Bugs item #3095590, was opened at 2010-10-26 14:41 Message generated for change (Tracker Item Submitted) made by gert_thijs You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3095590&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: 2.3.x Status: Open Resolution: None Priority: 5 Private: No Submitted By: gert thijs (gert_thijs) Assigned to: Nobody/Anonymous (nobody) Summary: problem with reading/converting aromatic molecule Initial Comment: I was testing Open Babel 2.3.0 for its ability to use it in a script to test for unique compounds when I encountered a problem concerning the processing of aromaticity when reading smiles input with some specific aromatic rings. Step 1: convert this protonated molecule to canonical smiles: $ echo "C1=CC=CC=C1N1[N-]C(=O)C=CC1(=O)" | babel -ismi -ocan O=c1ccc(=O)n([n-]1)c1ccccc1 Step 2: read the canonical smiles and convert it to canonical smiles : $ echo "O=c1ccc(=O)n([n-]1)c1ccccc1" | babel -ismi -ocan O=C1CCC(=O)[N-]N1c1ccccc1 One would expect that the result of step 2 would generate the same canonical smiles again, but as the example shows this is not happening. If I perform the same procedure but with neutral form the procedure is OK. $ echo "C1=CC=CC=C1N1NC(=O)C=CC1(=O)" | babel -ismi -ocan O=c1ccc(=O)n([nH]1)c1ccccc1 $ echo "O=c1ccc(=O)n([nH]1)c1ccccc1" | babel -ismi -ocan O=c1ccc(=O)n([nH]1)c1ccccc1 Gert Thijs gert.th...@silicos.com ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3095590&group_id=40728 ------------------------------------------------------------------------------ Nokia and AT&T present the 2010 Calling All Innovators-North America contest Create new apps & games for the Nokia N8 for consumers in U.S. and Canada $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store http://p.sf.net/sfu/nokia-dev2dev _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
