I've fixed this. It's a minor change so you could apply it locally if
you want. I just moved the call to DeleteHydrogens past the stereo
section when reading the InChI:
https://github.com/baoilleach/openbabel/commit/428ac8790d3b5307305912b892e9953c793b80dc
- Noel
On 26 June 2013 14:42, Jon F
Dear Chris and Fredrik,
Thanks for the information regarding this problem. The solution that I've
been using is to use an older version 2.3.0 to run my script.
Additional thanks for the information about the differences between obabel
and babel.
Best,
Jon
On 26 June 2013 15:01, Chris Morley
I think this is due to a bug in the stereo perception code which
appeared in v2.3.2 . It has been mentioned before on this and the
development list but a fix is not yet committed to the development code.
Version 2.3.1 works ok for me.
Incidentally, prefer obabel to the older babel. obabel is sa
Hi,
No, I never found a solution to this. I managed a workaround for the specific
problem (although I cannot remember for sure I believe I accepted some help
from ChemDraw…) so my needs fainted…
Kind regards,
Fredrik
25 jun 2013 kl. 14:33 skrev Jon Fuller :
> Hi Fredrik,
>
> Did you find a s
Hi Fredrik,
Did you find a solution to this problem? I found a similar example:
I pasted example code for pybel, but running the command below with both
inchis in the file inchi.txt:
babel -iinchi inchi.txt -osdf inchi.sdf
Will result in "Segmentation fault: 11"
Remove the second inchi and the com
Hi again,
Some more information…
The InChI "InChI=1S/C8H12/c1-2-4-6-8-7-5-3-1/h1-2,7-8H,3-6H2/b2-1-,8-7-" gives
the same problem.
I have now updated the ubuntu box to also run ob 2.3.2 and it segfaults now as
well, so it seems it has something to do with differences between 2.3.1 and
2.3.2.
Ki
Hi,
I get a segmentation fault when running the following command:
obabel -iinchi
-:"InChI=1S/2C8H12.Ni/c2*1-2-4-6-8-7-5-3-1;/h2*1-2,7-8H,3-6H2;/b2*2-1-,8-7-;"
-osmi
I'm running Open Babel 2.3.2 on a MacBook Pro, OSX 10.8.3 (installed via
homerbrew).
I have also tried it on an Ubuntu box (10.0
