I am trying to standardize my compounds with KNIME and RDKit. I am using a Python node and the MolVS library.
Now first I am generating RDKit molecules from SDF. In the node (RDKit from Molecule) I did tick everything in the Advanced Tab, apart from keep hydrogens. (So partial sanitization, reperceive aromaticity and correct stereochemistry). Except for one Molecule there is no error. Now the Molecules are sent to the Python node where the MolVS library is called. The first call the library makes when standardising is Chem.Sanitize(mol). Now here I get a failure for some molecules.
I would expect that sanitization in the node and the base library should be the same, hence if I already sanitized the molecules before with RDKit they should not fail later on.
Most errors relate to kekulization, some are related to valences (but to be honest these are quite weird molecules with Ru, Os or similar so here I would expect that it probably does not work)
Or is there something I am missing?
Also it would be good to know which sanitization I should trust more. Can I just ignore the errors related to aromaticity for standardisation of the library?
It would be great if someone could help me out here. I can also provide the failed molecules if that helps.
I am using Knime 3.6.2,
And Python 3 with conda:
conda version : 4.5.11
conda-build version : 3.16.2
python version : 3.7.0.final.0
on Ubuntu 16.04 LTS