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Project description
mofchecker
What does it do?
Perform quick sanity checks on your MOF:
- Find open metal sites (OMS) in metal-organic frameworks (MOFs).
- Find atomic overlaps.
- Find overvalent (CN>4) carbons or nitrogens.
- Check if there is metal, carbon or hydrogen.
- Check if there is floating atoms or molecules.
The idea is to have nothing to fancy but a fast tool that we can run to eliminate the really unreasonable structures. The code is basically a rewrite of the checking tools that we implemented in structure_comp.
A basic CLI is in development.
OMS detection
If works similar to the OMS detector used for the CoRE-MOF database but it attempts to be a bit more lightweight and correct in some cases (like paddlewheels).
We use pymatgen to calculate the order-parameters proposed by Zimmermann and Jain. Note that we introduce some weighting factors.
Identifying OMS is important as our force-fields fail to describe them correctly.
Overlapping atoms
Overlapping atoms are detected based on the pairwise distance matrix and the covalent radii.
Why check for carbons?
I think it is a pretty fast check if there is something organic ... And we know that in both the CSD subset and the CoRE-MOF database there are several structures that do not contain carbon.
Floating molecule detection
This check basically analyzes if there are unconnected subgraphs.
Installation
Development version:
pip install git+https://github.com/kjappelbaum/mofchecker.git
Usage
In Python
from mofchecker import MOFChecker
mofchecker = MOFChecker.from_cif(<path_to_cif>)
# 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())
CLI
For example, you can use
mofchecker <cif> --has-oms
You can get an overview over all options with
mofchecker --help
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