RDKit: MetricMatrixCalc.h Source File

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MetricMatrixCalc.h
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1// $Id$
2//
3// Copyright (C) 2003-2006 Rational Discovery LLC
4//
5// @@ All Rights Reserved @@
6// This file is part of the RDKit.
7// The contents are covered by the terms of the BSD license
8// which is included in the file license.txt, found at the root
9// of the RDKit source tree.
10//
11#include <RDGeneral/export.h>
12#ifndef __RD_METRICMATRIXCAL_H__
13#define __RD_METRICMATRIXCAL_H__
14
15#include "MetricFuncs.h"
16#include <RDGeneral/Invariant.h>
17
18namespace RDDataManip {
19
20/*! \brief A generic metric matrix calculator (e.g similarity matrix or
21 * distance matrix)
22 *
23 * This templated class needs some explanation
24 * vectType is a container that can support [] operator
25 * entryType is the type of entry that is returned by the [] operator
26 * Examples of the container include PySequenceHolder which is wrapper around
27 * a python sequence objects like lists and tuples.
28 * Examples of the entryType include a sequence of double, floats, and
29 *ExplicitBitVects
30 *
31 */
32template <class vectType, class entryType>
33 class MetricMatrixCalc {
34 public:
35 /*! \brief Default Constructor
36 *
37 */
38 MetricMatrixCalc() {}
39
40 /*! \brief Set the metric function
41 *
42 * Set the pointer to the mertic funvtion to be used by the metric calculator
43 *
44 * ARGUMENTS:
45 *
46 * mFunc - pointer to the metric function
47 */
48 void setMetricFunc(double (*mFunc)(const entryType &, const entryType &,
49 unsigned int)) {
50 dp_metricFunc = mFunc;
51 }
52
53 /*! \brief The calculator function
54 *
55 * ARGUMENTS:
56 *
57 * descrips - vectType container with a entryType for each item
58 * nItems - the number of item in the descripts.
59 * In several cases this argument is irrelvant since vectType
60 *probably supports
61 * a size() member function, But we would like this interface to
62 *take for example
63 * a double** and correctly parse the row and columns.
64 * dim - the dimension of the sequences
65 * distMat - pointer to an array to write the distance matrix to
66 * it is assumed that the right sized array has already be
67 *allocated.
68 *
69 * FIX: we can probably make this function create the correct sized distMat
70 *and return
71 * it to the caller, but when pushing he result out to a python array not sure
72 *how to
73 * avoid copy the entire distance matrix in that case
74 *
75 * RETURNS:
76 *
77 * pointer to a 1D array of doubles. Only the lower triangle elements are
78 * included in the array
79 */
80 void calcMetricMatrix(const vectType &descripts, unsigned int nItems,
81 unsigned int dim, double *distMat) {
82 CHECK_INVARIANT(distMat, "invalid pointer to a distance matix");
83
84 for (unsigned int i = 1; i < nItems; i++) {
85 unsigned int itab = i * (i - 1) / 2;
86 for (unsigned int j = 0; j < i; j++) {
87 distMat[itab + j] = dp_metricFunc(descripts[i], descripts[j], dim);
88 }
89 }
90 }
91
92 private:
93 // pointer to the metric function
94 /*! \brief pointer to the metric function
95 *
96 * In several cases the last argument 'dim' should be irrelevant,
97 * For example when entryType is a bit vector the size is of the vector
98 * or the dimension can be obtained by asking the bit vector itself. However
99 * we woul like this interface to support other containers lines double*
100 * in which case the 'dim' value is useful in cumputing the metric.
101 */
102 double (*dp_metricFunc)(const entryType &, const entryType &, unsigned int);
103};
104}; // namespace RDDataManip
105
106#endif
Invariant.h
CHECK_INVARIANT
#define CHECK_INVARIANT(expr, mess)
Definition Invariant.h:100
MetricFuncs.h
RDDataManip::MetricMatrixCalc::setMetricFunc
void setMetricFunc(double(*mFunc)(const entryType &, const entryType &, unsigned int))
Set the metric function.
Definition MetricMatrixCalc.h:48
RDDataManip::MetricMatrixCalc::calcMetricMatrix
void calcMetricMatrix(const vectType &descripts, unsigned int nItems, unsigned int dim, double *distMat)
The calculator function.
Definition MetricMatrixCalc.h:80
RDDataManip::MetricMatrixCalc::MetricMatrixCalc
MetricMatrixCalc()
Default Constructor.
Definition MetricMatrixCalc.h:38
export.h
RDDataManip
Definition MetricFuncs.h:17