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.