Bugs item #3528927, was opened at 2012-05-22 13:33 Message generated for change (Tracker Item Submitted) made by cjames53 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3528927&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: 2.3.x Status: Open Resolution: None Priority: 5 Private: No Submitted By: Craig (cjames53) Assigned to: Nobody/Anonymous (nobody) Summary: SMILES parser loses aromaticity of fullerene Initial Comment: The aromaticity of the attached SDF (C70 fullerene, see http://www.emolecules.com/cgi-bin/more?vid=30316111) is lost when it is read as a SMILES: $ babel fullerene.sdf -o smi c12c3c4c5c6c7c8c9c%10c%11c%12c%13c(c5c5c3c3c%14c1c1c%15c%14c%14c%16c3c5c%13c3c%16c5c%14c%13c%15c%14c%15c1c1c2c4c2c6c8c4c6c9c8c%10c9c%12c3c3c9c9c8c8c6c6c4c2c1c%15c6c1c%14c%13c(c53)c9c81)c7%11 $ babel fullerene.sdf -o smi | babel -i smi -o can C12C3C4C5C6C7C3C3C8C1C1C9C%10C2C2C4C4C5C5C%11C6C6C%12C7C3C3C7C8C1C1C8C9C9C%13C%10C2C2C4C4C5C5C%11C%10C6C6C%12C3C3C7C1C1C8C7C9C8C%13C2C4C2C8C4C7C7C1C3C6C7C%10C4C52 You can see that the problem occurs while parsing the SMILES by doing this: $ babel fullerene.sdf -o smi | babel -i smi -o sdf The resulting SDFs atom block seems to show two hydrogens on every carbon (which doesn't make sense) and the bond block is all single bonds. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3528927&group_id=40728 ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
