mofchecker 0.8.2

Perform sanity checks on MOF structures

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())