Weekly Notes for Week 19

• This weeks topics:

  • Continuation of canonicalization.
  • Network expansion using graph transformation.
  • Integer Linear Programming (ILP):
    • Introduction
    • Examples
    • Exercises
  • Autocatalytic solutions via ILP.
  • If time allows, we will start with Minimum Cycle Bases.

• Wrt. the first mandatory assignment I will

  • introduce the strategy framework of mød
  • explain the revive strategy in mød

• Exercises:

  • Exercise Sheet 03

• Reading Material:

  • For canonicalization: still Chapter 4 of the PhD thesis by Jakob Lykke Andersen.
  • For network strategies and network expansion: Chapter 9 of the same thesis.
  • Link for visualising graph canonicalization as shown in the first lecture: http://jakobandersen.github.io/graph_canon_vis
  • 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.
  • 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).
  • Voluntary: de Pina runtime / minimum cycle bases article

• Additional slides:

  • ILP slides
  • Canonicalization add-on slides
  • Canonicalization traces

• Code snippets:

  • code-snippets directory
  • SMILES counter-example