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
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
|
// $Id$
//
// Copyright (C) 2005-2012 Greg Landrum and 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/Invariant.h>
#include <GraphMol/RDKitBase.h>
#include "MolDescriptors.h"
#include <map>
#include <list>
#include <algorithm>
#include <sstream>
namespace RDKit {
namespace Descriptors {
const std::string amwVersion = "1.0.0";
double calcAMW(const ROMol &mol, bool onlyHeavy) {
double res = 0.0;
for (ROMol::ConstAtomIterator atomIt = mol.beginAtoms();
atomIt != mol.endAtoms(); ++atomIt) {
int atNum = (*atomIt)->getAtomicNum();
if (atNum != 1 || !onlyHeavy) {
res += (*atomIt)->getMass();
}
// add our implicit Hs if we need to:
if (!onlyHeavy) {
const PeriodicTable *table = PeriodicTable::getTable();
res += (*atomIt)->getTotalNumHs() * table->getAtomicWeight(1);
}
}
return res;
}
const std::string exactmwVersion = "1.1.0";
double calcExactMW(const ROMol &mol, bool onlyHeavy) {
double res = 0.0;
int nHsToCount = 0;
const PeriodicTable *table = PeriodicTable::getTable();
for (ROMol::ConstAtomIterator atomIt = mol.beginAtoms();
atomIt != mol.endAtoms(); ++atomIt) {
int atNum = (*atomIt)->getAtomicNum();
if (atNum != 1 || !onlyHeavy) {
if (!(*atomIt)->getIsotope()) {
res += table->getMostCommonIsotopeMass(atNum);
} else {
res += (*atomIt)->getMass();
}
res -= constants::electronMass * (*atomIt)->getFormalCharge();
}
// add our implicit Hs if we need to:
if (!onlyHeavy) {
nHsToCount += (*atomIt)->getTotalNumHs(false);
}
}
if (!onlyHeavy) {
res += nHsToCount * table->getMostCommonIsotopeMass(1);
}
return res;
}
namespace {
bool HillCompare(const std::pair<unsigned int, std::string> &v1,
const std::pair<unsigned int, std::string> &v2) {
bool nCompare = (v1.first < v2.first);
// special cases: Cs, Hs, Ds, and Ts go at the beginning
if (v1.second == "C") {
if (v2.second != "C") return true;
return nCompare;
} else if (v2.second == "C")
return false;
if (v1.second == "H") {
if (v2.second != "H") return true;
return nCompare;
} else if (v2.second == "H")
return false;
if (v1.second == "D")
return true;
else if (v2.second == "D")
return false;
if (v1.second == "T")
return true;
else if (v2.second == "T")
return false;
// finally, just compare the symbols and the isotopes:
if (v1 != v2)
return v1 < v2;
else
return nCompare;
}
}
static std::string _molFormulaVersion = "1.3.0";
std::string calcMolFormula(const ROMol &mol, bool separateIsotopes,
bool abbreviateHIsotopes) {
std::ostringstream res;
std::map<std::pair<unsigned int, std::string>, unsigned int> counts;
int charge = 0;
unsigned int nHs = 0;
const PeriodicTable *table = PeriodicTable::getTable();
for (ROMol::ConstAtomIterator atomIt = mol.beginAtoms();
atomIt != mol.endAtoms(); ++atomIt) {
int atNum = (*atomIt)->getAtomicNum();
std::pair<unsigned int, std::string> key =
std::make_pair(0, table->getElementSymbol(atNum));
if (separateIsotopes) {
unsigned int isotope = (*atomIt)->getIsotope();
if (abbreviateHIsotopes && atNum == 1 && (isotope == 2 || isotope == 3)) {
if (isotope == 2)
key.second = "D";
else
key.second = "T";
} else {
key.first = isotope;
}
}
if (counts.find(key) != counts.end()) {
counts[key] += 1;
} else {
counts[key] = 1;
}
nHs += (*atomIt)->getTotalNumHs();
charge += (*atomIt)->getFormalCharge();
}
if (nHs) {
std::pair<unsigned int, std::string> key = std::make_pair(0, "H");
if (counts.find(key) != counts.end()) {
counts[key] += nHs;
} else {
counts[key] = nHs;
}
}
std::list<std::pair<unsigned int, std::string> > ks;
for (std::map<std::pair<unsigned int, std::string>,
unsigned int>::const_iterator countIt = counts.begin();
countIt != counts.end(); ++countIt) {
ks.push_back(countIt->first);
}
ks.sort(HillCompare);
for (std::list<std::pair<unsigned int, std::string> >::const_iterator kIter =
ks.begin();
kIter != ks.end(); ++kIter) {
const std::pair<unsigned int, std::string> &key = *kIter;
if (key.first > 0) {
res << "[" << key.first << key.second << "]";
} else {
res << key.second;
}
if (counts[key] > 1) res << counts[key];
}
if (charge > 0) {
res << "+";
if (charge > 1) res << charge;
} else if (charge < 0) {
res << "-";
if (charge < -1) res << -1 * charge;
}
return res.str();
}
} // end of namespace Descriptors
} // end of namespace RDKit
|
