Weekly Notes for Week 37

• The course content will not be based on one book only. Besides the books to be listed on the course webpage original research article will be used. The book chapters, notes, and articles needed will be provided in the Blackboard System. Note, that I will use so-called “WebFolders” from the Blackboard BB9 system, you should be able to access all data via the WebDav resource, (authentication via blackboard user / password). Mounting WebDav resources is very easy and naively supported by basically all operating systems without the need to install and additional software. See for example this link for how to access a WebDav resource using Ubuntu.

• Topics of week 37: Introduction to the course, introduction to Polya enumeration, Double Pushout Approach, Starting with “Generative Chemistries”.

• We will discuss Generative Chemistries”: Double Pushout approach, graph grammars, exploring chemical spaces via graph grammars, (sub-)graph Iso-/Monomorphism, …”

• The project work for DM840 will consists of mandatory assignments. A preliminary version of the first mandatory assignment will already be published end of the week. If you want, you can already start looking at the examples from https://cheminf.imada.sdu.dk/mod/index.html

• Reading Material (will be uploaded during week 37):

  • Mandatory Reading: Articles by Weininger (SMILES1 and SMILES2).
  • Recommended Reading: Chapter 2 of the book by Gasteiger.
  • Very recommended Reading: Chapter Chemical Graphs of Graph Theory 1736-1936 (Biggs, Lloys, Wilson, 1986)
  • Recommended Reading: Chapter 8 of Combinatorics: Ancient and Modern: Early Graph Theory
  • Link for visualising graph canonicalization as shown in the first lecture: http:// jakobandersen.github.io/graph_canon_vis