Dear Stan,
OpenBabel Version: 2.4.1
>
> Operating System: Windows/Jupyter Notebook
>
>
>
> I have been trying to use the instructions at this link
> <https://openbabel.org/docs/dev/UseTheLibrary/Python_Pybel.html> and also
> in the original Chemistry Central Journal
> <https://ccj.springeropen.com/articles/10.1186/1752-153X-2-5>
> publication. I am able to convert .sdf files over to .smi files without
> any problem. However, when I try to convert .cdx files to .sdf or .smi
> files, the system crashes and I get an error in the command window that
> tells me that there is no ‘ChemDraw Header’ that pybel/openbabel is
> expecting to see.
>
>
>
> I have included a .cdx file that I’ve been using. Any chance that you
> guys can help me figure out what’s going on?
>
With the command line (Open Babel 2.4.1, Linux)
obabel -icdx multiNitroCompounds.cdx -OmultiNitroCompounds.sdf
the conversion is done without problem, but with one warning: "Alias O2N
was not chemically interpreted"
Indeed, nitro groups are not all represented in the same way in the sdf
file (see picture).
I think that it should not be linked to the "no ChemDraw header" message,
however.
What's the message exactly? May you share the corresponding part of your
Pybel script?
Without using Pybel, does the Open Babel GUI convert the .cdx file?
Regards,
Pascal
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