Bugs item #3316498, was opened at 2011-06-14 16:53 Message generated for change (Tracker Item Submitted) made by bentsm You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3316498&group_id=40728
Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Library Functions Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Bent (bentsm) Assigned to: Nobody/Anonymous (nobody) Summary: Errors in group-contribution data files Initial Comment: The data files used computing logP and MR (data/logp.txt, data/mr.txt) have errors in them (some appear to be misinterpretations of the original source paper, but some are just plain errors). Some of the errors include (these are from logp.txt; mr.txt has similar errors): [OX1-*][#15;#33;#43;#53] -1.189 (it's rather hard for an atom to simultaneously be phosphorus, arsenic, technetium, and iodine; those semicolons should be commas) [B,Si,Ga,Ge,As,Se,Sn,Te,Pb,Nc,Nr,Kr,Xe,Rn] -0.3808 (Nc and Nr should be Ne and Ar, respectively) [N+0](A)(A)A -0.3187 (this appears to be a misinterpretation of the source paper; while the SMARTS expression is copied verbatim from the paper, there is a subtle [but important] difference between what the paper means by 'A' and what 'A' means w.r.t. [Daylight] SMARTS: for the paper, 'A' represents a *non-hydrogen* aliphatic element; with SMARTS, A represents *any* aliphatic element; for an example of the problem this creates, the nitrogen in 'N' gets matched (improperly) to this entry when computing logP) [CX4][!#6;!#7;!#8;!#9;!#15;!#16;!#17;!#35;!#53;!#1] 0.2148 (unfortunately, this does not achieve what it is meant to; it should be something to the effect of "[CX4;!$(*[#6,#7,#8,#9,#15,#16,#17,#35,#53])][!#1]") I've been working on fixing up logp.txt and have attached a (mostly) fixed version. Technical details: I'm using Open Babel 2.3.0 (from source) on Mac OS X, compiled with GCC 4.5.1 (self-compiled). ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3316498&group_id=40728 ------------------------------------------------------------------------------ EditLive Enterprise is the world's most technically advanced content authoring tool. Experience the power of Track Changes, Inline Image Editing and ensure content is compliant with Accessibility Checking. http://p.sf.net/sfu/ephox-dev2dev _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
