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

Starter backbone

Copyright Schrodinger, LLC. All rights reserved.

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

__contains__

Return key in self.

__init__

Initialize self. See help(type(self)) for accurate signature.

__len__

Return len(self).

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_known_options(usage: str, options: List[schrodinger.application.desmond.starter.ui.cmdline.Option], argv: List[str]) → Tuple[argparse.Namespace, Optional[str]]

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:

(Known parsed options, unknown options)
Raises:

SystemExit – If no arguments given, show the usage and exit.
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, Optional[str]]

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 or if there is unknown arguments, 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)

Bases: object

Base class for arguments.

__init__(opt: argparse.Namespace)
Parameters:
  • opt – Command line options with corresponding values.
  • inp_file – Input file name
validate()

Validate the parameters.

Raises:SystemExit – For invalid parameters.
copy_parser_attributes(opt)

Copy parser options (e.g: time, buffer, …) from ArgumentParser to self.

Subclass needs to call this method in __init__

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.