Bugs item #3511528, was opened at 2012-03-26 11:40 Message generated for change (Tracker Item Submitted) made by You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3511528&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: None Group: 2.3.x Status: Open Resolution: None Priority: 5 Private: No Submitted By: Samuele Sommariva () Assigned to: Nobody/Anonymous (nobody) Summary: Smarts problem Initial Comment: I'm using the r4724 developer version (where radical valence have been corrected) I am intensively using group additivity and I found the following problem: I defined an ObGroupContrib in plugindefines as follow OBGroupContrib LnIntSymm LnInternalSymm.txt LOWER BOUND: ln internal symmetry number I defined the following groups in LnInternalSymm.txt (methyl, single substituted c6 aromatic ring, meta substituted c6 aromatic ring) ;heavy [CH3]-* 1 *-c1:[cH]:[cH]:[cH]:[cH]:[cH]:1 10 *-c1:[cH]:[cH]:[c](-*):[cH]:[cH]:1 100 I checked my smiles using http://www.daylight.com/daycgi_tutorials/depictmatch.cgi I expected 11 for toluene, 202 for para xylene (the "meta" substitution will be found twice), 2 for orto and meta xylene. I got 10 for toluene, 200 for para xylene, 2 for orto and meta xylene. I tried to "understand" the error: 1 - If I leave only the methyl group, it is properly recognized. Toluene gives 1, xylenes 2) 2 - If I swap 1st and 2nd group in LnInternalSymm.txt Toluene will give 1, while para-xylene, mantains 200. 3 - If I put methyl groups as the last group. Only the number of methyl groups is found. (1 for toluene, 2 for any xylene) It seems to me that if on a bond both conditions match, then only the "last one" is considered. I don't need a fix for this: modifying the smiles as follow (i.e. considering only the atoms on "one side" of the bond), I have the correct results: ;heavy [CH3v4] 1 [cH0v4]1:[cH]:[cH]:[cH]:[cH]:[cH]:1 10 [cH0v4]1:[cH]:[cH]:[cH0v4]:[cH]:[cH]:1 100 Still, I think that is a bug and should be corrected on your next release Samuele Sommariva ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3511528&group_id=40728 ------------------------------------------------------------------------------ This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
