Dear all,
I tried to load a periodate from its smiles (I think these are correct), but it
failed as according to rdkit, Iodine cannot have a valence of 7. However, it
can when stabilised with oxygens (at least from what I recall from my
undergraduate course!).
In [23]: Chem.MolFromSmiles('[O-]I(=O)(=O)=O')
[15:29:04] Explicit valence for atom # 1 I, 7, is greater than permitted
In [24]: Chem.MolFromSmiles('OI(=O)(=O)=O')
[15:24:21] Explicit valence for atom # 1 I, 7, is greater than permitted
In [25]: Chem.MolFromSmiles('[H]OI(=O)(=O)=O')
[15:24:26] Explicit valence for atom # 1 I, 7, is greater than permitted
I don’t know if the file rdkit/Code/GraphMol/atomic_data.cpp is where the
valences are configured for rdkit, but in the file, I saw that the allowed
valence states are +1, +2(?) and +5 but not +7. A few of the other elements
are also similarly conservative, such as Br only allowing +1. Should these be
expanded, or is this deliberate?
For a comparison with another toolkit, on the OpenEye docs
(https://docs.eyesopen.com/toolkits/cpp/oechemtk/valence.html
<https://docs.eyesopen.com/toolkits/cpp/oechemtk/valence.html>) they allow many
more valences - even allowing N +5.
Thanks,
Rich
--
Richard Lewis
PhD Candidate
Centre for Molecular Informatics
University of Cambridge
http://www.ch.cam.ac.uk/group/bender/person/rl403
<http://www.ch.cam.ac.uk/group/bender/person/rl403>
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