- check remove dead code in 'cif_molecule' (@Y.R.)

- check and remove commented code in 'cif_molecule' (@Y.R.)

- !!! Inspect and refactor duplicated code in cif_molecule (@Y.R.)

- check if variable '%seen_molecules' in 'cif_molecule' and 'cif_p1'
  is needed and if not, remove it. (@S.G.).

- check the polymer span generation from the new polymer detection
  code that uses factor-graphs. (@Y.R., S.G.)
