void OpenBabel::onPerceiveBondsFinished(const QByteArray &output)
{
m_progress->setLabelText(tr("Updating molecule from CML..."));
// CML --> molecule
Core::Molecule mol;
if (!Io::FileFormatManager::instance().readString(mol, output.constData(),
"cml")) {
m_progress->reset();
QMessageBox::critical(qobject_cast<QWidget*>(parent()),
tr("Error"),
tr("Error interpreting obabel CML 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.
// Check that the atom count hasn't changed:
if (mol.atomCount() != m_molecule->atomCount()) {
m_progress->reset();
QMessageBox::critical(qobject_cast<QWidget*>(parent()),
tr("Error"),
tr("Number of atoms in obabel output (%1) does not "
"match the number of atoms in the original "
"molecule (%2).")
.arg(mol.atomCount()).arg(m_molecule->atomCount()),
QMessageBox::Ok);
return;
}
m_molecule->clearBonds();
for (size_t i = 0; i < mol.bondCount(); ++i) {
Avogadro::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::Bonds | Molecule::Added |
Molecule::Removed | Molecule::Modified);
m_progress->reset();
}
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();
}