Package Pmv :: Module secondaryStructureCommands :: Class ComputeSecondaryStructureCommand

Class ComputeSecondaryStructureCommand

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

Class ComputeSecondaryStructureCommand

__init__(self) (Constructor)

onRemoveObjectFromViewer(self, obj)

onAddCmdToViewer(self)

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

doit(self, nodes, molModes=None)

savesets(self, mol)

clean(self, mol)

buildFormDescr(self, formName)

guiCallback(self)

init(self)
(Constructor)

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