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Mol Writer

LigandScout Extensions for the KNIME Workbench version 1.7.9 by InteLigand GmbH

The Mol Writer node saves molecules into MDL Mol-files.



Output directory
Path to the output Mol-file directory. As required by the Mol file format, each molecule will be written to a separate file inside this directory.
Filename template
Naming scheme of the output files. Allows placeholders for the row of the respective input molecule (%i%) and the conformation index (%c%).
(Default: name_%i%-%c%.mol)
Structure column
Column from the input table to be treated as molecule structure.
(Default: First column with a supported molecule structure type)
Use column as molecule title
Column from the input table to be used as molecule name in the output table.
(Default: "Name" or "Drug Name" depending on the input table. "Row ID" if no such column is available.)
Don't overwrite existing files
If selected, existing files will not be overriden. The node will only output molecules where the respective file does not yet exist.
(Default: false)
Export all conformations
If selected, each conformation of a given molecule will be exported to a separate file.
(Default: true)
Export in the V3000 format
If selected, the V3000 variant of the Mol file format will be used.
(Default: false)
Export 2D-coordinates
This option is available if only a single conformation is exported per molecule. If selected, only 2D-coordinates will be written to the output Mol-file.
(Default: false)

Input Ports

Table containing the molecule(s) to write to the specified output Mol-file

Best Friends (Incoming)


To use this node in KNIME, install LigandScout Extensions for the KNIME Workbench from the following update site:


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