Converting string data type to SMILES

For KNIME to interpret SMILES strings as molecules, it needs to recognize that they are not random sequences of characters but rather molecular notation. Depending on the input, this might necessitate the use of a Molecular Type Cast node. This does not change the string but only how KNIME interprets it.

This workflow demonstrates the use of the Molecule Type Cast node, which converts strings containing SMILES to the actual SMILES data format.

In a second step, the SMILES strings are canonicalized for further use using an RDKit node. Canonicalization means determining which of all possible SMILES will be used as the reference SMILES for further use.

Read a file containing strings that are actually SMILES

Ideally, the file format can be set directly under the "Transformation" tab in the respective reader's configuration!