Perform sanity checks on MOF structures
Project description
mofchecker
What does it do?
mofchecker
performs quick sanity checks on crystal structures of metal-organic frameworks (MOFs).
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.
Usage
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_overlapping_atoms
# 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())
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