It's been a while since I've studied chemistry. Now, I am reading the documentation of RDKit. At a certain point, the term "kekulization" is mentioned. What is kekulization (in RDKit, if this is not a standard chemical term)?
This is a method to generate alternate Lewis structures of the same molecule. Here are two examples from the cumulative dissertation by Sascha Urbaczek:
If you were to search for the left molecule in panel (1) using an image search or a SMILES string, you might miss the right molecule in that panel.
According to the RDkit document cited in the question, the software routinely generates the alternate position of double bonds, and then (in a second step they call "aromatization") labels the ring as aromatic. In panel (2), there are three possible Lewis structures contributing to the actual structure (i.e. there is resonance), so the software would have to generate all three to be able to search for identical structures.
- Urbaczek, Sascha. A consistent cheminformatics framework for automated virtual screening. Ph.D. Thesis, Universität Hamburg, August 2014. URL: http://ediss.sub.uni-hamburg.de/volltexte/2015/7349/; URN: urn:nbn:de:gbv:18-73491; PDF via Semantic Scholar
SMILES also exist in kekulized and non-kekulized forms. The kekulized form makes the double bonds in aromatic rings explicit. Instead, the normal (canonical) SMILES omits the double bond symbol
= in favor of lowercase characters to denote aromaticity. For example: