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
177
178
179
180
181
|
// $Id$
//
// Copyright (C) 2014 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/test.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/MonomerInfo.h>
#include <GraphMol/RDKitQueries.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <RDGeneral/types.h>
#include <RDGeneral/RDLog.h>
#include <RDGeneral/Dict.h>
#include <iostream>
using namespace std;
using namespace RDKit;
void testBasics() {
BOOST_LOG(rdInfoLog) << "-----------------------\n Basic Allocations"
<< std::endl;
auto *a1 = new Atom(6);
auto *b1 = new Bond();
auto *m1 = new ROMol();
(void)a1;
(void)b1;
(void)m1;
a1 = nullptr; // intentional leak
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testSMILES() {
BOOST_LOG(rdInfoLog) << "-----------------------\n SMILES Read" << std::endl;
string smi = "CCOC";
ROMol *m = SmilesToMol(smi);
(void)m; // leak al the things
m = SmilesToMol(smi, 0, false);
smi = "C1COC1";
RWMol *m2 = SmilesToMol(smi);
m2 = SmilesToMol(smi, 0, false);
m2 = SmilesToMol(smi, 0, false);
unsigned int failed;
MolOps::sanitizeMol(*m2, failed,
MolOps::SANITIZE_CLEANUP | MolOps::SANITIZE_PROPERTIES);
m2 = SmilesToMol(smi, 0, false);
MolOps::sanitizeMol(*m2, failed,
MolOps::SANITIZE_CLEANUP | MolOps::SANITIZE_PROPERTIES);
MolOps::symmetrizeSSSR(*m2);
m2 = SmilesToMol(smi, 0, false);
MolOps::sanitizeMol(*m2);
m2 = SmilesToMol(smi, 0, false);
MolOps::sanitizeMol(*m2);
MolOps::assignStereochemistry(*m2, true, true, false);
m2 = SmilesToMol(smi, 0, false);
MolOps::sanitizeMol(*m2);
MolOps::assignStereochemistry(*m2, true, true, true);
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testMol() {
auto *m1 = new RWMol();
m1->addAtom(new Atom(6), true, true);
m1->addAtom(new Atom(6), true, true);
m1->addAtom(new Atom(7), true, true);
m1->addAtom(new Atom(6), true, true);
m1->addBond(0, 1, Bond::SINGLE);
m1->addBond(1, 2, Bond::SINGLE);
m1->addBond(2, 3, Bond::SINGLE);
MolOps::sanitizeMol(*m1);
}
void testMols() {
std::string smis[] = {
"CN1CCC[C@H]1c2cccnc2", "CC1(C)[C@@H](N2[C@@H](CC2=O)S1(=O)=O)C(=O)O",
"C[C@]1(Cn2ccnn2)[C@@H](N3[C@@H](CC3=O)S1(=O)=O)C(=O)O",
"CCN(CC)C(=O)[C@@H]1CN(C)[C@H]2Cc3c[nH]c4cccc(C2=C1)c34",
"CCCN(CCC)[C@H]1CCc2c(O)cccc2C1",
"CC(=O)NC[C@H]1CN(C(=O)O1)c2ccc(cc2)C(=O)C",
"CC1(C)Oc2ccc3C=CC(=O)Oc3c2[C@@H](OC(=O)C45CCC(C)(C(=O)O4)C5(C)C)[C@H]"
"1OC(=O)C67CCC(C)(C(=O)O6)C7(C)C",
"CCC(C)(C)C(=O)C(=O)N1CCC[C@H]1C(=O)OCCCc2cccnc2",
"CN1N=C(S/C/1=N/C(=O)C)S(=O)(=O)N",
"COc1ccc(cc1)[C@@H]2Sc3ccccc3N(CCN(C)C)C(=O)[C@@H]2OC(=O)C", "EOS"};
for (int i = 0; smis[i] != "EOS"; ++i) {
SmilesToMol(smis[i], 0, false);
}
for (int i = 0; smis[i] != "EOS"; ++i) {
RWMol *m = SmilesToMol(smis[i], 0, false);
MolOps::sanitizeMol(*m);
}
}
void testProps() {
BOOST_LOG(rdInfoLog) << "-----------------------\n properties" << std::endl;
string smi = "C1COC1";
RWMol *m = SmilesToMol(smi, 0, false);
m = SmilesToMol(smi, 0, false);
for (ROMol::AtomIterator ai = m->beginAtoms(); ai != m->endAtoms(); ++ai) {
unsigned int v = 1;
(*ai)->setProp("foo", v, true);
}
m = SmilesToMol(smi, 0, false);
for (ROMol::BondIterator ai = m->beginBonds(); ai != m->endBonds(); ++ai) {
unsigned int v = 1;
(*ai)->setProp("foo", v, true);
}
m = SmilesToMol(smi, 0, false);
for (ROMol::AtomIterator ai = m->beginAtoms(); ai != m->endAtoms(); ++ai) {
unsigned int v = 1;
(*ai)->setProp("foo", v, true);
(*ai)->setProp("bar", v, true);
}
m = SmilesToMol(smi, 0, false);
for (ROMol::AtomIterator ai = m->beginAtoms(); ai != m->endAtoms(); ++ai) {
unsigned int v = 1;
(*ai)->setProp("foo", v, true);
(*ai)->setProp("bar", v, true);
(*ai)->setProp("baz", v, true);
}
m = SmilesToMol(smi, 0, false);
for (ROMol::AtomIterator ai = m->beginAtoms(); ai != m->endAtoms(); ++ai) {
unsigned int v = 1;
(*ai)->setProp("foo", v, false);
}
m = SmilesToMol(smi, 0, false);
for (ROMol::AtomIterator ai = m->beginAtoms(); ai != m->endAtoms(); ++ai) {
unsigned int v = 1;
(*ai)->setProp("foo", v, false);
(*ai)->setProp("bar", v, false);
}
m = SmilesToMol(smi, 0, false);
for (ROMol::AtomIterator ai = m->beginAtoms(); ai != m->endAtoms(); ++ai) {
unsigned int v = 1;
(*ai)->setProp("foo", v, false);
(*ai)->setProp("bar", v, false);
(*ai)->setProp("baz", v, false);
}
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testDict() {
BOOST_LOG(rdInfoLog) << "-----------------------\n dict" << std::endl;
int val = 1;
auto *d = new Dict();
d = new Dict();
d->setVal<int>("foo", val);
d = new Dict();
d->setVal<int>("foo", val);
d->setVal<int>("bar", val);
d = new Dict();
d->setVal<int>("foo", val);
d->setVal<int>("bar", val);
d->setVal<int>("baz", val);
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
// -------------------------------------------------------------------
int main() {
RDLog::InitLogs();
// boost::logging::enable_logs("rdApp.info");
// test1(); // <- this doesn't seem to actually do anything
#if 1
// testBasics();
// testSMILES();
// testMol();
// testMols();
// testProps();
testDict();
#endif
return 0;
}
|
