Package Pmv :: Module extrusionCommands :: Class ComputeSheet2DCommand

Class ComputeSheet2DCommand

ViewerFramework.VFCommand.Command --+    
                                    |    
                  mvCommand.MVCommand --+
                                        |
                                       ComputeSheet2DCommand

The ComputeSheet2DCommand class implements methods to compute the sheet2D for each chain of the contained in the current selection. Need to specify two control atoms.
    
Package : Pmv
    
Module  : extrusionCommands
    
Class   : ComputeSheet2DCommand
    
Command name : computeSheet2D
    
Synopsis:

        None <- ComputeSheet2D(nodes, buildIsHelix=1, nbrib=2,
                               nbchords=4, width=1.5, offset=1.2, **kw)
    
Required Arguments:
   
        nodes --- any set for MolKit nodes describing molecular components
     
Optional Arguments:
    
        ctlAtmsName --- tuple of two atom name specifying the two control atoms
                      the second atom is used to limit the torsion of the sheet
                      2D.
        
buildIsHelix --- flag when set to 1 specifies that an helix is defined.
        
nbrib --- integer specifying the number of ribbon of the sheet2D.
        
nbchords --- integer specifying the number of points per residues
        
width  --- float specifying the width of the sheet2D
        
offset --- float specifying the offset of ?

    
Required Packages:

      MolKit, DejaVu, mglutil, OpenGL, Tkinter, Pmw, types, ViewerFramework
    
Required Commands:

      ExtrusionCommands.ComputeSheet2D, 
    
Known bugs:

      None
    
Examples:

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

Instance Methods

[hide private]

__init__(self)

__call__(self, nodes, sheet2DName, ctlAtmName, torsAtmName, buildIsHelix=False, nbrib=2, nbchords=4, width=1.5, offset=1.2, **kw)
None <- ComputeSheet2D(nodes, sheet2DName, ctlAtmName, torsAtmName, buildIsHelix=0, nbrib=2, nbchords=4, width=1.5, offset=1.2, **kw) nodes --- any set for MolKit nodes describing molecular components ctlAtmName --- tuple of two atom name specifying the two control atoms the second atom is used to limit the torsion of the sheet 2D.

getSheet2DRes(self, chain, ctlAtmName, torsAtmName, buildIsHelix=False)

doit(self, nodes, sheet2DName, ctlAtmName, torsAtmName, buildIsHelix=False, nbrib=2, nbchords=4, width=1.5, offset=1.2)
virtual method.

buildFormDescr(self, formName)
descr <- buildFormDescr(self, formName): this virtual method is implemented in the classes derived from Command.

guiCallback(self)

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, onAddCmdToViewer, 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__

call(self, nodes, sheet2DName, ctlAtmName, torsAtmName, buildIsHelix=False, nbrib=2, nbchords=4, width=1.5, offset=1.2, **kw)
(Call operator)

source code

None <- ComputeSheet2D(nodes, sheet2DName, ctlAtmName, torsAtmName,
                               buildIsHelix=0, nbrib=2, nbchords=4,
                               width=1.5, offset=1.2, **kw)
        
nodes  --- any set for MolKit nodes describing molecular components
        
ctlAtmName --- tuple of two atom name specifying the two control atoms
                      the second atom is used to limit the torsion of the sheet
                      2D.
        
buildIsHelix ---- Boolean flag when set to True specifies that an helix is defined.
        
nbrib --- integer specifying the number of ribbon of the sheet2D.
        
nbchords --- integer specifying the number of points per residues
        
width  --- float specifying the width of the sheet2D
        
offset --- float specifying the offset of ?

Overrides: ViewerFramework.VFCommand.Command.__call__

getSheet2DRes(self, chain, ctlAtmName, torsAtmName, buildIsHelix=False)

source code

None

doit(self, nodes, sheet2DName, ctlAtmName, torsAtmName, buildIsHelix=False, nbrib=2, nbchords=4, width=1.5, offset=1.2)

source code

virtual method. Has to be implemented by the sub classes

Overrides: ViewerFramework.VFCommand.Command.doit: (inherited documentation)

buildFormDescr(self, formName)

source code

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)

guiCallback(self)

source code

None

Overrides: mvCommand.MVCommand.guiCallback

Class ComputeSheet2DCommand

__init__(self) (Constructor)

__call__(self, nodes, sheet2DName, ctlAtmName, torsAtmName, buildIsHelix=False, nbrib=2, nbchords=4, width=1.5, offset=1.2, **kw) (Call operator)

getSheet2DRes(self, chain, ctlAtmName, torsAtmName, buildIsHelix=False)

doit(self, nodes, sheet2DName, ctlAtmName, torsAtmName, buildIsHelix=False, nbrib=2, nbchords=4, width=1.5, offset=1.2)

buildFormDescr(self, formName)

guiCallback(self)

init(self)
(Constructor)

call(self, nodes, sheet2DName, ctlAtmName, torsAtmName, buildIsHelix=False, nbrib=2, nbchords=4, width=1.5, offset=1.2, **kw)
(Call operator)