schrodinger.application.bioluminate.antibody.antibody_modeling_yaml module

schrodinger.application.bioluminate.antibody.antibody_modeling_yaml.read_yaml(yaml_filename: str) → Dict[str, Any]

Read a yaml file and return the contents as a dictionary.

Yaml_filename

The name of the yaml file to read.

schrodinger.application.bioluminate.antibody.antibody_modeling_yaml.get_jobname(yaml_file_contents: Dict[str, Any], yaml_filename: str) → str

Get the jobname

Parameters

• yaml_file_contents – The contents of the yaml file.

• yaml_filename – The name of the yaml file.

schrodinger.application.bioluminate.antibody.antibody_modeling_yaml.graft_structures(yaml_contents: Dict[str, Any]) → Dict[str, schrodinger.structure._structure.Structure]

Get the structures for the sequences in the input dictionary.

Parameters

yaml_contents – A dictionary describing the sequences to find scaffolds for and graft onto scaffolds. The dictionary can also contain other options.

schrodinger.application.bioluminate.antibody.antibody_modeling_yaml.model_fv_with_immunebuilder(seqs_by_ab_format: Dict[str, str])

Model the Fv with immunebuilder.

Parameters

seqs_by_ab_format – A dictionary containing the sequences for the input antibody format.

schrodinger.application.bioluminate.antibody.antibody_modeling_yaml.get_output_filename(jobname: str) → str

Get the output filename from the jobname.

Parameters

jobname – The name of the job.

schrodinger.application.bioluminate.antibody.antibody_modeling_yaml.run_from_yaml(yaml_contents: Dict[str, Any], jobname='antibody_modeling') → None

Run the antibody modeling pipeline from a yaml dictionary.

Parameters

yaml_contents – A dictionary containing the inputs for the antibody modeling pipeline.

schrodinger.application.bioluminate.antibody.antibody_modeling_yaml.add_fv_modeling_mode(assembly_dict: dict, use_ai: bool)