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Incorrect resonance structures in presence of dative bonds #3349

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IvanChernyshov opened this issue Aug 20, 2020 · 4 comments · Fixed by #3354
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Incorrect resonance structures in presence of dative bonds #3349

IvanChernyshov opened this issue Aug 20, 2020 · 4 comments · Fixed by #3354
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@ptosco
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bug
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2020_09_1

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@IvanChernyshov
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If an atom which is a part of a conjugated system forms a dative bond, it drops out of the resonance:

from rdkit import Chem
mol = Chem.MolFromSmiles('CC(=O)[O-]')
print(len(Chem.ResonanceMolSupplier(mol)))
> 2
mol = Chem.MolFromSmiles('CC(=O)[O-]->[*]')
print(len(Chem.ResonanceMolSupplier(mol)))
> 1

I think, if an atom forms a dative bond as a donor, then such dative bonds must be ignored.
@greglandrum
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I agree.
@ptosco : seem right to you too?

@ptosco ptosco self-assigned this Aug 20, 2020
@ptosco
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ptosco commented Aug 20, 2020

Sure. At the moment the algorithm does not account for dative bonds. I'll look into fixing this over the weekend.
@IvanChernyshov Thanks for reporting this!

ptosco added a commit to ptosco/rdkit that referenced this issue Aug 22, 2020
@ptosco
- fixed rdkit#3349
c8b4824 
- fixed a few typos
- removed const from operator(), which should be allowed to modify the owning object
- added missing const to some getters
@ptosco ptosco mentioned this issue Aug 22, 2020
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greglandrum pushed a commit that referenced this issue Sep 2, 2020
@ptosco
- fixed #3349 (#3354)
5a8db40 
- fixed a few typos
- removed const from operator(), which should be allowed to modify the owning object
- added missing const to some getters
@greglandrum greglandrum added this to the 2020_03_6 milestone Sep 2, 2020
@greglandrum greglandrum modified the milestones: 2020_03_6, 2020_09_1 Sep 18, 2020
@greglandrum
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I'm changing the milestone on this one because the merge to the release branch is non-trivial

@ptosco
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ptosco commented Sep 18, 2020 •
edited

@greglandrum may I help? I guess the release branch misses some dative bond awareness that this requires?

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Fixes #3349 ptosco/rdkit
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@greglandrum @ptosco @IvanChernyshov