schrodinger.application.desmond.starter.ui.fep_plus module

FEP+ command line UI Version 0.1

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.application.desmond.starter.ui.fep_plus.FepPlusArgs(opt: argparse.Namespace, argv=None)

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

PROGRAM_NAME: str = 'FEP+'
SUPPORTED_FEP_TYPES: List[str] = ['small_molecule', 'metalloprotein', 'covalent_ligand', 'protein_selectivity', 'prm_stability', 'ligand_selectivity', 'prm_protein_binding', 'prm_ligand_binding', 'prm_thermostability']
__init__(opt: argparse.Namespace, argv=None)
Parameters

opt – Command line options with corresponding values.

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 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.

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_plus.ui(argv: List[str]) schrodinger.application.desmond.starter.ui.fep_plus.FepPlusArgs

Parse the arguments and return an object containing the values.

Parameters

argv – List of command line arguments

Returns

Parsed FEP+ options

schrodinger.application.desmond.starter.ui.fep_plus.get_fep_plus_options() List[schrodinger.application.desmond.starter.ui.cmdline.Option]

Return a list of options for fep_plus

Returns

list of fep_plus options