VizChemoton

Philosophy of SCINE VizChemoton

VizChemoton is an open-source framework aimed at displaying the information of a reaction network exploration performed by Chemoton in a standalone visualization HTML file. Once the file is generated, it allows users to access and visualize all the compounds, reactions, and transition states found by Chemoton, without requiring any specific library dependency nor any particular operating system. It is worth highlighting that VizChemoton should not be confused with Heron, as the latter is the full-fledged graphical user interface which allows monitoring and controlling the exploration on-the-fly.

Technical Details

VizChemoton is implemented in Python and JavaScript, and it can be installed via PIP. To generate the HTML file of the reaction network, it requires the following SCINE modules to extract the chemical data from the exploration:

  • SCINE Chemoton, which is necessary to create a Pathfinder object for each exploration,
  • the SCINE database wrapper, which is necessary to query the MongoDB to obtain reaction and energy data,
  • SCINE Utilities, which a library of common functionality used across all SCINE modules.
Apart from the SCINE dependencies, VizChemoton also requires the amk-tools package to convert the data from the exploration into a single HTML file.
These components do not need to be installed manually; rather, they are automatically installed when setting up VizChemoton.

Current Features

  • Generate the HTML file from a local (or remote) MongoDB where the exploration data is collected. The user can define the method family (e.g. "cc", "dft"), the specific method, the basis set, and the program.
  • Generate the HTML file from a JSON file written by Pathfinder containing a set of elementary steps and reactions. The Pathfinder JSON file can be either read of written using VizChemoton.
  • Generate the HTML file from a pair of custom data files: compounds.json and reactions.csv. This allows running VizChemoton without an active MongoDB, as well as storing the reaction data in plain text files.
  • Define the name, size and layout of the dashboard displaying the reaction network in the HTML file.
  • Search any given compound in the reaction network by its index name or SMILES. The former can be obtained searching the structure in ioChem-BD at the server hosted in the Barcelona Supercomputer Center (more information in the documentation).

Download

SCINE VizChemoton is distributed as an open source code. Visit our GitHub page to download it.

Future Releases

  • Implement more Chemoton input variables in the configuration file
  • Make the HTML file appearance more chemically intuitive

Documentation

Documentation is provided in the source code; you can also access it here.

Support

Despite intense testing of the program, questions may arise with respect to the usage of SCINE VizChemoton. Do not hesitate to contact the developers via scine@phys.chem.ethz.ch in case of any questions and suggestions.

References

  • Primary reference for VizChemoton 1.0.0:
    E. Petrus, D. Garay-Ruiz, C. Bo, M. Reiher, T. B. Hofstetter, "VizChemoton: v1.0.0 (Version 1.0.0)", Zenodo, 2025. DOI
  • First application:
    E. Petrus, L. A. Hunkeler, U. von Gunten, M. Reiher, T. B. Hofstetter, "Automated Reaction Exploration of Ozonation Processes for Model Olefins in Water", ChemRxiv, 2025. DOI