schrodinger.application.livedesign.ld_strain_rescore_utils module

schrodinger.application.livedesign.ld_strain_rescore_utils.deduplicate_strain_rescore_input(input_file: str, corpid_dict: Dict[str, str]) → Tuple[str, Dict[str, str]]

Rename duplicate ligands in the input file.

Parameters

  • input_file – Input ligand file

  • corpid_dict – Dict of structure titles to corp_id

Returns

File name of the deduplicated input file and a dict of ligand titles

schrodinger.application.livedesign.ld_strain_rescore_utils.process_strain_rescore_outfiles(strain_rescore_outfiles: List[str]) → Tuple[Dict[str, Dict[str, float]], Dict[str, Dict[str, str]], Dict[str, Dict[str, float]]]

Parse the results from the Ligand Strain calculation.

Parameters

strain_rescore_outfiles – List of output file from the Strain Rescore calculation

Returns

Dictionaries of Corp ID to strain energy, structure file, and MMGBSA results

schrodinger.application.livedesign.ld_strain_rescore_utils.write_result_row(corp_id: str, lig_title: str, strain_energy_dict: Dict[str, Dict[str, float]], mmgbsa_dict: Dict[str, Dict[str, float]], st_file_dict: Dict[str, Dict[str, str]], st_type: str, prot: Optional[str] = None, grid_file: Optional[str] = None) → Dict[str, Union[str, float]]

Write the result row for the strain rescore calculation.

Parameters

  • corp_id – Corporate ID of the ligand

  • lig_title – Title of the ligand to query the dict

  • strain_energy_dict – A dictionary of strain energy results

  • mmgbsa_dict – A dictionary of MMGBSA results

  • st_file_dict – A dictionary of structure files

  • st_type – orig_st, local_st, or global_st

  • prot – Protein structure file

  • grid_file – The grid file used for the best Glide docking

Returns

A dictionary containing the results

schrodinger.application.livedesign.ld_strain_rescore_utils.parse_strain_rescore_results(strain_rescore_outfiles: List[str], lig_prot_dict: Dict[str, str], corpid_dict: Dict[str, str], backend: schrodinger.job.jobcontrol._Backend, grid_file: Optional[str] = None) → Tuple[List[Dict[str, Union[str, float]]], set]

Parse the results from the Ligand Strain calculation.

Parameters

  • strain_rescore_outfiles – List of output file from the Strain Rescore calculation

  • lig_prot_dict – A dictionary of ligand-protein complexes

  • corpid_dict – dict of structure titles to corp_id

  • backend – the _Backend object of Jobcontrol

  • grid_file – The grid file used for the best Glide docking

Returns

A list of result dictionaries and Corp IDs of completed ligands