Avogadro2 Atom symbols and Neighbors

atomtype.cpp

  auto graph = m_molecule->graph();

  for (Index i = 0; i < m_molecule->atomCount(); ++i)
  {
    // print the symbol for the atom
    Core::Atom atom = m_molecule->atom(i);
    std::string atomType = Core::Elements::symbol(atom.atomicNumber());
    std::cout << "Atom " << atomType << " (" << i << ")" << std::endl;

    // check neighbors
    if (graph.neighbors(i).size() > 0) {
      std::cout << "Neighbors of " << atomType << " (" << i << "): ";
      for (const auto neighbor : graph.neighbors(i)) {
        Core::Atom neighborAtom = m_molecule->atom(neighbor);

        // check the bond order between the atoms
        auto bond = m_molecule->bond(i, neighbor);
        char bondOrder = ' ';
        switch (bond.order()) {
          case 1:
            bondOrder = '-';
            break;
          case 2:
            bondOrder = '=';
            break;
          case 3:
            bondOrder = '#';
            break;
          default:
            bondOrder = '?';
            break;
        }        

        std::string neighborType = Core::Elements::symbol(neighborAtom.atomicNumber());
        std::cout << bondOrder << neighborType << " (" << neighbor << "), ";
      }
      std::cout << std::endl;
    }
  }