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
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
|
// $Id$
//
// Created by Greg Landrum, July 2008
//
//
// Expected test results here correspond to v1.0 of the open-source avalontoolkit
//
#include <RDGeneral/RDLog.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <RDGeneral/Invariant.h>
#include <DataStructs/ExplicitBitVect.h>
#include "AvalonTools.h"
#include <string>
using namespace RDKit;
void test1(){
BOOST_LOG(rdInfoLog) << "testing canonical smiles generation" << std::endl;
{
ROMol *m = static_cast<ROMol *>(SmilesToMol("c1ccccc1"));
TEST_ASSERT(m);
std::string smi=AvalonTools::getCanonSmiles(*m);
TEST_ASSERT(smi=="c1ccccc1");
delete m;
}
{
ROMol *m = static_cast<ROMol *>(SmilesToMol("c1cccnc1"));
TEST_ASSERT(m);
std::string smi=AvalonTools::getCanonSmiles(*m);
TEST_ASSERT(smi=="c1ccncc1");
delete m;
}
{
ROMol *m = static_cast<ROMol *>(SmilesToMol("n1ccccc1"));
TEST_ASSERT(m);
std::string smi=AvalonTools::getCanonSmiles(*m);
TEST_ASSERT(smi=="c1ccncc1");
delete m;
}
{
std::string smi=AvalonTools::getCanonSmiles("n1ccccc1",true);
TEST_ASSERT(smi=="c1ccncc1");
}
{
std::string smi=AvalonTools::getCanonSmiles("c1cccnc1",true);
TEST_ASSERT(smi=="c1ccncc1");
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void test2(){
BOOST_LOG(rdInfoLog) << "testing coordinate generation" << std::endl;
#if 1
{
RWMol *m = SmilesToMol("c1cccnc1");
TEST_ASSERT(m);
unsigned int confId=AvalonTools::set2DCoords(*m);
TEST_ASSERT(m->getNumConformers()==1);
TEST_ASSERT(confId==0);
delete m;
}
#endif
{
std::string molb = AvalonTools::set2DCoords("c1cccnc1",true);
TEST_ASSERT(molb!="");
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void test3(){
BOOST_LOG(rdInfoLog) << "testing fingerprint generation" << std::endl;
{
ROMol *m = static_cast<ROMol *>(SmilesToMol("c1ccccn1"));
TEST_ASSERT(m);
ExplicitBitVect bv(512);
AvalonTools::getAvalonFP(*m,bv,512,false,true,0x00006FFF);
BOOST_LOG(rdInfoLog) << "c1ccccn1 " << bv.getNumOnBits() << std::endl;
TEST_ASSERT(bv.getNumOnBits()==18);
delete m;
}
{
ROMol *m = static_cast<ROMol *>(SmilesToMol("c1ccccc1"));
TEST_ASSERT(m);
ExplicitBitVect bv(512);
AvalonTools::getAvalonFP(*m,bv,512,false,true,0x006FFF);
BOOST_LOG(rdInfoLog) << "c1ccccn1 " << bv.getNumOnBits() << std::endl;
TEST_ASSERT(bv.getNumOnBits()==6);
delete m;
}
{
ROMol *m = static_cast<ROMol *>(SmilesToMol("c1nnccc1"));
TEST_ASSERT(m);
ExplicitBitVect bv(512);
AvalonTools::getAvalonFP(*m,bv,512,false,true,0x006FFF);
BOOST_LOG(rdInfoLog) << "c1nnccc1 " << bv.getNumOnBits() << std::endl;
TEST_ASSERT(bv.getNumOnBits()==28);
delete m;
}
{
ROMol *m = static_cast<ROMol *>(SmilesToMol("c1ncncc1"));
TEST_ASSERT(m);
ExplicitBitVect bv(512);
AvalonTools::getAvalonFP(*m,bv,512,false,true,0x006FFF);
BOOST_LOG(rdInfoLog) << "c1ncncc1 " << bv.getNumOnBits() << std::endl;
TEST_ASSERT(bv.getNumOnBits()==25);
delete m;
}
{
ExplicitBitVect bv(512);
AvalonTools::getAvalonFP("c1cccnc1",true,bv,512,false,true,0x006FFF);
BOOST_LOG(rdInfoLog) << "c1cccnc1 " << bv.getNumOnBits() << std::endl;
TEST_ASSERT(bv.getNumOnBits()==18);
}
{
ExplicitBitVect bv(512);
AvalonTools::getAvalonFP("c1ccccc1",true,bv,512,false,true,0x006FFF);
BOOST_LOG(rdInfoLog) << "c1ccccc1 " << bv.getNumOnBits() << std::endl;
TEST_ASSERT(bv.getNumOnBits()==6);
}
{
ROMol *m = static_cast<ROMol *>(SmilesToMol("c1cccnc1"));
TEST_ASSERT(m);
ExplicitBitVect bv(1024);
AvalonTools::getAvalonFP(*m,bv,1024,false,true,0x006FFF);
BOOST_LOG(rdInfoLog) << "c1cccnc1 " << bv.getNumOnBits() << std::endl;
TEST_ASSERT(bv.getNumOnBits()==19);
delete m;
}
{
ExplicitBitVect bv(2048);
AvalonTools::getAvalonFP("c1cocc1",true,bv,2048,false,true,0x006FFF);
BOOST_LOG(rdInfoLog) << "c1cocc1 " << bv.getNumOnBits() << std::endl;
TEST_ASSERT(bv.getNumOnBits()==48);
}
{
ExplicitBitVect bv(2048);
AvalonTools::getAvalonFP("C1=COC=C1",true,bv,2048,false,true,0x006FFF);
BOOST_LOG(rdInfoLog) << "C1=COC=C1 " << bv.getNumOnBits() << std::endl;
TEST_ASSERT(bv.getNumOnBits()==48);
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testRDK151(){
BOOST_LOG(rdInfoLog) << "testing Jira issue RDK-151: pyAvalonTools not generating chiral smiles from molecules" << std::endl;
{
std::string tSmi="C[C@H](F)Cl";
ROMol *m = static_cast<ROMol *>(SmilesToMol(tSmi));
TEST_ASSERT(m);
std::string smi=AvalonTools::getCanonSmiles(tSmi,true);
CHECK_INVARIANT(smi==tSmi,smi+"!="+tSmi);
smi=AvalonTools::getCanonSmiles(*m);
CHECK_INVARIANT(smi==tSmi,smi+"!="+tSmi);
delete m;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testSmilesFailures(){
BOOST_LOG(rdInfoLog) << "testing handling of bad smiles strings" << std::endl;
{
std::string tSmi="C1C";
std::string smi=AvalonTools::getCanonSmiles(tSmi,true);
CHECK_INVARIANT(smi=="",smi);
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testSubstructFps(){
BOOST_LOG(rdInfoLog) << "testing substructure fingerprints " << std::endl;
{
ExplicitBitVect bv1(512),bv2(512);
AvalonTools::getAvalonFP("c1ccccc1",true,bv1,512,true,true,AvalonTools::avalonSSSBits);
AvalonTools::getAvalonFP("c1ccccc1C(F)(F)F",true,bv2,512);
TEST_ASSERT((bv1&bv2)==bv1);
AvalonTools::getAvalonFP("c1ccccc1C(F)(F)F",true,bv1,512);
TEST_ASSERT((bv1&bv2)==bv1);
AvalonTools::getAvalonFP("c1cccc(C)c1C(F)(F)F",true,bv2,512);
TEST_ASSERT((bv1&bv2)==bv1);
}
{
ExplicitBitVect bv1(512),bv2(512);
AvalonTools::getAvalonFP("c1ccccc1O",true,bv1,512,true,true,AvalonTools::avalonSSSBits);
AvalonTools::getAvalonFP("c1ccccc1OC",true,bv2,512);
TEST_ASSERT((bv1&bv2)==bv1);
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testStruChk(){
BOOST_LOG(rdInfoLog) << "testing structure checking " << std::endl;
{
int errs = 0;
RDKit::ROMOL_SPTR m = AvalonTools::checkMol(errs, "c1ccccc1",true);
TEST_ASSERT(errs==0);
m = AvalonTools::checkMol(errs, "c1c(R)cccc1C1(CC-C(C)C1)C",true);
TEST_ASSERT(errs!=0);
}
{
int errs = 0;
std::string res;
boost::tie(res,errs)=AvalonTools::checkMolString("c1ccccc1",true);
TEST_ASSERT(errs==0);
TEST_ASSERT(res!="");
boost::tie(res,errs)=AvalonTools::checkMolString("c1c(R)cccc1C1(CC-C(C)C1)C",true);
TEST_ASSERT(errs==1);
TEST_ASSERT(res=="");
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testBadMolfile() {
BOOST_LOG(rdInfoLog) << "testing handling bad molecules " << std::endl;
// some tests around dealing with bad mol blocks
{
std::string molb="SNAP007157A\n\
MACCS-II3194121345\n\
\n\
0 0 0 0 0";
std::string smi=AvalonTools::getCanonSmiles(molb,false);
CHECK_INVARIANT(smi=="",smi);
ExplicitBitVect bv(1024);
AvalonTools::getAvalonFP(molb,false,bv,1024);
TEST_ASSERT(bv.getNumOnBits()==0);
std::string oMolb;
AvalonTools::set2DCoords(molb,false);
CHECK_INVARIANT(oMolb=="",oMolb);
}
}
void testSmilesSegFault() {
BOOST_LOG(rdInfoLog) << "testing a canonical smiles case that led to seg faults " << std::endl;
// some tests around dealing with bad mol blocks
{
std::string inSmi(1024,'C');
std::string smi=AvalonTools::getCanonSmiles(inSmi,true);
TEST_ASSERT(smi==inSmi);
}
{
std::string inSmi(1534,'C');
std::string smi=AvalonTools::getCanonSmiles(inSmi,true);
TEST_ASSERT(smi==inSmi);
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
int main(int argc,char *argv[]){
RDLog::InitLogs();
#if 1
test1();
test2();
test3();
testRDK151();
testSmilesFailures();
testSubstructFps();
testStruChk();
testBadMolfile();
#endif
testSmilesSegFault();
return 0;
}
|
