Bugs item #3106596, was opened at 2010-11-10 12:09 Message generated for change (Tracker Item Submitted) made by filipspl You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3106596&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: filips (filipspl) Assigned to: Nobody/Anonymous (nobody) Summary: wrong mol2 -> SMILES conversion Initial Comment: there is a problem with indicating Z/E isomers in SMILES generated from mol2 files. Eg. for 1,2-dichloroethane. For structures saved in mol files, smiles (smi or can) are generated correctly: >babel Z.mol -o can Cl/C=C\Cl Z 1 molecule converted 32 audit log messages >babel E.mol -o can Cl/C=C/Cl E 1 molecule converted 32 audit log messages while for files saved in mol2 format, we dont get the E/Z isomerism: >babel Z.mol2 -o can ClC=CCl Z 1 molecule converted 32 audit log messages >babel E.mol2 -o can ClC=CCl E 1 molecule converted 32 audit log messages Converting mol2 back to mol fixes the problem. greetings, F ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3106596&group_id=40728 ------------------------------------------------------------------------------ The Next 800 Companies to Lead America's Growth: New Video Whitepaper David G. Thomson, author of the best-selling book "Blueprint to a Billion" shares his insights and actions to help propel your business during the next growth cycle. Listen Now! http://p.sf.net/sfu/SAP-dev2dev _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
