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;
}
/**
* Use unit vectors NC and NCalpha Add them. Calc unit vector and substract it from N. C
* coordinates are from amino acid i-1 N, CA atoms from amino acid i
*
* <p>see also:
*
* @link
* {http://openbioinformatics.blogspot.com/2009/08/how-to-calculate-h-atoms-for-nitrogens.html}
*/
private static Atom calc_H(Atom C, Atom N, Atom CA) throws StructureException {
Atom nc = Calc.substract(N, C);
Atom nca = Calc.substract(N, CA);
Atom u_nc = Calc.unitVector(nc);
Atom u_nca = Calc.unitVector(nca);
Atom added = Calc.add(u_nc, u_nca);
Atom U = Calc.unitVector(added);
// according to Creighton distance N-H is 1.03 +/- 0.02A
Atom H = Calc.add(N, U);
H.setName("H");
H.setFullName(" H ");
// this atom does not have a pdbserial number ...
return H;
}