global.h

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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
// $Id: global.h,v 1.25 2005/10/23 12:02:19 oliver Exp $
//

#ifndef BALL_KERNEL_GLOBAL_H
#define BALL_KERNEL_GLOBAL_H

#ifndef BALL_KERNEL_ATOM_H
# include <BALL/KERNEL/atom.h>
#endif

#ifndef BALL_KERNEL_BOND_H
# include <BALL/KERNEL/bond.h>
#endif

namespace BALL 
{
  template <class AtomContainerType>
  void cloneBonds(const AtomContainerType& atom_container, AtomContainerType& cloned)
  {
    typedef HashMap<const Atom*, Atom*> AtomMap;
    AtomMap atom_map;

    std::list<const Bond*> bond_list;

    // iterate over the two composite structures in parallel
    // caveat: if the two composite structures are not isomorphous, bonds
    // are created between unrelated atoms!
    Atom::BondConstIterator bond_iter;    
    AtomConstIterator atom_iter_a(atom_container.beginAtom());
    AtomIterator atom_iter_b(cloned.beginAtom());

    for (; +atom_iter_a && +atom_iter_b; ++atom_iter_a, ++atom_iter_b)
    {
      // create a hash map containing a 1:1 relation for the atom pointers
      // atom_map maps atom pointers of atom_container to atom pointers in cloned
      atom_map.insert(std::pair<const Atom*, Atom*>(&*atom_iter_a, &*atom_iter_b));

      // iterate over all bonds and store the bonds in a list
      // to get each bond exactly once, we check the first atom
      for (bond_iter = atom_iter_a->beginBond(); bond_iter != atom_iter_a->endBond(); ++bond_iter) 
      {
        if (bond_iter->getFirstAtom() == &(*atom_iter_a))
        {
          bond_list.push_back(&(*bond_iter));
        }
      }
    }

    // iterate over all bonds and create a bond in the cloned structure
    // if both atoms of the bond are contained in the cloned structure,
    // thus preventing the copying of bonds between atoms of atom_container
    // and atoms outside atom_container
    std::list<const Bond*>::iterator list_iter = bond_list.begin();
    for ( ; list_iter != bond_list.end(); ++list_iter)
    {
      if (atom_map.has((*list_iter)->getFirstAtom()) && atom_map.has((*list_iter)->getSecondAtom()))
      {
        Atom* a1 = atom_map[(*list_iter)->getFirstAtom()];
        Atom* a2 = atom_map[(*list_iter)->getSecondAtom()];
        Bond* tmp_bond = static_cast<Bond*>((*list_iter)->create(false, true));
        tmp_bond->createBond(*tmp_bond, *a1, *a2);
        *tmp_bond = **list_iter;
        tmp_bond->setFirstAtom(a1);
        tmp_bond->setSecondAtom(a2);
        tmp_bond->finalize();
      }
    }
  }

  extern bool clone_bonds;
} // namespace BALL  

#endif // BALL_KERNEL_GLOBAL_H