions are further subdivided to account for the cases of multispecifics such as L1_0, L1_1.

Parameters: st (structure.Structure) – antibody st (this is modified in place)