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