Quantcast

Re: Cis-trans streochemistry lost on upgrading to 2.3.0?

Previous Topic Next Topic
 
classic Classic list List threaded Threaded
1 message Options
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: Cis-trans streochemistry lost on upgrading to 2.3.0?

Miguel Quirós Olozábal
Hello. Sorry I have taken this long (one month!) to answer but I have
been very busy with other subjects. Also I am not a developer and I was
a little scared about using a "development version" (after all, it
compiled smoothly exactly the same as the "stable version", I've got
version labelled 4341).

In any case, in a few test I have made, it seems indeed that the problem
has vanished.

Thanks a lot!

Miguel Quirós.

El mar, 16-11-2010 a las 17:20 +0000, Noel O'Boyle escribió:

> Hi Miguel,
>
> I think it's now fixed in the development version.
>
> - Noel
>
> 2010/11/15 Miguel Quirós Olozábal <[hidden email]>:
> > 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 <[hidden email]>:
> >> > 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 <[hidden email]>:
> >> >> > 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
> >
> >
--
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


------------------------------------------------------------------------------
Lotusphere 2011
Register now for Lotusphere 2011 and learn how
to connect the dots, take your collaborative environment
to the next level, and enter the era of Social Business.
http://p.sf.net/sfu/lotusphere-d2d
_______________________________________________
OpenBabel-discuss mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Loading...