Open Babel is a widely used open source toolkit for cheminformatics. One of its important functions is 3D structure prediction of input molecules. Open Babel’s coordinate generation function was improved in speed and stereochemical accuracy by the new fragment-based coordinate generation method implemented as a GSoC 2018 project. However, the stereochemistry accuracy is not as high as the distance geometry method of RDKit.

In this project, I will improve the coordinate generation of Open Babel by implementing a new method which combines the fragment-based method of Open Babel and the distance geometry method of RDKit. This new implementation is expected to be faster than current RDKit and more accurate in stereochemistry than current Open Babel. Implementing a better prediction method could be beneficial for a wide range of applications such as drug design.



Naruki Yoshikawa


  • Geoff Hutchison
  • Greg Landrum