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RDKit SMILES Headers

RDKit Nodes for Knime version 4.0.1.v202006261025 by NIBR

Sets, changes and/or retrieves SMILES structures of RDKit table header properties, which can be made visible using the RDKit Interactive View.

Beside the column title a KNIME column can have properties assigned. Use this node to manipulate the property that controls the SMILES value used by the RDKit Interactive View to render a molecule in the column header. This node will not change any of the column titles / names.

This node takes a Data Table as first input - the data of the table remains unchanged, only the column properties get affected by the change. You may either use existing column titles of the Data Table as SMILES properties (if they are valid SMILES), or read SMILES values from a SMILES Definition Table that is connected to the second input port.

If a SMILES Definition Table is connected it needs to contain at least two columns: One defines a SMILES value and the other the name of the target column that should receive the SMILES value in the header property. The node will now walk through all columns of the Data Table and checks, if a SMILES value is available in the SMILES Definition Table for that column. If the name of the column is found in the SMILES Definition Table it will set the associated SMILES value as a column property, and the SMILES will show up in subsequent RDKit Interactive Views. If there is no SMILES value but an empty cell defined for that column, the SMILES property gets removed instead.

The Data Table is available with the manipulated column properties on the first output port. The second output table contains information about all columns that have SMILES values as properties attached. It can be used to manipulate these structure (e.g. canonicalizing them) and to reassign them afterwards again to make these changes visible in the column headers.

Optionally, it is possible to remove all SMILES information from the column properties before applying any new SMILES values to them.


Use column titles of Data Table as SMILES property definitions
Flag this option to use column titles as SMILES values. This option is only visible and takes only effect, if there is no SMILES Definition Table connected and if it is checked. Invalid SMILES values in header titles are ignored without warnings or errors.
Column with target column names
The input column of the SMILES Definition Table that defines which Data Table column headers shall be changed.
Column with new SMILES values
The new SMILES values to be set for the specified Data Table columns. Note, that an empty or missing cell will actually remove the SMILES header information.
Remove existing SMILES values in all headers first
Flag this option to remove all existing SMILES values from the properties of all(!) header columns of the data table before setting new SMILES values based on the SMILES Definition Table.

Input Ports

Data Table whose header properties (not titles) shall be manipulated.
Defines target column names of the Data Table and SMILES values to be set as column header properties.

Output Ports

Same table as input data table, but with potentially changed column header properties.
Table with all column header SMILES properties in Result Data Table.


Interactive Table View
Displays the data in a table view. Has the capability to show chemical structures in the headers of the substructure count columns.

Best Friends (Incoming)

Best Friends (Outgoing)


To use this node in KNIME, install RDKit KNIME JUnit Test from the following update site:

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