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