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 QTAIMEngine::process(const Core::Molecule &coreMolecule,
Rendering::GroupNode &node)
{
const QtGui::Molecule *molecule =
dynamic_cast<const QtGui::Molecule*>(&coreMolecule);
if (!molecule)
return;
// Create sphere/cylinder nodes.
GeometryNode *geometry = new GeometryNode;
node.addChild(geometry);
SphereGeometry *spheres = new SphereGeometry;
geometry->addDrawable(spheres);
CylinderGeometry *cylinders = new CylinderGeometry;
geometry->addDrawable(cylinders);
// Render the bond paths
if(
molecule->property("QTAIMFirstNCPIndexVariantList").isValid() &&
molecule->property("QTAIMSecondNCPIndexVariantList").isValid() &&
molecule->property("QTAIMLaplacianAtBondCriticalPoints").isValid() &&
molecule->property("QTAIMEllipticityAtBondCriticalPoints").isValid() &&
molecule->property("QTAIMBondPathSegmentStartIndex").isValid() &&
molecule->property("QTAIMBondPathSegmentEndIndex").isValid() &&
molecule->property("QTAIMXBondPaths").isValid() &&
molecule->property("QTAIMYBondPaths").isValid() &&
molecule->property("QTAIMZBondPaths").isValid()
)
{
QVariant firstNCPIndexVariant=molecule->property("QTAIMFirstNCPIndexVariantList");
QVariant secondNCPIndexVariant=molecule->property("QTAIMSecondNCPIndexVariantList");
QVariant laplacianAtBondCriticalPointsVariant=molecule->property("QTAIMLaplacianAtBondCriticalPoints");
QVariant ellipticityAtBondCriticalPointsVariant=molecule->property("QTAIMEllipticityAtBondCriticalPoints");
QVariant bondPathSegmentStartIndexVariant=molecule->property("QTAIMBondPathSegmentStartIndex");
QVariant bondPathSegmentEndIndexVariant=molecule->property("QTAIMBondPathSegmentEndIndex");
QVariant xBondPathsVariant=molecule->property("QTAIMXBondPaths");
QVariant yBondPathsVariant=molecule->property("QTAIMYBondPaths");
QVariant zBondPathsVariant=molecule->property("QTAIMZBondPaths");
QVariantList firstNCPIndexVariantList=firstNCPIndexVariant.toList();
QVariantList secondNCPIndexVariantList=secondNCPIndexVariant.toList();
QVariantList laplacianAtBondCriticalPointsVariantList=laplacianAtBondCriticalPointsVariant.toList();
QVariantList ellipticityAtBondCriticalPointsVariantList=ellipticityAtBondCriticalPointsVariant.toList();
QVariantList bondPathSegmentStartIndexVariantList=bondPathSegmentStartIndexVariant.toList();
QVariantList bondPathSegmentEndIndexVariantList=bondPathSegmentEndIndexVariant.toList();
QVariantList xBondPathsVariantList=xBondPathsVariant.toList();
QVariantList yBondPathsVariantList=yBondPathsVariant.toList();
QVariantList zBondPathsVariantList=zBondPathsVariant.toList();
for( qint64 i=0 ; i < firstNCPIndexVariantList.length() ; ++i )
{
qint64 start=bondPathSegmentStartIndexVariantList.at(i).toLongLong();
qint64 end=bondPathSegmentEndIndexVariantList.at(i).toLongLong();
if( laplacianAtBondCriticalPointsVariantList.at(i).toReal() > 0.0 )
{
const qint64 step=4;
Vector3f xyz;
Vector3ub color(255, 255, 255);
for( qint64 j=start ; j < end-1 ; j=j+step )
{
xyz << xBondPathsVariantList.at(j).toFloat(),
yBondPathsVariantList.at(j).toFloat(),
zBondPathsVariantList.at(j).toFloat();
spheres->addSphere(xyz, color, 0.025f);
}
}
else
{
const qint64 step=1;
Vector3ub color(255, 255, 255);
double radius=0.025;
Vector3f v1;
Vector3f v2;
Vector3f direction;
for( qint64 j=start ; j < end-1 ; j=j+step )
{
v1 << xBondPathsVariantList.at(j).toFloat(),
yBondPathsVariantList.at(j).toFloat(),
zBondPathsVariantList.at(j).toFloat();
v2 << xBondPathsVariantList.at(j+1).toFloat(),
yBondPathsVariantList.at(j+1).toFloat(),
zBondPathsVariantList.at(j+1).toFloat();
direction = v2 - v1;
float length = direction.norm();
direction /= length;
cylinders->addCylinder(v1, direction, length, radius, color);
}
}
} // bond path
}
if( molecule->property("QTAIMXNuclearCriticalPoints").isValid() &&
molecule->property("QTAIMYNuclearCriticalPoints").isValid() &&
molecule->property("QTAIMZNuclearCriticalPoints").isValid() )
{
QVariant xNuclearCriticalPointsVariant=molecule->property("QTAIMXNuclearCriticalPoints");
QVariant yNuclearCriticalPointsVariant=molecule->property("QTAIMYNuclearCriticalPoints");
QVariant zNuclearCriticalPointsVariant=molecule->property("QTAIMZNuclearCriticalPoints");
QVariantList xNuclearCriticalPointsVariantList=xNuclearCriticalPointsVariant.toList();
QVariantList yNuclearCriticalPointsVariantList=yNuclearCriticalPointsVariant.toList();
QVariantList zNuclearCriticalPointsVariantList=zNuclearCriticalPointsVariant.toList();
if( xNuclearCriticalPointsVariantList.length() == yNuclearCriticalPointsVariantList.length() &&
xNuclearCriticalPointsVariantList.length() == zNuclearCriticalPointsVariantList.length() )
{
Vector3f xyz;
Vector3ub color(255, 64, 255);
for( qint64 i=0 ; i < xNuclearCriticalPointsVariantList.length() ; ++i )
{
xyz << xNuclearCriticalPointsVariantList.at(i).toFloat(),
yNuclearCriticalPointsVariantList.at(i).toFloat(),
zNuclearCriticalPointsVariantList.at(i).toFloat();
// map->setFromPrimitive(ncp);
spheres->addSphere(xyz, color, 0.1f);
}
}
}
if( molecule->property("QTAIMXBondCriticalPoints").isValid() &&
molecule->property("QTAIMYBondCriticalPoints").isValid() &&
molecule->property("QTAIMZBondCriticalPoints").isValid() )
{
QVariant xBondCriticalPointsVariant=molecule->property("QTAIMXBondCriticalPoints");
QVariant yBondCriticalPointsVariant=molecule->property("QTAIMYBondCriticalPoints");
QVariant zBondCriticalPointsVariant=molecule->property("QTAIMZBondCriticalPoints");
QVariantList xBondCriticalPointsVariantList=xBondCriticalPointsVariant.toList();
QVariantList yBondCriticalPointsVariantList=yBondCriticalPointsVariant.toList();
QVariantList zBondCriticalPointsVariantList=zBondCriticalPointsVariant.toList();
if( xBondCriticalPointsVariantList.length() == yBondCriticalPointsVariantList.length() &&
xBondCriticalPointsVariantList.length() == zBondCriticalPointsVariantList.length() )
{
Vector3ub color(255, 255, 32);
Vector3f xyz;
for( qint64 i=0 ; i < xBondCriticalPointsVariantList.length() ; ++i )
{
xyz << xBondCriticalPointsVariantList.at(i).toFloat(),
yBondCriticalPointsVariantList.at(i).toFloat(),
zBondCriticalPointsVariantList.at(i).toFloat();
// map->setFromPrimitive(ncp);
spheres->addSphere(xyz, color, 0.1f);
}
}
}
if( molecule->property("QTAIMXElectronDensitySources").isValid() &&
molecule->property("QTAIMYElectronDensitySources").isValid() &&
molecule->property("QTAIMZElectronDensitySources").isValid() )
{
QVariant xElectronDensitySourcesVariant=molecule->property("QTAIMXElectronDensitySources");
QVariant yElectronDensitySourcesVariant=molecule->property("QTAIMYElectronDensitySources");
QVariant zElectronDensitySourcesVariant=molecule->property("QTAIMZElectronDensitySources");
QVariantList xElectronDensitySourcesVariantList=xElectronDensitySourcesVariant.toList();
QVariantList yElectronDensitySourcesVariantList=yElectronDensitySourcesVariant.toList();
QVariantList zElectronDensitySourcesVariantList=zElectronDensitySourcesVariant.toList();
if( xElectronDensitySourcesVariantList.length() == yElectronDensitySourcesVariantList.length() &&
xElectronDensitySourcesVariantList.length() == zElectronDensitySourcesVariantList.length() )
{
Vector3ub color(64, 64, 255);
Vector3f xyz;
for( qint64 i=0 ; i < xElectronDensitySourcesVariantList.length() ; ++i )
{
xyz << xElectronDensitySourcesVariantList.at(i).toFloat(),
yElectronDensitySourcesVariantList.at(i).toFloat(),
zElectronDensitySourcesVariantList.at(i).toFloat();
// map->setFromPrimitive(ncp);
spheres->addSphere(xyz, color, 0.1f);
}
}
}
}
