schrodinger.application.bioluminate.antibody.annotate module

class schrodinger.application.bioluminate.antibody.annotate.Properties(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)

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, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)

Bases: enum.Enum

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_l: set[str]

res_ids_h: set[str]

property res_id_set_by_domain_type: dict[schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciType, set[str]]

residueIsInZone(kabat_res_id: str, domain: schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciType) → 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.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)

schrodinger.application.bioluminate.antibody.annotate.is_special_residue(res_info: schrodinger.application.bioluminate.anarci.anarci_adapter.ResInfo, anarci_chain_type: schrodinger.application.bioluminate.anarci.anarci_adapter.AnarciType, res_type: schrodinger.application.bioluminate.antibody.annotate.SpecialResidueTypes) → bool

schrodinger.application.bioluminate.antibody.annotate.get_chain_sequence(chain)