code: public static void translateAllPositive(IAtomContainer atomCon) {
          double minX = Double.MAX_VALUE;
          double minY = Double.MAX_VALUE;
          Iterator<IAtom> atoms = atomCon.atoms().iterator();
          while (atoms.hasNext()) {
              IAtom atom = (IAtom) atoms.next();
              if (atom.getPoint2d() != null) {
                  if (atom.getPoint2d().x < minX) {
                      minX = atom.getPoint2d().x;
                  }
                  if (atom.getPoint2d().y < minY) {
                      minY = atom.getPoint2d().y;
                  }
              }
          }
          logger.debug("Translating: minx=" + minX + ", minY=" + minY);
          translate2D(atomCon, minX * -1, minY * -1);
      }
docs: Adds an automatically calculated offset to the coordinates of all atoms
  such that all coordinates are positive and the smallest x or y coordinate
  is exactly zero.
  See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets
  
  @param  atomCon  AtomContainer for which all the atoms are translated to
  positive coordinates