schrodinger.application.desmond.starter.ui.fep_plus module

FEP+ command line UI Version 0.1

Copyright Schrodinger, LLC. All rights reserved.

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

set_restart()

Set the RESTART flag if only the checkpoint is given.

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.

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

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

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