mofchecker 0.9.6
Perform sanity checks for MOFs.
License: MIT
Requires Python: >=3.8

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## 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](https://pubs.acs.org/doi/10.1021/jz3008485)

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](https://github.com/kjappelbaum/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](https://anaconda.org/conda-forge/zeopp-lsmo) 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](https://github.com/kjappelbaum/webmofchecker) and deployed on [MatCloud](http://mofchecker.matcloud.xyz/).

## 💪 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.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](https://github.com/kjappelbaum/mofchecker/blob/master/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](https://cordis.europa.eu/project/id/666983)), by the [NCCR-MARVEL](https://www.nccr-marvel.ch/), funded by the Swiss National Science Foundation, and by the Swiss National Science Foundation (SNSF) under Grant 200021_172759.