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object --+ | GeomAnalyzerBase --+ | VolumeMapper
This class takes the coordinates of provided particles and maps them onto a discretized grid using kernel density estimation as implemented in scipy. The returned occupancy object is a volumetric np.array which contains the probability density of the selected particles. Note: The trajectory provided for this method should already be pre-aligned onto the selection of interest. For example, to calculate the water occupancy around a protein, the provided trajectory should already contain the necessary transformations on the protein. Basic usage: ana = VolumeMapper(cms_model, 'mol.num 1') results = analyze(tr, ana)
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Inherited from Inherited from Inherited from |
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x.__init__(...) initializes x; see help(type(x)) for signature
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