Hi everyone, I am going to work on the GSoC 2019 project "More Improved Coordinate Generation for Open Babel: Combining Fragment-based Method and Distance Geometry" https://summerofcode.withgoogle.com/projects/#5547940045651968 Although this is a project for Open Babel, I'd like to introduce to developers of RDKit too.
The goal of this project is to improve the current coordinate generation method by incorporating the distance geometry method, which is implemented in RDKit. If it turns out to be efficient, I'd like to contribute to RDKit in addition to Open Babel. I heard some people are working on the distance geometry code. If you give me any suggestions, I'd appreciate it. You can read my proposal for more details: https://drive.google.com/file/d/14xUVci1dbcrwCeWc088votLBZxp5Jiq8/ Project abstract: 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. Thanks, Naruki --- Naruki Yoshikawa Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences The University of Tokyo _______________________________________________ Rdkit-devel mailing list Rdkit-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-devel
