Hi Aileen,
I've just been reading the blog post again: "One problem that became
immediately apparent was that because the 2D structure obtained was
just a projection of the 3D structure along the a cell axis.....". How
exactly did you create the 2D depictions? Are they present in the CIF
file? Because Open Babel doesn't project 3D structures onto 2D to
create a depiction.
I would have thought that the CIF file contains 3D coordinates and
that you could generate a 2D depiction using "--gen2d" (which layouts
out the molecular structure as best it can in 2D). There's no mention
of "gen2d" in the post though.
Regards,
Noel
On 9 December 2013 16:44, daya <d...@rsc.org> wrote:
> I’ve just supervised a student project in which we used OpenBabel to convert
> over 44,000 Royal Society of Chemistry CIF structures to mol files, then a
> student checked over 4,000 of these conversions so that we could upload the
> successfully processed CIFs to ChemSpider for the corresponding ChemSpider
> compounds. A summary of the results of that project are detailed here:
> http://www.chemspider.com/blog/adding-rsc-cifs-to-chemspider.html
> It seemed like a valuable opportunity to identify the most frequent
> OpenBabel bugs when doing a CIF to Mol conversion so these are documented in
> there, along with test cases to identify the problems and with a view to
> fixing them and making OpenBabel more bulletproof.
> We’re taking a bit of a break from this project for now, but in the next
> phase of the project will see if we can fix at least some of the bugs
> identified if they haven’t already been.
> But we’re sharing these results here for now though since we thought you
> would be interested in the project and the performance of OpenBabel when run
> over such a large and varied test set, possibly even enough to look into
> some of them yourselves…
> Looking forward to working with you on some of them in the future…
> Aileen Day (Informatics Analyst, RSC ChemSpider)
>
>
>
> --
> View this message in context:
> http://forums.openbabel.org/Converting-CIFs-to-mols-using-OpenBabel-tp4657031.html
> Sent from the General discussion mailing list archive at Nabble.com.
>
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