Package Pmv :: Module repairCommands :: Class ModifyNTerminus
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Class ModifyNTerminus

source code

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

This command is used to modify residues which become internal n-termini
because some residues are missing within a chain in a crystal structure. 
Hydrogens are added or subtracted from nitrogen atom of the internal 
n-terminus so that the natom ends up with one sp2-hydrogen which is what it
would have in an intact chain.
   
Package : Pmv
   
Module  : repairCommands
   
Class   : ModifyNTerminus
   
Command : modifyNTerminus
   
Synopsis:

        None<--- modifyNTerminus(res,**kw)
   
Required Arguments:
    
        resSet --- set of residues which are inside a chain and not bonded to a previous residue
    



Instance Methods [hide private]
  onAddCmdToViewer(self)
method called when an instance of this command is added to the viewer.
  __call__(self, resSet, renumber=1, **kw)
None<---modifyNTerminus(res,**kw)
  doit(self, resSet, renumber)
None <--- modifyNTerminus(resSet)
  buildCoords(self, atom)

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, resSet, renumber=1, **kw)
(Call operator)

source code 

None<---modifyNTerminus(res,**kw)

resSet --- set of residues which are inside a chain and not bonded to a previous residue
Overrides: ViewerFramework.VFCommand.Command.__call__

doit(self, resSet, renumber)

source code 
None <--- modifyNTerminus(resSet)
Overrides: ViewerFramework.VFCommand.Command.doit

buildCoords(self, atom)

source code 
None