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

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

schrodinger.application.desmond.starter.ui.cmdline.get_sim_time_message(default_time: float, leg_type: Optional[str] = None, default_arg: Optional[str] = None)¶: Get the help message for the sim time arguments to the FEP interfaces

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

Bases: NamedTuple

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

group: str¶: Alias for field number 4

class schrodinger.application.desmond.starter.ui.cmdline.SingleOptionAction(*args, **kwargs)¶

Bases: argparse.Action

Argparse action handler that only allows a flag to be used once.

__init__(*args, **kwargs)¶

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 scripts.

schrodinger.application.desmond.starter.ui.cmdline.get_common_fep_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, List[str], argparse.ArgumentParser]¶

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) → argparse.Namespace¶

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_discontinued_args(args: List[str])¶: Check for the presence of arguments that have been removed and exit if any are used.

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.

SUPPORTED_OPLS_VERSIONS = (16, 17)¶

__init__(opt: argparse.Namespace)¶

Parameters: opt – Command line options with corresponding values.

property mode: schrodinger.application.desmond.constants.UiMode¶

classmethod get_supported_ff_names() → List[str]¶

Return the display names of the supported forcefields for the FEP+ workflow.

Other names are supported since they map to the same version, but for simplicity we only show the display names to the user.

validate() → List[str]¶

Validate the parameters.

Returns: a list of error messages for invalid parameters

copy_parser_attributes(opt: argparse.Namespace)¶: Copy parser options (e.g: time, buffer, …) from opt to self. Subclass needs to call this method in __init__

generate_jobname()¶: If the JOBNAME was not set and this is a new job, 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.

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

Bases: schrodinger.application.desmond.starter.ui.cmdline.BaseArgs

PROGRAM_NAME: str¶

SUPPORTED_FEP_TYPES: List[str]¶

property mode: schrodinger.application.desmond.constants.UiMode¶

copy_parser_attributes(opt: argparse.Namespace)¶: Copy parser options (e.g: time, buffer, …) from opt to self. Subclass needs to call this method in __init__

validate() → List[str]¶

Validate the parameters.

Returns: a list of error messages for invalid parameters

check_ppj()¶

Raise a warning if restarting and trying to set ppj.

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

check_duplicate_titles(sts: List[schrodinger.structure._structure.Structure])¶

get_time_for_leg(leg_type: str) → Optional[float]¶: Get simulation time for FEP leg. Implemented in subclasses of FepArgs.

schrodinger.application.desmond.starter.ui.cmdline.get_fep_supported_ff_names(use_display_name: bool = True) → List[str]¶

Return a list of OPLS names that are supported by FEP products. The function first gets the available OPLS, and eliminates OPLS versions specified by UNSUPPORTED_OPLS_VERSIONS.

Parameters: use_display_name – whether to return OPLS in their common name or display name
Returns: A tuple containing all the OPLS supported by FEP

schrodinger.application.desmond.starter.ui.cmdline.verify_args_validate(args_obj: schrodinger.application.desmond.starter.ui.cmdline.BaseArgs)¶

Verifies that no validation error occurs

Parameters: args_obj – instance of BaseArgs or its subclass
Raises: SystemExit – for invalid arguments