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
toself
. 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