void ThreeDMolDialog::updateTextBrowser()
{
QString text = "<script src='http://3Dmol.csb.pitt.edu/build/3Dmol-min.js'></script>\n";
// MDL representation
std::string mol;
bool writeSDF = Io::FileFormatManager::instance().writeString(*m_molecule, mol, "sdf");
text.append("<div style='height: 400px; width: 400px; position: relative;' class='viewer_3Dmoljs' data-element='molecule'");
if (writeSDF)
text.append(" data-type='sdf' data-backgroundcolor='0xffffff' data-style='stick'></div>\n");
else
text.append(" data-type='xyz' data-backgroundcolor='0xffffff' data-style='stick'></div>\n");
text.append("<textarea id='molecule' style='display: none;'>");
if (writeSDF) {
text.append(mol.c_str());
} else {
// couldn't write MDL for some reason, write XYZ
size_t numAtoms = m_molecule->atomCount();
text.append(QString::number(numAtoms) + "\n");
text.append("Generated by Avogadro.\n");
for(size_t i = 0; i < numAtoms; ++i) {
Core::Atom atom = m_molecule->atom(i);
QString line("%1 %2 %3 %4\n");
text.append( line.arg(Core::Elements::symbol(atom.atomicNumber()))
.arg(atom.position3d().x())
.arg(atom.position3d().y())
.arg(atom.position3d().z()) );
} // end for(atoms)
}
text.append("</textarea>");
m_ui->plainTextEdit->setPlainText(text);
}
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);
}
}
}
}
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();
}