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(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)¶

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, output_file: str = None, ab_scheme: schrodinger.infra.util.AntibodyCDRScheme = None, tcr_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_all_models(model: ImmuneBuilder.ABodyBuilder2.Antibody | ImmuneBuilder.TCRBuilder2.TCR | ImmuneBuilder.NanoBodyBuilder2.Nanobody, model_type: schrodinger.application.bioluminate.immunebuilder.immunebuilder_adapter.ImmuneBuilderType, dirname: str = None, filename: str = None, ab_scheme: schrodinger.infra.util.AntibodyCDRScheme = None, tcr_scheme: schrodinger.infra.util.AntibodyCDRScheme = None)¶: Save all structures to files, refine the best-ranked structure, and add error estimates.

schrodinger.application.bioluminate.immunebuilder.immunebuilder_adapter.save_refined_model(model: ImmuneBuilder.ABodyBuilder2.Antibody | ImmuneBuilder.TCRBuilder2.TCR | ImmuneBuilder.NanoBodyBuilder2.Nanobody, model_type: schrodinger.application.bioluminate.immunebuilder.immunebuilder_adapter.ImmuneBuilderType, filename: str = None, ab_scheme: schrodinger.infra.util.AntibodyCDRScheme = None, tcr_scheme: schrodinger.infra.util.AntibodyCDRScheme = None)¶: Save and refine the top-ranked structure, retry if necessary, and log failures.

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