Package Pmv :: Module repairCommands :: Class RepairMissingAtoms
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Class RepairMissingAtoms

source code

ViewerFramework.VFCommand.Command --+    
                                    |    
                  mvCommand.MVCommand --+
                                        |
                                       RepairMissingAtoms

This command compares atoms present in residues with those expected by the dictionary used to assign Kollman charges, qkollua. It builds the missing atoms.
    
Package : Pmv
   
Module  : repairCommands
   
Class   : RepairMissingAtoms
   
Command : repairMissingAtoms
   
Synopsis:

        dictOfMissingAts <--- repairMissingAtoms(nodes, **kw)
   
Required Arguments:
        
        nodes --- TreeNodeSet holding the current selection
    



Instance Methods [hide private]
  onRemoveObjFromViewer(self, obj)
  onAddCmdToViewer(self)
method called when an instance of this command is added to the viewer.
  getRefMol(self, resType, ptype=<class MolKit.pdbParser.PdbParser at 0xb77b7e6c>)
  doit(self, resSet)
virtual method.
  __call__(self, nodes, **kw)
dictOfMissingAts <--- checkForMissingAtoms(nodes, **kw)

Inherited from mvCommand.MVCommand: __init__, guiCallback, strArg

Inherited from mvCommand.MVCommand (private): _strArg

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


Class Variables [hide private]

Inherited from ViewerFramework.VFCommand.Command: negateKw, objArgOnly


Method Details [hide private]

onRemoveObjFromViewer(self, obj)

source code 
None

onAddCmdToViewer(self)

source code 
method called when an instance of this command is added to the viewer. This enable viewer-addition time initializations
Overrides: ViewerFramework.VFCommand.Command.onAddCmdToViewer
(inherited documentation)

getRefMol(self, resType, ptype=<class MolKit.pdbParser.PdbParser at 0xb77b7e6c>)

source code 
None

doit(self, resSet)

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virtual method. Has to be implemented by the sub classes
Overrides: ViewerFramework.VFCommand.Command.doit
(inherited documentation)

__call__(self, nodes, **kw)
(Call operator)

source code 

dictOfMissingAts <--- checkForMissingAtoms(nodes, **kw)

nodes --- TreeNodeSet holding the current selection
Overrides: ViewerFramework.VFCommand.Command.__call__