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 ------------------------------------------------------------------------------ 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
