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)));
}
}
