Package Pmv :: Module superImposeCommands :: Class SuperimposeCoordsCommand
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Class SuperimposeCoordsCommand

source code

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

Instance Methods [hide private]
  onAddCmdToViewer(self)
method called when an instance of this command is added to the viewer.
  doit(self, refAtoms, inAtoms, inAllAtoms=None)
The SuperimposeCoordsCommand takes two set of Atoms of the same length refAtoms and inAtoms, a subset of inAllAtoms, plus an optional third set, inAllAtoms, It computes the rotation and translation matrices to superimpose the inAtoms onto the refAtoms using rigidFit module.
  __call__(self, refAtoms, inAtoms, inAllAtoms=None, **kw)
None <- superimposeCoords(refAtoms, inAtoms, inAllAtoms, **kw) refAtoms: atoms in reference structure inAtoms: corresponding atoms in structure to be moved by rigidFit to refAtoms inAllAtoms: complete set of all atoms whose coords are to be transformed bytranslation and rotation matrices from rigidFit.

Inherited from mvCommand.MVCommand: __init__, 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]

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)

doit(self, refAtoms, inAtoms, inAllAtoms=None)

source code 
The SuperimposeCoordsCommand takes two set of Atoms of the same length refAtoms and inAtoms, a subset of inAllAtoms, plus an optional third set, inAllAtoms, It computes the rotation and translation matrices to superimpose the inAtoms onto the refAtoms using rigidFit module. Then transforms the coords of inAllAtoms.
Overrides: ViewerFramework.VFCommand.Command.doit

__call__(self, refAtoms, inAtoms, inAllAtoms=None, **kw)
(Call operator)

source code 

None <- superimposeCoords(refAtoms, inAtoms, inAllAtoms, **kw)
refAtoms: atoms in reference structure
inAtoms: corresponding atoms in structure to be moved 
    by rigidFit to refAtoms
inAllAtoms: complete set of all atoms whose coords are to be
    transformed bytranslation and rotation matrices from rigidFit.
    (Possibly inAtoms will contain all atoms in molecule to be 
    moved so inAllAtoms will be None.)

Overrides: ViewerFramework.VFCommand.Command.__call__