Package Pmv :: Module amberCommands :: Class FixAmberHAtomNamesCommand
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Class FixAmberHAtomNamesCommand

source code

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

This class checks hydrogen atom names and modifies them to conform to
    
Package : Pmv
    
Module  : amberCommands
    
Class   : FixAmberHAtomNamesCommand
    
Command : fixAmberHAtomNamesCommand
    
Synopsis:

    None <- fixAmberHNames(nodes, **kw)

    
Arguments:

    nodes --- TreeNodeSet holding the current selection

    
Amber conventions:

        Single hydrogen atoms bonded to N are named 'H'.
 
        Single hydrogen atoms bonded to atoms with 2 or 3 character names are named 'H'+ bonded-atom's name[ 1: ].  
    
eg: 
        
hydrogen bonded to atom 'CA' is named 'HA'
        
hydrogen bonded to atom 'OG1' of THR is named 'HG1'.
        
Pairs of hydrogens bonded to atoms append '2' or '3' to names formed as above.
    
eg: 
        
hydrogens bonded to n-terminus 'N' of PRO are named 'H2' and 'H3'.
        
hydrogens bonded to atom 'CA' of GLY are named 'HA2' and 'HA3'.
        
hydrogens bonded to atom 'CG1' of ILE are named 'HG12' and 'HG13'.
        
Trios of hydrogens bonded to atoms append '1', '2' or '3' to 
    names formed as above.
    
eg: 
        
hydrogens bonded to n-terminus 'N' of ALA are named 'H1', 'H2' and 'H3'.
        
hydrogens bonded to atom 'CB' of ALA are named 'HB1','HB2' and 'HB3'.
        
hydrogens bonded to atom 'CB' of ALA are named 'HB1','HB2' and 'HB3'.
        
hydrogens bonded to atom 'CD1' of ILE are named 'HD11','HD12' and 'HD13'.
    



Instance Methods [hide private]
  __init__(self, func=None)
  doit(self, nodes)
virtual method.
  __call__(self, nodes, **kw)
None <- fixAmberHNames(nodes, **kw)

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, onAddCmdToViewer, 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__

doit(self, nodes)

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

__call__(self, nodes, **kw)
(Call operator)

source code 

None <- fixAmberHNames(nodes, **kw)

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