Data structures for crystallography
crystals is a library of data structure and algorithms to manipulate
abstract crystals in a Pythonic way.
crystals helps with reading
crystallographic files (like .cif and .pdb), provides access to atomic
positions, scattering utilities, allows for symmetry determination, and
indexing of diffraction peaks. Although
crystals can be used on its own,
it was made to be integrated into larger projects (like
Take a look at the documentation for more information and examples.
crystals is available on the Python Package Index:
pip install crystals
For users of the conda package manager,
crystals is also available
from the conda-forge channel:
conda install -c conda-forge crystals
crystals can also be installed from source:
git clone https://github.com/LaurentRDC/crystals.git cd crystals python setup.py install
You can install the latest development version using
pip as well:
python -m pip install git+git://github.com/LaurentRDC/crystals.git
To build documentation, you will need a few more packages, listed in
dev-requirements.txt. For example, to build documentation from source:
git clone https://github.com/LaurentRDC/crystals.git cd crystals pip install -r dev-requirements.txt python setup.py build_sphinx
The documentation, including user guides as well as detailed reference, is available here: https://crystals.readthedocs.io/
Tests can be run with the
python -m pytest --pyargs crystals
Some optional tests might be skipped if dependencies are not installed, e.g. ASE.
As this package is a spinoff from
scikit-ued, please consider citing
the following publication if you find
L. P. René de Cotret, M. R. Otto, M. J. Stern. and B. J. Siwick, An open-source software ecosystem for the interactive exploration of ultrafast electron scattering data, Advanced Structural and Chemical Imaging 4:11 (2018) DOI: 10.1186/s40679-018-0060-y.
Underlying algorithms provided by
spglib are described in the
A. Togo and I. Tanaka, spglib: a software library for crystal symmetry search. https://arxiv.org/abs/1808.01590 (written at version 1.10.4).
Structure parsing from CIF files has been tested for correctness against CIF2CELL, detailed here:
Torbjorn Bjorkman, CIF2Cell: Generating geometries for electronic structure programs, Computer Physics Communications 182, 1183-1186 (2011) DOI: 10.1016/j.cpc.2011.01.013
Structure parsing from PDB files has been tested for correctness against
Bio.PDB, detailed here:
Hamelryck, T., Manderick, B. PDB parser and structure class implemented in Python. Bioinformatics 19: 2308–2310 (2003)
Atomic weights are reported in the following publication:
Meija, J., Coplen, T., Berglund, M., et al. (2016). Atomic weights of the elements 2013 (IUPAC Technical Report). Pure and Applied Chemistry, 88(3), pp. 265-291. Retrieved 30 Nov. 2016, DOI:10.1515/pac-2015-0305
Covalent radii are reported in the following article:
Cordero, B. et al. (2008). Covalent radii revisited. Dalton Transactions, issue 21, pp. 2832-2838. The Royal Society of Chemistry. DOI: 10.1039/B801115j
Support / Report Issues
All support requests and issue reports should be filed on Github as an issue.
crystals is made available under the GPLv3 license. For more
details, see LICENSE.
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