void OpenBabel::onHydrogenOperationFinished(const QByteArray &mdl) { m_progress->setLabelText(tr("Reading obabel output...")); // MDL --> molecule Core::Molecule mol; if (!Io::FileFormatManager::instance().readString(mol, mdl.constData(), "mol")) { m_progress->reset(); qWarning() << "Bad MDL: " << mdl; QMessageBox::critical(qobject_cast<QWidget*>(parent()), tr("Error"), tr("Error interpreting obabel MDL output."), QMessageBox::Ok); return; } /// @todo cache a pointer to the current molecule in the above slot, and /// verify that we're still operating on the same molecule. // Update molecule m_molecule->clearAtoms(); for (Index i = 0; i < mol.atomCount(); ++i) { Core::Atom atom = mol.atom(i); m_molecule->addAtom(atom.atomicNumber()).setPosition3d(atom.position3d()); } for (Index i = 0; i < mol.bondCount(); ++i) { Core::Bond bond = mol.bond(i); m_molecule->addBond(m_molecule->atom(bond.atom1().index()), m_molecule->atom(bond.atom2().index()), bond.order()); } m_molecule->emitChanged(Molecule::Atoms | Molecule::Bonds | Molecule::Added | Molecule::Removed | Molecule::Modified); m_progress->reset(); }
void BallAndStick::process(const Molecule &molecule, Rendering::GroupNode &node) { // Add a sphere node to contain all of the spheres. GeometryNode *geometry = new GeometryNode; node.addChild(geometry); SphereGeometry *spheres = new SphereGeometry; spheres->identifier().molecule = &molecule; spheres->identifier().type = Rendering::AtomType; geometry->addDrawable(spheres); for (Index i = 0; i < molecule.atomCount(); ++i) { Core::Atom atom = molecule.atom(i); unsigned char atomicNumber = atom.atomicNumber(); const unsigned char *c = Elements::color(atomicNumber); Vector3ub color(c[0], c[1], c[2]); spheres->addSphere(atom.position3d().cast<float>(), color, static_cast<float>(Elements::radiusVDW(atomicNumber)) * 0.3f); } float bondRadius = 0.1f; CylinderGeometry *cylinders = new CylinderGeometry; cylinders->identifier().molecule = &molecule; cylinders->identifier().type = Rendering::BondType; geometry->addDrawable(cylinders); for (Index i = 0; i < molecule.bondCount(); ++i) { Core::Bond bond = molecule.bond(i); Vector3f pos1 = bond.atom1().position3d().cast<float>(); Vector3f pos2 = bond.atom2().position3d().cast<float>(); Vector3ub color1(Elements::color(bond.atom1().atomicNumber())); Vector3ub color2(Elements::color(bond.atom2().atomicNumber())); Vector3f bondVector = pos2 - pos1; float bondLength = bondVector.norm(); bondVector /= bondLength; switch (bond.order()) { case 3: { Vector3f delta = bondVector.unitOrthogonal() * (2.0f * bondRadius); cylinders->addCylinder(pos1 + delta, bondVector, bondLength, bondRadius, color1, color2, i); cylinders->addCylinder(pos1 - delta, bondVector, bondLength, bondRadius, color1, color2, i); } default: case 1: cylinders->addCylinder(pos1, bondVector, bondLength, bondRadius, color1, color2, i); break; case 2: { Vector3f delta = bondVector.unitOrthogonal() * bondRadius; cylinders->addCylinder(pos1 + delta, bondVector, bondLength, bondRadius, color1, color2, i); cylinders->addCylinder(pos1 - delta, bondVector, bondLength, bondRadius, color1, color2, i); } } } }