broken topology parsing
At least two issues in topology parsing:
- when index is not provided, hydrogens are not filtered out (while with index hydrogens are not permited :-( )
- for some reasons, dihed9 contain redundancies with our trpcage topology & index: array([[0, 1, 4, 5], [0, 1, 4, 5], [0, 1, 4, 5], [0, 1, 4, 5], [0, 1, 4, 5], [0, 1, 4, 5], [2, 1, 4, 5], [0, 1, 2, 3], [0, 1, 2, 8], ...