fix: update dihedrals, make pairs unique #383
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jmbuhr
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Fixes #376
There were two problems.
Inner dihedrals in MultipleDihedrals were all written in the same dict (new_dihedrals), for all multidihedrals. Did not matter though, as this dict was not fed back into the multidihedrals.
Second, multiple dihedrals had the same start and end, with different middle atoms. The start and end were used for pairs, leading to duplicate definitions of the same pair. On top, the pair was updated, so it got updated a second time, leading to a miss match of dict keys and content in the pairs.
https://github.com/hits-mbm-dev/kimmdy/blob/9f9b162c40aaf91f691b3963578030592f0ec0a5/src/kimmdy/topology/topology.py#L529-L567