Creating a COMPOUND_CTAB file from a file containing SMILES strings

If you need to create the file but you only have your compound structures as SMILES strings.

We provide an examble 2-column Excel workbook to show how input data should be organised for these tools.

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CIDX_smiles.xlsx

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Using KNIME

Install KNIME, which you can find here. https://www.knime.com/installation Open the workflow in KNIME. KNIME will prompt you to let it install the plugin dependencies for this workflow.

Double-click the first node and change the File path to wherever you downloaded the CIDX_SMILES.xlxs file to.

Double-click the final node and change the File path to wherever you would like the output to go to.

Select the final node again and either press the execute button (right-facing triangle) or press F7 to run the workflow. At this point you will probably want to save the workflow to keep your own file paths.

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smiles2SDF.knwf

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Using a Jupyter Notebook

If you are more familiar with coding, we also have a Jupyter notebook tool here.

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smiles2SDF_RDKit.ipynb

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