Package Pmv :: Module amberCommands :: Class FixAmberResNamesAndOrderAtomsCommand
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Class FixAmberResNamesAndOrderAtomsCommand

source code

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

This class reorders atoms to conform to Amber conventions. 
    
Package : Pmv
    
Module  : amberCommands
    
Class   : FixAmberResNamesAndOrderAtomsCommand
    
Command : fixAmberResNamesAndOrderAtomsCommand
    
Synopsis:
 
    
  None<-fixAmberResNamesAndOrderAtomsCommand(nodes)
    
for residues with no cycles:
    
N,[H*],_A,[HA*],_B,[HB*],_G,[HG*],_D,[HD*],_E,[HE*],_Z,[HZ*],_H,[HH*],C,O
    for HIS:

    HID: (has HD1)

    N,[H*],CA,HA,CB,HB2,HB3,CG,ND1,HD1,CE1,HE1,NE2,CD2,HD2,C,O

    HIE: (has HE2)

    N,[H*],CA,HA,CB,HB2,HB3,CG,ND1,CE1,HE1,NE2,HE2,CD2,HD2,C,O

    HIP: (has both)

    N,[H*],CA,HA,CB,HB2,HB3,CG,ND1,HD1,CE1,HE1,NE2,HE2,CD2,HD2,C,O

    for PHE:

    N,[H*],CA,HA,CB,HB2,HB3,CG,CD1,HD1,CE1,HE1,CZ,HZ,CE2,HE2,CD2,HD2,C,O

    for PRO:

    N,[H*], CD, HD2, HD3, CG, HG2, HG3, CB, HB2, HB3, CA, HA, C, O

    for TRP:

    N,[H*],CA,HA,CB,HB2,HB3,CG,CD1,HD1,NE1,HE1,CE2,CZ2,HZ2,CH2,HH2,CZ3,HZ3,CE3,HE3,CD2,C,O

    for TYR:

    N,[H*],CA,HA,CB,HB2,HB3,CG,CD1,HD1,CE1,HE1,CZ,OH,HH,CE2,HE2,CD2,HD2,C,O

    



Instance Methods [hide private]
  onAddCmdToViewer(self)
method called when an instance of this command is added to the viewer.
  reorderAtoms(self, res, atList)
  doit(self, nodes)
virtual method.

Inherited from mvCommand.MVCommand: __init__, guiCallback, strArg

Inherited from mvCommand.MVCommand (private): _strArg

Inherited from ViewerFramework.VFCommand.Command: __call__, __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)

reorderAtoms(self, res, atList)

source code 
None

doit(self, nodes)

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