antibody_utils.structure.models¶

Antibody chains in a structure, and the Fvs that pair them.

These classes wrap a gemmi.Structure rather than copying it. Each AntibodyChain maps the numbered positions of its variable domain to residues of the structure, which keep their original numbering. Treat the structure as read-only while these objects are in use: adding or removing chains or residues invalidates the mapping.

Classes

`AntibodyChain`(chain, numbered, indices)	A chain of a structure with a numbered antibody variable domain.
`AntibodyStructure`(structure, chains, scheme, ...)	A structure with its antibody chains identified and numbered.
`Fv`(heavy, light)	A variable fragment: a heavy and a light chain that pair.

class antibody_utils.structure.models.AntibodyChain(chain, numbered, indices)[source]¶

Bases: object

A chain of a structure with a numbered antibody variable domain.

Only the residues of the variable domain are numbered. Any others on the chain (such as a constant domain, a tag, ligands or water) are left out here, but remain in the structure.

property chain: Chain¶: Whether this is a heavy or a light chain.

property gemmi_chain: Chain¶: The whole chain in the structure, including unnumbered residues.

property name: str¶: The chain’s name in the structure.

property numbered: NumberedSequence¶: The numbered variable domain.

region_residues(definition)[source]¶

Group the residues of the domain by region.

Regions are assigned with antibody_utils.regions.annotate_regions, as for antibody_utils.sequence.region_sequences.

Parameters:: definition (Definition | str) – The region definition to apply.
Return type:: dict[Region, list[Residue]]
Returns:: The residues of each region present, in sequence order.

property residues: list[Residue]¶: The residues of the numbered domain, in sequence order.

property scheme: Scheme¶: The numbering scheme.

class antibody_utils.structure.models.AntibodyStructure(structure, chains, scheme, model)[source]¶

Bases: object

A structure with its antibody chains identified and numbered.

Create one with antibody_utils.structure.read_structure or antibody_utils.structure.from_gemmi.

chains¶: The antibody chains, in the order they appear in the structure.

property heavy_chains: tuple[AntibodyChain, ...]¶: The heavy chains.

property light_chains: tuple[AntibodyChain, ...]¶: The light chains.

property model: Model¶: The model that the antibody chains belong to.

property other_chains: list[Chain]¶: The chains of the model that are not antibody chains.

scheme¶: The numbering scheme.

structure¶: The underlying GEMMI structure, with its original numbering.

class antibody_utils.structure.models.Fv(heavy, light)[source]¶

Bases: object

A variable fragment: a heavy and a light chain that pair.

Chains are not paired automatically: choose the pair yourself, for example from the structure’s metadata: Fv(structure[“H”], structure[“L”]).

property heavy: AntibodyChain¶: The heavy chain.

property light: AntibodyChain¶: The light chain.

property name: str¶: The heavy and light chain names, joined, such as “HL”.

property numbered: tuple[NumberedSequence, NumberedSequence]¶

The numbered heavy and light domains.

These can be passed straight to antibody_utils.sequence.identity and antibody_utils.sequence.similarity.

region_residues(definition)[source]¶

Group the residues of both domains by region.

Parameters:: definition (Definition | str) – The region definition to apply.
Returns:: the heavy chain’s, then the light chain’s.
Return type:: dict[Region, list[Residue]]

property scheme: Scheme¶: The numbering scheme.