On 2016-01-29 17:02, Rich Lewis wrote:
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 [*2**3*]: 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?
Hi Rich,
The file rdkit/Code/GraphMol/atomic_data.cpp is indeed where the
valences are configured. There was a similar discussion in 2015 that
resulted in additional valence data being added to P.
http://sourceforge.net/p/rdkit/mailman/message/34131420/
You can try out the valence change locally by adding it to
atomic_data.cpp (TAB-delimited format) and rebuilding RDKit.
Cheers
-- Jan Holst Jensen
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