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
|
/**********************************************************************
aromatest.cpp - Test Open Babel aromaticity perception
Copyright (C) 2005-2006 Geoffrey R. Hutchison
This file is part of the Open Babel project.
For more information, see <http://openbabel.org/>
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation version 2 of the License.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
***********************************************************************/
// used to set import/export for Cygwin DLLs
#ifdef WIN32
#define USING_OBDLL
#endif
#include <cstdlib>
#include <openbabel/babelconfig.h>
#include <openbabel/mol.h>
#include <openbabel/atom.h>
#include <openbabel/obiter.h>
#include <openbabel/obconversion.h>
#include <openbabel/elements.h>
#if !HAVE_STRNCASECMP
extern "C" int strncasecmp(const char *s1, const char *s2, size_t n);
#endif
#include <stdio.h>
#include <iostream>
#include <fstream>
using namespace std;
using namespace OpenBabel;
// Molecules aromatized in error (in the course of porting from SMARTS patterns)
void NegativeTestCases(int &molCount, unsigned int &testCount)
{
// Check that not every atom is aromatic (i.e. negative test cases)
const char* smiles[] = { "c1ccc2[N+]=c3ccccc3=Nc2c1", // N radical found in eMolecules
"N1S[SH+]C=C1",
"S1C=[NH+]=[NH+]=C1",
"C1(N23)=CC=CC2=CC=CC3=CC=C1", // pyrido[2,1,6-de]quinolizine - no atom is Daylight aromatic
nullptr };
OBMol mol;
OBConversion conv;
conv.SetInFormat("smi");
for (int i = 0; smiles[i]; ++i) {
mol.Clear();
conv.ReadString(&mol, smiles[i]);
molCount++;
bool found_non_aromatic = false;
FOR_ATOMS_OF_MOL(atom, mol) {
if (atom->GetAtomicNum() == OBElements::Hydrogen)
continue;
if (!atom->IsAromatic()) {
found_non_aromatic = true;
break;
}
}
if (found_non_aromatic)
cout << "ok " << ++testCount << "\n";
else
cout << "not ok " << ++testCount << " # all atoms are aromatic in molecule " << molCount << " "
<< mol.GetTitle() << "\n";
}
}
int aromatest(int argc, char* argv[])
{
int defaultchoice = 1;
int choice = defaultchoice;
if (argc > 1) {
if(sscanf(argv[1], "%d", &choice) != 1) {
printf("Couldn't parse that input as a number\n");
return -1;
}
}
cout << endl << "# Testing aromaticity perception... " << endl;
#ifdef TESTDATADIR
string testdatadir(TESTDATADIR);
string filename = testdatadir + "aromatics.smi";
#else
string filename = "files/aromatics.smi";
#endif
#ifdef FORMATDIR
char env[BUFF_SIZE];
snprintf(env, BUFF_SIZE, "BABEL_LIBDIR=%s", FORMATDIR);
putenv(env);
#endif
ifstream ifs(filename.c_str());
if (!ifs)
{
cout << "Bail out! Cannot read input file!" << endl;
return(-1);
}
OBConversion conv(&ifs, &cout);
OBFormat* pFormat;
pFormat = conv.FormatFromExt("aromatics.smi");
if (pFormat == nullptr)
{
cout << "Bail out! Cannot read file format!" << endl;
return(-1);
}
// Finally, we can do some work!
OBMol mol;
unsigned int testCount = 0;
if (! conv.SetInAndOutFormats(pFormat, pFormat))
{
cout << "Bail out! File format isn't loaded" << endl;
return (-1);
}
int molCount;
switch(choice) {
case 1:
molCount = 0;
while(ifs.peek() != EOF && ifs.good())
{
mol.Clear();
conv.Read(&mol);
molCount++;
for (int N = 0; N < 2; ++N)
{
if (N == 0)
mol.AddHydrogens();
else
mol.DeleteHydrogens();
FOR_ATOMS_OF_MOL(atom, mol)
{
if (atom->GetAtomicNum() == OBElements::Hydrogen)
continue;
if (atom->IsAromatic())
cout << "ok " << ++testCount << "\n";
else
{
cout << "not ok " << ++testCount << " # atom isn't aromatic!\n";
cout << "# atom idx " << atom->GetIdx()
<< " in molecule " << molCount << " "
<< mol.GetTitle() << "\n";
}
}
}
} // while reading molecules
NegativeTestCases(molCount, testCount);
break;
default:
cout << "Test number " << choice << " does not exist!\n";
return -1;
}
return(0);
}
|
