Molfile Reader

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.

Options

Directory: 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.

Input Ports

This node has no input ports

Output Ports

: Table with the read molecules

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Workflows

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Installation

To use this node in KNIME, install the extension KNIME Base Chemistry Types & Nodes from the below update site following our NodePit Product and Node Installation Guide:

v5.4

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

Plugin provider: KNIME AG, Zurich, Switzerland

Plugin version: 5.4.0.v202410111128

On NodePit since: 2024-12-06

Last update: 2024-12-17

KNIME versions: Since v3.6

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