Hi all,
I'm trying to work with Chembl23, calculating ChemFP fingerprints. Some
compounds contain non-standard heavy atoms, e.g. this one containing Te:
CC(C)(/C(=C\\Cl)/[Te](c1ccc(cc1)OC)(Cl)Cl)O
My workflow is to convert SDF format to SMILES as I find it easier to correct
any minor errors. I'm trying to calculate the fingerprints using ChemFP and
RDKit as follows:
rdkit2fps \
--id-tag "Molecule Name" \
chembl_23.fixed.smi \
-o rdkit_chembl_23.fixed.fps
but I get the following error:
[11:37:55] Explicit valence for atom # 6 Te, 4, is greater than permitted
ERROR: Cannot parse the SMILES 'CC(C)(/C(=C\\Cl)/[Te-2](c1ccc(cc1)OC)(Cl)Cl)O'
at line 155850 of chembl_23.fixed.smi. Exiting.[11:39:23] Explicit valence for
atom # 6 Te, 6, is greater than permitted
How should atoms non-standard heavy atoms like Te be treated?
Thanks
Markus
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