Package Pmv :: Module msmsCommands :: Class ComputeMSMSApprox
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Class ComputeMSMSApprox

source code

 ViewerFramework.VFCommand.Command --+        
                                     |        
                   mvCommand.MVCommand --+    
                                         |    
ViewerFramework.VFCommand.ICOM --+       |    
                                 |       |    
                  mvCommand.MVICOM --+   |    
                                     |   |    
                  mvCommand.MVAtomICOM --+    
                                         |    
                               ComputeMSMS --+
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                                            ComputeMSMSApprox

Computes an approximative molecular surface for a selected set of atoms by molecule.
 
    Package : Pmv

    Module  : msmsCommands

    Class   : ComputeMSMSApprox

    Command name : computeMSMSApprox

    
Description:

    This approximation is done by replacing each residue by a sphere. The center of the sphere is geometric center of the atoms in the  residue. The radius is set to include all atoms.

    
Synopsis:

    None<---mv.computeMSMSapprox(nodes,surfName='MSMSMOL',pRadius=1.5,density=1.0,nbSphPerRes=1, perMol=True, display=1)

    
Required Arguments :

        nodes --- current selection

    
Optional Arguments:

    surfName --- name of the surfname which will be used as the key in
                mol.geomContainer.msms dictionary. If the surfName is
                already a key of the msms dictionary the surface is
                recreated. By default MSMS-MOL

    pRadius  --- probe radius (1.5)

    density --- triangle density to represent the surface. (1.0)

    perMol  --- when this flag is True a surface is computed for each molecule
                having at least one node in the current selection
                else the surface is computed for the current selection.
                (True)

    display --- flag when set to 1 the displayMSMS will be executed to
                display the new msms surface.

                
    nbSphPerRes --- number of approximating spheres per residue,default=1, possible values 1 or 2


    



Instance Methods [hide private]
  computeResidueSpheres(self, residues, nbSphPerRes=1)
Compute the geometric centers and the radii of the spheres that will cover each residue
  doit(self, nodes, surfName='MSMS-MOL', pRadius=1.5, density=1.0, perMol=True, display=True, nbSphPerRes=1)
Required Arguments: nodes --- current selection surfName --- name of the surfname which will be used as the key in mol.geomContainer.msms dictionary.
  __call__(self, nodes, surfName='MSMS-MOL', pRadius=1.5, density=1.0, nbSphPerRes=1, perMol=True, display=True, **kw)
None<---mv.computeMSMSapprox(nodes,surfName='MSMSMOL',pRadius=1.5,density=1.0,nbSphPerRes=1, perMol=True, display=1) Required Arguments: nodes --- current selection Optional arguments: surfName --- name of the surfname which will be used as the key in mol.geomContainer.msms dictionary.
  guiCallback(self)

Inherited from ComputeMSMS: __init__, atomPropToVertices, buildFormDescr, checkDependencies, entryValidate, fixValues, onAddCmdToViewer, onAddObjectToViewer, perMol_cb, pickedVerticesToAtoms, pickedVerticesToBonds, saveSel_cb, setTexCoords, updateCBB, updateForm, updateTexCoords

Inherited from mvCommand.MVCommand: strArg

Inherited from mvCommand.MVCommand (private): _strArg

Inherited from ViewerFramework.VFCommand.Command: __repr__, addCallbackAfter, addCallbackBefore, addUndoCall, afterDoit, beforeDoit, buildLogArgList, cleanup, customizeGUI, doitWrapper, getArguments, getHelp, getLastUsedValues, getLogArgs, getValNamedArgs, log, logString, onAddNewCmd, onCmdRun, setLastUsedValues, setupUndoAfter, setupUndoBefore, showForm, tkCb, updateGeom, warningMsg

Inherited from mvCommand.MVAtomICOM: getObjects

Inherited from ViewerFramework.VFCommand.ICOM: initICOM, startICOM, stopICOM


Class Variables [hide private]

Inherited from ViewerFramework.VFCommand.Command: negateKw, objArgOnly


Method Details [hide private]

computeResidueSpheres(self, residues, nbSphPerRes=1)

source code 
Compute the geometric centers and the radii of the spheres that will cover each residue

doit(self, nodes, surfName='MSMS-MOL', pRadius=1.5, density=1.0, perMol=True, display=True, nbSphPerRes=1)

source code 
Required Arguments:
        
        nodes   ---  current selection

        surfName --- name of the surfname which will be used as the key in
                    mol.geomContainer.msms dictionary.

        
Optional Arguments:  
      
        pRadius  --- probe radius (1.5)

        density  --- triangle density to represent the surface. (1.0)

        perMol   --- when this flag is True a surface is computed for each 
                    molecule having at least one node in the current selection
                    else the surface is computed for the current selection.
                    (True)

        display  --- flag when set to True the displayMSMS will be executed with
                    the surfName else not.

        hdset    --- Atom set for which high density triangualtion 
                     will be generated
        hdensity --- vertex density for high density
        

Overrides: ComputeMSMS.doit
(inherited documentation)

__call__(self, nodes, surfName='MSMS-MOL', pRadius=1.5, density=1.0, nbSphPerRes=1, perMol=True, display=True, **kw)
(Call operator)

source code 
None<---mv.computeMSMSapprox(nodes,surfName='MSMSMOL',pRadius=1.5,density=1.0,nbSphPerRes=1, perMol=True, display=1)

           
Required Arguments:
 
           nodes    ---  current selection

           
Optional arguments:

           surfName --- name of the surfname which will be used as the key in mol.geomContainer.msms dictionary. If the surfName is already a key of the msms dictionary the surface is recomputed. (default MSMS-MOL)

           pRadius  --- probe radius (1.5)

           density  --- triangle density to represent the surface. (1.0)

           nbSphPerRes --- number of approximating spheres per residue,default=1, possible values 1 or 2

           perMol   --- when this flag is True a surface is computed for each molecule having at least one node in the current selection else the surface is computed for the current selection.(True)

           display  --- flag when set to 1 the displayMSMS will be executed with the surfName else not.

Overrides: ComputeMSMS.__call__

guiCallback(self)

source code 
None
Overrides: ComputeMSMS.guiCallback