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mofchecker

Tests PyPI PyPI - Python Version PyPI - License Documentation Status Code style: black

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:

pip install git+https://github.com/kjappelbaum/mofchecker.git

Latest stable release

pip install mofchecker

Note that you need to install zeopp if you want to use the porosity features.

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

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

from mofchecker import MOFChecker
mofchecker = MOFChecker.from_cif(<path_to_cif>)
# or: MOFChecker(structure=my_pymatgen_structure)

# Test for OMS
mofchecker.has_oms

# Test for clashing atoms
mofchecker.has_atomic_overlaps

# Run basic checks on a list of cif paths (sample_structures)
results = []

for structure in sample_structures:
    mofchecker = MOFChecker.from_cif(structure)
    results.append(mofchecker.get_mof_descriptors())

👐 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 Union’s 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.