schrodinger.application.desmond.starter.ui.bpfep module

Binding-pose FEP command line UI

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.application.desmond.starter.ui.bpfep.Args(opt: argparse.Namespace)

Bases: schrodinger.application.desmond.starter.ui.cmdline.BaseArgs

__init__(opt: argparse.Namespace)

Parameters:opt – Command line options with corresponding values.

validate()

Validate the parameters.

Raises:SystemExit – For invalid parameters.

check_ppj()

Raise a warning if restarting and trying to set ppj.

Raises:UserWarning – If ppj set for a restarted job.

copy_parser_attributes(opt: argparse.ArgumentParser)

Copy parser options (e.g: time, buffer, …) from opt to self. Subclass needs to call this method in __init__

generate_jobname()

If the JOBNAME was not set and not RESTART’ing, automatically generate a job name.

set_mps_factor(val)

Set the mps oversubcription factor. If val is auto, the mps factor will be determined automatically. Otherwise it is set directly, and should have an int value. 0 is treated equivalently to the value 1.

set_restart()

Set the RESTART flag if only the checkpoint is given.

schrodinger.application.desmond.starter.ui.bpfep.ui(argv: List[str]) → schrodinger.application.desmond.starter.ui.bpfep.Args