mirror of
https://github.com/openbabel/openbabel.git
synced 2025-02-25 18:55:23 -06:00
fdf43c17a0
encountering a bond between two potential radical or aromatic
atoms. Previously marked bond as double, now mark as 5 -
potentially aromatic bond. Appears to fix PR#1493148.
* src/kekulize.cpp (NewPerceiveKekuleBonds): Make sure that
bestorden is reset when traversing cycle. Previous code would only
check one atom for adding extra electrons. Appears to fix
PR#1445453.
* test/aromatest.cpp: Make sure to test that all ring bonds are
aromatic to confirm that above bugs do not come back.
* test/files/aromatics.smi: Add additional test cases for above bugs.
129 lines
3.2 KiB
C++
129 lines
3.2 KiB
C++
/**********************************************************************
|
|
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 "babelconfig.h"
|
|
#include "mol.h"
|
|
#include "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 = 1;
|
|
|
|
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-1 << endl;
|
|
|
|
return(0);
|
|
}
|