current Net implementation does not work if branching index is used via multiple images

[kjappelbaum]

reason for why #100 is not resolved

[kjappelbaum]

the issue is that i currently do this via a dict that is indexed with the site index

[kjappelbaum]

the issue is that i no longer remember in what cases we needed already

     self.mapping_from_original_indices = defaultdict(list)
        for ori_index, index in zip(self._original_indices, range(len(molecule))):
            self.mapping_from_original_indices[ori_index].append(index)

[kjappelbaum]

while this is now fixed, it makes issues in the net construction, where we currently have a similar assumption