schrodinger.application.bioluminate.immunebuilder.immunebuilder_adapter module¶

This module allows use of ImmuneBuilder structure prediction, replacing (and disabling) the third-party modules openmm and pdbfixer.

WARNING: Importing this module will prevent the caller from using the third party modules openmm and pdbfixer.

class schrodinger.application.bioluminate.immunebuilder.immunebuilder_adapter.MockOpenMM¶

Bases: object

These mocked modules are imported by ImmuneBuilder, but we don’t need them.

class Unit¶

Bases: object

kilocalories_per_mole = 1¶

angstroms = 1¶

class App¶

Bases: object

ForceField()¶

app¶: alias of schrodinger.application.bioluminate.immunebuilder.immunebuilder_adapter.MockOpenMM.App

LangevinIntegrator = None¶

CustomExternalForce = None¶

CustomTorsionForce = None¶

OpenMMException = None¶

Platform = None¶

unit¶: alias of schrodinger.application.bioluminate.immunebuilder.immunebuilder_adapter.MockOpenMM.Unit

class schrodinger.application.bioluminate.immunebuilder.immunebuilder_adapter.ImmuneBuilderType¶

Bases: enum.Enum

TCR = 'TCR'¶

ANTIBODY = 'Antibody'¶

NANOBODY = 'Nanobody'¶

schrodinger.application.bioluminate.immunebuilder.immunebuilder_adapter.predict_and_refine_model(model_type: schrodinger.application.bioluminate.immunebuilder.immunebuilder_adapter.ImmuneBuilderType, seq_dict: dict[str, str], refine: bool = True) → schrodinger.structure._structure.Structure¶: Predict models of TCR, Antibody, or Nanobody

schrodinger.application.bioluminate.immunebuilder.immunebuilder_adapter.predict_model(model_type: schrodinger.application.bioluminate.immunebuilder.immunebuilder_adapter.ImmuneBuilderType, seq_dict: dict[str, str], model_weights_dir=None) → ImmuneBuilder.ABodyBuilder2.Antibody | ImmuneBuilder.TCRBuilder2.TCR | ImmuneBuilder.NanoBodyBuilder2.Nanobody¶: Predict models of TCR, Antibody, or Nanobody

schrodinger.application.bioluminate.immunebuilder.immunebuilder_adapter.get_default_weights_dir()¶

schrodinger.application.bioluminate.immunebuilder.immunebuilder_adapter.refine_model(model: ImmuneBuilder.ABodyBuilder2.Antibody | ImmuneBuilder.TCRBuilder2.TCR | ImmuneBuilder.NanoBodyBuilder2.Nanobody)¶: Save and refine the top-ranked structure.

schrodinger.application.bioluminate.immunebuilder.immunebuilder_adapter.run_prepwizard(input_file: str, model_type: schrodinger.application.bioluminate.immunebuilder.immunebuilder_adapter.ImmuneBuilderType, output_file: str = None, scheme: schrodinger.infra.util.AntibodyCDRScheme = None)¶: Run PrepWizard to minimize and clean up a predicted structure

schrodinger.application.bioluminate.immunebuilder.immunebuilder_adapter.cleanup_after_prep_calculation(directory: str = '.')¶: Remove intermediate files and hidden files created by Prep Wizard.

schrodinger.application.bioluminate.immunebuilder.immunebuilder_adapter.build_peptide_bonds(st: schrodinger.structure._structure.Structure)¶: Manually build peptide bonds between residues in a structure to ensure that PrepWizard preserves them.

schrodinger.application.bioluminate.immunebuilder.immunebuilder_adapter.save_and_refine_models(seqs: dict[str, str], model_type: schrodinger.application.bioluminate.immunebuilder.immunebuilder_adapter.ImmuneBuilderType, dirname: str = None, filename: str = None, scheme: schrodinger.infra.util.AntibodyCDRScheme = None, num_structures_to_save: int = 1) → int¶

Save all structures to files, refine the best-ranked structure, and add error estimates.

Parameters

seqs – A dictionary of sequences to model.
model_type – The ImmuneBuilder modeling type.
dirname – The directory to save the files.
filename – The filename to save the refined structure.
scheme – The numbering scheme to use.
num_structures_to_save – The number of structures to save.

Returns

The number of successful models saved.

schrodinger.application.bioluminate.immunebuilder.immunebuilder_adapter.get_critical_reliability_issues(input_file: str)¶: Check for critical reliability issues in a structure.

schrodinger.application.bioluminate.immunebuilder.immunebuilder_adapter.get_scheme_for_arg(scheme_arg: str) → schrodinger.infra.util.AntibodyCDRScheme | None¶: Get the antibody CDR scheme based on the provided argument.

schrodinger.application.bioluminate.immunebuilder.immunebuilder_adapter.get_compatible_sequences_from_fasta(fasta_file: str, model_type: schrodinger.application.bioluminate.immunebuilder.immunebuilder_adapter.ImmuneBuilderType) → dict[str, str]¶

schrodinger.application.bioluminate.immunebuilder.immunebuilder_adapter.get_seqs_from_fasta_file(fasta_file: str) → list[str]¶: Read a FASTA file and return the sequences as a list

schrodinger.application.bioluminate.immunebuilder.immunebuilder_adapter.get_compatible_sequences_dict(sequences: list[str], model_type: schrodinger.application.bioluminate.immunebuilder.immunebuilder_adapter.ImmuneBuilderType) → dict[str, str]¶: Read a FASTA file and return a dictionary of sequences to model with the provided ImmuneBuilder modeling type

schrodinger.application.bioluminate.immunebuilder.immunebuilder_adapter.get_arg_parser(model_type: schrodinger.application.bioluminate.immunebuilder.immunebuilder_adapter.ImmuneBuilderType, program_name: str, description: str, exp_fasta_contents: str, allowed_schemes: list[str] = None) → argparse.ArgumentParser¶

class schrodinger.application.bioluminate.immunebuilder.immunebuilder_adapter.ValidateNumStructures(option_strings, dest, nargs=None, const=None, default=None, type=None, choices=None, required=False, help=None, metavar=None)¶: Bases: argparse.Action