OEFPVariogram
class OEFPVariogram : public OEFPHistogram
OEFPVariogram class is used to generate a variogram of similarity scores and related empirical measurements. An OEFPVariogram object is a OEFPHistogram with additional variogram data regarding user provided measurements.
The empirical variogram has the form :
\(\hat{\gamma}(h)=\frac{1}{2|N(h)|}\sum\limits_{(i,j)\in N(h)} |z_i-z_j|^2\)
Where \(N(h)\) is the set of pairs that have a distance close to \(h\) and \(z_i\) is the measurement provided for the \(i\) th molecule.
For all of our built-in similarity measures, except for Tversky, distance is calculated a \(1-similarity\). It is not possible to calculate an empirical variogram using Tversky similarity.
The measurement in the context of a variogram can be any user provided value per fingerprint e.g. bioassay data or calculated properties.
The following methods are publicly inherited from OEFPHistogram:
See also
Constructors
OEFPVariogram(size_t numBins = 200, double min = 0, double max = 1)
OEFPVariogram(const OEFPVariogram&)
Creates an OEFPVariogram object with the given number of bins and similarity range.
- numBins
Number of bins in the histogram. (default = 200)
- min
Minimum bound (inclusive) of the similarity range. (default = 0.0)
- max
Maximum bound (inclusive) of the similarity range. (default = 1.0)
AddSample
size_t AddSample(const float sim, const float obs)
Adds a sample representing a pair of molecules into the variogram
- sim
Similarity between fingerprints i and j
- obs
Measured difference between the relevant fingerprints \(z_i-z_j\)
Note
Since we are dealing with \(|z_i-z_j|^2\) this relationship is actually symmetrical.
GetVariogram
OESystem::OEIterBase<double>* GetVariogram() const
Returns an iterator over the empirical variogram.