code: private void calculateHAtoms() throws StructureException {
  
  		for ( int i = 0 ; i < groups.length-1  ; i++) {
  
  			SecStrucGroup a  = groups[i];
  			SecStrucGroup b  = groups[i+1];
  
  			if ( !b.hasAtom("H") ) {
  				//Atom H = calc_H(a.getC(), b.getN(), b.getCA());
  				Atom H = calcSimple_H(a.getC(), a.getO(), b.getN());
  				b.setH(H);
  			}
  		}
  	}
docs: Calculate the coordinates of the H atoms. They are usually
  missing in the PDB files as only few experimental methods allow
  to resolve their location.