Le 30/08/2011 16:35, Noel O'Boyle a écrit :
> For some time I have been using hashizume.cif (in
> scripts/python/examples) to test the Python bindings. Some time ago,
> the test started to fail due to the text below which now appears which
> hashizume.cif is read:
>
> user@ubuntu904desktop:~/Tools/openbabel/nightly/ob-build/test$
> ../../ob-build/bin/obabel
> ../../openbabel/scripts/python/examples/hashizume.cif -osmi
> ==============================
> *** Open Babel Error in ExtractUnitCell
> CIF ERROR: missing a,b or c value - cannot interpret structure !
> ==============================
> *** Open Babel Warning in ExtractSpacegroup
> CIF ERROR: missing spacegroup description: defaulting to P1...
> O=C(NC(=O)NCC)CCC(C)C 1-ethyl-3-(4-methylpentanoyl)urea
>
> Are these errors correct? I opened the file in Mercury and the entries
> have a,b and c values and a spacegroup of P-1.
Well, the errors are correct: In this CIF file, there are *two* data
entries, "data_global" and "data_ethyl98K".
In the first (data_global) there are just journal and author
information, and no crystal structure - which causes the errors.
The second data entry (data_ethyl98K) has all the correct information,
and is interpreted correctly without warning - this gives the structure
output.
If you remove the "data_global" entry the error disappears.
In a CIF file there may be a number of independent data_** entries,
any of which may or may not contain a crystal structure, or diffraction
data,. OB currently tries to interpret all the data entries.
This raises the question of what should OB do in such a case: simply
ignore, or a warning, or an error...
At the very least the message could include the name of the data
statement, and say something less ominous like:
"while reading the data_global , the following error was encountered:
missing a,b or c value.
This may be caused by a non-crystallographic data_ field".
Alternatively, data_ entries without any apparent structure information
(no cell, spacegroup or atomic positions) may also be ignored, or just
issue a warning
What do you think ?
Vincent
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