This fixes issue #384. However, there is one caveat: Now the modification can have an order attribute. This originates from the way we treat the atoms when making interactions. Even though we maybe don't want this, having order attributes is most consistent in my opinion with the fact that modifications is a subclass of Link. I would propose to later down the line disentangle the Modifications object from the Link, because they are really very separate things. As far as I can asses it makes no difference between having order attributes as to not having them in the current code.
This fixes issue #384. However, there is one caveat: Now the modification can have an order attribute. This originates from the way we treat the atoms when making interactions. Even though we maybe don't want this, having order attributes is most consistent in my opinion with the fact that modifications is a subclass of
Link. I would propose to later down the line disentangle the Modifications object from the Link, because they are really very separate things. As far as I can asses it makes no difference between having order attributes as to not having them in the current code.