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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
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Inherited from |
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inputParametersNames = 'trajectory', 'timeinfo', 'sfa', 'pyros
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shortName = 'SFA'
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canBeEstimated = True
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The constructor. Insures that the class can not be instanciated directly from here.
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Initializes the analysis (e.g. parses and checks input parameters, set some variables ...). |
Calculates the contribution for one frame.
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Finalizes the calculations (e.g. averaging the total term, output files creations ...). |
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 |
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inputParametersNames
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