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sulfate sulfur marked as _ChiralityPossible

Open jasondbiggs opened this issue 2 years ago • 2 comments

Describe the bug The sulfur in sulfuric acid or a sulfate group is marked with the "_ChiralityPossible" flag, even though it has identical substituents.

To Reproduce

rdmolops.SetUseLegacyStereoPerception(False) # unless you already have this set
ps = Chem.SmilesParserParams()
ps.removeHs = False
sa = MolFromSmiles('O=S(=O)(O[H])O[H]', ps)
for atom in sa.GetAtoms():
	if(atom.HasProp('_ChiralityPossible')):
		print(atom.GetIdx())

#output: 1

Expected behavior I would expect this to not be marked as a potential stereocenter since it is tetrahedral and has identical substituents, like how carbon is treated.

Configuration (please complete the following information): I see this in RDKit version "2022.09.3"

jasondbiggs avatar Apr 21 '23 16:04 jasondbiggs

This also seems to affect phosphorus atoms, so the P in O=P(O)(O)O is marked as a possible stereocenter.

I have set up a check in my code when looking for unmarked stereocenters to check that the underlying atom is not sulfur or phosphorus, but I would rather not use such a hack

jasondbiggs avatar May 11 '23 16:05 jasondbiggs

This issue was marked as stale because it has been open for 90 days with no activity.

github-actions[bot] avatar Oct 19 '24 02:10 github-actions[bot]

This issue was closed because it has been inactive for 14 days since being marked as stale.

github-actions[bot] avatar Nov 04 '24 02:11 github-actions[bot]