ChemReactionUtils: remove unused/specialized functions from interface

- specialized utils functions only used in the pgsql cartridge were removed
  from the interface
Merge pull request #319 from NadineSchneider/master

ChemReactionUtils: remove unused/specialized functions from interface
Fix defaults in ReactionFp parameter struct
Merge pull request #321 from NadineSchneider/master

Fix defaults in ReactionFp parameter struct
backup
Issue #320 Making GetBestRMS more idiot-proof

- minor changes,
- improve docs, note about the combinatorial explosion,
- suggest alternative in AlignMol,
- issue a warning if number of matches is above an aribtrary cutoff
smiles tests now pass as well
some code cleanup
Merge pull request #322 from jandom/Issue_320

Issue #320 Making GetBestRMS more idiot-proof
Adapt tests for python3.
Add preprocessor option for use of Eigen3 library in Alignment code.
Merge remote-tracking branch 'upstream/master'