Package Pmv :: Module secondaryStructureCommands
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Module secondaryStructureCommands

source code

Classes [hide private]
  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.
  ExtrudeSecondaryStructureCommand
The ExtrudeCommand allows the user to represent the secondary structure elements by extruding 2D geometries along a 3D path.To execute this command use the entry 'extrude Secondary Structure' under the 'Compute' menu in the menu bar.
  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.
  UndisplayExtrudedSSCommand
UndisplaySSCommand is an interactive command to undisplay part of the molecule when represented as extruded secondary structure.
  RibbonCommand
The RibbonCommand is a shortcut to visualize a traditional Ribbon representation of the current selection.
  ColorBySSElementType
Command to color the given geometry by secondary structure element.

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

Variables [hide private]
  colorBySecondaryStructureTypeGuiDescr = {'menuBarName': 'menuRoot', 'menuButtonName': 'Color...
  ColorBySSElementTypeGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  computeSSGuiDescr = {'separatorAbove': 1, 'menuBarName': 'menuRoot', 'me...
  computeSSGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  extrudeSSGuiDescr = {'menuBarName': 'menuRoot', 'menuButtonName': 'Compu...
  ExtrudeSSGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  displaySSGuiDescr = {'menuBarName': 'menuRoot', 'menuButtonName': 'Displ...
  DisplaySSGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  ribbonGuiDescr = {'menuBarName': 'menuRoot', 'menuButtonName': 'Compu...
  RibbonGUI = <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]

colorBySecondaryStructureTypeGuiDescr

None
Value:
{'menuBarName': 'menuRoot',
 'menuButtonName': 'Color',
 'menuEntryLabel': 'By SS Element Type',
 'widgetType': 'Menu'}                                                 
      

ColorBySSElementTypeGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb2ba4a6c>          
      

computeSSGuiDescr

None
Value:
{'menuBarName': 'menuRoot',
 'menuButtonName': 'Compute',
 'menuEntryLabel': 'Compute Secondary Structure',
 'separatorAbove': 1,
 'widgetType': 'Menu'}                                                 
      

computeSSGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb2ba4aac>          
      

extrudeSSGuiDescr

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

ExtrudeSSGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb2ba4acc>          
      

displaySSGuiDescr

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

DisplaySSGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb2ba4aec>          
      

ribbonGuiDescr

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

RibbonGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb2ba4b0c>          
      

commandList

None
Value:
[{'cmd': self.,
  'gui': <ViewerFramework.VFCommand.CommandGUI instance at 0xb2ba4aac>
,
  'name': 'computeSecondaryStructure'},
 {'cmd': self.,
  'gui': <ViewerFramework.VFCommand.CommandGUI instance at 0xb2ba4acc>
,
  'name': 'extrudeSecondaryStructure'},
...