protected void set(Atom atom1, Atom atom2, Distance distance, int swapFactor) {
this.atom1 = atom1;
this.atom2 = atom2;
this.swapFactor = swapFactor;
distanceVal = distance.distance();
dDistanceDx = distance.dDistanceDx();
dDistanceDy = distance.dDistanceDy();
dDistanceDz = distance.dDistanceDz();
}
/*
* @parm obj is Distance
*/
public boolean accept(Object obj) {
Distance dis = (Distance) obj;
HB_AtomAttribute atom1Attribute =
(HB_AtomAttribute) (dis.atom1().getAttribute(HB_AtomAttribute.key));
HB_AtomAttribute atom2Attribute =
(HB_AtomAttribute) (dis.atom2().getAttribute(HB_AtomAttribute.key));
if (atom1Attribute == null
|| atom2Attribute == null) // meens that at list one of the atom is not H or O
// since we add attribute just to H or O
return false;
return ((atom1Attribute.isH && atom2Attribute.isO)
|| (atom1Attribute.isO && atom2Attribute.isH));
}