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Molfile Writer

KNIME Chemistry Base nodes version 4.4.0.v202104131254 by KNIME AG, Zurich, Switzerland

This nodes writes molecules from a Mol column into separate files into a local directory or a remote location denoted by a URL. The files may optionally be compressed with gzip.
Note that if the destination location is a remote URL not all options are available because in general it's not possible to determine whether the remote location exists. In this case it will always be overwritten.


The directory into which the Molfiles should be written. The directory must already exist. You can also specify remote URLs, in this case the final destination URLs are built by directly appending the file name to this base URL.
Use molecule title as file name
If selected, the molecules' titles are used as file names. You have to make sure, that the titles are unique. Otherwise files may be overwritten or the node fails, depending on the "Overwrite existing files" option. If unselected, the row ID is used as file name.
Structure column
Select the column containing the Mol structures here.
Overwrite existing files
If selected, existing files are overwritten, if unselected, the node fails if a file already exists.
Compress files
If selected, the output files will be compressed with gzip.

Input Ports

A table with at least a Mol column

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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