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, inp_file: str = None)

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

set_restart()

Set the RESTART flag if only the checkpoint is given.

validate()

Validate the parameters for missing files.

Raises:SystemExit – For invalid parameters.

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