Use the MDL format instead of CML for optimization

The CML format suffers from a bug in obabel on the Mac (reported on the
Open Babel developer list). For geometry optimization and add/remove
hydrogens the MDL format is a great second choice (atoms and bonds
supported in a simple format) that side steps the obabel bug while
retaining all other desired functionality. Verified correct operation
with latest obabel on Mac OS X.

Change-Id: Id9a8f76ec9190a555b94f41bc347b54649c3fea8
Merge topic 'openbabel-mdl' into master

e0e0ad72 Use the MDL format instead of CML for optimization