Package Pmv :: Module colorCommands :: Class ColorByResidueType
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Class ColorByResidueType

source code

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

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

    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


      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)

source code 
Overrides: ColorFromPalette.__init__

getColors(self, nodes)

source code 
Overrides: ColorFromPalette.getColors