Bugs item #3010741, was opened at 2010-06-02 23:31 Message generated for change (Tracker Item Submitted) made by tjbear You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3010741&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: Command-line Tools Group: 2.2.x Status: Open Resolution: None Priority: 5 Private: No Submitted By: TJ O'Donnell (tjbear) Assigned to: Nobody/Anonymous (nobody) Summary: incorrect cansmi: rings with =O substituents Initial Comment: For some smiles, cansmiles yields incorrect results. PROBLEM: echo 'O=c1[nH]c(=O)c2cccc3c2c1ccc3' | babel -ismi -osmi O=[C]1=[NH][C](=O)=C2C=CC=C3C2C1C=CC3 1 molecule converted 4 info messages 33 audit log messages The resulting SMILES in not correct. I expected the result to be identical to the input, because the input came from a canonicalization of another SMILES. BACKGROUND: The input SMILES above came from here. echo 'O=C1NC(=O)C2=CC=CC3=C2C1=CC=C3' | babel -ismi -osmi O=c1[nH]c(=O)c2cccc3c2c1ccc3 1 molecule converted 1 info messages 33 audit log messages This resulting cansmiles is correct, but I cannot convert it properly (see PROBLEM). Another way to think of this is cansmiles(x) = cansmiles(cansmiles(x)) This is not true for x = 'O=c1[nH]c(=O)c2cccc3c2c1ccc3' I think this is a general problem with aromatic rings having =O subtitutions and how to aromatize them. Linux/ubuntu openbabel 2.2.3 TJ t...@gnova.com ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3010741&group_id=40728 ------------------------------------------------------------------------------ ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental unit. See the prize list and enter to win: http://p.sf.net/sfu/thinkgeek-promo _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
