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