Neither PDB nor XYZ files store the bond order. XYZ files do not even store
which atoms are connected to which atoms. If you want to learn more about
this, you should open chemical structure files in a text editor and
familiarise yourself with the information contained within. I gave a talk
which touches upon some of this (see slide 3 of
https://www.slideshare.net/baoilleach/so-i-have-an-sd-file-what-do-i-do-next-51825001
).
- Noel
On 27 June 2018 at 20:31, Biruk Abreha <abreh...@husky.neu.edu> wrote:
> Hello,
>
> I’ve been having trouble converting between formats. I have generated some
> MOL files using RDKit for various substituted subphthalocyanines (attached
> below) which, when opened with any molecule viewer, show the correct bond
> order (1 or 2 depending on the atom) between the nitrogen and carbon atoms
> surrounding the central boron. However, when I convert to any other format
> (such as PDB or XYZ) with OpenBabel, the bond order between each nitrogen
> atom and the adjacent carbon atom is reduced to 1.
>
> Is there an option that I haven’t included that can solve this problem, or
> is this a bug that hasn’t been addressed? Any help would be appreciated.
>
> Thanks,
> Biruk
>
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
>
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
