CheS-Mapper Node for KNIME (trusted extension)


About CheS-Mapper

CheS-Mapper is a 3D-viewer for small molecule datasets (see It supports clustering and 3D-embbeding based on the compound features (compounds with similar feature values will be located close to each other). It has been published here: Gütlein, Karwath and Kramer (2012).

About the node

The CheS-Mapper KNIME node is a pure visualization node. The input has to contain chemical structure information and/or properties (e.g. from an SDF-file, CSV-file with SMILES or InCHI column).

Two different views are available:

  • Start CheS-Mapper 3D-Viewer directly
    Starts CheS-Mapper visualization directly, using all features in the dataset for 3D-embedding (clustering is disabled).
  • Start CheS-Mapper Wizard
    Starts CheS-Mapper Wizard first. The user can configure the visualization, e.g. skip features from the 3D-embedding, or enable clustering.



An Example on how to use the CheS-Mapper Node can be found at the CheS-Mapper wiki pages.

Source Code

The source code can be accessed at


The CheS-Mapper extension is released under GPLv3.


Please send an e-mail if you have any sorts of questions, feedback, etc.: Martin Gütlein,


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