code: private void translateStructure(Point3d originalCoord, Point3d newCoord, IAtomContainer ac) {
          Point3d transVector = new Point3d(originalCoord);
          transVector.sub(newCoord);
          for (int i = 0; i < ac.getAtomCount(); i++) {
              if (!(ac.getAtom(i).getFlag(CDKConstants.ISPLACED))) {
                  ac.getAtom(i).getPoint3d().sub(transVector);
                  //ac.getAtomAt(i).setFlag(CDKConstants.ISPLACED, true);
              }
          }
      }
docs: Translates the template ring system to new coordinates.
  
  @param  originalCoord  original coordinates of the placed ring atom from template
  @param  newCoord       new coordinates from branch placement
  @param  ac             AtomContainer contains atoms of ring system