Skip to main content

Data structures for crystallography

Project description

Documentation Status AppVeyor Build Status PyPI Package latest release Supported Python versions Code formatting style

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, and allows for symmetry determination. Although crystals can be used on its own, it was made to be integrated into larger projects (like scikit-ued).

Take a look at the documentation for more information.

Usage example

crystals is all about constructing crystals and getting information about the resulting object. Crystals can be built from a variety of sources:

Here’s a quick example of building a crystal from the internal database:

>>> from crystals import Crystal
>>> vo2 = Crystal.from_database('vo2-m1')
>>> print(vo2)         # Short string representation
< Crystal object with following unit cell:
    Atom O  @ (0.90, 0.79, 0.80)
    Atom O  @ (0.90, 0.71, 0.30)
    Atom O  @ (0.61, 0.31, 0.71)
    Atom O  @ (0.39, 0.69, 0.29)
    Atom O  @ (0.61, 0.19, 0.21)
    Atom O  @ (0.10, 0.29, 0.70)
    Atom O  @ (0.10, 0.21, 0.20)
    Atom O  @ (0.39, 0.81, 0.79)
    Atom V  @ (0.76, 0.03, 0.97)
    Atom V  @ (0.76, 0.48, 0.47)
    ... omitting 2 atoms ...
Lattice parameters:
    a=5.743Ã…, b=4.517Ã…, c=5.375Ã…
    α=90.000°, β=122.600°, γ=90.000°
Chemical composition:
    O: 66.667%
    V: 33.333%
    (...omitted...)\crystals\cifs\vo2-m1.cif >

Symmetry information is also readily available:

>>> print(vo2.symmetry())
{'international_symbol': 'P2_1/c',
 'hall_symbol': '-P 2ybc',
 'international_number': 14,
 'hall_number': 81,
 'international_full': 'P 1 2_1/c 1',
 'pointgroup': 'C2h'}


crystals is available on the Python Package Index:

pip install crystals

From source

crystals can also be installed from source:

git clone
cd crystals
python install

You can install the latest development version using pip as well:

python -m pip install git+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
cd crystals
pip install -r dev-requirements.txt
python build_sphinx


The documentation, including a user guide as well as detailed reference, is available here:


Tests can be run with the standard library’s unittest module:

python -m unittest discover

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 crystals useful:

[1]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 following publication:

  1. Togo and I. Tanaka, spglib: a software library for crystal symmetry search. (written at version 1.10.4).

Structure parsing from CIF files has been tested for correctness against CIF2CELL, detailed here:

[3]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:

[4]Hamelryck, T., Manderick, B. PDB parser and structure class implemented in Python. Bioinformatics 19: 2308–2310 (2003)


This package depends on the work of some amazing people. Of note are the spglib contributors

Support / Report Issues

All support requests and issue reports should be filed on Github as an issue.


crystals is made available under the BSD 3-clause license. For more details, see LICENSE.txt.

Project details

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Filename, size & hash SHA256 hash help File type Python version Upload date
crystals-0.5-py3-none-any.whl (202.3 kB) Copy SHA256 hash SHA256 Wheel py3
crystals-0.5.tar.gz (103.5 kB) Copy SHA256 hash SHA256 Source None

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN SignalFx SignalFx Supporter DigiCert DigiCert EV certificate StatusPage StatusPage Status page