Class OrderParameterContactModel
source code
Analysis.Analysis --+
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OrderParameterContactModel
Sets up an order parameter analysis using the contact model .
A Subclass of nMOLDYN.Analysis.Analysis.
Constructor: OrderParameterContactModel(|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.
* opcm -- 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 adapted from the s2predict code developped by F. Zhang and R. Bruschweiler and available in:
http://nmr.clarku.edu/software/S2/s2predict.html
- For more details about the method: Zhang, F., Bruschweiler, R. J. AM. Chem. Soc. 2002, 124, 12654-12655.
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calc(self,
frameIndex,
trajname)
Calculates the contribution for one group. |
source code
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Inherited from Analysis.Analysis :
analysisTime ,
buildJobInfo ,
buildTimeInfo ,
deuterationSelection ,
groupSelection ,
parseInputParameters ,
preLoadTrajectory ,
runAnalysis ,
saveAnalysis ,
setInputParameters ,
subsetSelection ,
updateJobProgress ,
weightingScheme
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inputParametersNames = 'trajectory', 'timeinfo', 'opcm', 'pyro...
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shortName = 'OPCM'
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canBeEstimated = True
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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__
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Initializes the analysis (e.g. parses and checks input parameters, set
some variables ...).
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Calculates the contribution for one group.
- Parameters:
frameIndex (integer.) - the index of the frame in |self.frameIndexes| array.
trajname (string) - the name of the trajectory file name.
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Finalizes the calculations (e.g. averaging the total term, output
files creations ...).
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inputParametersNames
- Value:
'trajectory', 'timeinfo', 'opcm', 'pyroserver',
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