Hi, On Tue, Oct 5, 2010 at 11:51 PM, Craig A. James <cja...@emolecules.com> wrote: > Hi Tim, > > I was looking through the new canon.cpp code, and it looks like a huge > improvement over the original, and the tests we've been running are > confirming this. This is a big step forward. > > But I noticed a rather alarming lack of comments in the new code. There are > some unfinished general comments towards the end of the file, but the various > data structs and methods aren't explained, and I couldn't find anything about > the overall algorithms you've implemented.
Yes, I'll update the docs tonight. > The reason this came up was because of the "c1(ccccc1)O" or "ugly SMILES" > bug. I was hoping to be able to look at your new code and make some > suggestions, but after an hour or two of scratching my head I was still lost. > I hope you'll have some time to write down all of the knowledge you put into > the new canon.cpp code. I think I know how to make the smiles look better again using your suggestions. Right now, the highest symmetry class is used to start labeling which tends to be ring atoms, metals, ... Once I commit the docs, I'll try modify the code and post the resulting smiles. This would change the smiles again but perhaps we should just declare canonical smiles stable when we release 2.3? I didn't do very much the last 3 days since I was sick but I should be able to get some work done again. Tim > Thanks, > Craig > > ------------------------------------------------------------------------------ > Beautiful is writing same markup. Internet Explorer 9 supports > standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. > Spend less time writing and rewriting code and more time creating great > experiences on the web. Be a part of the beta today. > http://p.sf.net/sfu/beautyoftheweb > _______________________________________________ > OpenBabel-Devel mailing list > OpenBabel-Devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-devel > ------------------------------------------------------------------------------ Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today. http://p.sf.net/sfu/beautyoftheweb _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
