This script, sf_reader.py, written for the CLI of Python 3, retrieves
information from the .sqlite data base StructureFinder (by Kratzert and
Krossing) writes.
StructureFinder (https://www.xs3.uni-freiburg.de/research/structurefinder, https://github.com/dkratzert/StructureFinder) provides the infrastructure to set up a local database of crystallographic data in .cif files. It is desirable to complement structural information with applications like DataWarrior (http://openmolecules.org/datawarrior/index.html) already offering access to the Crystallographic Open Database (http://www.crystallography.net/cod/index.php) with a snapshot ( http://www.openmolecules.org/datawarrior/datafiles.html) with model data not yet in the public, too (dkratzert/StructureFinder#3).
By a call of
python sf_reader.py example.sqlite
the script will retrieve a minimal subset of data from the .sqlite data base StructureFinder writes: lattice constants, space group symmetry, symmetry operators; atom label, atom label and atom coordinates.
The script does not consider additional crystallographic information such as site occupancy factors used to describe positional disorder, or anisotropic displacement parameters.
Note that script restores the file name of the .cif, rather than
the model name of the within the script. This reflects that more
often than wanted .cif provided as supporting information do not
provide a (as possibly meaningful) name to the structure model, and
publishers include in the name the .cif accessible e.g. a part
of the doi of the corresponding publication.
Equally note that the retrieval should be restricted to .cif which
originally (i.e., when read by StructureFinder) contained only one
single model per file.
As a training, the repository contains test data. File
three_data.sqlite is a test data base written by StructureFinder
(version 47) while accessing structure models ACSALA01.cif,
ADRENL.cif, and BAPLOT01.cif; these files are part of CCDC's freely
accessible teaching subset,
section Drug molecules,
and are copied in sub-folder input.
Running python sf_reader.py three_data.sqlite restores the three
.cif files deposit in sub-folder output.
Additional paramaters the script accepts are
-h to access the help screen -v to access the version information