Weekly Notes for Week 20

This weeks topics:
- Integer Linear Programming, Autocatalysis
- Ring Perception, 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)
```
  – (week 20) 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 will show/showed in class can be found on github (repository from Nikolai 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.