from a list of compounds names to the corresponding SMILES

KNIME Analytics Platform
1

hi,
I have only been approaching with KNIME for few days and i am encountering some difficulties.
i have an excel file with a column reporting names of compounds of which i need the corresponding SMILES.
what is the best way to obtain them? what are the nodes that i need for the process?
thank you in advance!

2

Hi and welcome!
I would start with either the OPSIN – KNIME Community Hub or the RDKit From IUPAC – KNIME Community Hub nodes.
The first one uses a web service, so you may not be able to use that.
If you have a lot of missing values because of the use of trivial or commercial names, then it’s possible to construct a workflow to use PubChem or similar to retrieve SMILES strings.

(the other)
Simon

1 Like
3

thank you so much! i did it

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