/**
* calculate distance between two atoms.
*
* @param a an Atom object
* @param b an Atom object
* @return a double
* @throws StructureException ...
*/
public static BigDecimal getPreciseDistance(Atom a, Atom b) throws StructureException {
double x = a.getX() - b.getX();
double y = a.getY() - b.getY();
double z = a.getZ() - b.getZ();
double s = x * x + y * y + z * z;
BigSqrt sqrt = new BigSqrt();
BigDecimal d = new BigDecimal(s);
BigDecimal dist = sqrt.sqrt(d);
return dist;
}
private static Atom calcSimple_H(Atom c, Atom o, Atom n) throws StructureException {
Atom h = Calc.substract(c, o);
double dist = Calc.getDistance(o, c);
// System.out.println(dist);
double x = n.getX() + h.getX() / dist;
double y = n.getY() + h.getY() / dist;
double z = n.getZ() + h.getZ() / dist;
h.setX(x);
h.setY(y);
h.setZ(z);
h.setName("H");
h.setFullName(" H ");
return h;
}