crystals
========
[](https://crystals.readthedocs.io/) [](https://pypi.python.org/pypi/crystals) [](https://anaconda.org/conda-forge/crystals) [](https://doi.org/10.1186/s40679-018-0060-y)
`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
[scikit-ued](https://github.com/LaurentRDC/scikit-ued)).
Take a look at the [documentation](https://crystals.readthedocs.io/) for
more information and examples.
Installation
------------
`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
### From source
`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
Documentation
-------------
The documentation, including user guides as well as detailed reference,
is available here: <https://crystals.readthedocs.io/>
Development
-----------
Tests can be run with the `pytest` package:
python -m pytest --pyargs crystals
Some optional tests might be skipped if dependencies are not installed,
e.g. [ASE](https://wiki.fysik.dtu.dk/ase/).
Citations
---------
As this package is a spinoff from `scikit-ued`, please consider citing
the following publication if you find `crystals` useful:
> 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.](https://ascimaging.springeropen.com/articles/10.1186/s40679-018-0060-y)
Underlying algorithms provided by `spglib` are described in the
following publication:
> A. Togo and I. Tanaka, *spglib: a software library for crystal symmetry search*. [https://arxiv.org/abs/1808.01590](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](https://doi.org/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](https://doi.org/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](https://dx.doi.org/10.1039/B801115J)
Support / Report Issues
-----------------------
All support requests and issue reports should be [filed on Github as an
issue](https://github.com/LaurentRDC/crystals/issues).
License
-------
`crystals` is made available under the GPLv3 license. For more
details, see [LICENSE](https://github.com/LaurentRDC/crystals/blob/master/LICENSE).
Related projects
----------------
- Streaming operations on NumPy arrays are available in the [npstreams
package](https://pypi.org/pypi/npstreams).
- Interactive exploration of ultrafast electron diffraction data with
the [iris-ued package](https://pypi.org/project/iris-ued/).
- Data structures and algorithms to handle ultrafast electron
scattering data in the [scikit-ued
package](https://pypi.org/project/scikit-ued).
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"description": "crystals\n========\n[](https://crystals.readthedocs.io/) [](https://pypi.python.org/pypi/crystals) [](https://anaconda.org/conda-forge/crystals) [](https://doi.org/10.1186/s40679-018-0060-y)\n\n`crystals` is a library of data structure and algorithms to manipulate\nabstract crystals in a Pythonic way. `crystals` helps with reading\ncrystallographic files (like .cif and .pdb), provides access to atomic\npositions, scattering utilities, allows for symmetry determination, and\nindexing of diffraction peaks. Although `crystals` can be used on its own, \nit was made to be integrated into larger projects (like\n[scikit-ued](https://github.com/LaurentRDC/scikit-ued)).\n\nTake a look at the [documentation](https://crystals.readthedocs.io/) for\nmore information and examples.\n\nInstallation\n------------\n\n`crystals` is available on the Python Package Index:\n\n pip install crystals\n\nFor users of the conda package manager, `crystals` is also available\nfrom the conda-forge channel:\n\n conda install -c conda-forge crystals\n\n### From source\n\n`crystals` can also be installed from source:\n\n git clone https://github.com/LaurentRDC/crystals.git\n cd crystals\n python setup.py install\n\nYou can install the latest development version using `pip` as well:\n\n python -m pip install git+git://github.com/LaurentRDC/crystals.git\n\nTo build documentation, you will need a few more packages, listed in\n`dev-requirements.txt`. For example, to build documentation from source:\n\n git clone https://github.com/LaurentRDC/crystals.git\n cd crystals\n pip install -r dev-requirements.txt\n python setup.py build_sphinx\n\nDocumentation\n-------------\n\nThe documentation, including user guides as well as detailed reference,\nis available here: <https://crystals.readthedocs.io/>\n\nDevelopment\n-----------\n\nTests can be run with the `pytest` package:\n\n python -m pytest --pyargs crystals\n\nSome optional tests might be skipped if dependencies are not installed,\ne.g. [ASE](https://wiki.fysik.dtu.dk/ase/).\n\nCitations\n---------\n\nAs this package is a spinoff from `scikit-ued`, please consider citing\nthe following publication if you find `crystals` useful:\n\n> L. P. Ren\u00e9 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.](https://ascimaging.springeropen.com/articles/10.1186/s40679-018-0060-y)\n\nUnderlying algorithms provided by `spglib` are described in the\nfollowing publication:\n\n> A. Togo and I. Tanaka, *spglib: a software library for crystal symmetry search*. [https://arxiv.org/abs/1808.01590](https://arxiv.org/abs/1808.01590) (written at version 1.10.4).\n\nStructure parsing from CIF files has been tested for correctness against\nCIF2CELL, detailed here:\n\n> Torbjorn Bjorkman, *CIF2Cell: Generating geometries for electronic structure programs*, Computer Physics Communications 182, 1183-1186 (2011) [DOI: 10.1016/j.cpc.2011.01.013](https://doi.org/10.1016/j.cpc.2011.01.013)\n\nStructure parsing from PDB files has been tested for correctness against\n`Bio.PDB`, detailed here:\n\n> Hamelryck, T., Manderick, B. *PDB parser and structure class implemented in Python*. Bioinformatics 19: 2308\u20132310 (2003)\n\nAtomic weights are reported in the following publication:\n\n> 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](https://doi.org/10.1515/pac-2015-0305)\n\nCovalent radii are reported in the following article:\n\n> Cordero, B. et al. (2008). *Covalent radii revisited*. Dalton Transactions, issue 21, pp. 2832-2838. The Royal Society of Chemistry. [DOI: 10.1039/B801115j](https://dx.doi.org/10.1039/B801115J)\n\nSupport / Report Issues\n-----------------------\n\nAll support requests and issue reports should be [filed on Github as an\nissue](https://github.com/LaurentRDC/crystals/issues).\n\nLicense\n-------\n\n`crystals` is made available under the GPLv3 license. For more\ndetails, see [LICENSE](https://github.com/LaurentRDC/crystals/blob/master/LICENSE).\n\nRelated projects\n----------------\n\n- Streaming operations on NumPy arrays are available in the [npstreams\n package](https://pypi.org/pypi/npstreams).\n- Interactive exploration of ultrafast electron diffraction data with\n the [iris-ued package](https://pypi.org/project/iris-ued/).\n- Data structures and algorithms to handle ultrafast electron\n scattering data in the [scikit-ued\n package](https://pypi.org/project/scikit-ued).\n\n\n",
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