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RDKitConverter fails to infer bond orders/charges correctly #3339

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cbouy opened this issue May 27, 2021 · 2 comments
Open

RDKitConverter fails to infer bond orders/charges correctly #3339

cbouy opened this issue May 27, 2021 · 2 comments

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@cbouy
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cbouy commented May 27, 2021

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

  • Which version are you using? 2.0.0b0
@orbeckst
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Will the issue be fixed by PR #3044 ?

@cbouy
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cbouy commented Mar 30, 2022

Nope! This issue keeps track of the cases that are known to fail even after PR#3044.

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