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, 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_chain_structures_from_model(modeled_structures: Dict[tuple, Structure])¶
Get the chain structures from the modeled structures.
- Parameters:
modeled_structures – A dictionary containing the modeled structures.
- schrodinger.application.bioluminate.antibody.antibody_modeling_yaml.get_output_filename(output_file_set_value: str, jobname: str) str¶
Get the output filename from the jobname.
- Parameters:
output_file_set_value – The current output file value.
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_wam_property(filename: str)¶
- schrodinger.application.bioluminate.antibody.antibody_modeling_yaml.add_fv_modeling_mode(assembly_dict: dict, use_ai: bool)¶
- schrodinger.application.bioluminate.antibody.antibody_modeling_yaml.remove_pdb_id_label(st: Structure) None¶
Remove the PDB ID label from the structure.
- Parameters:
st – The structure to remove the PDB ID label from.
- schrodinger.application.bioluminate.antibody.antibody_modeling_yaml.remove_labels(st: Structure) None¶
Remove the labels from the structure. These labels include “Flip” and “HIE” labels.
- Parameters:
st – The structure to remove the labels from.
- schrodinger.application.bioluminate.antibody.antibody_modeling_yaml.remove_hetatms(st: Structure) None¶
Finds all het groups in the st and removes them. A “het” is a group of atoms which are bound to each other and are not in any standard residues. This includes ligands (including covalently bound ones), ions, cofactors, etc.
Instead of using ‘include_hydrogens=True’ in the ‘find_hets’ function, we remove the hydrogen atoms from the het groups by iterating over the atoms in the group and checking if they are bonded to a hydrogen atom.
- Parameters:
st – The structure to remove the hetatms from.