schrodinger.application.desmond.starter.ui.fep_absolute_binding module

Absolute binding FEP command line UI

Copyright Schrodinger, LLC. All rights reserved.

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

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

PROGRAM_NAME: str = 'Absolute Binding FEP'
SUPPORTED_FEP_TYPES: List[str] = ['absolute_binding']
copy_parser_attributes(opt: argparse.Namespace)

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


Validate the parameters.


SystemExit – For invalid parameters.

get_time_for_leg(leg_type: str) Optional[float]

Get simulation time for FEP leg. Implemented in subclasses of FepArgs.

__init__(opt: argparse.Namespace)

opt – Command line options with corresponding values.

check_duplicate_titles(sts: List[schrodinger.structure._structure.Structure])

Raise a warning if restarting and trying to set ppj.


UserWarning – If ppj set for a restarted job.


If the JOBNAME was not set and this is a new job, automatically generate a job name.

property mode: schrodinger.application.desmond.constants.UiMode

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_absolute_binding.ui(argv: List[str]) schrodinger.application.desmond.starter.ui.fep_absolute_binding.Args