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object --+
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GeomAnalyzerBase --+
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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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