schrodinger.application.desmond.msj_generator.fep.small_molecule module

class schrodinger.application.desmond.msj_generator.fep.small_molecule.SmallMoleculeMsjGenerator(jobname, cd_params, **kwargs)

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

WorkflowParamsCls

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

property fep_type

modify_fep_launcher_stage(msj)

Add the fragment linking and vacuum jobs to the fep_launcher stage. Other jobs are added from FepBaseMsjGenerator.

generate_subjob_msj(leg_type='complex', protocol='default', **kwargs)

write_subjob_msjs()

Write the msjs for each leg type. Subclasses which run additional legs should override and write the additional msjs

write_complex_msj()

Write the complex subjob msjs.

write_solvent_msj()

Write the solvent subjob msjs.

write_vacuum_msj()

generate_vacuum_msj(protocol='default') → schrodinger.application.desmond.multisim.parser.Msj