AtomPair.java

Map<AtomPair,IBond> bondMap = new HashMap<>();

for (IBond bond : container.bonds())
    bondMap.put(new AtomPair(bond.getAtom(0), bond.getAtom(1)), 
                bond);
                
class AtomPair { 
    IAtom a, b;
    AtomPair(IAtom a, IAtom b) {
        this.a = a, this.b = b;
    }
    public int hashCode() {
       return a.hashCode() ^ b.hashCode();
    }
    public boolean equals(Object obj) {
        // null check etc
	AtomPair that = (AtomPair) obj;
        return this.a.equals(that.a) && this.b.equal(that.b) || this.a.equals(that.b) && this.b.equal(that.a);
    } 
}