Better error message if it can't save a reaction for some strange reason.
Don't insert a blank line in the SMILES.txt every time.

Just a new line is sufficient.
Save the kinetics file (and prune the unmatched reactions) at the start.

This will help speed up the generation of the partial kinetics.py files, but also
speed up the general algorithm, as reactions that are not "unmatched" can
be taken out of consideration sooner. (If I remember correctly how this works!)