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
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
|
// $Id: itertest.cpp 1625 2011-01-13 04:22:56Z glandrum $
//
// Copyright (C) 2002-2006 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 <GraphMol/RDKitBase.h>
#include <GraphMol/RDKitQueries.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <RDGeneral/RDLog.h>
#include <iostream>
#include <stdlib.h>
#include <vector>
using namespace RDKit;
using namespace std;
typedef class ROMol Mol;
void test1(){
string smi="CCOC";
Mol *m = SmilesToMol(smi);
Mol::AtomIterator atIt;
unsigned int idx=0;
for(atIt=m->beginAtoms();atIt!=m->endAtoms();atIt++){
CHECK_INVARIANT((*atIt)->getIdx()==idx,"bad idx");
idx++;
}
atIt=m->beginAtoms();
CHECK_INVARIANT((*(atIt+2))->getIdx()==2,"bad idx");
atIt=m->beginAtoms();
Mol::AtomIterator atIt2=m->beginAtoms();
CHECK_INVARIANT(atIt==atIt2,"iterators don't compare equal");
atIt++;
CHECK_INVARIANT((*atIt)->getIdx()==1,"bad idx");
atIt+=2;
CHECK_INVARIANT((*atIt)->getIdx()==3,"bad idx");
atIt-=1;
CHECK_INVARIANT((*atIt)->getIdx()==2,"bad idx");
CHECK_INVARIANT(atIt!=atIt2,"iterators don't compare different");
CHECK_INVARIANT(atIt2<atIt,"iterator inequality failed");
CHECK_INVARIANT(atIt2<=atIt,"iterator inequality failed");
CHECK_INVARIANT(atIt>atIt2,"iterator inequality failed");
CHECK_INVARIANT(atIt>=atIt2,"iterator inequality failed");
atIt--;
--atIt;
CHECK_INVARIANT((*atIt)->getIdx()==0,"bad idx");
CHECK_INVARIANT(atIt==atIt2,"iterator inequality failed");
atIt++;
++atIt;
CHECK_INVARIANT((*atIt)->getIdx()==2,"bad idx");
atIt = m->beginAtoms();
atIt = atIt + 2;
atIt = atIt - 2;
CHECK_INVARIANT((*atIt)->getIdx()==0,"bad idx");
atIt2 = m->beginAtoms();
atIt2 += 2;
CHECK_INVARIANT(atIt2-atIt==2,"subtraction failed");
CHECK_INVARIANT(atIt-atIt2==-2,"subtraction failed");
// past the end stuff
atIt2 = m->endAtoms();
atIt = m->beginAtoms()+10;
CHECK_INVARIANT(atIt>=atIt2,"past-the-end failed");
// this is whack
atIt = m->beginAtoms();
atIt -= 10;
CHECK_INVARIANT(atIt>=atIt2,"past-the-end failed");
BOOST_LOG(rdInfoLog)<< "test1 done" << endl;
};
void test2(){
string smi="C1COC1";
Mol *m = SmilesToMol(smi);
Mol::BondIterator bondIt;
unsigned int idx=0;
for(bondIt=m->beginBonds();bondIt!=m->endBonds();bondIt++){
CHECK_INVARIANT((*bondIt)->getIdx()==idx,"bad idx");
idx++;
}
bondIt=m->beginBonds();
Mol::BondIterator bondIt2=m->beginBonds();
CHECK_INVARIANT(bondIt==bondIt2,"iterators don't compare equal");
bondIt++;
CHECK_INVARIANT((*bondIt)->getIdx()==1,"bad idx");
bondIt++;
bondIt++;
bondIt--;
CHECK_INVARIANT((*bondIt)->getIdx()==2,"bad idx");
CHECK_INVARIANT(bondIt!=bondIt2,"iterators don't compare different");
bondIt--;
--bondIt;
CHECK_INVARIANT((*bondIt)->getIdx()==0,"bad idx");
CHECK_INVARIANT(bondIt==bondIt2,"iterator inequality failed");
bondIt++;
++bondIt;
CHECK_INVARIANT((*bondIt)->getIdx()==2,"bad idx");
// past the end stuff
bondIt2 = m->endBonds();
bondIt = m->beginBonds();
bondIt--;
BOOST_LOG(rdInfoLog)<< "test2 done" << endl;
};
void test3(){
string smi="C1COCCNCOCNSCC1";
unsigned char heteros[]={2,5,7,9,10};
Mol *m = SmilesToMol(smi);
Mol::HeteroatomIterator heteroIt;
unsigned int nSeen=0;
for(heteroIt=m->beginHeteros();heteroIt!=m->endHeteros();heteroIt++){
CHECK_INVARIANT((*heteroIt)->getIdx()==heteros[nSeen],"bad hetero");
nSeen++;
}
heteroIt = m->beginHeteros();
heteroIt++;
heteroIt++;
heteroIt--;
CHECK_INVARIANT((*heteroIt)->getIdx()==heteros[1],"bad hetero");
CHECK_INVARIANT((*--heteroIt)->getIdx()==heteros[0],"bad hetero");
CHECK_INVARIANT((*heteroIt)->getIdx()==heteros[0],"bad hetero");
BOOST_LOG(rdInfoLog)<< "test3 done" << endl;
};
void test4(){
string smi="C1COCCNCOCNSCC1";
unsigned int heteros1[]={2,7};
Mol *m = SmilesToMol(smi);
QueryAtom *q= new QueryAtom();
q->setQuery(makeAtomNumEqualsQuery(8));
Mol::QueryAtomIterator queryIt;
unsigned int nSeen=0;
for(queryIt=m->beginQueryAtoms(q);queryIt!=m->endQueryAtoms();queryIt++){
CHECK_INVARIANT((*queryIt)->getIdx()==heteros1[nSeen],"bad query");
nSeen++;
}
queryIt = m->beginQueryAtoms(q);
queryIt++;
queryIt--;
CHECK_INVARIANT((*queryIt)->getIdx()==heteros1[0],"bad query");
CHECK_INVARIANT((*++queryIt)->getIdx()==heteros1[1],"bad query");
CHECK_INVARIANT((*queryIt)->getIdx()==heteros1[1],"bad query");
smi = "CC(C)CC(C)CC(C)CC(C)C";
unsigned int heteros2[]={1,4,7,10};
m = SmilesToMol(smi);
//m->debugMol(cout);
q->setQuery(makeAtomImplicitValenceQuery(1));
nSeen = 0;
for(queryIt=m->beginQueryAtoms(q);queryIt!=m->endQueryAtoms();queryIt++){
CHECK_INVARIANT((*queryIt)->getIdx()==heteros2[nSeen],"bad query");
nSeen++;
}
BOOST_LOG(rdInfoLog)<< "test4 done" << endl;
};
void test5(){
string smi="CCCC";
Mol *m = SmilesToMol(smi);
Mol::BondIterator bondIt;
unsigned int idx=0;
for(bondIt=m->beginBonds();bondIt!=m->endBonds();bondIt++){
CHECK_INVARIANT((*bondIt)->getIdx()==idx,"bad idx");
idx++;
}
CHECK_INVARIANT(idx==3,"bad idx");
idx = 0;
for(bondIt=m->beginBonds();bondIt!=m->endBonds();bondIt++){
CHECK_INVARIANT((*bondIt)->getIdx()==idx,"bad idx");
idx++;
}
CHECK_INVARIANT(idx==3,"bad idx");
idx = 0;
Mol::BondIterator beginP(m->beginBonds());
Mol::BondIterator endP(m->endBonds());
for(bondIt=beginP;bondIt!=endP;bondIt++){
CHECK_INVARIANT((*bondIt)->getIdx()==idx,"bad idx");
idx++;
}
CHECK_INVARIANT(idx==3,"bad idx");
BOOST_LOG(rdInfoLog)<< "test5 done" << endl;
}
#if 1
void _test6Help(const ROMol *m){
Mol::ConstAtomIterator atIt;
unsigned int idx=0;
for(atIt=m->beginAtoms();atIt!=m->endAtoms();atIt++){
CHECK_INVARIANT((*atIt)->getIdx()==idx,"bad idx");
idx++;
}
atIt=m->beginAtoms();
CHECK_INVARIANT((*(atIt+2))->getIdx()==2,"bad idx");
atIt=m->beginAtoms();
Mol::ConstAtomIterator atIt2=m->beginAtoms();
CHECK_INVARIANT(atIt==atIt2,"iterators don't compare equal");
atIt++;
CHECK_INVARIANT((*atIt)->getIdx()==1,"bad idx");
atIt+=2;
CHECK_INVARIANT((*atIt)->getIdx()==3,"bad idx");
atIt-=1;
CHECK_INVARIANT((*atIt)->getIdx()==2,"bad idx");
CHECK_INVARIANT(atIt!=atIt2,"iterators don't compare different");
CHECK_INVARIANT(atIt2<atIt,"iterator inequality failed");
CHECK_INVARIANT(atIt2<=atIt,"iterator inequality failed");
CHECK_INVARIANT(atIt>atIt2,"iterator inequality failed");
CHECK_INVARIANT(atIt>=atIt2,"iterator inequality failed");
atIt--;
--atIt;
CHECK_INVARIANT((*atIt)->getIdx()==0,"bad idx");
CHECK_INVARIANT(atIt==atIt2,"iterator inequality failed");
atIt++;
++atIt;
CHECK_INVARIANT((*atIt)->getIdx()==2,"bad idx");
atIt = m->beginAtoms();
atIt = atIt + 2;
atIt = atIt - 2;
CHECK_INVARIANT((*atIt)->getIdx()==0,"bad idx");
atIt2 = m->beginAtoms();
atIt2 += 2;
CHECK_INVARIANT(atIt2-atIt==2,"subtraction failed");
CHECK_INVARIANT(atIt-atIt2==-2,"subtraction failed");
// past the end stuff
atIt2 = m->endAtoms();
atIt = m->beginAtoms()+10;
CHECK_INVARIANT(atIt>=atIt2,"past-the-end failed");
// this is whack
atIt = m->beginAtoms();
atIt -= 10;
CHECK_INVARIANT(atIt>=atIt2,"past-the-end failed");
}
void test6(){
string smi="CCOC";
Mol *m = SmilesToMol(smi);
_test6Help(m);
BOOST_LOG(rdInfoLog)<< "test6 done" << endl;
};
#endif
void test7(){
string smi="c1ccccc1C";
#if 1
Mol *m = SmilesToMol(smi);
Mol::AromaticAtomIterator atomIt;
Mol::AromaticAtomIterator beginP(m->beginAromaticAtoms());
Mol::AromaticAtomIterator endP(m->endAromaticAtoms());
unsigned int idx=0;
for(atomIt=beginP;atomIt!=endP;atomIt++){
TEST_ASSERT((*atomIt)->getIdx()==idx);
idx++;
}
TEST_ASSERT(idx==6);
atomIt = beginP;
atomIt++;
atomIt--;
TEST_ASSERT((*atomIt)->getIdx()==0);
delete m;
smi = "Cc1ccccc1";
m = SmilesToMol(smi);
beginP = m->beginAromaticAtoms();
endP = m->endAromaticAtoms();
idx=0;
for(atomIt=beginP;atomIt!=endP;atomIt++){
TEST_ASSERT((*atomIt)->getIdx()==idx+1);
idx++;
}
TEST_ASSERT(idx==6);
#endif
BOOST_LOG(rdInfoLog)<< "test7 done" << endl;
}
void testIssue263(){
string smi="c1ccccc1C";
#if 1
Mol *m = SmilesToMol(smi);
Mol::AtomIterator atomIt;
unsigned int idx=0;
for(atomIt=m->beginAtoms();atomIt!=m->endAtoms();++atomIt){
TEST_ASSERT((*atomIt)->getIdx()==idx);
idx++;
}
TEST_ASSERT(idx==7);
Mol::BondIterator bondIt;
idx = 0;
for(bondIt=m->beginBonds();bondIt!=m->endBonds();++bondIt){
CHECK_INVARIANT((*bondIt)->getIdx()==idx,"bad idx");
idx++;
}
CHECK_INVARIANT(idx==7,"bad idx");
#endif
BOOST_LOG(rdInfoLog)<< "testIssue263 done" << endl;
}
int main(){
RDLog::InitLogs();
test1();
test2();
test3();
test4();
test5();
test6();
test7();
testIssue263();
return 0;
}
|
