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)¶