JChem External Tool 2:1

Allows running an external program on the data. It will write out the incoming datatable into a temporary file as specified format which can be used as an input to an external tool. After the tool finishes the node will read in an output file the tool has (hopefully) created.

Options

Structure 1 column
Column in the input data table containing the structure to be converted.
Structure 2 column
Column in the input data table containing the structure to be converted.
Input 1 format
The structure format for the input file which can be used as an input to an external tool.
Input 2 format
The structure format for the input file which can be used as an input to an external tool.
External Tool
Specify an existing and executable file that will be called with the specified command line arguments. Before executing this external tool, the current working directory is set to the specified directory. The string '%input_1%' for specifying the input file, the string '%output_1%' for specifying the output file.
Output format
The structure format for the output file which will be created by the external tool.

Input Ports

Icon
Input table that contains structure in Structure(Mrv, Sdf, Smiles, etc.) format for the external tool.
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Input table that contains structure in Structure(Mrv, Sdf, Smiles, etc.) format for the external tool.

Output Ports

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Output table that contains structure from the output file of the tool.

Popular Predecessors

Popular Successors

Views

Tool Output
The text sent to standard output during the execution of the external tool. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)
NOTE: Keeping the view open may slow down the process significantly, if it produces a lot of output in a short amount of time.
Tool Error
The text sent to standard error during the execution of the external tool. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)

Workflows

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Links

Developers

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Installation

To use this node in KNIME, install the extension ChemAxon/Infocom JChem Extensions Feature from the below update site following our NodePit Product and Node Installation Guide:

v5.9

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

Plugin provider: Infocom Corporation
Plugin version: 4.7.0.v250304
On NodePit since: 2025-12-17
Last update: 2026-01-06
KNIME versions: v5.9, v5.8, v5.7, v5.6, v5.5, v5.4, v5.3, v5.2, v5.1, v4.7, v4.6, v4.5, v4.4, v4.3, v4.2, v4.1, v4.0

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