void testGithub336() {
BOOST_LOG(rdInfoLog) << "testing github issue 336: bad canonical smiles for "
"conjugated double bonds" << std::endl;
// some tests around dealing with bad mol blocks
{
std::string pathName = getenv("RDBASE");
pathName += "/External/AvalonTools/test_data/";
std::ifstream ins((pathName + "EZ_test.2.sdf").c_str());
std::string mb((std::istreambuf_iterator<char>(ins)),
std::istreambuf_iterator<char>());
ROMol *m = MolBlockToMol(mb);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms() == 17);
std::string smi1 = AvalonTools::getCanonSmiles(mb, false);
std::string smi2 = AvalonTools::getCanonSmiles(*m);
std::cerr << "smi1: " << smi1 << std::endl;
std::cerr << "smi2: " << smi2 << std::endl;
TEST_ASSERT(smi1 == smi2);
delete m;
}
{
std::string pathName = getenv("RDBASE");
pathName += "/External/AvalonTools/test_data/";
std::ifstream ins((pathName + "heterocycle.mol").c_str());
std::string mb((std::istreambuf_iterator<char>(ins)),
std::istreambuf_iterator<char>());
RWMol *m = MolBlockToMol(mb, false);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms() == 6);
m->updatePropertyCache();
MolOps::cleanUp(*m);
MolOps::setAromaticity(*m);
std::string smi1 = AvalonTools::getCanonSmiles(mb, false);
std::string smi2 = AvalonTools::getCanonSmiles(*m);
std::cerr << "smi1: " << smi1 << std::endl;
std::cerr << "smi2: " << smi2 << std::endl;
TEST_ASSERT(smi1 == smi2);
TEST_ASSERT(smi1 == "CC1C=NNC=1");
delete m;
}
{
std::string pathName = getenv("RDBASE");
pathName += "/External/AvalonTools/test_data/";
std::ifstream ins((pathName + "heterocycle2.mol").c_str());
std::string mb((std::istreambuf_iterator<char>(ins)),
std::istreambuf_iterator<char>());
RWMol *m = MolBlockToMol(mb, false);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms() == 11);
m->updatePropertyCache();
MolOps::cleanUp(*m);
MolOps::setAromaticity(*m);
std::string smi1 = AvalonTools::getCanonSmiles(mb, false);
std::string smi2 = AvalonTools::getCanonSmiles(*m);
std::cerr << "smi1: " << smi1 << std::endl;
std::cerr << "smi2: " << smi2 << std::endl;
TEST_ASSERT(smi1 == smi2);
TEST_ASSERT(smi1 == "CN2C=CC1=CC(=O)NC=C12");
delete m;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void DrawDemo() {
#if 1
{
RWMol *mol = SmilesToMol("c1c(C#N)cccc1C~C2CC2");
std::string svg = MolToSVG(*mol);
std::ofstream ostr("blah.svg");
ostr << svg << std::endl;
delete mol;
}
{
RWMol *mol =
SmilesToMol("[Mg]c1c(C#N)cc(C(=O)NCc2sc([NH3+])c([NH3+])c2)cc1");
std::string svg = MolToSVG(*mol);
std::ofstream ostr("blah3.svg");
ostr << svg << std::endl;
delete mol;
}
{
RWMol *mol = SmilesToMol(
"[Mg]c1c(C#N)cc(C(=O)NCCCCCC(CCCCCCCCCCC(CCCCCCCCC)(CCCCCCCCCC)CCCCCC)"
"CCCCCCCCCCCCCCCCCCCCCc2sc([NH3+])c([NH3+])c2)cc1");
std::string svg = MolToSVG(*mol);
std::ofstream ostr("blah4.svg");
ostr << svg << std::endl;
delete mol;
}
{
RWMol *mol = SmilesToMol("BrO");
std::string svg = MolToSVG(*mol);
std::ofstream ostr("blah2.svg");
ostr << svg << std::endl;
delete mol;
}
{
RWMol *mol = SmilesToMol("BrC(O)(Cl)N");
std::string svg = MolToSVG(*mol);
std::ofstream ostr("blah5.svg");
ostr << svg << std::endl;
delete mol;
}
{
RWMol *mol = SmilesToMol("[14NH2+]=[14NH2+]");
std::string svg = MolToSVG(*mol);
std::ofstream ostr("blah6.svg");
ostr << svg << std::endl;
delete mol;
}
#endif
#ifdef USE_CAIRO
{
RWMol *mol =
SmilesToMol("[Mg]c1c(C#N)cc(C(=O)NCc2sc([NH3+])c([NH3+])c2)cc1");
cairo_surface_t *surface =
cairo_image_surface_create(CAIRO_FORMAT_ARGB32, 200, 200);
cairo_t *cr = cairo_create(surface);
MolToCairo(*mol, cr, 200, 200);
cairo_destroy(cr);
cairo_surface_write_to_png(surface, "mol1.png");
cairo_surface_destroy(surface);
delete mol;
}
{
RWMol *mol = SmilesToMol("c1c[12cH]ccn1");
cairo_surface_t *surface =
cairo_image_surface_create(CAIRO_FORMAT_ARGB32, 300, 300);
cairo_t *cr = cairo_create(surface);
MolToCairo(*mol, cr, 300, 300);
cairo_destroy(cr);
cairo_surface_write_to_png(surface, "mol2.png");
cairo_surface_destroy(surface);
delete mol;
}
{
RWMol *mol = SmilesToMol("Nc1ccc(cc1)S(=O)(=O)c1ccc(N)cc1");
cairo_surface_t *surface =
cairo_image_surface_create(CAIRO_FORMAT_ARGB32, 300, 300);
cairo_t *cr = cairo_create(surface);
MolToCairo(*mol, cr, 300, 300);
cairo_destroy(cr);
cairo_surface_write_to_png(surface, "mol3.png");
cairo_surface_destroy(surface);
delete mol;
}
{
RWMol *mol = SmilesToMol("Nccc(CCO)n", 0, false);
mol->updatePropertyCache();
cairo_surface_t *surface =
cairo_image_surface_create(CAIRO_FORMAT_ARGB32, 300, 300);
cairo_t *cr = cairo_create(surface);
MolToCairo(*mol, cr, 300, 300);
cairo_destroy(cr);
cairo_surface_write_to_png(surface, "mol4.png");
cairo_surface_destroy(surface);
delete mol;
}
{
RWMol *mol = SmilesToMol("N~ccc(CCO)n", 0, false);
mol->updatePropertyCache();
cairo_surface_t *surface =
cairo_image_surface_create(CAIRO_FORMAT_ARGB32, 300, 300);
cairo_t *cr = cairo_create(surface);
MolToCairo(*mol, cr, 300, 300);
cairo_destroy(cr);
cairo_surface_write_to_png(surface, "mol5.png");
cairo_surface_destroy(surface);
delete mol;
}
{
RWMol *mol = SmilesToMol("BrO", 0, false);
mol->updatePropertyCache();
cairo_surface_t *surface =
cairo_image_surface_create(CAIRO_FORMAT_ARGB32, 300, 300);
cairo_t *cr = cairo_create(surface);
MolToCairo(*mol, cr, 300, 300);
cairo_destroy(cr);
cairo_surface_write_to_png(surface, "mol6.png");
cairo_surface_destroy(surface);
delete mol;
}
{
RWMol *mol = SmilesToMol(
"[Mg]c1c(C#N)cc(C(=O)NCCCCCC(CCCCCCCCCCC(CCCCCCCCC)(CCCCCCCCCC)CCCCCC)"
"CCCCCCCCCCCCCCCCCCCCCc2sc([NH3+])c([NH3+])c2)cc1");
cairo_surface_t *surface =
cairo_image_surface_create(CAIRO_FORMAT_ARGB32, 300, 300);
cairo_t *cr = cairo_create(surface);
MolToCairo(*mol, cr, 300, 300);
cairo_destroy(cr);
cairo_surface_write_to_png(surface, "mol7.png");
cairo_surface_destroy(surface);
delete mol;
}
{
RWMol *mol = SmilesToMol("[NH3+][NH3+]", 0, false);
mol->updatePropertyCache();
cairo_surface_t *surface =
cairo_image_surface_create(CAIRO_FORMAT_ARGB32, 300, 300);
cairo_t *cr = cairo_create(surface);
MolToCairo(*mol, cr, 300, 300);
cairo_destroy(cr);
cairo_surface_write_to_png(surface, "mol8.png");
cairo_surface_destroy(surface);
delete mol;
}
#endif
}
