Weekly Notes for Week 39

• This weeks topics:
  • More details on SMILES
  • Graph Canonicalization recap: Individualisation Refinement Paradigm / Equitable partitions / search tree

  • Ring Perception, Hanser Algorithm, Horton’s algorithm, de Pina’s algorithm.

  • Mandatory Reading (ring perception):

    – Franziska Berger, Christoph Flamm, Petra M. Gleiss, Josef Leydold, Peter F. Stadler: Counterexamples in Chemical Ring Perception. Journal of Chemical Information and Modeling 44(2): 323-331 (2004)

    – Hanser T, Jauffret P, Kaufmann G, (1996), A New Algorithm for Exhaustive Ring Perception in a Molecular Graph. J Chem Inf Comput Sci, 36(6):1146-1152. DOI:10.1021/c

  • Recommended reading if you are more interested:

    – Downs, G.M., Gillet, V.J., Holliday, J.D., Lynch, M.F.: Theoretical aspects of ring perception and development of the extended set of smallest rings concept. Journal of Chemical Information and Computer Sciences, 187-206 (1989)

• The graph grammar rule editor I willshow/showed in the last lecture can be found on github (repository fromNikolai Nøjgaard). The following sequence of command should work in order to make the editor work. Use at your own risk ;)

   git clone https://github.com/Nojgaard/mod-RuleMaker.git
   sudo apt install npm
   cd mod-RuleMaker/
   pip3 install websockets jsonschema
   npm install
   npm run build
  

  After that you should be able start the rule editor webserver with npm run start. Open the file mod-RuleMaker/index.html in a web browser and you should be able to edit graph grammar rules.

• The examples of how to use wildcards (will be presented/was presented in the) can be found online (folder Material/assignment1).