schrodinger.application.desmond.starter.generator.fep_plus module¶
FEP+ generator Version 0.1
Copyright Schrodinger, LLC. All rights reserved.
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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
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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.
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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.
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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.