Package Pmv :: Module amberCommands :: Class MolecularDynamicsAmber94
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Class MolecularDynamicsAmber94

source code

ViewerFramework.VFCommand.Command --+    
                                    |    
                  mvCommand.MVCommand --+
                                        |
                                       MolecularDynamicsAmber94


    This class allows you to select an Amber94 instance from Amber94Config whose keys are ids specified in setup_Amber94 for the Amber94 instances.You can also set md options, freeze atoms, specify constrained atoms and anchor atoms and set maxStep. The md 
can be run repeatedly.
    
Package : Pmv
    
Module  : amberCommands
    
Class   : MolecularDynamicsAmber94
    
Command : molecularDynamicsAmber94
    
Synopsis:

    return_code<-md_Amber94(key, maxStep, **kw)

    
Arguments
:
    key --- is key into Amber94Config dictionary

    



Instance Methods [hide private]
  __call__(self, key, maxStep, **kw)
return_code<-md_Amber94(key, maxStep, **kw) possible return codes: >0 converged, final iteration number -1 bad line search, probably an error in the relation of the funtion to its gradient (perhaps from round-off if you push too hard on the minimization).
  doit(self, key, maxStep, **kw)
virtual method.
  updateCoords(self, cbNum=0, nbat=300, coords=[], energies=[], step=[])
  Close_cb(self, ifd, event=None)
  buildForm(self)
  disableCallbackFreq(self, event=None)
  set_filename(self, event=None)
  Accept_cb(self, event=None)
  setMdOpts(self, event=None)
  setFrozenAtoms(self, event=None)
  setConstrainedAtoms(self, event=None)
  update(self, event=None)
  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, 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]

__call__(self, key, maxStep, **kw)
(Call operator)

source code 
return_code<-md_Amber94(key, maxStep, **kw)


possible return codes:

        >0    converged, final iteration number

        -1    bad line search, probably an error in the relation
                of the funtion to its gradient (perhaps from
                round-off if you push too hard on the minimization).

        -2    search direction was uphill

        -3    exceeded the maximum number of iterations

        -4    could not further reduce function value

        -5    stopped via signal   (bsd)

key is key into Amber94Config dictionary

        

Overrides: ViewerFramework.VFCommand.Command.__call__

doit(self, key, maxStep, **kw)

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

updateCoords(self, cbNum=0, nbat=300, coords=[], energies=[], step=[])

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None

Close_cb(self, ifd, event=None)

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None

buildForm(self)

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None

disableCallbackFreq(self, event=None)

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None

set_filename(self, event=None)

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None

Accept_cb(self, event=None)

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None

setMdOpts(self, event=None)

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None

setFrozenAtoms(self, event=None)

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None

setConstrainedAtoms(self, event=None)

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None

update(self, event=None)

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None

guiCallback(self)

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Default callback function called by the gui
Overrides: mvCommand.MVCommand.guiCallback