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

Common command line arguments Lightweight framework for defining new command line arguments.

Copyright Schrodinger, LLC. All rights reserved.

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

Bases: tuple

name: Union[str, List]

Alias for field number 0

default: object

Alias for field number 1

help: str

Alias for field number 2

dest: Dict

Alias for field number 3

__contains__(key, /)

Return key in self.

__len__()

Return len(self).

count(value, /)

Return number of occurrences of value.

index(value, start=0, stop=9223372036854775807, /)

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, dest).

schrodinger.application.desmond.starter.ui.cmdline.auto_int(string)

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.

schrodinger.application.desmond.starter.ui.cmdline.suppress_options(options: List[schrodinger.application.desmond.starter.ui.cmdline.Option], excluded: Set[str])

Modify the options as specified by excluded by replacing the help text with argparse.SUPPRESS, which will effectively hide the specified options in the command line. No effects if either options or excluded is an empty container.

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

Return a command-line parser with the given options.

Parameters

• usage – Usage to display if no arguments given.

• options – List of options

• add_help – Whether to add help flag to the parser

Returns

Configured command-line parser

schrodinger.application.desmond.starter.ui.cmdline.parse_known_options(usage: str, options: List[schrodinger.application.desmond.starter.ui.cmdline.Option], argv: List[str], add_subhost: bool = True) → 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], add_subhost: bool = True) → 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, dest).

• argv – List of input arguments

• add_subhost – Add the -SUBHOST option?

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.check_jobname(jobname: str) → Optional[str]

Check whether the given job name contains problematic characters. It cannot start with a “-” or contain a “=”.

class schrodinger.application.desmond.starter.ui.cmdline.BaseArgs(opt: argparse.Namespace)

Bases: object

Base class for arguments. A subclass of this class contains all the command-line arguments. The jobcontrol-related arguments, which are consumed by the toplevel script, are recovered.

__init__(opt: argparse.Namespace)

Parameters

opt – Command line options with corresponding values.

validate()

Validate the parameters.

Raises

SystemExit – For invalid parameters.

copy_parser_attributes(opt: argparse.ArgumentParser)

Copy parser options (e.g: time, buffer, …) from opt 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.

set_mps_factor(val)

Set the mps oversubcription factor. If val is auto, the mps factor will be determined automatically. Otherwise it is set directly, and should have an int value. 0 is treated equivalently to the value 1.