schrodinger.application.desmond.mxmd.mxmd_stage module

Multisim stages that relate to Mixed solvent MD.

class schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventSetup(should_pack=True)

Bases: schrodinger.application.desmond.cmj.StageBase

Multisim stage that builds a cosolvent system. Setting acetonitrile, isopropanol and pyrimidine as default probes as they are water-miscible.

NAME = 'mixed_solvent_setup'

PARAM = <schrodinger.utils.sea.Map object>

crunch()

This is where jobs of this stage are created. This function should be overriden by the subclass.

class schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventAnalysis(should_pack=True)

Bases: schrodinger.application.desmond.cmj.StageBase

Analyze cosolovent probes around a the protein.

NAME = 'mixed_solvent_analysis'

PARAM = <schrodinger.utils.sea.Map object>

crunch()

Calculate occupancy grids, write .cns and .raw files

class schrodinger.application.desmond.mxmd.mxmd_stage.MixedSolventCleanup(should_pack=True)

Bases: schrodinger.application.desmond.cmj.StageBase

NAME = 'mixed_solvent_cleanup'

TAG = 'MIXED_SOLVENT_CLEANUP'

PARAM = <schrodinger.utils.sea.Map object>

crunch()

This is where jobs of this stage are created. This function should be overriden by the subclass.

poststage()