Package nMOLDYN :: Package Analysis :: Module Structure :: Class ScrewFitAnalysis
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Class ScrewFitAnalysis

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Analysis.Analysis --+
                    |
                   ScrewFitAnalysis

Set up a Screw Fit analysis.

A Subclass of nMOLDYN.Analysis.Analysis. 

Constructor: ScrewFit(|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.
        * sfa         -- the output NetCDF file name. A CDL version of this file will also be generated with the '.cdl' extension
                         instead of the '.nc' extension.
        * 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.
    
Comments:
                                          
    - This code is based on a first implementation made by Paolo Calligari.
    
    - For more details: Kneller, G.R., Calligari, P. Acta Crystallographica , D62, 302-311

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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findQuaternionMatrix(self, peptide, point_ref, conf1, conf2=None, matrix=True)
Returns the complete matrix of quaternions compatibles with linear trasformation.|conf1| is the reference configuration.
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findGenericTransformation(self, peptide, point_ref, conf1, conf2=None) source code
 
angularDistance(self, chain) source code
 
screwMotionAnalysis(self, chain) source code

Inherited from Analysis.Analysis: analysisTime, buildJobInfo, buildTimeInfo, deuterationSelection, groupSelection, parseInputParameters, preLoadTrajectory, runAnalysis, saveAnalysis, setInputParameters, subsetSelection, updateJobProgress, weightingScheme

Class Variables [hide private]
  inputParametersNames = 'trajectory', 'timeinfo', 'sfa', 'pyros...
  shortName = 'SFA'
  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 ...).

findQuaternionMatrix(self, peptide, point_ref, conf1, conf2=None, matrix=True)

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Returns the complete matrix of quaternions compatibles with linear trasformation.|conf1| is the reference configuration. |point_ref| is the reference point about which the fit is calculated


Class Variable Details [hide private]

inputParametersNames

Value:
'trajectory', 'timeinfo', 'sfa', 'pyroserver',