IconMolecule to CDK0 ×

KNIME CDK Integration version 1.5.700.v201711101057 by KNIME GmbH, Konstanz and EMBL-EBI, Cambridge

Converts the elements in one of the input table's columns into an internal format (CDKCell), which can then be rendered as molecule or used for further computations. The target column must contain string representations of molecules (SDF, Mol2, SMILES [no stereo information], CML, InChI).

For on untyped InChI or SMILES string, the line notation is inferred. If the string starts with "InChI=", the InChI parser is used, the SMILES parser otherwise. The option's dialog will not automatically select an input column as a string cell may not contain the right input, in contrast to typed SDF, Mol2, or SMILES cells.

This node uses CDK classes to parse and display structures.


Molecule Column
The column that contains the molecules.
Replace Column
Select this to replace the molecule column with the column containing the converted CDK molecules. Otherwise a new column will be appended.
New column name
Enter the name of the new column here if the original column is not replaced (see option above).
Generate 2D coordinates
Enabling this option will generate 2D coordinates for the converted molecules so that they can be visualized.
Force 2D generation
Without this option, 2D coordinates will only be generated for molecules that do not only have any (usually detected by an all zero z-coordinate). If this options is enabled the coordinates will be generated in any case.
An experimental feature that tries to infer double bonds in an aromatic system if not given by the input file. E.g., when the bond order in a SDFile is used to indicate aromaticity (bond order 4).

Input Ports

Table containing molecules to parse

Output Ports

Table with the parsed molecules

Best Friends (Incoming)

Best Friends (Outgoing)


Update Site

To use this node in KNIME, install KNIME CDK Integration from the following update site:

Wait a sec! You want to explore and install nodes even faster? We highly recommend our NodePit for KNIME extension for your KNIME Analytics Platform.