Hello.
Sorry if it has taken me too long (almost one month to continue with
this thread!) to elaborate a list of files with representative examples
to illustrate OpenBabel performance on inorganic compounds. I have not
found till now time for doing this. As you can see (I prevent you!) the
message
Thanks a lot for your message.
It probably will take some time to prepare such set. I would like to
include files containing a single different problem each one, with
compounds as simple as possible and without purely crystallographic
problems (molecules in symmetry elements, disorder, ...). All t
That's a pretty bad regression, and I will investigate the two examples you
sent.
Certainly if you can prepare a test set (in whatever format) that would be
extremely helpful, since it could be added as a unit test. Not only would this
ensure all such examples will be fixed, but future versions
El 13/12/2013 22:16, Geoffrey Hutchison escribió:
>> I need to review and, in most cases, fix the SMILES chains coming
>> out
>> from OpenBabel for inorganic compounds (either manually or
>> semiautomatically). I am also stuck to version 2.2.3 because
>> versions
>> newer than this perform wors
> I need to review and, in most cases, fix the SMILES chains coming out
> from OpenBabel for inorganic compounds (either manually or
> semiautomatically). I am also stuck to version 2.2.3 because versions
> newer than this perform worse for inorganic compounds.
If you can give some bug reports or
This is very interesting - sounds like you came across the same issues as we
did and came to the same conclusions too.
We're also very interested to hear that you've got smiles for so many of
your structures which would indeed make it straightforward to link
ChemSpider to COD. We'll be in touch!
A colleague has pointed out to me the likely problem with the
depictions. Mol files can have either 2D or 3D coordinates. I'm
guessing that 3D mol files are not interpreted correctly by the
drawing program you used to view the structures; it must have set the
z coordinate to 0 without any warning.
Hello. A very interesting initiative and rather related to what I am
working in.
I am working in the Crystallography Open Database (COD,
www.crystallography.net), a large collection of openly accessible CIF
files. I have posted a few times messages previously to this list. COD
contains today 2453
On 12/10/2013 11:47 AM, Geoffrey Hutchison wrote:
>> OpenBabel crash more nicely with an error message rather than
>> entering an infinite loop…
>
> Right. Infinite loops are a clear bug, and "crash" certainly is too.
> I think what you really mean is that it'll refuse to translate the
> CIF beca
> OpenBabel crash more nicely with an error message rather than entering an
> infinite loop…
Right. Infinite loops are a clear bug, and "crash" certainly is too. I think
what you really mean is that it'll refuse to translate the CIF because there's
nothing in it.
Anyway, these are helpful - la
Thanks for the reply Noel,
Ah, I didn't know about the "--gen2d" option - sounds like I should have
used that. I'll try it out...
And it looks like I misunderstood the --unique option...
How does the nitro normalisation work? That would definitely be something
we're interested in...
Thanks again,
Thanks Dimitri,
Thanks for the tips - they'll come in useful. A lot of these are problems
with our badly behaved CIF files rather than OpenBabel, so all I was
thinking of doing e.g. for the missing loop example was just making
OpenBabel crash more nicely with an error message rather than entering a
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? Bec
Thanks Aileen,
This is very useful and may help spur improvement in CIF file format
support. I didn't realise that CIF is yet another format that does not
store the chemical structure; Open Babel has to guess what the chemist
already knew (which always makes me shake my head).
Just to note though
On 12/09/2013 10:44 AM, daya wrote:
...
> 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.
When you do, note a couple of caveats for
Category: CIF_MISSIN
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 ChemSpi
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