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)¶

Bases: enum.Enum

An enumeration.

NO_MODIFY = 1¶

USE_SCAFFOLD_LOOP = 2¶

USE_LOOP_DB = 3¶

USE_STRUCTURE = 4¶

class schrodinger.application.bioluminate.antibody.grafting.LoopTypes(value)¶

Bases: enum.Enum

An enumeration.

LOOP_1 = 1¶

LOOP_2 = 2¶

LOOP_3 = 3¶

class schrodinger.application.bioluminate.antibody.grafting.ChainTypes(value)¶

Bases: enum.Enum

An enumeration.

HEAVY = 1¶

LIGHT = 2¶

class schrodinger.application.bioluminate.antibody.grafting.LoopGraftingInput(loop_type: schrodinger.application.bioluminate.antibody.grafting.LoopTypes, chain_type: schrodinger.application.bioluminate.antibody.grafting.ChainTypes, start_residue: str, end_residue: str, source_pdb: schrodinger.structure._structure.Structure, instruction: schrodinger.application.bioluminate.antibody.grafting.LoopGraftingInstruction = <LoopGraftingInstruction.NO_MODIFY: 1>)¶

Bases: object

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

chain_type: schrodinger.application.bioluminate.antibody.grafting.ChainTypes¶

start_residue: str¶

end_residue: str¶

source_pdb: schrodinger.structure._structure.Structure¶

instruction: schrodinger.application.bioluminate.antibody.grafting.LoopGraftingInstruction = 1¶

property cdr_name: str¶

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

class schrodinger.application.bioluminate.antibody.grafting.GraftingInput(alignment: schrodinger.application.prime.packages.antibody.AntibodyAlignment, loop_grafting_inputs: List[schrodinger.application.bioluminate.antibody.grafting.LoopGraftingInput], loop_databases: List[str], job_name: str, scaffold: schrodinger.structure._structure.Structure = None, num_models: int = 1)¶

Bases: object

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

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

loop_databases: List[str]¶

job_name: str¶

scaffold: schrodinger.structure._structure.Structure = None¶

num_models: int = 1¶

__init__(alignment: schrodinger.application.prime.packages.antibody.AntibodyAlignment, loop_grafting_inputs: List[schrodinger.application.bioluminate.antibody.grafting.LoopGraftingInput], loop_databases: List[str], job_name: str, scaffold: Optional[schrodinger.structure._structure.Structure] = None, num_models: int = 1) → None¶

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

Bases: object

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

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

schrodinger.application.bioluminate.antibody.grafting.build_chain_settings(alignment: schrodinger.application.prime.packages.antibody.AntibodyAlignment, filename: str, db_files: Optional[List[str]] = None, models: int = 1, multimodel_loop: str = 'H1,H2,H3,L1,L2,L3', mode: str = 'antibody', loops=None, temp_ct=None, antigens=None, ligands=None, params=None)¶

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

Parameters

alignment – The alignment to use for the Framework structure
filename – The basename of filenames for this job
models – The number of models to produce
multimodel_loop (str) – The CDR loops that are allowed to have structural variability to generate multiple models.
models – the build mode: antibody, knowledge, energy
loops (dict) – Keys are CDR names (H1, H2, H3, L1, L2, L3), values are calculation types - either ‘auto’, or a loop model file such as ‘loop.mae’
temp_ct (CT object) – if provided, this CT will be used for writing out the template
antigens (list) – a list of antigen chain names
ligands (list) – a list of tuples (resname, chain:resnum, prot) describing ligands, with the third element optional (it should be passed in if the ligands come from different templates)
scheme (string) – one of the numbering schemes
dict (params) – a dictionary of any keyword and value pair

schrodinger.application.bioluminate.antibody.grafting.write_alignment_file(bld_align_file, alignment)¶: 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.derive_base_name(job_name: str) → str¶

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