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Ring stereochemistry not properly removed from N atoms #3631

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greglandrum opened this issue Dec 10, 2020 · 0 comments
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Ring stereochemistry not properly removed from N atoms #3631

greglandrum opened this issue Dec 10, 2020 · 0 comments
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greglandrum commented Dec 10, 2020

Here's the reproducible:

In [11]: Chem.CanonSmiles('C[N@]1C[C@@](F)(Cl)C1')
Out[11]: 'C[N@]1C[C@@](F)(Cl)C1'

In [12]: Chem.CanonSmiles('C[N@]1O[C@@](F)(Cl)C1')
Out[12]: 'CN1C[C@](F)(Cl)O1'

That three-coordinate N shouldn't be a chiral center. The stereochem is correctly removed when it's "normal" chirality, but it persists when ring stereo is involved (the first example).

The reason this happens is that the logic which allows ring stereo essentially passes all atoms through, even those which aren't allowed to have atomic chirality (like these Ns).

@greglandrum greglandrum added this to the 2020_09_3 milestone Dec 10, 2020
@greglandrum greglandrum self-assigned this Dec 10, 2020
greglandrum added a commit to greglandrum/rdkit that referenced this issue Dec 11, 2020
Still worth investigating *why* this happened.
greglandrum added a commit that referenced this issue Dec 12, 2020
* Fixes #3631

Still worth investigating *why* this happened.

* a bit of simplification/refactoring
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