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
|
// $Id$
//
// Copyright (C) 2004-2006 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 "DiscreteDistMat.h"
#include "DiscreteValueVect.h"
#include <iostream>
#include "DatastructsException.h"
namespace RDKit {
void _fillDistMat(unsigned int dmat[], unsigned int nBits) {
unsigned int i, j, a, b, ta, tb, dist;
int temp;
unsigned int mask = ((1 << nBits) - 1);
for (i = 0; i < 256; ++i) {
for (j = 0; j < 256; ++j) {
dist = 0;
a = i;
b = j;
while (a || b) {
ta = a & mask;
tb = b & mask;
temp = ta - tb;
if (temp > 0) {
dist += temp;
} else {
dist -= temp;
}
a >>= nBits;
b >>= nBits;
}
dmat[i * 256 + j] = dist;
}
}
}
DiscreteDistMat::DiscreteDistMat() {
// fill in the distance matrix table
// one bit per value table
_fillDistMat(d_oneBitTab, 1);
// two bits per value table
_fillDistMat(d_twoBitTab, 2);
// four bits per value table
_fillDistMat(d_fourBitTab, 4);
}
unsigned int DiscreteDistMat::getDist(
unsigned char v1, unsigned char v2,
DiscreteValueVect::DiscreteValueType type) {
unsigned int res = 0;
int temp;
unsigned int id =
static_cast<unsigned int>(v1) * 256 + static_cast<unsigned int>(v2);
switch (type) {
case DiscreteValueVect::ONEBITVALUE:
res = d_oneBitTab[id];
break;
case DiscreteValueVect::TWOBITVALUE:
res = d_twoBitTab[id];
break;
case DiscreteValueVect::FOURBITVALUE:
res = d_fourBitTab[id];
break;
case DiscreteValueVect::EIGHTBITVALUE:
temp = static_cast<unsigned int>(v1) - static_cast<unsigned int>(v2);
if (temp < 0) {
res -= temp;
} else {
res += temp;
}
break;
default:
// ummm.. we shouldn't have come here
throw DatastructsException("We shouldn't be here");
}
return res;
}
static DiscreteDistMat discreteDMat;
DiscreteDistMat *getDiscreteDistMat() { return &discreteDMat; }
}
|
