void VanDerWaals::process(const Core::Molecule &molecule,
Rendering::GroupNode &node)
{
// Add a sphere node to contain all of the VdW 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 (size_t 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)));
}
}
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();
}