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 }