Hi Miguel, I think it's now fixed in the development version.
- Noel 2010/11/15 Miguel Quirós Olozábal <mqui...@ugr.es>: > Thank you very much. If some testing is needed at any stage of the bug > solving process, just tell me. > > Miguel. > > El lun, 15-11-2010 a las 17:28 +0000, Noel O'Boyle escribió: >> Thanks for letting us know - it looks like a serious bug. I've >> confirmed it for another 3D format, xyz, so it looks like it's a >> general problem. All of my test cases for stereochemistry use the SDF >> format which, naturally, works fine. >> >> I'll file a bug and chase it up. >> >> - Noel >> >> 2010/11/9 Miguel Quirós Olozábal <mqui...@ugr.es>: >> > Sure. I am attaching the same file of the example in my message. I have >> > seen the same behaviour with many other files. >> > >> > Miguel. >> > >> > El mar, 09-11-2010 a las 14:08 +0100, Noel O'Boyle escribió: >> >> Can you provide an example cif file for testing? >> >> >> >> - Noel >> >> >> >> 2010/11/9 Miguel Quirós Olozábal <mqui...@ugr.es>: >> >> > Hello. >> >> > >> >> > When getting SMILES from CIF files, it seems that the stereochemistry >> >> > around double bonds is no longer indicated in the output after upgrading >> >> > to 2.3.0. >> >> > >> >> > For example, with a CIF file containing such a double bond, I get with >> >> > version 2.3.0: >> >> > >> >> > $ babel 2005910.cif -osmi >> >> > OC(=O)C=Cc1c(cc(cc1)N(=O)=O)N(=O)=O C9 H6 N2 O6 >> >> > 1 molecule converted >> >> > 34 audit log messages 1 debugging messages >> >> > >> >> > whereas for version 2.2.3, I used to get: >> >> > $ babel 2005910.cif -osmi >> >> > OC(=O)/C=C/c1c(cc(cc1)N(=O)=O)N(=O)=O C9 H6 N2 O6 >> >> > 1 molecule converted >> >> > 1 info messages 30 audit log messages 1 debugging messages >> >> > >> >> > As you can see, the cis-trans geometry does not appear after upgrading >> >> > openbabel. Is this a regression or there is an option (run-time or >> >> > compilation) that needs to be set to get the stereochemistry? >> >> > >> >> > Thanks for any reply, >> >> > Miguel Quirós >> >> > >> >> > -- >> >> > Miguel Quirós Olozábal >> >> > Departamento de Química Inorgánica. Facultad de Ciencias. >> >> > Universidad de Granada. 18071 Granada. SPAIN. >> >> > email: mquiros<at>ugr<dot>es >> >> > mquiros<arroba>ugr<punto>es >> >> > >> >> > >> >> > ------------------------------------------------------------------------------ >> >> > 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-discuss mailing list >> >> > OpenBabel-discuss@lists.sourceforge.net >> >> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >> >> > >> > -- >> > Miguel Quirós Olozábal >> > Departamento de Química Inorgánica. Facultad de Ciencias. >> > Universidad de Granada. 18071 Granada. SPAIN. >> > email: mquiros<at>ugr<dot>es >> > mquiros<arroba>ugr<punto>es >> > > -- > Miguel Quirós Olozábal > Departamento de Química Inorgánica. Facultad de Ciencias. > Universidad de Granada. 18071 Granada. SPAIN. > email: mquiros<at>ugr<dot>es > mquiros<arroba>ugr<punto>es > > ------------------------------------------------------------------------------ Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today http://p.sf.net/sfu/msIE9-sfdev2dev _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
