Package Pmv :: Module secondaryStructureCommands :: Class ComputeSecondaryStructureCommand
[hide private]
[frames] | no frames]

Class ComputeSecondaryStructureCommand

source code

ViewerFramework.VFCommand.Command --+    
                                    |    
                  mvCommand.MVCommand --+
                                        |
                                       ComputeSecondaryStructureCommand

The computeSecondaryStructure command gets the information on the secondary structure of each molecule contained in the current selection.This information is then used to create object describing the various secondary structure elements.
    
Package : Pmv
    
Module  : secondaryStructureCommands
    
Class   : ComputeSecondaryStructureCommand
    
Command name : computeSecondaryStructure
    
Description:
 
    The SS element object belonging to a chain are then grouped into sets.
    A new level is added in the 4 level hierarchy...
    The information is taken from the file when available or using stride when
    available.This command can be used as an interactive command.
    
Synopsis:

        None <--- ComputeSS(nodes, molMode={}, **kw)
    
Required Arguments:
   
        nodes --- any set for MolKit nodes describing molecular components
    
Optional Arguments:
    
        
molmode --- dictionary key: molecule name, value : 'From File' or 'From Stride'.
    
Required Packages:

      MolKit, DejaVu, mglutil, OpenGL, Tkinter, Pmw, types, ViewerFramework
    
Known bugs:

      None
    
Examples:

      mol = mv.Mols[0]
      
mv.computeSecondaryStructure(mv.getSelection())
    



Instance Methods [hide private]
  __init__(self)
  onRemoveObjectFromViewer(self, obj)
Method to delete sets created by this command.
  onAddCmdToViewer(self)
method called when an instance of this command is added to the viewer.
  __call__(self, nodes, molModes=None, **kw)
None <--- computeSecondaryStructure(nodes, molModes = None, **kw) nodes --- TreeNodeSet holding the current selection.
  doit(self, nodes, molModes=None)
virtual method.
  savesets(self, mol)
  clean(self, mol)
This method is called when getting the secondary structure information using stride after having from file and vice versa.
  buildFormDescr(self, formName)
Build the form description for the given form name.
  guiCallback(self)
Default callback function called by the gui

Inherited from mvCommand.MVCommand: strArg

Inherited from mvCommand.MVCommand (private): _strArg

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


Class Variables [hide private]

Inherited from ViewerFramework.VFCommand.Command: negateKw, objArgOnly


Method Details [hide private]

__init__(self)
(Constructor)

source code 
None
Overrides: mvCommand.MVCommand.__init__

onRemoveObjectFromViewer(self, obj)

source code 
Method to delete sets created by this command. This is done to prevent circular references and memory leaks.

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)

__call__(self, nodes, molModes=None, **kw)
(Call operator)

source code 
None <--- computeSecondaryStructure(nodes, molModes = None, **kw)
        
nodes --- TreeNodeSet holding the current selection.
        
moldMode --- dictionary {name of the protein: 'From File' or From Stride'},
                  'From File' to get the information from the file,
                  'From Stride' to use stride.
        

Overrides: ViewerFramework.VFCommand.Command.__call__

doit(self, nodes, molModes=None)

source code 
virtual method. Has to be implemented by the sub classes
Overrides: ViewerFramework.VFCommand.Command.doit
(inherited documentation)

savesets(self, mol)

source code 
None

clean(self, mol)

source code 
This method is called when getting the secondary structure information using stride after having from file and vice versa. It is used to delete all the secondary structure objects and attributes created previously.

buildFormDescr(self, formName)

source code 
Build the form description for the given form name.
Overrides: ViewerFramework.VFCommand.Command.buildFormDescr

guiCallback(self)

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