schrodinger.application.desmond.msj_generator.fep.solubility module

class schrodinger.application.desmond.msj_generator.fep.solubility.SolubilityMsjGenerator(jobname: str, cd_params: Dict[str, object], **kwargs)

Bases: schrodinger.application.desmond.msj_generator.common.BaseMsjGenerator

Generates the msj files needed to run the Solubility FEP workflow.

WorkflowParamsCls

alias of schrodinger.application.desmond.msj_generator.workflow_params.SolubilityWorkflowParams

__init__(jobname: str, cd_params: Dict[str, object], **kwargs)

See BaseMsjGenerator for a description of the input parameters.

In addition to these parameters, the following are supported.

Parameters

  • hydration_fep_sim_time – The simulation time for the Hydration FEP production stage.

  • sublimation_fep_sim_time – The simulation time for the Sublimation FEP production stage.

  • hydration_only – Set to True to only run the hydration leg.

  • solvation_only – Set to True to run the solvation protocol. Similar to hydration_only, but for non-water solvents.

  • rest_enabled – Set to True to enable REST sampling of ligand atoms for hydration/solvation legs and False to disable it. Default is True.

property fep_type
generate_main_msj() → schrodinger.utils.sea.sea.Map

Generate the main msj.

generate_solvation_msj() → schrodinger.application.desmond.multisim.parser.Msj
generate_subjob_msj(leg_type: schrodinger.application.desmond.constants.FepLegTypes) → schrodinger.application.desmond.multisim.parser.Msj
write_main_msj() → str

Write out the main msj and return the filename.

write_md_msj() → str

Write out the md msj and return the filename.

write_fep_msj()

Write out the fep msj files.