Package Pmv :: Module hbondCommands :: Class WriteAssemblyHBonds
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Class WriteAssemblyHBonds

source code

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

Command to write a file specifying >1 chain with hydrogen bonds. Chains which are hydrogen-bonded are written in one pdb file.  They may or may not be part of the same molecule.
    
Package : Pmv
   
Module  : hbondCommands
   
Class   : WriteAssemblyHBonds
   
Command : writeAssemblyHB
   
Synopsis:

        None <--- writeAssemblyHB(filename, nodes, **kw)
   
Required Arguments:
     
        filename --- name of the hbond file

        nodes --- TreeNodeSet holding the current selection
    



Instance Methods [hide private]
  onAddCmdToViewer(self)
method called when an instance of this command is added to the viewer.
  __call__(self, filename, nodes, **kw)
None <--- writeAssemblyHB(filename, nodes, **kw)
  fixIDS(self, chains)
  writeHYDBNDRecords(self, atoms, fptr)
  doit(self, filename, nodes)
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, filename, nodes, **kw)
(Call operator)

source code 

None <--- writeAssemblyHB(filename, nodes, **kw)

filename --- name of the hbond file

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

fixIDS(self, chains)

source code 
None

writeHYDBNDRecords(self, atoms, fptr)

source code 
None

doit(self, filename, nodes)

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