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The RDKitConverter should be able to infer correctly bond orders and formal charges for any molecule
Actual behavior
As mentioned in #3044, it currently fails for molecules with the following patterns:
R-[N+]#N
R-N=[N+]=[N-]
R-[O+]=R
R-[N+]#[C-]
Additionally, monatomic ions are converted to what I'd consider to be the most common charged forms, thus things like [Cu+1] and [Fe+3] will be converted to [Cu+2] and [Fe+2].
Expected behavior
The RDKitConverter should be able to infer correctly bond orders and formal charges for any molecule
Actual behavior
As mentioned in #3044, it currently fails for molecules with the following patterns:
R-[N+]#N
R-N=[N+]=[N-]
R-[O+]=R
R-[N+]#[C-]
Additionally, monatomic ions are converted to what I'd consider to be the most common charged forms, thus things like
[Cu+1]
and[Fe+3]
will be converted to[Cu+2]
and[Fe+2]
.Code to reproduce the behavior
See the RDKitConverter benchmark for examples of molecules
Current version of MDAnalysis
2.0.0b0
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