schrodinger.application.desmond.starter.ui.fep_absolute_binding module

Absolute binding FEP command line UI

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.application.desmond.starter.ui.fep_absolute_binding.Args(opt: argparse.Namespace)

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

PROGRAM_NAME: str = 'Absolute Binding FEP'

SUPPORTED_FEP_TYPES: List[str] = ['absolute_binding']

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 for Absolute Binding FEP command line UI

Returns

a list of error messages for invalid parameters

get_time_for_leg(leg_type: str) → Optional[float]

Get simulation time for FEP leg. Implemented in subclasses of FepArgs.

__init__(opt: argparse.Namespace)

Parameters

opt – Command line options with corresponding values.

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

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 this is a new job, automatically generate a job name.

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

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.

schrodinger.application.desmond.starter.ui.fep_absolute_binding.get_abfep_options() → List[schrodinger.application.desmond.starter.ui.cmdline.Option]

Return a list of options for Absolute Binding FEP

Returns

list of ABFEP options

schrodinger.application.desmond.starter.ui.fep_absolute_binding.get_abfep_args_instance(argv: List[str]) → schrodinger.application.desmond.starter.ui.fep_absolute_binding.Args

Parse the arguments and return an Args object containing the values.

Parameters

argv – List of command line strings

Returns

Args instance that stores parsed Absolute Binding FEP options

schrodinger.application.desmond.starter.ui.fep_absolute_binding.ui(argv: List[str]) → schrodinger.application.desmond.starter.ui.fep_absolute_binding.Args

Parse, validate arguments and return an Args object containing the values.

Parameters

argv – List of command line strings

Returns

validated Args instance that stores parsed Absolute Binding FEP options