Science Score: 49.0%
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○Scientific vocabulary similarity
Low similarity (15.9%) to scientific vocabulary
Keywords
Repository
Basic sanity checks for MOFs.
Basic Info
- Host: GitHub
- Owner: lamalab-org
- License: mit
- Language: Python
- Default Branch: main
- Homepage: https://mofchecker.readthedocs.io/en/latest/background.html
- Size: 8.82 MB
Statistics
- Stars: 30
- Watchers: 2
- Forks: 4
- Open Issues: 33
- Releases: 19
Topics
Metadata Files
README.md
mofchecker
What does it do?
mofchecker performs quick sanity checks on crystal structures of metal-organic frameworks (MOFs).
Try the live web app at https://github.com/kjappelbaum/webmofchecker !
Sanity checks:
- Presence of at least one metal, carbon and hydrogen atom
- Overlapping atoms (distance between atoms above covalent radius of the smaller atom)
- Overvalent carbons (coordination number above 4), nitrogens (heuristics), or hydrogens (CN > 1)
- Missing hydrogen on common coordination geometries of C and N (heuristics)
- Atoms with excessive EQeq partial charge
Basic analysis: - Presence of floating atoms or molecules - Hash of the atomic structure graph (useful to identify duplicates)
The sanity checks can be used to weed out really unreasonable structures (nothing too fancy). The code is a rewrite of similar tools in structure_comp.
Installation
Development version:
bash
pip install git+https://github.com/kjappelbaum/mofchecker.git
Latest stable release
bash
pip install mofchecker
Note that you need to install zeopp if you want to use the porosity features.
bash
conda install -c conda-forge zeopp-lsmo
A web app is currently being developed in another repository and deployed on MatCloud.
Getting Started
Command line interface
bash
mofchecker --help # list options
mofchecker structure1.cif structure2.cif # prints JSON output
mofchecker -d has_metal -d has_atomic_overlaps *.cif # compute only selected descriptors
In Python
```python from mofchecker import MOFChecker mofchecker = MOFChecker.fromcif(<pathto_cif>)
or: MOFChecker(structure=mypymatgenstructure)
Test for OMS
mofchecker.has_oms
Test for clashing atoms
mofchecker.hasatomicoverlaps
Run basic checks on a list of cif paths (sample_structures)
results = []
for structure in samplestructures: mofchecker = MOFChecker.fromcif(structure) results.append(mofchecker.getmofdescriptors()) ```
Contributing
Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See CONTRIBUTING.rst for more information on getting involved.
License
The code in this package is licensed under the MIT License.
Funding
The research was supported by the European Research Council (ERC) under the European Unions Horizon 2020 research and innovation programme (grant agreement 666983, MaGic), by the NCCR-MARVEL, funded by the Swiss National Science Foundation, and by the Swiss National Science Foundation (SNSF) under Grant 200021_172759.
Owner
- Name: Laboratory for AI for Materials
- Login: lamalab-org
- Kind: organization
- Repositories: 1
- Profile: https://github.com/lamalab-org
Research group led by Kevin Maik Jablonka
GitHub Events
Total
- Watch event: 6
- Issue comment event: 1
Last Year
- Watch event: 6
- Issue comment event: 1
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 83
- Total pull requests: 111
- Average time to close issues: about 2 months
- Average time to close pull requests: 10 days
- Total issue authors: 5
- Total pull request authors: 5
- Average comments per issue: 0.98
- Average comments per pull request: 0.76
- Merged pull requests: 79
- Bot issues: 0
- Bot pull requests: 69
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- kjappelbaum (71)
- Andrew-S-Rosen (5)
- ltalirz (5)
- akulpillai (1)
- danieleongari (1)
Pull Request Authors
- dependabot[bot] (33)
- kjappelbaum (26)
- github-actions[bot] (20)
- deepsource-autofix[bot] (16)
- ltalirz (16)
Top Labels
Issue Labels
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Dependencies
- actions/checkout v2 composite
- codecov/codecov-action v1 composite
- s-weigand/setup-conda v1 composite
- click *
- pymatgen *
- sphinx *
- sphinx-autodoc-typehints *
- sphinx-book-theme *
- sphinx-copybutton *