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

Module displayCommands

source code

Classes [hide private]
  DisplayCommand
The DisplayCommand class is the base class from which all the display commands implemented for PMV will derive.It implements the general functionalities to display/undisplay parts of a geometry representing a molecule.
  DisplayLines
The displayLines allows the user to display/undisplay the selected nodes using a lines for bonded atoms, dots for non bonded atoms and doted lines for an aromatic ring.
  UndisplayLines
The undisplayLines command is a picking command allowing the user to undisplay the lines geometry representing the picked nodes.This command can also be called from the Python shell with a set of nodes.
  DisplayCPK
The displayCPK command allows the user to display/undisplay the given nodes using a CPK representation, where each atom is represented with a sphere.
  DisplayCPKByProperty
The displayCPKByProperty command allows the user to specify a property used to display/undisplay the given nodes using a CPK representation, where each atom is represented with a sphere whose radius is set by the particular value of the property for that atom.
  UndisplayCPK
The undisplayCPK command is a picking command allowing the user to undisplay the CPK geometry representing the picked nodes when used as a picking command or the given nodes when called from the Python shell.
  DisplaySticksAndBalls
The displaySticksAndBalls command allows the user to display/undisplay the given nodes using the sticks and balls representation, where the bonds are represented by cylinders and the atoms by balls.The radii of the cylinders and the balls, and the quality of the spheres are user defined.
  DisplaySSSB
The displaySSSB command allows the user to display/undisplay the given chains using the sticks and balls representation for non protein chains and ribbon diagram for proteic chains.
  UndisplaySticksAndBalls
The UndisplaySticksAndBalls command is an interactive command to undisplay part of the molecule when represented as sticks and balls.
  DisplayBackboneTrace
The displayBackboneTrace command allows the user to display/undisplay the given nodes using the sticks and balls representation, where the bonds are represented by cylinders and the atoms by balls.The radii of the cylinders and the balls, and the quality of the spheres are user defined.
  UndisplayBackboneTrace
The UndisplayBackboneTrace command is an interactive command to undisplay part of the molecule when represented as sticks and balls.
  ShowMolecules
The showMolecules command allows the user to show or hide chosen molecules.
  BindGeomToMolecularFragmentBase
  BindGeomToMolecularFragment
Command to bind an Indexed Geometry to a molecule.
  DisplayBoundGeom
Command to display/undisplay geometries that were bound to molecules with 'bindGeomToMolecularFragment' command.
  UndisplayBoundGeom
  DisplayInteractionsCommand
The DisplayInteractionsCommand class is used to display interactions between a 'ligand' and a 'receptor' molecule: the ligand is displayed with a msms surface...

Functions [hide private]
    'name':'displayBondOrder', 'cmd': DisplayBondOrder(), 'gui':DisplayBOGUI}
  initModule(viewer)

Variables [hide private]
  displayLinesGuiDescr = {'menuBarName': 'menuRoot', 'menuButtonName': 'Displ...
  DisplayLinesGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  displayCPKGuiDescr = {'menuBarName': 'menuRoot', 'menuButtonName': 'Displ...
  DisplayCPKGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  displayCPKByPropertyGuiDescr = {'menuBarName': 'menuRoot', 'menuButtonName': 'Displ...
  DisplayCPKByPropertyGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  displaySticksAndBallsGuiDescr = {'menuBarName': 'menuRoot', 'menuButtonName': 'Displ...
  DisplaySticksAndBallsGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  displaySSSBDescr = {'menuBarName': 'menuRoot', 'menuButtonName': 'Displ...
  DisplaySSSBGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  displayBackboneTraceGuiDescr = {'menuBarName': 'menuRoot', 'menuButtonName': 'Displ...
  DisplayBackboneTraceGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  showMoleculeGuiDescr = {'barName': 'Toolbar', 'widgetType': <class Tkinter....
  ShowMoleculeGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  BHTree_CUT = 40.0
  BindGeomToMolecularFragmentGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  DisplayBoundGeomGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  displayInteractionsCommandGuiDescr = {'menuBarName': 'menuRoot', 'menuButtonName': 'Displ...
  DisplayInteractionsCommandGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
    'name':'displayBondOrder', 'cmd': DisplayBondOrder(), 'gui':DisplayBOGUI}
  commandList = [{'gui': <ViewerFramework.VFCommand.CommandGUI insta...

Function Details [hide private]

initModule(viewer)

source code 
None

Variables Details [hide private]

displayLinesGuiDescr

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

DisplayLinesGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb715706c>          
      

displayCPKGuiDescr

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

DisplayCPKGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb71570ec>          
      

displayCPKByPropertyGuiDescr

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

DisplayCPKByPropertyGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb715720c>          
      

displaySticksAndBallsGuiDescr

None
Value:
{'menuBarName': 'menuRoot',
 'menuButtonName': 'Display',
 'menuEntryLabel': 'Stick And Balls',
 'widgetType': 'Menu'}                                                 
      

DisplaySticksAndBallsGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb715728c>          
      

displaySSSBDescr

None
Value:
{'menuBarName': 'menuRoot',
 'menuButtonName': 'Display',
 'menuEntryLabel': 'ribbon and S&B',
 'widgetType': 'Menu'}                                                 
      

DisplaySSSBGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb71572cc>          
      

displayBackboneTraceGuiDescr

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

DisplayBackboneTraceGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb715732c>          
      

showMoleculeGuiDescr

None
Value:
{'barName': 'Toolbar',
 'buttonName': 'show/hide molecule',
 'widgetType': <class Tkinter.Button at 0xb7b9198c>}                   
      

ShowMoleculeGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb715742c>          
      

BHTree_CUT

None
Value:
40.0                                                                  
      

BindGeomToMolecularFragmentGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb71574ac>          
      

DisplayBoundGeomGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb71574ec>          
      

displayInteractionsCommandGuiDescr

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

DisplayInteractionsCommandGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb715778c>          
      

commandList

None
Value:
[{'cmd': self.,
  'gui': <ViewerFramework.VFCommand.CommandGUI instance at 0xb715732c>
,
  'name': 'displayBackboneTrace'},
 {'cmd': self.,
  'gui': <ViewerFramework.VFCommand.CommandGUI instance at 0xb715728c>
,
  'name': 'displaySticksAndBalls'},
...