mofchecker 0.1.0

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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