Dear Developers,
There are two plugins in openbabel for cif format I/O: cifformat.cpp and
mmcifformat.cpp.
A few months ago the cifformat.cpp reader was changed to mmcif by force
(commit 1014d1858d3c0ef820b7afaf50595dd2202b03fb), leaving no
possibility to use original cif reader (except manually delete
mmcifformat.o file from plugins folder). What was the reason of such
brute force change? Why it was not done in much soft way? Does it mean
that the cifformat plugin is obsolete and will be removed in a future?
I few years ago I change a cifformat.cpp to support atoms occupancy and
oxidations. About 30% of cif files in Inorganic Crystal Structure
Database (ICSD) has a partial occupancy. This property is crucial for my
code, which used Open Babel API for the I/O.
If cifformat.cpp file will be deprecated, it looks like that there is no
problem for me to implement the functionality in a new reader, but I
have quite a lot of question to mmcifformat WriteMolecule. The output of
the function is not at all oriented to crystallography.
1) All crystallography files has a fractional coordinates. Fractional
representation is really useful for special position "detection"
manually. The symmetry operations, listed in the file applying to
fractional coordination also.
2) Although, the cif format is quite flexible. For people, working in
crystallography field, there is a familiar special order of data, which
is also not he case of the mmcifformat WriteMolecule.
Don't you think, that it will be good to have 2 separate cif I/O
modules, one for inorganic systems and one for organic one? Or, at
least, two different WriteMolecule procedures?
Best regards,
Okhotnikov Kirill.
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