Package Pmv :: Module repairCommands :: Class AddOXT
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Class AddOXT

source code

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

This class uses add_sp2_hydrogen method of the AddHydrogens class from the PyBabel package to compute coordinates of oxygen to be added to carbon atom.The carbon atom is bonded to another oxygen and a CA. If it is bonded to a hydrogen, the hydrogen is removed and replaced by the new OXT atom.
   
Package : Pmv
   
Module  : repairCommands
   
Class   : AddOXT
   
Command : add_oxt
   
Synopsis:
 
        oxt<--- add_oxt(catom,**kw)
   
Required Arguments:
     
        catom --- carbon atom to get new oxt oxygen atom.
        oxt ---  the new oxygen atom
    



Instance Methods [hide private]
  onAddCmdToViewer(self)
method called when an instance of this command is added to the viewer.
  __call__(self, catom, polarOnly=0, method='noBondOrder', renumber=1, **kw)
oxt<- add_oxt(catom,**kw)
  doit(self, catom)
oxt <- add_oxt(catom)

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]

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)

__call__(self, catom, polarOnly=0, method='noBondOrder', renumber=1, **kw)
(Call operator)

source code 

oxt<- add_oxt(catom,**kw)

catom --- carbon atom to get new oxt oxygen atom.

oxt --- the new oxygen atom
Overrides: ViewerFramework.VFCommand.Command.__call__

doit(self, catom)

source code 
oxt <- add_oxt(catom)
Overrides: ViewerFramework.VFCommand.Command.doit