void StereoCenterItem::paint(QPainter *painter, const QStyleOptionGraphicsItem *option, QWidget *widget) { Molecule *mol = molecule(); painter->save(); painter->setPen(Qt::green); if (!mol) { // not connected: default behaviour (draw connectable box) MolInputItem::paint(painter, option, widget); painter->restore(); return; } const QList<Atom*> &atoms = mol->atoms(); OpenBabel::OBMol *obmol = mol->OBMol(); QPointF offset(-5.0, 5.0); #ifdef OPENBABEL2_TRUNK // need to calculate symmetry first std::vector<unsigned int> symmetry_classes; OpenBabel::OBGraphSym graphsym(obmol); graphsym.GetSymmetry(symmetry_classes); //std::vector<unsigned long> atomIds = FindTetrahedralAtoms(obmol, symmetry_classes); std::vector<OpenBabel::StereogenicUnit> units = FindStereogenicUnits(obmol, symmetry_classes); for (unsigned int i = 0; i < units.size(); ++i) { if (units.at(i).type == OpenBabel::OBStereo::Tetrahedral) { OpenBabel::OBAtom *obatom = obmol->GetAtomById(units.at(i).id); painter->drawEllipse(mapFromItem(mol, atoms[obatom->GetIndex()]->pos()), 10, 10); } else if (units.at(i).type == OpenBabel::OBStereo::CisTrans) { OpenBabel::OBBond *obbond = obmol->GetBondById(units.at(i).id); OpenBabel::OBAtom *obatom1 = obbond->GetBeginAtom(); OpenBabel::OBAtom *obatom2 = obbond->GetEndAtom(); painter->drawEllipse(mapFromItem(mol, atoms[obatom1->GetIndex()]->pos()), 10, 10); painter->drawEllipse(mapFromItem(mol, atoms[obatom2->GetIndex()]->pos()), 10, 10); } } #else using OpenBabel::OBMolAtomIter; FOR_ATOMS_OF_MOL(atom, obmol) if (atom->IsChiral()) painter->drawEllipse(mapFromItem(mol, atoms[atom->GetIdx()-1]->pos()), 10, 10); #endif // default behavious (draw the label()) MolInputItem::paint(painter, option, widget); painter->restore(); }
int main (int argc, char *argv[]) { if (argc < 2) { cout << "Usage: " << argv[0] << " {filename}" << endl; return 1; } Molecule mol; // loop through the filenames for (unsigned int a = 1; a < argc; ++a) { if (!readXYZ(mol, argv[a])) cout << "Cannot read the XYZ file" << endl; mol.perceiveBonds(); cout << "Molecule has " << mol.numberOfAtoms() << " atoms and " << mol.numberOfBonds() << " bonds." << endl; mol.doMatching(); std::vector<Atom*> atoms = mol.atoms(); unsigned int j = 0; for (std::vector<Atom*>::iterator i = atoms.begin(); i < atoms.end(); ++i, ++j) { if ((*i)->atomicNum() == 6 && (*i)->numberOfDoubleBonds() != 1) { // cout << " failed matching on atom " << j << endl; cout << " failed matching on atom " << *i << endl; cout << " has " << (*i)->numberOfDoubleBonds() << " double bonds" << endl; break; } } // end check loop // write an SD output char *filename = argv[a]; // change extension char *pExt = strrchr(filename, '.'); if (pExt != NULL) strcpy(pExt, ".sdf"); else strcat(filename, ".sdf"); if (!writeSDF(mol, filename)) cout << "Cannot write the SDF file" << endl; } // end (loop through command-line args) return 0; }