How to import a SMARTS string from a node generating SMARTS to the RDKit R Group Decomposition node?

Groups Cheminformatics
1

Dear Knime experts,

I am a Knime newbie and I would like to know how to import a SMARTS string from a node capable of generating SMARTS to the RDKit R Group Decomposition node.

I have a prinicipal worflow starting with a SD file followed by the RDKit R Group Decomposition node, then the workflow continues.

I have a second workflow in the same worflow panel generating the SMARTS string.

In the RDKit R Group Decomposition node configuration panel there is a field called "Core SMARTS" and I would like this field to be automatically filled by the another node generating the SMARTS string information.

Any idea?

Many thanks in advance.

Julien

2

Hi Julien,

You can do this by converting the cell containing the SMARTS to a flow variable and then using this to set the "Core SMARTS" value.

-greg

 

3

Thank you Greg for your help.

Problem solved!

I connected the node generating the SMARTS string to the 'Table Column to Variable' node. In this node, I selected the column containing the single row with the SMARTS string.

Then, I connected the variable to the 'RDKit R Group Decomposition' variable port. Finally, in the RDKit R Group Decomposition node, under Flow Variables, I selected "Row0" for smarts_value.

Julien