1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
|
//
// 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.
//
#include <RDGeneral/export.h>
#ifndef _RD_CORRMATGENERATOR_H_
#define _RD_CORRMATGENERATOR_H_
#include <RDGeneral/types.h>
#include <DataStructs/BitVects.h>
#include <boost/dynamic_bitset.hpp>
namespace RDInfoTheory {
// FIX: won't worry about it now, but this class can be templated by the type of
// container for the bit list and type of descriptors (fingerprint vs. real
// valued)
class BitCorrMatGenerator {
/*! \brief A class to generate a correlation matrix for a bunch of
*fingerprints
*
* The correlation matrix is done only for the bit IDs that are set by a call
*to the
* function setDescriptorIdList
*
* cr = CorrMatGenerator();
* cr.setDescriptorIdList(descList);
* for each fingerprint in list of fingerprints {
* cr.collectVotes(fingerprint);
* }
* double *corrMat = cr.getCorrMat()
*
* The resulting correlation matrix is a one dimension matrix with only the
*lower triangle elements
* of the symmetric matrix
*/
public:
BitCorrMatGenerator() { this->initGenerator(); };
~BitCorrMatGenerator() { delete[] dp_corrMat; }
void initGenerator() {
dp_corrMat = 0;
d_descs.resize(0);
d_nExamples = 0;
};
/*! \brief Set the list bits that we are interested in correlating
*
* \param bitIdList is a list of bit ids that need to be correlated e.g. a
*list top ranked ensemble
* of bits
*/
void setBitIdList(const RDKit::INT_VECT &bitIdList) {
d_descs = bitIdList;
int i, nd = d_descs.size();
int nelem = nd * (nd - 1) / 2;
delete[] dp_corrMat;
dp_corrMat = new double[nd * (nd - 1) / 2];
for (i = 0; i < nelem; i++) {
dp_corrMat[i] = 0.0;
}
};
//! \brief get the number of examples we used so far to compute the
//correlation matrix
int getNumExamples() const { return d_nExamples; };
//! \brief Get the list of bits ID that are used to generate the correlation
//matrix
RDKit::INT_VECT getCorrBitList() const { return d_descs; };
//! \brief Gets a pointer to the correlation matrix
double *getCorrMat() { return dp_corrMat; };
//! \brief For each pair of on bits (bi, bj) in fp increase the correlation
//count
// for the pair by 1
void collectVotes(const BitVect &fp) {
unsigned int nd = d_descs.size();
// use a temporary bit vector to first mask the fingerprint
ExplicitBitVect ebv(nd);
int bi;
for (unsigned int i = 0; i < nd; i++) {
bi = d_descs[i];
if (fp[bi]) {
ebv.setBit(i);
}
}
for (unsigned i = 1; i < nd; i++) {
unsigned int itab = i * (i - 1) / 2;
if (ebv[i]) {
for (unsigned int j = 0; j < i; j++) {
if (ebv[j]) {
dp_corrMat[itab + j] += 1;
}
}
}
}
d_nExamples++;
};
private:
RDKit::INT_VECT d_descs;
double *dp_corrMat;
int d_nExamples;
};
}
#endif
|
