Hello,
my name is Stephan. I am facing an issue with the two component reaction. The node is running but is returning an empty table. I am trying to formulate a reaction which includes a cylcization. Checking the SMARTS reaction with a visualization webtool shows the right reaction, so the generic SMARTS seems to be correct. But obviously the KNIME node has difficulties to match my list of reactants to the SMART reaction. How can I get a populated list of products instead of an empty one?
Hi Stephan! Welcome to the community! Can you share a workflow and data with an example of your problem?
Thank you.
Dear Carlos,
thank you for picking this up. I am not sure how to best share my workflow. It looks like this, combining the Smilescolumns of the two input tables
Two component reaction between two types of compounds, an aldehyde and a certain group of amino compound. The SMARTS reaction is defined as such
O=[C:1]*.[N:6][C:5](*)[C:7][c:8]1[c:9][NH:10][c:11]2[c:12][c:13][c:14][c:15][c:16]12>>*[C:1]3[N:6][C:5](*)[C:7][c:8]1[c:9]3[NH:10][c:11]2[c:12][c:13][c:14][c:15][c:16]12
A visualisation of this SMARTS looks correct, but I get back an empty table.
One example for such a combination of aldehyde and amino compound is OCC=O with
| OC(=O)C(N)Cc1c[NH]c2ccccc12 |
|---|
I hope you can help me with this.
Kind regards
Stephan
Hi Stephan,
Unfortunately, I cannot see your screenshots.
Try to follow this short tutorial to share a workflow https://youtu.be/g60JH-iJ7gU
You can save a sample of your data (not the whole file) in the data folder of your workflow folder before sharing it in the hub.
Cheers,
Carlos
