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 > ------------------------------------------------------------------------------ Centralized Desktop Delivery: Dell and VMware Reference Architecture Simplifying enterprise desktop deployment and management using Dell EqualLogic storage and VMware View: A highly scalable, end-to-end client virtualization framework. Read more! http://p.sf.net/sfu/dell-eql-dev2dev _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
