for extracting domain from xls for modification reaction it is now possible to get domain for component A ot component B (needed for PT).
StateFactory has now additional option - to get PT state - it returns source state for PT reaction (domain from componentA), product state is obtained through Covalent modification (domain from componentB).
Attribut added to Reaction - to_change_pt. It is used only for PT reactions, otherwisw None, used in run reaction function for PT.
Way a preliminary reaction is created in reactionFactory changed.
Tests updated.
Merge pull request #26 from thieme/debugging_pt

Debugging pt