Fix crash when save to files with stereo perception.

Need to make sure OBMol/OBAtom objects have correct
atom IDs. Fixes PR#675 for me -- save to MDL crash.

Change-Id: Idd11b4ba0fc172e462051dcffbc1c3263c5e4901
Merge topic 'FIX_save-stereo-crash' into master

40021e20 Fix crash when save to files with stereo perception.