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

__init__(opt: argparse.Namespace, inp_file: str = None)

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 for missing files.

Raises:SystemExit – For invalid parameters.

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.starter.ui.fep_plus', '__init__': <function FepPlusArgs.__init__>, 'set_restart': <function FepPlusArgs.set_restart>, 'validate': <function FepPlusArgs.validate>, '__doc__': None})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.desmond.starter.ui.fep_plus'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__()

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

check_ppj()

Raise a warning if restarting and trying to set ppj.

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

generate_jobname()

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

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