org.biojava.nbio.structure.Calc.subtract java code examples | Tabnine

/**
 * 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
 *
 * @link http://openbioinformatics.blogspot.com/
 *         2009/08/how-to-calculate-h-atoms-for-nitrogens.html
 */
@SuppressWarnings("unused")
private static Atom calc_H(Atom C, Atom N, Atom CA)
    throws StructureException {
  Atom nc  = Calc.subtract(N,C);
  Atom nca = Calc.subtract(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");
  // this atom does not have a pdbserial number ...
  return H;
}