Package schrodinger :: Package trajectory :: Module analysis :: Class CovarianceMatrix

Class CovarianceMatrix

analysistool.AnalysisTool --+
                            |
                           CovarianceMatrix

A tool to calculate covmatiant matrix.

Instance Methods

[hide private]

__init__(self, covmat_asl, ref_pos=None, fit_asl=None, ref_fit_pos=None, *args, **kwargs)
@type covmat_asl: AtomSelection instance @param covmat_asl: The atom selection from which to indetify atom indices to be compared.

doFrameInit(self, frame)
Initialize data that requires a frame instance for reference.

processFrame(self, frame)
Collect data for the provided frame.

postProcess(self)
Complete a post-processing step.

getFrameResults(self)
Return results as a numpy array for all values and frames with the first index being across frames.

getLabel(self)

plot(self, *args, **kwargs)
A generic matplotlib 2D plot implementation.

Inherited from analysistool.AnalysisTool: getDataLabels, getResults, plot2D, setSlice, shouldProcessFrame

Method Details

[hide private]

init(self, covmat_asl, ref_pos=None, fit_asl=None, ref_fit_pos=None, *args, **kwargs)
(Constructor)


@type covmat_asl: AtomSelection instance
@param covmat_asl:
    The atom selection from which to indetify atom indices to be
    compared.

@type fit_asl: AtomSelection instance
@param fit_asl:
    The atom selection from which to indetify atom indices to be
    transformed.

@type ref_fit_pos: numpy array with shape (n,3)
@param ref_fit_pos
    fitting position array of reference conformer structure.

Overrides: analysistool.AnalysisTool.__init__

doFrameInit(self, frame)

Initialize data that requires a frame instance for reference.

This method will be called once, with the first frame that is processed.

Overrides: analysistool.AnalysisTool.doFrameInit: (inherited documentation)

processFrame(self, frame)

Collect data for the provided frame.

Overrides: analysistool.AnalysisTool.processFrame: (inherited documentation)

postProcess(self)

Complete a post-processing step.

Defaults to doing nothing.

Overrides: analysistool.AnalysisTool.postProcess: (inherited documentation)

getFrameResults(self)

Return results as a numpy array for all values and frames with the first index being across frames.

So, if fr = analysis.getFrameResults(), and the analysis instance calculates three values for each frame, then fr[0] will be the three values for the first frame.

Overrides: analysistool.AnalysisTool.getFrameResults: (inherited documentation)

getLabel(self)

Overrides: analysistool.AnalysisTool.getLabel

plot(self, *args, **kwargs)

A generic matplotlib 2D plot implementation.

Overrides: analysistool.AnalysisTool.plot

Class CovarianceMatrix

__init__(self, covmat_asl, ref_pos=None, fit_asl=None, ref_fit_pos=None, *args, **kwargs) (Constructor)

doFrameInit(self, frame)

processFrame(self, frame)

postProcess(self)

getFrameResults(self)

getLabel(self)

plot(self, *args, **kwargs)

init(self, covmat_asl, ref_pos=None, fit_asl=None, ref_fit_pos=None, *args, **kwargs)
(Constructor)