Package Pmv :: Module msmsCommands :: Class ComputeMSMS
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Class ComputeMSMS

source code

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

The computeMSMS command will compute a triangulated solvent excluded surface for the current selection.

    Package : Pmv

    Module  : msmsCommands

    Class   : ComputeMSMS

    Command name : computeMSMS

    
Synopsis :

    None <--- mv.computeMSMS(nodes, surfName=None, pRadius=1.5,
                           density=1.0, 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 mol.name-MSMS

    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.

                    
    



Instance Methods [hide private]
  __init__(self, func=None)
  checkDependencies(self)
virtual method.
  onAddCmdToViewer(self)
method called when an instance of this command is added to the viewer.
  onAddObjectToViewer(self, obj)
  atomPropToVertices(self, geom, atoms, propName, propIndex=None)
Function called to map atomic properties to the vertices of the geometry
  pickedVerticesToBonds(self, geom, parts, vertex)
  pickedVerticesToAtoms(self, geom, vertInd)
Function called to convert picked vertices into atoms
  __call__(self, nodes, surfName='MSMS-MOL', pRadius=1.5, density=3.0, perMol=True, display=True, hdset='None', hdensity=6.0, **kw)
None <- mv.computeMSMS(nodes, surfName='MSMSMOL', pRadius=1.5,density=1.0,perMol=True, display=1) Required Arguments : nodes --- atomic fragment (string or objects) Optional Arguments : surfName --- name of the surfname which will be used as the key in mol.geomContainer.msms dictionary.
  fixValues(self, val)
  guiCallback(self)
Default callback function called by the gui
  doit(self, nodes, surfName='MSMS-MOL', pRadius=1.5, density=1.0, perMol=True, display=True, hdset=None, hdensity=6.0)
Required Arguments: nodes --- current selection surfName --- name of the surfname which will be used as the key in mol.geomContainer.msms dictionary.
  buildFormDescr(self, formName='default')
descr <- buildFormDescr(self, formName): this virtual method is implemented in the classes derived from Command.
  setTexCoords(self, mol, values)
  updateTexCoords(self, mol)
  updateForm(self, surfName)
  entryValidate(self, text)
Method to validate the name of the msms surface.
  updateCBB(self)
  perMol_cb(self, event=None)
  saveSel_cb(self, event=None)

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]

__init__(self, func=None)
(Constructor)

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None
Overrides: mvCommand.MVCommand.__init__

checkDependencies(self)

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virtual method. Has to be implemented by the sub classes. Method called when command is loaded, if all the dependencies are not found the command won't be loaded.
Overrides: ViewerFramework.VFCommand.Command.checkDependencies
(inherited documentation)

onAddCmdToViewer(self)

source code 
method called when an instance of this command is added to the viewer. This enable viewer-addition time initializations
Overrides: ViewerFramework.VFCommand.Command.onAddCmdToViewer
(inherited documentation)

onAddObjectToViewer(self, obj)

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atomPropToVertices(self, geom, atoms, propName, propIndex=None)

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Function called to map atomic properties to the vertices of the geometry

pickedVerticesToBonds(self, geom, parts, vertex)

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None

pickedVerticesToAtoms(self, geom, vertInd)

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Function called to convert picked vertices into atoms

__call__(self, nodes, surfName='MSMS-MOL', pRadius=1.5, density=3.0, perMol=True, display=True, hdset='None', hdensity=6.0, **kw)
(Call operator)

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


Required Arguments :

    nodes ---  atomic fragment (string or objects)


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)

    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.

    hdset    --- Atom set (or name) for which high density triangualtion will
                 be generated
    hdensity --- vertex density for high density

Overrides: ViewerFramework.VFCommand.Command.__call__

fixValues(self, val)

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None

guiCallback(self)

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Default callback function called by the gui
Overrides: mvCommand.MVCommand.guiCallback

doit(self, nodes, surfName='MSMS-MOL', pRadius=1.5, density=1.0, perMol=True, display=True, hdset=None, hdensity=6.0)

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: ViewerFramework.VFCommand.Command.doit

buildFormDescr(self, formName='default')

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descr <- buildFormDescr(self, formName): this virtual method is implemented in the classes derived from Command. This is where the inputFormDescr is created and the description of the widgets appended. If a command has several inputForm buildFormDescr should build all the inputFormDescr and you do a if / elif check to know which one to create. formName : string name of the form corresponding to this descr.
Overrides: ViewerFramework.VFCommand.Command.buildFormDescr
(inherited documentation)

setTexCoords(self, mol, values)

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None

updateTexCoords(self, mol)

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None

updateForm(self, surfName)

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None

entryValidate(self, text)

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Method to validate the name of the msms surface. This name will be used by other command to build Pmw widget so it can't contain an '_'.

updateCBB(self)

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None

perMol_cb(self, event=None)

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None

saveSel_cb(self, event=None)

source code 
None