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
|
/**********************************************************************
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.sourceforge.net/>
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 <openbabel/babelconfig.h>
#include <openbabel/mol.h>
#include <openbabel/obconversion.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;
int main(int argc,char *argv[])
{
// turn off slow sync with C-style output (we don't use it anyway).
std::ios::sync_with_stdio(false);
if (argc != 2)
{
cout << "Usage: aromatest <file>" << endl;
cout << " Tests aromaticity perception -- all non-hydrogen atoms"
<< " are expected to be aromatic." << endl;
return(-1);
}
cout << endl << "# Testing aromaticity perception... " << endl;
ifstream ifs(argv[1]);
if (!ifs)
{
cout << "Bail out! Cannot read input file!" << endl;
return(-1);
}
OBConversion conv(&ifs, &cout);
OBFormat* pFormat;
pFormat = conv.FormatFromExt(argv[1]);
if ( pFormat == NULL )
{
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 = 0;
while(ifs.peek() != EOF && ifs.good())
{
mol.Clear();
conv.Read(&mol);
molCount++;
FOR_ATOMS_OF_MOL(atom, mol)
{
if (atom->IsHydrogen())
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";
}
}
FOR_BONDS_OF_MOL(bond, mol)
{
if (bond->IsInRing() && !bond->IsAromatic())
{
cout << "not ok " << ++testCount << " # bond isn't aromatic!\n";
cout << "# begin atom " << bond->GetBeginAtomIdx()
<< " end atom " << bond->GetEndAtomIdx()
<< " bond order " << bond->GetBO();
cout << " in molecule " << molCount << " "
<< mol.GetTitle() << "\n";
}
else if (bond->IsInRing() && bond->IsAromatic())
{
cout << "ok " << ++testCount << "\n";
}
}
} // while reading molecules
// output the number of tests run
cout << "1.." << testCount << endl;
return(0);
}
|
