Package Pmv :: Module hbondCommands :: Class GetHydrogenBondEnergies
[hide private]
[frames] | no frames]

Class GetHydrogenBondEnergies

source code

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

This class allows user to get a list of energies of HydrogenBonds. For this calculation, the bond must have a hydrogen atom AND it must know its type.
Energy calculation based on "Protein Flexibility and dynamics using constraint
theory", J. Molecular Graphics and Modelling 19, 60-69, 2001. MF Thorpe, Ming
Lei, AJ Rader, Donald J.Jacobs and Leslie A. Kuhn.
   
Package : Pmv
   
Module  : hbondCommands
   
Class   : GetHydrogenBondEnergies
   
Command : getHBondEnergies
   
Synopsis:

        [energies] <- getHBondEnergies(nodes, **kw) 
   
Required Arguments:
     
        nodes --- TreeNodeSet holding the current selection
    



Instance Methods [hide private]
  __init__(self, func=None)
  onAddCmdToViewer(self)
method called when an instance of this command is added to the viewer.
  __call__(self, nodes, **kw)
[energies] <- getHBondEnergies(nodes, **kw)
  getEnergy(self, b)
  doit(self, hats)
virtual method.

Inherited from mvCommand.MVCommand: 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]

__init__(self, func=None)
(Constructor)

source code 
None
Overrides: mvCommand.MVCommand.__init__

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, **kw)
(Call operator)

source code 

[energies] <- getHBondEnergies(nodes, **kw)

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

getEnergy(self, b)

source code 
None

doit(self, hats)

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