schrodinger.application.desmond.starter.ui.fep_plus module¶
FEP+ command line UI Version 0.1
Copyright Schrodinger, LLC. All rights reserved.
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class
schrodinger.application.desmond.starter.ui.fep_plus.FepPlusArgs(opt: argparse.Namespace, argv=[])¶ Bases:
schrodinger.application.desmond.starter.ui.cmdline.BaseArgs-
__init__(opt: argparse.Namespace, argv=[])¶ Parameters: - opt – Command line options with corresponding values.
- inp_file – Input filename
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set_restart()¶ Set the RESTART flag if only the checkpoint is given.
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validate()¶ Validate the parameters.
Raises: SystemExit – For invalid parameters.
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check_ppj()¶ Raise a warning if restarting and trying to set ppj.
Raises: UserWarning – If ppj set for a restarted job.
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copy_parser_attributes(opt)¶ Copy parser options (e.g: time, buffer, …) from ArgumentParser to
self.Subclass needs to call this method in __init__
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generate_jobname()¶ If the JOBNAME was not set and not RESTART’ing, automatically generate a job name.
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schrodinger.application.desmond.starter.ui.fep_plus.ui(argv: List[str]) → schrodinger.application.desmond.starter.ui.fep_plus.FepPlusArgs¶ Parse the arguments and return an object containing the values.
Parameters: argv – List of command line arguments Returns: Parsed FEP+ options
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schrodinger.application.desmond.starter.ui.fep_plus.get_fep_plus_parser(add_help: bool = True) → argparse.ArgumentParser¶ Return a parser configured with fep_plus command line options
Parameters: add_help – Whether to add help flag to the parser Returns: fep_plus command line parser
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schrodinger.application.desmond.starter.ui.fep_plus.get_fep_plus_options() → List[schrodinger.application.desmond.starter.ui.cmdline.Option]¶ Return a list of options for fep_plus
Returns: list of fep_plus options