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remove_hs function removes deuterium/tritium atoms #438
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@markarchibald You are right about deuterium and tritium - Regarding H atoms that are required to define stereochemistry, those are not actually present in the molecule graph, they are only added on-the-fly for visualization. You may avoid that those Hs are added by calling |
@ptosco thanks for the quick reply. Do you have a guess for when the change will find its way into a release? (Regarding Hs defining stereo, I do want these to be displayed but it's useful to understand it better.) |
The |
That's great, thank you |
Using the remove_hs function to remove unnecessary explicit H atoms, I found that while it does not remove H atoms that are required to define stereochemistry, it does remove H atoms that are labelled as the isotopes deuterium or tritium – altering the chemical structure. The analogous Chem.RemoveHs function in core RDKit does not remove deuterium/tritium.
Can be reproduced on the RDKitJS demo page (https://www.rdkitjs.com/#introduction) by running this code using a mol block for D2O:
which produces this depiction:
Expected behavior
Expected behaviour is that D atoms are not removed (as they define chemical information that is otherwise lost), resulting in this depiction:
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