Dear Toby, On Fri, Nov 4, 2011 at 1:55 PM, Toby Wright <toby.wri...@inhibox.com> wrote: > > On line 11 of the file Data/Crippen.txt the label says "C2" but the > SMARTS expression, "log p" and MR values are as expected for case "C3" > from Wildman&Crippen '99, which suggests that the thing wrong is > simply the label.
Yes, good catch. I've fixed this. > I also have a question that might be a bit foolish as I'm not an > accomplished chemist, but does the SMARTS for O11 deal correctly when > the Oxygen in question is bonded to aromatic atoms? If I understand > correctly it should match either aromatic or aliphatic elements (apart > from the Carbon), but the SMARTS as written will only match in the > aliphatic case. Another good one. Here's what is in the paper; O11 carbonyl heteroatom ‘[O]=C([A#X])[A#X]’, ‘[O]=C([A#X])[a#X]’, ‘[O]=C([a#X])[a#X]’ The [A#X] notation is, I believe, a MOE extension to SMARTS that means "Aliphatic heteroatom". Crippen.txt just has the first part of the Wildman definition: O11 [O]=C([A;!#1;!#6])[A;!#1;!#6] I just modified it to; O11 [O]=C([!#1;!#6])[!#1;!#6] The changes will go into svn this morning and will be in the next RDKit release. Here's the bug report: https://sourceforge.net/tracker/?func=detail&aid=3433771&group_id=160139&atid=814650 Thanks for pointing this out! -greg ------------------------------------------------------------------------------ RSA(R) Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1 _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
