Package schrodinger :: Package application :: Package desmond :: Package packages :: Module analysis :: Class VolumeMapper
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Class VolumeMapper

      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)

Instance Methods [hide private]
 
__init__(self, cms_model, asl, origin=[0.0, 0.0, 0.0], spacing=[1.0, 1.0, 1.0], length=[10.0, 10.0, 10.0])
x.__init__(...) initializes x; see help(type(x)) for signature
 
_postcalc(self, _, pbc, fr)
 
reduce(self, *_, **__)

Inherited from GeomAnalyzerBase: __call__

Inherited from GeomAnalyzerBase (private): _precalc

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, cms_model, asl, origin=[0.0, 0.0, 0.0], spacing=[1.0, 1.0, 1.0], length=[10.0, 10.0, 10.0])
(Constructor)

 

x.__init__(...) initializes x; see help(type(x)) for signature

Parameters:
Overrides: object.__init__

_postcalc(self, _, pbc, fr)

 
Overrides: GeomAnalyzerBase._postcalc
(inherited documentation)