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

Module colorCommands

source code


This Module implements commands to color the current selection different ways.
for example:
    by atoms.
    by residues.
    by chains.
    etc ...
    



Classes [hide private]
  ColorCommand
The ColorCommand class is the base class from which all the color commands implemented for PMV will derive.
  ColorFromPalette
The ColorFromPalette class is the base class from which all the color commands using a colorPalette implemented for PMV will derive.
  ColorByAtomType
The colorByAtomType command allows the user to color the given geometry representing the given nodes using the atomtype coloring scheme where:N :Blue ; C : White ; O : Red ; S : Yellow ; H : Cyan; P: Magenta;UNK:green.
  ColorByDG
The colorByDG command allows the user to color the given geometries representing the given nodes using the following David Goodsell coloring scheme.
  ColorByResidueType
The colorByResidueType command allows the user to color the given geometries representing the given nodes using the Rasmol coloring scheme.
  ColorShapely
The colorByShapely command allows the user to color the given geometries representing the given nodes using the Shapely coloring scheme where each residue has a different color.
  ColorFromRamp
The colorFromRamp class implements the functionality to color the given geometries representing the given nodes using a colorMap created from the Ramp.
  ColorByChain
The colorByChain command allows the user to color the given geometries representing the given nodes by chain.
  ColorByMolecule
The colorByChain command allows the user to color the given geometries representing the given nodes by molecules.
  ColorByInstance
Command to color the current selection by instance using a Rainbow palette.
  ColorByProperties
Command to color the current selection according to the integer or float properties, or by defining a function.
  ColorByExpression
The colorByExpression command allows the user to color the given geometries representing the given nodes evaluated by python function or lambda function.

Functions [hide private]
  initModule(viewer)

Variables [hide private]
  colorGuiDescr = {'menuBarName': 'menuRoot', 'menuButtonName': 'Color...
  ColorGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  colorByAtomTypeGuiDescr = {'menuBarName': 'menuRoot', 'menuButtonName': 'Color...
  ColorByAtomTypeGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  colorByDGGuiDescr = {'menuBarName': 'menuRoot', 'menuButtonName': 'Color...
  ColorByDGGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  colorByResdueTypeGuiDescr = {'menuBarName': 'menuRoot', 'menuCascadeName': 'by R...
  ColorByResidueTypeGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  colorShapelyGuiDescr = {'menuBarName': 'menuRoot', 'menuCascadeName': 'by R...
  ColorShapelyGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  colorByChainGuiDescr = {'menuBarName': 'menuRoot', 'menuButtonName': 'Color...
  ColorByChainGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  colorByMoleculeGuiDescr = {'menuBarName': 'menuRoot', 'menuButtonName': 'Color...
  ColorByMoleculeGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  colorByInstanceGuiDescr = {'menuBarName': 'menuRoot', 'menuButtonName': 'Color...
  ColorByInstanceGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  colorByPropertiesGuiDescr = {'menuBarName': 'menuRoot', 'menuButtonName': 'Color...
  ColorByPropertiesGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  colorByExpressionGuiDescr = {'menuBarName': 'menuRoot', 'menuButtonName': 'Color...
  ColorByExpressionGUI = <ViewerFramework.VFCommand.CommandGUI instance at 0x...
  commandList = [{'gui': <ViewerFramework.VFCommand.CommandGUI insta...

Function Details [hide private]

initModule(viewer)

source code 
None

Variables Details [hide private]

colorGuiDescr

None
Value:
{'menuBarName': 'menuRoot',
 'menuButtonName': 'Color',
 'menuEntryLabel': 'Choose Color',
 'widgetType': 'Menu'}                                                 
      

ColorGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb6d12b2c>          
      

colorByAtomTypeGuiDescr

None
Value:
{'menuBarName': 'menuRoot',
 'menuButtonName': 'Color',
 'menuEntryLabel': 'by Atom Type',
 'widgetType': 'Menu'}                                                 
      

ColorByAtomTypeGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb6d12bec>          
      

colorByDGGuiDescr

None
Value:
{'menuBarName': 'menuRoot',
 'menuButtonName': 'Color',
 'menuEntryLabel': 'by DG colors',
 'widgetType': 'Menu'}                                                 
      

ColorByDGGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb6d12c4c>          
      

colorByResdueTypeGuiDescr

None
Value:
{'menuBarName': 'menuRoot',
 'menuButtonName': 'Color',
 'menuCascadeName': 'by Residue Type',
 'menuEntryLabel': 'RasmolAmino',
 'widgetType': 'Menu'}                                                 
      

ColorByResidueTypeGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb6d12cac>          
      

colorShapelyGuiDescr

None
Value:
{'menuBarName': 'menuRoot',
 'menuButtonName': 'Color',
 'menuCascadeName': 'by Residue Type',
 'menuEntryLabel': 'Shapely',
 'widgetType': 'Menu'}                                                 
      

ColorShapelyGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb6d12d0c>          
      

colorByChainGuiDescr

None
Value:
{'menuBarName': 'menuRoot',
 'menuButtonName': 'Color',
 'menuEntryLabel': 'by Chain',
 'widgetType': 'Menu'}                                                 
      

ColorByChainGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb6d12d8c>          
      

colorByMoleculeGuiDescr

None
Value:
{'menuBarName': 'menuRoot',
 'menuButtonName': 'Color',
 'menuEntryLabel': 'by Molecules',
 'widgetType': 'Menu'}                                                 
      

ColorByMoleculeGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb6d12dec>          
      

colorByInstanceGuiDescr

None
Value:
{'menuBarName': 'menuRoot',
 'menuButtonName': 'Color',
 'menuEntryLabel': 'by Instance',
 'widgetType': 'Menu'}                                                 
      

ColorByInstanceGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb6d12e4c>          
      

colorByPropertiesGuiDescr

None
Value:
{'menuBarName': 'menuRoot',
 'menuButtonName': 'Color',
 'menuEntryLabel': 'by Properties',
 'widgetType': 'Menu'}                                                 
      

ColorByPropertiesGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb6d12f8c>          
      

colorByExpressionGuiDescr

None
Value:
{'menuBarName': 'menuRoot',
 'menuButtonName': 'Color',
 'menuEntryLabel': 'by Expression',
 'widgetType': 'Menu'}                                                 
      

ColorByExpressionGUI

None
Value:
<ViewerFramework.VFCommand.CommandGUI instance at 0xb6d2106c>          
      

commandList

None
Value:
[{'cmd': self.,
  'gui': <ViewerFramework.VFCommand.CommandGUI instance at 0xb6d12b2c>
,
  'name': 'color'},
 {'cmd': self.,
  'gui': <ViewerFramework.VFCommand.CommandGUI instance at 0xb6d12bec>
,
  'name': 'colorByAtomType'},
...