Package Pmv :: Module secondaryStructureCommands :: Class DisplayExtrudedSSCommand
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Class DisplayExtrudedSSCommand

source code

 ViewerFramework.VFCommand.Command --+        
                                     |        
                   mvCommand.MVCommand --+    
                                         |    
ViewerFramework.VFCommand.ICOM --+       |    
                                 |       |    
                  mvCommand.MVICOM --+   |    
                                     |   |    
                  mvCommand.MVAtomICOM --+    
                                         |    
            displayCommands.DisplayCommand --+
                                             |
                                            DisplayExtrudedSSCommand

The DisplaySSCommand displays the geometries representing the secondary structure elements of the current selection.To execute this command use the 'Display Secondary Structure' entry under the 'Display' menu in the menu bar.
    
Package : Pmv
    
Module  : secondaryStructureCommands
    
Class   : DisplayExtrudedSSCommand
    
Command name : displaySecondaryStructure
    
Synopsis:

        None <- displaySecondaryStructure(nodes, only=False,
                   negate=False,**kw)
    
Required Arguments:

        nodes --- TreeNodeSet holding the current selection
    
Optional Arguments:

        only --- allows the user to display only the current selection when set to 1
        
negate --- allows to undisplay the current selection when set to 1.
    
This command is undoable.
    



Instance Methods [hide private]
  getNodes(self, nodes)
expand nodes argument into a list of residues sets and a list of molecules.
  onAddCmdToViewer(self)
  setupUndoBefore(self, nodes, only=False, negate=False)
This method builds the self.undoCmds string.
  doit(self, nodes, only=False, negate=False)
displays the secondary structure for the selected treenodes
  cleanup(self)
Method called by afterDoit to clean up things eventhough the doit failes.
  __call__(self, nodes, only=False, negate=False, **kw)
None <- displaySecondaryStructure(nodes, only=False,...
  getResiduesBySS(self, residues, chain)

Inherited from displayCommands.DisplayCommand: __init__, buildFormDescr, getFormValues, getLastUsedValues, guiCallback, handleDisplayValue, handleNegateOnly, setLastUsedValues, updateGeom

Inherited from mvCommand.MVCommand: strArg

Inherited from mvCommand.MVCommand (private): _strArg

Inherited from ViewerFramework.VFCommand.Command: __repr__, addCallbackAfter, addCallbackBefore, addUndoCall, afterDoit, beforeDoit, buildLogArgList, checkDependencies, customizeGUI, doitWrapper, getArguments, getHelp, getLogArgs, getValNamedArgs, log, logString, onAddNewCmd, onCmdRun, setupUndoAfter, showForm, tkCb, 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]

getNodes(self, nodes)

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expand nodes argument into a list of residues sets and a list of molecules. this function is used to prevent the expansion operation to be done in both doit and setupUndoBefore The nodes.findType( Residue ) is the operation that is potentially expensive
Overrides: displayCommands.DisplayCommand.getNodes

onAddCmdToViewer(self)

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None
Overrides: displayCommands.DisplayCommand.onAddCmdToViewer

setupUndoBefore(self, nodes, only=False, negate=False)

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This method builds the self.undoCmds string. This method should have the same signature than the __call__. When this string is executed it should undo the actions of this command. This string will be appended to the undoCmdStack list if the command is successfuly carried out. This method handles only commands with the negateKw. Other commands have to overwrite it.
Overrides: ViewerFramework.VFCommand.Command.setupUndoBefore
(inherited documentation)

doit(self, nodes, only=False, negate=False)

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displays the secondary structure for the selected treenodes
Overrides: ViewerFramework.VFCommand.Command.doit

cleanup(self)

source code 
Method called by afterDoit to clean up things eventhough the doit failes.
Overrides: ViewerFramework.VFCommand.Command.cleanup

__call__(self, nodes, only=False, negate=False, **kw)
(Call operator)

source code 
None <- displaySecondaryStructure(nodes, only=False,
                   negate=False,**kw)
        
Required Arguments:

            
nodes  ---  TreeNodeSet holding the current selection
        
Optional Arguments:

            
only ---  flag when set to 1 only the current selection will be displayed as secondarystructures
            
negate ---  flag when set to 1 undisplay the current selection

Overrides: ViewerFramework.VFCommand.Command.__call__

getResiduesBySS(self, residues, chain)

source code 
None