SyGMa Metabolites

Predict metabolites from parent molecules using Sygma ( https://github.com/3D-e-Chem/sygma ).

Resolving "'sygma' Python package not found" error

This node requires the ' sygma ' Python package.

If the sygma Python package was not installed then go to https://github.com/3D-e-Chem/sygma#installation and follow the installation instructions. To test if the package is installed run sygma --version on the command line, it should print a version number if installed.

Options

Parents molecule column
Column containing smile string which will be metabolized.
Phase 1 cycles
Number of times phase 1 rules should be applied
Phase 2 cycles
Number of times phase 2 rules should be applied
Sygma path
Path to sygma executable.

Input Ports

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Parent molecules

Output Ports

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Predicted metabolites

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Installation

To use this node in KNIME, install the extension 3D-e-Chem KNIME nodes from the below update site following our NodePit Product and Node Installation Guide:

v5.9
Plugin provider: Netherlands eScience Center
Plugin version: 3.0.0.v202507210712
On NodePit since: 2025-12-11
Last update: 2026-01-20
KNIME versions: v5.9, v5.8, v5.7, v5.6, v5.5, v5.3, v5.2, v5.1, v4.7, v4.6, v4.5, v4.4, v4.3, v4.2, v4.1, v4.0, v3.7, v3.6

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