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

FEP+ command line UI Version 0.1

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

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)¶

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()¶

Validate the 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.

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.

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.

schrodinger.application.desmond.starter.ui.fep_plus.get_fep_plus_parser(add_help: bool = True) → argparse.ArgumentParser¶

Return a parser configured with fep_plus command line 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