IterateOverAllAtomPairsInAnAtomContainer

How can I iterate over all atom pairs in an AtomContainer ?

Iterating over all atom pairs of an AtomContainer using the BALL_FOREACH_ATOM_PAIR-macro:

#include <BALL/KERNEL/forEach.h>

using namespace BALL;
...
AtomContainer ac;
AtomIterator ait1, ait2;			
BALL_FOREACH_ATOM_PAIR(ac, ait1, ait2)
{
  // Compute the distance of the current atom pair
  float dist = ait1->getPosition().getDistance(ait2->getPosition());
 
  // Print the distance
  std::cout << dist <<  " " << ait1->getFullName() << " " << ait2->getFullName()  << std::endl;
}

Note: Using a simple nested AtomIterator-BondIterator-construction will consider each atom-pair twice!

Note: Never try to add or remove atoms from the AtomContainer while running over it! Your programm will crash!

Note: the BALL_FOREACH_ATOM_PAIR-macro gets an AtomContainer. BALL-objects, that can be runtime-cast to an AtomContainer are for example a Chain, a Residue, a Molecule, a Protein, or a System.