Here's the place to leave comments about my "Dealing with SSSR" article. In it I describe my experience in trying to develop a toolkit-indendent means of specifying some of the PubChem bits which require ESSSR. I concluded saying that I couldn't - without reimplementing ESSSR myself for each toolkit - handle those bits so I would be ignoring them.
I also wondered why people use SSSR, and how well they've tested their SSSR-based algorithms, including testing in the face of differing atom order.
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Nice post (of many)!
Two comments: 1. I'm with OpenEye on using number of ring bonds, rather than rings an atom is in. Much faster to compute. 2. Forget about the aromaticity concept. It suck, and it's useless. An 'aromatic ring'? Yeah, sure. Very much along the same lines of why OpenEye changed the meaning of 'R', just forget about aromatic rings. Just work with rings that *can* delocalize, and just drop the ambiguous 'aromaticity' concept. It does wonders for fingerprints:
http://chem-bla-ics.blogspot.com/2010/07/new-cdk-default-fingerprinter.html
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