schrodinger.application.bioluminate.antibody.grafting module¶

This class handles the mapping from scaffold search output to grafted, build antibody variable domain structures.

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

Bases: enum.Enum

USE_SCAFFOLD_LOOP = 'off'¶

USE_LOOP_DB = 'auto'¶

USE_STRUCTURE = 1¶

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

Bases: enum.Enum

LOOP_1 = 1¶

LOOP_2 = 2¶

LOOP_3 = 3¶

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

Bases: enum.Enum

HEAVY = 1¶

LIGHT = 2¶

class schrodinger.application.bioluminate.antibody.grafting.LoopGraftingInput(loop_type: 'LoopTypes', chain_type: 'ChainType', start_residue: 'str', end_residue: 'str', source_pdb: 'Structure', instruction: 'LoopGraftingInstruction' = <LoopGraftingInstruction.USE_SCAFFOLD_LOOP: 'off'>)¶

Bases: object

loop_type: schrodinger.application.bioluminate.antibody.grafting.LoopTypes¶

chain_type: schrodinger.application.prime.packages.antibody.ChainType¶

start_residue: str¶

end_residue: str¶

source_pdb: schrodinger.structure._structure.Structure¶

instruction: schrodinger.application.bioluminate.antibody.grafting.LoopGraftingInstruction = 'off'¶

property cdr_name: str¶

__init__(loop_type: schrodinger.application.bioluminate.antibody.grafting.LoopTypes, chain_type: schrodinger.application.prime.packages.antibody.ChainType, start_residue: str, end_residue: str, source_pdb: schrodinger.structure._structure.Structure, instruction: schrodinger.application.bioluminate.antibody.grafting.LoopGraftingInstruction = LoopGraftingInstruction.USE_SCAFFOLD_LOOP) → None¶

class schrodinger.application.bioluminate.antibody.grafting.GraftingInput(alignment: 'antibody.AntibodyAlignment', scaffold: 'Structure', loop_grafting_inputs: 'List[LoopGraftingInput]', job_name: 'str' = 'Grafting', antigen_chains: 'List[str]' = <factory>, loop_databases: 'List[str]' = <factory>, ligands: 'List[Tuple[str]]' = <factory>, num_models: 'int' = 1)¶

Bases: object

alignment: schrodinger.application.prime.packages.antibody.AntibodyAlignment¶

scaffold: schrodinger.structure._structure.Structure¶

loop_grafting_inputs: List[schrodinger.application.bioluminate.antibody.grafting.LoopGraftingInput]¶

job_name: str = 'Grafting'¶

antigen_chains: List[str]¶

loop_databases: List[str]¶

ligands: List[Tuple[str]]¶

num_models: int = 1¶

property bld_align_file: str¶

property bld_scaffold_file: str¶

active_cdr_names() → str¶

get_loop_instructions() → Dict[str, str]¶

classmethod fromScaffoldMatch(scaffold, options)¶

__init__(alignment: schrodinger.application.prime.packages.antibody.AntibodyAlignment, scaffold: schrodinger.structure._structure.Structure, loop_grafting_inputs: typing.List[schrodinger.application.bioluminate.antibody.grafting.LoopGraftingInput], job_name: str = 'Grafting', antigen_chains: typing.List[str] = <factory>, loop_databases: typing.List[str] = <factory>, ligands: typing.List[typing.Tuple[str]] = <factory>, num_models: int = 1) → None¶

class schrodinger.application.bioluminate.antibody.grafting.GraftingOutput(grafted_sts: 'List[Structure]')¶

Bases: object

grafted_sts: List[schrodinger.structure._structure.Structure]¶

write(file_name: str) → None¶: Write the grafted structures to a structure file.

__init__(grafted_sts: List[schrodinger.structure._structure.Structure]) → None¶

schrodinger.application.bioluminate.antibody.grafting.build_chain_settings(grafting_input: schrodinger.application.bioluminate.antibody.grafting.GraftingInput, params=None)¶

Build a chain settings dict compatible with blstruct.build_model() Should be modeled after search_antibody.write_bld_input()

Parameters

grafting_input – Object with inputs to massage into the format that bldstruct expects.
params – a dictionary of any keyword and value pair

schrodinger.application.bioluminate.antibody.grafting.write_alignment_file(bld_align_file, alignment) → None¶: Write sequence alignment file for bldstruct.py to use.

schrodinger.application.bioluminate.antibody.grafting.make_cdr_shifts(loop_grafting_inputs: List[schrodinger.application.bioluminate.antibody.grafting.LoopGraftingInstruction]) → Dict[str, str]¶

schrodinger.application.bioluminate.antibody.grafting.graft(grafting_input: schrodinger.application.bioluminate.antibody.grafting.GraftingInput) → schrodinger.application.bioluminate.antibody.grafting.GraftingOutput¶