schrodinger.application.desmond.starter.ui.fep_solubility module¶
FEP+ solubility command line UI
Copyright Schrodinger, LLC. All rights reserved.
-
class
schrodinger.application.desmond.starter.ui.fep_solubility.
FepSolubilityArgs
(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 for missing files.
- Raises
SystemExit – For invalid parameters.
-
set_restart
()¶ Set the RESTART flag if only the checkpoint is given.
-
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
toself
. 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 anint
value.0
is treated equivalently to the value1
.
-
-
schrodinger.application.desmond.starter.ui.fep_solubility.
ui
(argv: List[str]) → schrodinger.application.desmond.starter.ui.fep_solubility.FepSolubilityArgs¶ Parse the arguments and return an object containing the values.
- Parameters
argv – List of command line arguments
- Returns
Parsed command line options