schrodinger.application.desmond.starter.ui.cmdline module¶

Starter backbone

class schrodinger.application.desmond.starter.ui.cmdline.Option(name, default, help, dest, other_kwargs)¶

Bases: tuple

name¶: Alias for field number 0

default¶: Alias for field number 1

help¶: Alias for field number 2

dest¶: Alias for field number 3

other_kwargs¶: Alias for field number 4

__add__¶: Return self+value.

__annotations__ = {'default': <class 'object'>, 'dest': typing.Dict, 'help': <class 'str'>, 'name': <class 'str'>, 'other_kwargs': typing.Dict}¶

__class__¶: alias of builtins.type

__contains__¶: Return key in self.

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__getitem__¶: Return self[key].

__getnewargs__()¶: Return self as a plain tuple. Used by copy and pickle.

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__¶: Initialize self. See help(type(self)) for accurate signature.

__init_subclass__()¶

This method is called when a class is subclassed.

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

__iter__¶: Implement iter(self).

__le__¶: Return self<=value.

__len__¶: Return len(self).

__lt__¶: Return self<value.

__module__ = 'schrodinger.application.desmond.starter.ui.cmdline'¶

__mul__¶: Return self*value.n

__ne__¶: Return self!=value.

static __new__(_cls, name, default, help, dest=None, other_kwargs={})¶: Create new instance of Option(name, default, help, dest, other_kwargs)

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__()¶: Return a nicely formatted representation string

__rmul__¶: Return self*value.

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__slots__ = ()¶

__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).

count(value) → integer -- return number of occurrences of value¶

index(value[, start[, stop]]) → integer -- return first index of value.¶: Raises ValueError if the value is not present.

schrodinger.application.desmond.starter.ui.cmdline.define_options(parser: argparse.ArgumentParser, options: List[schrodinger.application.desmond.starter.ui.cmdline.Option])¶

Define the options on a specified parser.

Parameters:	parser – Add options to this parser. options – List of options in the format (name, default, help, destination).

schrodinger.application.desmond.starter.ui.cmdline.parse_options(usage: str, options: List[schrodinger.application.desmond.starter.ui.cmdline.Option], argv: List[str]) → Tuple[argparse.Namespace, Union[str, NoneType]]¶

Parse and return the parsed options.

Parameters:	usage – Usage to display if no arguments given. options – List of options in the format (name, default, help, destination). argv – List of input arguments.
Returns:	Parsed options.
Raises:	SystemExit – If no arguments given, show the usage and exit.

schrodinger.application.desmond.starter.ui.cmdline.get_parser(usage: str, options: List[schrodinger.application.desmond.starter.ui.cmdline.Option], add_help: bool = True) → argparse.ArgumentParser¶

Return a parser with the specified options.

Parameters:	usage – Usage to display if no arguments given. options – List of options in the format (name, default, help, destination). add_help – Whether to add help flag to the parser
Returns:	Configured parser

schrodinger.application.desmond.starter.ui.cmdline.get_common_options() → List[schrodinger.application.desmond.starter.ui.cmdline.Option]¶

Return list of options common to all fep scripts.

Returns:	List of options that are common to all fep scripts.

class schrodinger.application.desmond.starter.ui.cmdline.BaseArgs(opt: argparse.Namespace, inp_file: str = None)¶

Bases: object

Base class for arguments.

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

Parameters:	opt – Command line options with corresponding values. inp_file – Input file name

validate()¶

Validate the parameters for missing files.

Raises:	SystemExit – For invalid parameters.

check_ppj()¶

Raise a warning if restarting and trying to set ppj.

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

set_restart()¶: Set the RESTART flag if only the checkpoint is given.

generate_jobname()¶: If the JOBNAME was not set and not RESTART’ing, automatically generate a job name.

__str__()¶: Return str(self).

__class__¶: alias of builtins.type

__delattr__¶: Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.starter.ui.cmdline', '__doc__': '\n Base class for arguments.\n ', '__init__': <function BaseArgs.__init__>, 'validate': <function BaseArgs.validate>, 'check_ppj': <function BaseArgs.check_ppj>, 'set_restart': <function BaseArgs.set_restart>, 'generate_jobname': <function BaseArgs.generate_jobname>, '__str__': <function BaseArgs.__str__>, '__dict__': <attribute '__dict__' of 'BaseArgs' objects>, '__weakref__': <attribute '__weakref__' of 'BaseArgs' objects>})¶

__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).