cleanup of SubstitutionProbability. Addition of SubstitutionPredictor, which
does half of what the Substitutor currently does, but more cleanly.
refactor SubstitutionPredictorTransformation to use SubstitutionPredictor
instead of Substitutor
minor changes to substitutor for compatibility with modified
SubstitutionProbability
added method to get underlying element object from specie
clean up anonymous formula
minor changes to substitution_probability
Cleanup doc. New version.
Merge remote-tracking branch 'mpmaster/master'
 Minor changes