Package nMOLDYN :: Package Analysis :: Module Dynamics :: Class GlobalMotionFilteredTrajectory
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Class GlobalMotionFilteredTrajectory

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Analysis.Analysis --+
                    |
                   GlobalMotionFilteredTrajectory

Sets up a Global Motion Trajectory Filter analysis.

A Subclass of nMOLDYN.Analysis.Analysis. 

Constructor: GlobalMotionFilteredTrajectory(|parameters| = None)

Arguments:

    - |parameters| -- a dictionnary of the input parameters, or 'None' to set up the analysis without parameters.
        * trajectory -- a trajectory file name or an instance of MMTK.Trajectory.Trajectory class.
        * timeinfo   -- a string of the form 'first:last:step' where 'first' is an integer specifying the first frame 
                        number to consider, 'last' is an integer specifying the last frame number to consider and 
                        'step' is an integer specifying the step number between two frames.
        * subset     -- a selection string specifying the atoms to consider for the analysis.
        * gmft       -- the output NetCDF file name.
        * pyroserver -- a string specifying if Pyro will be used and how to run the analysis.
    
Running modes:

    - To run the analysis do: a.runAnalysis() where a is the analysis object.
    - To estimate the analysis do: a.estimateAnalysis() where a is the analysis object.
    - To save the analysis to 'file' file name do: a.saveAnalysis(file) where a is the analysis object.

Instance Methods [hide private]
 
__init__(self)
The constructor.
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initialize(self)
Initializes the analysis (e.g.
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calc(self, frameIndex, trajname)
Calculates the contribution for one frame.
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combine(self, frameIndex, x) source code
 
finalize(self)
Finalizes the calculations (e.g.
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Inherited from Analysis.Analysis: analysisTime, buildJobInfo, buildTimeInfo, deuterationSelection, groupSelection, parseInputParameters, preLoadTrajectory, runAnalysis, saveAnalysis, setInputParameters, subsetSelection, updateJobProgress, weightingScheme

Class Variables [hide private]
  inputParametersNames = 'trajectory', 'timeinfo', 'subset', 'gm...
  shortName = 'GMFT'
  canBeEstimated = True
Method Details [hide private]

__init__(self)
(Constructor)

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The constructor. Insures that the class can not be instanciated directly from here.

Parameters:
  • parameters - a dictionnary that contains parameters of the selected analysis.
  • statusBar - if not None, an instance of nMOLDYN.GUI.Widgets.StatusBar. Will attach a status bar to the selected analysis.
Overrides: Analysis.Analysis.__init__

initialize(self)

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Initializes the analysis (e.g. parses and checks input parameters, set some variables ...).

calc(self, frameIndex, trajname)

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Calculates the contribution for one frame.

Parameters:
  • frameIndex (integer.) - the index of the frame in |self.frameIndexes| array.
  • trajname (string) - the name of the trajectory file name.

finalize(self)

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Finalizes the calculations (e.g. averaging the total term, output files creations ...).


Class Variable Details [hide private]

inputParametersNames

Value:
'trajectory', 'timeinfo', 'subset', 'gmft', 'pyroserver',