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);
    }
    }
  }
}
Ejemplo n.º 2
0
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)));
  }
}
Ejemplo n.º 3
0
  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);
        }
      }
    }
  }