schrodinger.application.desmond.starter.generator.fep_plus module

FEP+ generator Version 0.1

Copyright Schrodinger, LLC. All rights reserved.

schrodinger.application.desmond.starter.generator.fep_plus.is_covalent(filename)

Determine if the given file is for covalent FEP. The file is either a .mae or a .fmp file, but for covalent FEP, it has to be the latter (a .mae file will cause this function to return False directly), and this function will check the fep_type graph property and return True if its value is ‘COVALENT_LIGAND’, or False if not.

Return type:bool

schrodinger.application.desmond.starter.generator.fep_plus.validate_covalent_fmp(filename)

Make sure the fmp file is generated by >= 19-2 release that adds i_fep_cov_protein_bb_atom to atom’s property.

schrodinger.application.desmond.starter.generator.fep_plus.prepare_report_stage_for_restart(engine: schrodinger.application.desmond.cmj.Engine, rst_stage_idx: int) → List[str]

If the FepMapperReport or FepMapperCleanup stage is present after the restart stage, include the FepMapper stage when restarting the job.

Parameters:

• engine – Represents the current job state.
• rst_stage_idx – The restart stage index.

Returns:

List of filenames to be used for restarting the job.

schrodinger.application.desmond.starter.generator.fep_plus.generate(args: schrodinger.application.desmond.starter.ui.fep_plus.FepPlusArgs) → List[str]

Generate the files and command line to run multisim for the FEP+ workflow.

Parameters:args – Object with input arguments. Returns:Command line to launch multisim Raises:SystemExit – If preparing the job without launching it.