{"id":17603484,"url":"https://github.com/laurentrdc/crystals","last_synced_at":"2025-08-09T03:43:57.858Z","repository":{"id":37458425,"uuid":"156432089","full_name":"LaurentRDC/crystals","owner":"LaurentRDC","description":"Data structures, algorithms, and parsing for crystallography","archived":false,"fork":false,"pushed_at":"2025-01-16T16:59:41.000Z","size":854,"stargazers_count":47,"open_issues_count":0,"forks_count":12,"subscribers_count":7,"default_branch":"master","last_synced_at":"2025-03-26T02:51:11.379Z","etag":null,"topics":["bioinformatics","crystal-structure","crystallography","indexing-algorithms","materials-science","python3"],"latest_commit_sha":null,"homepage":"https://crystals.readthedocs.io/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/LaurentRDC.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.rst","contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2018-11-06T18:53:33.000Z","updated_at":"2025-02-10T04:20:20.000Z","dependencies_parsed_at":"2024-01-08T01:21:02.069Z","dependency_job_id":"d4711439-e3e3-40bf-ada0-b7a443747e38","html_url":"https://github.com/LaurentRDC/crystals","commit_stats":{"total_commits":475,"total_committers":6,"mean_commits":79.16666666666667,"dds":"0.11368421052631583","last_synced_commit":"d0ae10847550467170a7a5a2ad0e1f69c28308eb"},"previous_names":[],"tags_count":14,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LaurentRDC%2Fcrystals","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LaurentRDC%2Fcrystals/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LaurentRDC%2Fcrystals/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LaurentRDC%2Fcrystals/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/LaurentRDC","download_url":"https://codeload.github.com/LaurentRDC/crystals/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248536990,"owners_count":21120683,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bioinformatics","crystal-structure","crystallography","indexing-algorithms","materials-science","python3"],"created_at":"2024-10-22T13:53:22.316Z","updated_at":"2025-04-12T07:41:09.939Z","avatar_url":"https://github.com/LaurentRDC.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"crystals\n========\n[![Documentation Status](https://readthedocs.org/projects/crystals/badge/?version=master)](https://crystals.readthedocs.io/) [![PyPI Package latest release](https://img.shields.io/pypi/v/crystals.svg)](https://pypi.python.org/pypi/crystals) [![Conda-forge Version](https://img.shields.io/conda/vn/conda-forge/crystals.svg)](https://anaconda.org/conda-forge/crystals) [![DOI badge](https://img.shields.io/badge/DOI-10.1186%2Fs40679--018--0060--y-blue)](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\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\nDocumentation\n-------------\n\nThe documentation, including user guides as well as detailed reference,\nis available here: \u003chttps://crystals.readthedocs.io/\u003e\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\u003e 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)\n\nUnderlying algorithms provided by `spglib` are described in the\nfollowing publication:\n\n\u003e 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\u003e 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\u003e Hamelryck, T., Manderick, B. *PDB parser and structure class implemented in Python*. Bioinformatics 19: 2308–2310 (2003)\n\nAtomic weights are reported in the following publication:\n\n\u003e 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\u003e 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","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flaurentrdc%2Fcrystals","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flaurentrdc%2Fcrystals","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flaurentrdc%2Fcrystals/lists"}