Fragmenter

Fragmenter cleaves single bonds to generate molecular fragments. The cleavage rules correspond to chemical reactions in order to enhance synthetic accessibility. The cleavage points on the fragments are labeled with the cleavage rules.

Options

Filename
The path to the configuration XML file.
The maximum number of fragments per fragment set
Sets the maximum number of fragments per fragment set to be created.
The maximum number of fragment sets per molecule
Sets the maximum number of fragment sets per molecule.
Include extendable cut sets
Sets the extendable cut sets be included.
Set fragment cut data in atom labels
Set fragment cut data in atom labels.
Fragment attachment points
Sets the atom type added to denote attachment points.
Structure column
The structure column.

Input Ports

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Input table that contains structure in Structure(Mrv, Sdf, Smiles, etc.) format.

Output Ports

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Output table that contains fragments structure in Marvin format.

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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:

v4.2

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

Plugin provider: Infocom Corporation
Plugin version: 4.0.0.v192100
On NodePit since: 2020-07-13
Last update: 2024-04-14
Tags: Streamable
KNIME versions: From v4.0 to v4.2

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