Bugs item #3550066, was opened at 2012-07-27 09:11 Message generated for change (Tracker Item Submitted) made by jgerlits You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3550066&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: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: John Gerlits (jgerlits) Assigned to: Nobody/Anonymous (nobody) Summary: sdf to smi conversion - aromaticity of rings fails Initial Comment: RE: sdf to smi conversion - aromaticity of rings fails After conversion the aromaticity of the ring system is not valid. Does this go beyond what OpenBabel is intended to do, or is this a bug? This is an one example of a compound listed at DrugBank: www.drugbank.ca Compound ID: DB02920 SMILES from DrugBank: CC1=C(C=C)C2=CC3=[N-]4C(=CC5=C(CCC(O)=O)C(C)=C6N5[Zn++]44N2C1=CC1=[N-]4C(C(C)=C1C=C)=C6O)C(CCC(O)=O)=C3C This was converted to the absolute SMILES at: http://cdb.ics.uci.edu/cgibin/BabelWeb.py ChemDB / Babel: Molecule Format Converter SMILES: Cc1c(c2=CC3=[N-]4C(=Cc5c(c(c6n5[Zn+2]47n2c1=CC8=[N-]7C(=C6O)C(=C8C=C)C)C)CCC(=O)O)C(=C3C)CCC(=O)O)C=C This SMILES was converted to sdf and back to SMI with OpenBabel GUI. Resulting SMILES: Cc1c(c2=Cc3[n-]4c(=Cc5c(c(c6n5[Zn+2]54n2c1=Cc1[n-]5c(=C6O)c(c1C=C)C)C)CCC(=O)O)c(c3C)CCC(=O)O)C=C This SMILES gives and error instead of structure at: ChemDB / Smi2Depict: Generate 2D Images from Molecule Files: http://cdb.ics.uci.edu/cgibin/Smi2DepictWeb.py The connections of the structure are valid but it apparently does not conform to aromaticity rules and so the ChemDB viewer will not display it. John Gerlits jg_erli...@hotmail.com WindowsXP OpenBabel version 2.3.1 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3550066&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
