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RDKit From Molecule

RDKit Nodes for Knime version 4.0.1.v202006261025 by NIBR

Generates RDKit molecule column from a molecule string representation (SMILES, SDF or SMARTS) and appends it to the table. Depending on the input format of the molecule the usage of some options is not possible. All grayed out options are not taken into account when the RDKit molecule gets generated, regardless if flagged or not.


Molecule column
The column that contains the molecules (SMILES, SDF or SMARTS type column). If the input column type supports multiple molecule types, the node will take SMILES before SDF before SMARTS.
Treat as query
Flag that can be used for SMILES and SDF input columns. Select it to prepare the resulting RDKit molecules as queries. This forces a full sanitization, keeps hydrogens in the molecule and merges query hydrogens.
New column name
Name of the new column in the output table.
Remove source column
Toggles removal of the input molecule column in the output table.
Error Handling
If the molecule in an input row cannot be converted, you can select if this row should be separated from the output table and be delivered at the second port, or if a missing value should be inserted instead of the RDKit molecule in the result table.

Also, it is possible to get additional error information added for all structures that failed conversion. If this option is checked, you need to specify the name of the error column.
Generate 2D Coordinates
Select this option to generate 2D coordinates for the molecules. The coordinates are used for, among other things, 2D renderings of the structures. If not selected, the renderer will (re-)compute coordinates on demand.
Force Generation
Select this box to enforce 2D coordinate generation. Coordinates may already be available in the (SDF) input, so this option allows you to discard the original coordinates and recompute from scratch.


Keep Hydrogens
Switch this option on to prevent the RDKit from removing hydrogens from molecules constructed from SDF. This option has no effect for SMILES or SMARTS input.
Partial Sanitization
The RDKit does a fair amount of work when compounds are loaded to make sure that they are chemically reasonable and correct. This is called sanitization. When switching on partial sanitization the following options allow specific aspects of the sanitization to be turned off:
Partial Sanitization Option - Reperceive Aromaticity
If enabled (the default) all molecules are converted to a Kekule form and then Hueckel's rules are applied to determine aromaticity. If disabled, whatever aromaticity information is present in the input will be used. NOTE: SDF/MOL data contains no information about aromaticity.
Partial Sanitization Option - Correct Stereochemistry
If enabled (the default) all stereochemistry specifications will be checked to ensure that they are not redundant or that stereochemistry markers are not set on either atoms or double bonds that should not have them.

Input Ports

Data with Smiles or SDF representation of molecules

Output Ports

Data with RDKit molecule column
Rows that could not be converted to a RDKit molecule

Best Friends (Incoming)

Best Friends (Outgoing)



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


A zipped version of the software site can be downloaded here.

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