Dear all,
I noticed another small issue when importing mol / sd data and calculating
RDKIT descriptors.
There is a difference between direct import and smiles (or second mol-block
conversion):
Take Mercury as an simplified example: [Hg+]
If imported as smiles Descriptors.NumRadicalElectrons() reports 1.0
>>> smiMol = Chem.MolFromSmiles("[Hg+]")
>>> Descriptors.NumRadicalElectrons(smiMol)
1.0
If I use this mdl molfile:
mdl="""Mercury
Mrv0541 03241519412D
1 0 0 0 0 0 999 V2000
5.2935 -7.2164 0.0000 Hg 0 3 0 0 0 0 0 0 0 0 0 0
M CHG 1 1 1
M END"""
>>> mdlMol = Chem.MolFromMolBlock(mdl)
>>> Descriptors.NumRadicalElectrons(mdlMol)
0.0
BUT if converted twice I get the same as with the Smiles input:
>>> mdlMol2 = Chem.MolFromMolBlock(Chem.MolToMolBlock(mdlMol))
>>> Descriptors.NumRadicalElectrons(mdlMol2)
1.0
The difference in the Mol file is that the valency in the ctab is set to
15 (0) when exported using MolToMolBlock.
I am wondering if there might be a standardization / assignment step
missing in the MolFromMolBlock when called with an "external" mol file as
input?
Best,
Michael
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