https://github.com/laurentrdc/crystals
Data structures, algorithms, and parsing for crystallography
Science Score: 49.0%
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 14 DOI reference(s) in README -
✓Academic publication links
Links to: arxiv.org -
○Committers with academic emails
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (14.8%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
Data structures, algorithms, and parsing for crystallography
Basic Info
- Host: GitHub
- Owner: LaurentRDC
- License: gpl-3.0
- Language: Python
- Default Branch: master
- Homepage: https://crystals.readthedocs.io/
- Size: 834 KB
Statistics
- Stars: 50
- Watchers: 7
- Forks: 11
- Open Issues: 0
- Releases: 14
Topics
Metadata Files
README.md
crystals
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).
Take a look at the documentation 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
You can install the latest development version using pip as well:
python -m pip install git+git://github.com/LaurentRDC/crystals.git
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.
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.
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 (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.
License
crystals is made available under the GPLv3 license. For more
details, see LICENSE.
Related projects
- Streaming operations on NumPy arrays are available in the npstreams package.
- Interactive exploration of ultrafast electron diffraction data with the iris-ued package.
- Data structures and algorithms to handle ultrafast electron scattering data in the scikit-ued package.
Owner
- Name: Laurent P. René de Cotret
- Login: LaurentRDC
- Kind: user
- Location: Montréal
- Company: @bitnomial
- Website: https://laurentrdc.xyz
- Repositories: 34
- Profile: https://github.com/LaurentRDC
Scientific computing, functional programming, and hardtech innovation. Board member of the @haskellfoundation
GitHub Events
Total
- Release event: 1
- Watch event: 7
- Delete event: 1
- Issue comment event: 1
- Push event: 18
- Pull request event: 1
- Create event: 1
Last Year
- Release event: 1
- Watch event: 7
- Delete event: 1
- Issue comment event: 1
- Push event: 18
- Pull request event: 1
- Create event: 1
Committers
Last synced: 9 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Laurent P. René de Cotret | l****t@o****m | 488 |
| Chazeon | c****o@g****m | 5 |
| GitHub Actions | 2 | |
| Sebastian Hammer | 1****b | 1 |
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 16
- Total pull requests: 5
- Average time to close issues: 6 days
- Average time to close pull requests: 10 days
- Total issue authors: 10
- Total pull request authors: 5
- Average comments per issue: 4.0
- Average comments per pull request: 2.8
- Merged pull requests: 3
- Bot issues: 0
- Bot pull requests: 1
Past Year
- Issues: 0
- Pull requests: 1
- Average time to close issues: N/A
- Average time to close pull requests: about 2 months
- Issue authors: 0
- Pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 1.0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 1
Top Authors
Issue Authors
- errhernandez (4)
- eggplants (2)
- StarostinV (2)
- Cs137 (2)
- pllim (1)
- azkhadiev (1)
- craldaz (1)
- KeysBit (1)
- patquem (1)
- bokertof (1)
Pull Request Authors
- dependabot[bot] (2)
- chazeon (1)
- subangstrom (1)
- LaurentRDC (1)
- HammerSeb (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 2
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Total downloads:
- pypi 1,435 last-month
- Total docker downloads: 30
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Total dependent packages: 5
(may contain duplicates) -
Total dependent repositories: 9
(may contain duplicates) - Total versions: 53
- Total maintainers: 1
pypi.org: crystals
Data structures for crystallography
- Homepage: http://crystals.readthedocs.io
- Documentation: https://crystals.readthedocs.io/
- License: GPLv3
-
Latest release: 1.7.0
published over 1 year ago
Rankings
Maintainers (1)
conda-forge.org: crystals
crystals provides data structure to manipulate crystal structures, including parsing crystal files, determining symmetries, and accessing atomic information.
- Homepage: https://crystals.readthedocs.io
- License: GPL-3.0-only
-
Latest release: 1.6.0
published over 3 years ago
Rankings
Dependencies
- ase >=3,<4 development
- biopython >=1,<2 development
- pytest >=6 development
- sphinx >=3 development
- sphinx_rtd_theme >=0.4 development
- wheel * development
- numpy >=1.20,<2
- pycifrw >=4.4.1,<5
- requests >=2,<3
- spglib >=1.15,<2
- actions/cache v2 composite
- actions/checkout v2 composite
- actions/download-artifact v2 composite
- actions/setup-python v2 composite
- actions/upload-artifact v2 composite
- pypa/gh-action-pypi-publish release/v1 composite
- softprops/action-gh-release v1 composite
- actions/checkout v2 composite