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

Class ColorByResidueType

source code

ViewerFramework.VFCommand.Command --+            
                                    |            
                  mvCommand.MVCommand --+        
                                        |        
                             ColorCommand --+    
                                            |    
   ViewerFramework.VFCommand.ICOM --+       |    
                                    |       |    
                     mvCommand.MVICOM --+   |    
                                        |   |    
                     mvCommand.MVAtomICOM --+    
                                            |    
                             ColorFromPalette --+
                                                |
                                               ColorByResidueType

The colorByResidueType command allows the user to color the given geometries representing the given nodes using the Rasmol coloring scheme.
    
Package : Pmv
    
Module  : colorCommands
    
Class   : ColorByResidueType
    
Command : colorByResidueType
    
where:

    ASP, GLU    bright red       CYS, MET       yellow

    LYS, ARG    blue             SER, THR       orange

    PHE, TYR    mid blue         ASN, GLN       cyan

    GLY         light grey       LEU, VAL, ILE  green

    ALA         dark grey        TRP            pink

    HIS         pale blue        PRO            flesh

    
Synopsis:

      None <- colorByResidueType(nodes, geomsToColor='all', **kw)

      nodes --- any set of MolKit nodes describing molecular components.

      geomsToColor --- list of the name of geometries to color default is 'all'

    Keywords --- color, Rasmol, residue type

    



Instance Methods [hide private]
  __init__(self, func=None)
  getColors(self, nodes)

Inherited from ColorFromPalette: __call__, doit, guiCallback, onAddCmdToViewer, setupUndoBefore

Inherited from ColorCommand: addNewEntries, buildFormDescr, cleanup, color_cb, deselectall_cb, dismiss_cb, getAvailableGeoms, getChildrenGeomsName, getNodes, selectall_cb, showForm, showUndisplayed_cb

Inherited from mvCommand.MVCommand: strArg

Inherited from mvCommand.MVCommand (private): _strArg

Inherited from ViewerFramework.VFCommand.Command: __repr__, addCallbackAfter, addCallbackBefore, addUndoCall, afterDoit, beforeDoit, buildLogArgList, checkDependencies, customizeGUI, doitWrapper, getArguments, getHelp, getLastUsedValues, getLogArgs, getValNamedArgs, log, logString, onAddNewCmd, onCmdRun, setLastUsedValues, setupUndoAfter, tkCb, updateGeom, warningMsg

Inherited from mvCommand.MVAtomICOM: getObjects

Inherited from ViewerFramework.VFCommand.ICOM: initICOM, startICOM, stopICOM


Class Variables [hide private]

Inherited from ViewerFramework.VFCommand.Command: negateKw, objArgOnly


Method Details [hide private]

__init__(self, func=None)
(Constructor)

source code 
None
Overrides: ColorFromPalette.__init__

getColors(self, nodes)

source code 
None
Overrides: ColorFromPalette.getColors