schrodinger.application.desmond.stage.app.mxmd module

Multisim stages that relate to Mixed solvent MD.

schrodinger.application.desmond.stage.app.mxmd.normalize_probe_occupancy_grid(grid)

Convert the grid counts to z-scores by normalizing the grid. Since the grid contains probe occupancies, this matrix is mostly sparse (with ~1% of non- zero values) we need to omit all the zero-containing values from calculating of mean and standard deviation.

class schrodinger.application.desmond.stage.app.mxmd.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. Provide a custom_probe_dir to use custom <probe>.box.mae files. This should be a relative path pointing to a subdirectory of the launch directory

NAME = 'mixed_solvent_setup'

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

check_param()

Check that the necessary box .mae files for the specified probes exist

collect_inputfile()

Get any probe boxes specified by user that are in the provided custom directory

crunch()

Generate a solvent box for each specified cosolvent

class schrodinger.application.desmond.stage.app.mxmd.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.sea.Map object>

crunch()

Calculate occupancy grids, write .cns and .raw files

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

Bases: schrodinger.application.desmond.cmj.StageBase

NAME = 'mixed_solvent_cleanup'

TAG = 'MIXED_SOLVENT_CLEANUP'

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

crunch()

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

poststage()

class schrodinger.application.desmond.stage.app.mxmd.GenerateMxmdBox(*args, **kwargs)

Bases: schrodinger.application.desmond.cmj.StructureStageBase

Solvate cosolvent CT with water to produce an output system with 50% water:cosolvent weight/weight

NAME = 'generate_mxmd_box'

run(jobname: str, cms_fname: str) → str

Parameters

• jobname – Jobname for this stage.

• input_fname – Filename for the input structure.

Returns

Filename for the output structure or None if there was an error generating the output.

class schrodinger.application.desmond.stage.app.mxmd.AnalyzeMxmdProbeMixture(should_pack=True)

Bases: schrodinger.application.desmond.cmj.StageBase

Analyze the solvent/cosolvent trajectories to determine miscibility.

NAME = 'analyze_mxmd_probe_mixture'

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

crunch()

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