/usr/include/rdkit/DataManip/MetricMatrixCalc/MetricMatrixCalc.h is in librdkit-dev 201503-3.
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//
// Copyright (C) 2003-2006 Rational Discovery LLC
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#ifndef __RD_METRICMATRIXCAL_H__
#define __RD_METRICMATRIXCAL_H__
#include "MetricFuncs.h"
#include <RDGeneral/Invariant.h>
namespace RDDataManip {
/*! \brief A generic metric matrix calculator (e.g similarity matrix or
* distance matrix)
*
* This templated class needs some explanation
* vectType is a container that can support [] operator
* entryType is the type of entry that is returned by the [] operator
* Examples of the container include PySequenceHolder which is wrapper around
* a python sequence objects like lists and tuples.
* Examples of the entryType include a sequence of double, floats, and ExplicitBitVects
*
*/
template <class vectType, class entryType> class MetricMatrixCalc {
public:
/*! \brief Default Constructor
*
*/
MetricMatrixCalc() {};
/*! \brief Set the metric function
*
* Set the pointer to the mertic funvtion to be used by the metric calculator
*
* ARGUMENTS:
*
* mFunc - pointer to the metric funtion
*/
void setMetricFunc(double (*mFunc)(const entryType &, const entryType &, unsigned int)) {
dp_metricFunc = mFunc;
}
/*! \brief The calculator function
*
* ARGUMENTS:
*
* descrips - vectType container with a entryType for each item
* nItems - the number of item in the descripts.
* In several cases this argument is irrelvant since vectType probably supports
* a size() member function, But we would like this interface to take for example
* a double** and correctly parse the row and columns.
* dim - the dimension of the sequences
* distMat - pointer to an array to write the distance matrix to
* it is assumed that the right sized array has already be allocated.
*
* FIX: we can probably make this function create the correct sized distMat and return
* it to the caller, but when pushing he result out to a python array not sure how to
* avoid copy the entire distance matrix in that case
*
* RETURNS:
*
* pointer to a 1D array of doubles. Only the lower triangle elements are
* included in the array
*/
void calcMetricMatrix(const vectType &descripts, unsigned int nItems, unsigned int dim,
double *distMat) {
CHECK_INVARIANT(distMat, "invalid pointer to a distance matix");
for (unsigned int i = 1; i < nItems; i++) {
unsigned int itab = i*(i-1)/2;
for (unsigned int j = 0; j < i; j++) {
distMat[itab+j] = dp_metricFunc(descripts[i], descripts[j], dim);
}
}
};
private:
// pointer to the metric function
/*! \brief pointer to the metric function
*
* In several cases the last argument 'dim' should be irrelevant,
* For example when entryType is a bit vector the size is of the vector
* or the dimension can be obtained by asking the bit vector itself. However
* we woul like this interface to support other containers lines double*
* in which case the 'dim' value is useful in cumputing the metric.
*/
double (*dp_metricFunc)(const entryType &, const entryType &, unsigned int);
};
};
#endif
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