MedØlDatschgerl (MØD) is a software package developed for graph-based cheminformatics. It includes a general graph transformation system for automatically generating reaction networks from graph grammar formulations of chemistries.
The software is primarily implemented in C++, but the package includes comprehensive Python 3 binding that provides easy access most functionality. The package also includes a large visualisation module that makes it possible to automatically visualise molecules, reactions, and reaction networks. Examples of how to use the Python interface and the visualisation capabilities can be seen in the examples section, and they can all be accessed interactively in the Live Playground.
Source Code and Documentation¶
If you use MØD in your research, you may want to cite some of the following papers. You may also be interested in the Graph Grammar Library, which has been used in early versions of MØD.
- 50 Shades of Rule Composition — From Chemical Reactions to Higher Levels of AbstractionJakob L. Andersen, Christoph Flamm, Daniel Merkle, and Peter F. Stadler. Formal Methods in Macro-Biology, 8738:117-135, 2014. [ DOI ]
- Conference version: Towards an Optimal DNA-Templated Molecular AssemblerJakob L. Andersen, Christoph Flamm, Martin M. Hanczyc, and Daniel Merkle. ALIFE 14: The Fourteenth Conference on the Synthesis and Simulation of Living Systems, 14:557-564, 2014. [ DOI | http ]Journal version: Towards Optimal DNA-Templated ComputingJakob L. Andersen, Christoph Flamm, Martin M. Hanczyc, and Daniel Merkle. International Journal of Unconventional Computing, 11(3-4):185-203, 2015. [ http ]