Package Pmv :: Module repairCommands :: Class ModifyTermini
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Class ModifyTermini

source code

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

This class detects residues within a chain which are not bonded to a previous
residue in the chain and those not bonded to a subsequent residue in the
chain.  It calls ModifyNTerminus to edit hydrogens bonded to the nitrogen
atom of the first kind of residue  and ModifyCTerminus to edit hydrogens bonded terminal carbon in the second kind of intra-chain breaks.
   
Package : Pmv
   
Module  : repairCommands
   
Class   : ModifyTermini 
   
Command : modifyTermini
   
Synopsis:

        None<- modifyTermini(res, check, **kw)
   
Required Arguments:
 
        
nodes to be checked for intrachain deletions. 
        
check --- if check, each molecule in nodes.top is checked to be sure that each of its residues is a standard type. If not, looking for peptide connection breaks doesn't make sense so command exits with an error.If the user's molecule has non-standard residues, he can call this with check=0... 
    



Instance Methods [hide private]
  onAddCmdToViewer(self)
method called when an instance of this command is added to the viewer.
  __call__(self, nodes, check=1, **kw)
None<- modifyTermini(res, check, **kw)
  doit(self, nodes, check)
virtual method.
  guiCallback(self)
Default callback function called by the gui

Inherited from mvCommand.MVCommand: __init__, 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, nodes, check=1, **kw)
(Call operator)

source code 

None<- modifyTermini(res, check, **kw)

nodes to be checked for intrachain deletions.

check --- if check, each molecule in nodes.top is checked to be sure that each of its residues is a standard type. If not, looking for peptide connection breaks doesn't make sense so command exits with an error.If the user's molecule has non-standard residues, he can call this with check=0...
Overrides: ViewerFramework.VFCommand.Command.__call__

doit(self, nodes, check)

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

guiCallback(self)

source code 
Default callback function called by the gui
Overrides: mvCommand.MVCommand.guiCallback