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.

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