Package Pmv :: Module traceCommands
[hide private]
[frames] | no frames]

Module traceCommands

source code

Module for Compute,Extrude and Display Trace.
This module provides a set of commands:
- ComputeTraceCommand (computeTrace) to compute a trace and the corresponding
  sheet2D using the given control atoms and torsion atoms. Typically used to
  compute a CA trace for a protein
- ExtrudeTraceCommand (extrudeTrace) to extrude a 2D geometry along the 3D
  path to represent the given trace.
- DisplayTraceCommand (displayTrace) to display, undisplay or display only
  parts of the molecule using the geometry created to represent the given
  trace.
  Keywords:
  Trace, CA 
  



Classes [hide private]
  ComputeTraceCommand
This command computes the oriented spline (trace) for the molecules in the current selection.
  ExtrudeTraceCommand
This command extrude a shape 2D along the path 3D of a given trace computed by the computeTrace command.
  DisplayTraceCommand
This command allows the user to display, undisplay or display only the current selection using the extruded trace representation of the given traceName.
  CustomTraceCommand
This command computes and extrudes Trace Package : Pmv Module : traceCommands Class : CustomTraceCommand Command : customTrace keywords: custom trace Synopsis: None<---customTrace(nodes,traceName='CATrace',shape2D=None,frontCap=1, endCap=1,ctlAtmName='CA',torsAtmName='O',nbchords=4,display=1,**kw) Required Arguments: nodes --- TreeNodeSet holding the current selection Optional Arguments: : traceName --- string representing the name of the computed trace.
  ComputeExtrudeTraceCommand
This command computes and Extrudes Trace with default arguements...

Functions [hide private]
  initModule(viewer)
initializes commands for secondary structure and extrusion.

Variables [hide private]
  computeTraceGuiDescr = {'separatorAbove': 1, 'menuBarName': 'Compute', 'men...
  ComputeTraceGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  extrudeTraceGuiDescr = {'menuBarName': 'menuRoot', 'menuButtonName': 'Compu...
  ExtrudeTraceGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  computeExtrudeTraceGuiDescr = {'menuBarName': 'menuRoot', 'menuButtonName': 'Compu...
  ComputeExtrudeTraceGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  customTraceGuiDescr = {'menuBarName': 'menuRoot', 'menuButtonName': 'Custo...
  CustomTraceGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  displayTraceGuiDescr = {'menuBarName': 'menuRoot', 'menuButtonName': 'Displ...
  DisplayTraceGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  commandList = [{'gui': <ViewerFramework.VFCommand.CommandGUI insta...

Function Details [hide private]

initModule(viewer)

source code 
initializes commands for secondary structure and extrusion. Also imports the commands for Secondary Structure specific coloring, and initializes these commands also.

Variables Details [hide private]

computeTraceGuiDescr

None
Value:
{'menuBarName': 'Compute',
 'menuButtonName': 'Compute CA Trace',
 'separatorAbove': 1,
 'widgetType': 'Menu'}                                                 
      

ComputeTraceGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb2eaa12c>          
      

extrudeTraceGuiDescr

None
Value:
{'menuBarName': 'menuRoot',
 'menuButtonName': 'Compute',
 'menuEntryLabel': 'Extrude Trace',
 'widgetType': 'Menu'}                                                 
      

ExtrudeTraceGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb2eaa16c>          
      

computeExtrudeTraceGuiDescr

None
Value:
{'menuBarName': 'menuRoot',
 'menuButtonName': 'ComputeExtrude CA Trace',
 'menuEntryLabel': 'ComputeExtrude Trace',
 'widgetType': 'Menu'}                                                 
      

ComputeExtrudeTraceGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb2eaa18c>          
      

customTraceGuiDescr

None
Value:
{'menuBarName': 'menuRoot',
 'menuButtonName': 'Custom CA Trace',
 'menuEntryLabel': 'Custom Trace',
 'widgetType': 'Menu'}                                                 
      

CustomTraceGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb2eaa1ac>          
      

displayTraceGuiDescr

None
Value:
{'menuBarName': 'menuRoot',
 'menuButtonName': 'Display',
 'menuEntryLabel': 'Display Trace',
 'widgetType': 'Menu'}                                                 
      

DisplayTraceGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb2eaa1cc>          
      

commandList

None
Value:
[{'cmd': self.,
  'gui': <ViewerFramework.VFCommand.CommandGUI instance at 0xb2eaa12c>
,
  'name': 'computeTrace'},
 {'cmd': self.,
  'gui': <ViewerFramework.VFCommand.CommandGUI instance at 0xb2eaa16c>
,
  'name': 'extrudeTrace'},
...