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Molfile Reader

KNIME Chemistry Base nodes version 4.3.0.v202011191214 by KNIME AG, Zurich, Switzerland

This node reads Molfiles (*.mol) from a directory and creates a row for each file. The row ID is either taken from the file name or extracted from the molecule itself. The node can also read gzipped files ending with *.mol.gz.


The directory in which the Molfiles are
Use molecule name as row ID
If selected, the row ID will be the same as the molecules' titles. You have to ensure, that the titles are unique, otherwise the node will fail. If unchecked, the row ID is extracted from the file names (the part before the file type suffix).
Extract molecule name
If selected, the molecules' names are put into a column called 'Molecule name' in the output table. This option can be used together with the previous one.
Output column name
Enter the name of the column containing the molecules in the output table.

Output Ports

Table with the read molecules

Best Friends (Incoming)

Best Friends (Outgoing)



To use this node in KNIME, install KNIME Base Chemistry Types & Nodes from the following update site:


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

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