MOFid 2024

A system for rapid identification and analysis of metal-organic frameworks.

Please cite DOI: 10.1021/acs.cgd.9b01050 if you use MOFid in your work.

Table of Contents

1. Objective
2. Usage and Installation Instructions
   1. Browser-based MOFid
   2. Compiling from Source
   3. Containerized MOFid
3. Output Overview
4. Repository Overview
5. Background and Troubleshooting
6. Credits

Objective

Supplement the current MOF naming conventions with a canonical, machine-readable identifier to facilitate data mining and searches. Accomplish this goal by representing MOFs according to their nodes and linkers and topology.

Usage and Installation Instructions

There are three main ways in which you can use MOFid.

1. From your browser.
2. By compiling the MOFid source code and running it locally.
3. By using Singularity or Docker to run a pre-built image of the MOFid code locally.

Browser-based MOFid

Visit Web MOFid to quickly and easily run MOFid in your browser! No programming skills are required.

Compiling from Source

See Compiling for how to compile and run MOFid from source.

Containerized MOFid

See Singularity for how to run MOFid via a Singularity container.

Output Overview

By default, the SBU binary and utility scripts write files to a user-specified Output directory. The base directory contains the original adjacency matrix of single bonds for the MOF in orig_mol.txt. If a single structure is analyzed in Python by invoking Python/run_mofid.py or the Python API, two files containing the MOFid and MOFkey are written to this directory. Similar files are written for an entire folder of CIFs by Scripts/run_folder.sh.

The results of four MOF deconstruction algorithms are written to labeled subdirectories (MetalOxo, SingleNode, AllNode, StandardIsolated) and contain information about…

• MOF building blocks (nodes, linkers).
• Solvents (bound/free).
  • The MOF structure with only free solvent removed (FSR).
  • The MOF structure with all solvent removed (ASR).
• The simplified net.
  • A topology.cgd file for Systre.
  • A simplified topology CIF.
• Statistics about MOF linkers.

The directory for the SingleNode and AllNode simplification algorithms additionally contain the crystal structures of the node SBUs (including carboxylates or bound heterocycles) and the AllNode directory contains the identities of branch points in the simplified net. Results from the standard simplification algorithm are written to Output/StandardIsolated but have not been analyzed for the paper.

Repository Overview

• Resources: contains data files for testing and continuous integration using GitHub Actions.
• Scripts: provides contains utilities for studying folders of structures.
• Analysis: contains supplementary information source code for figures in the paper.
• Python: contains wrappers for the SBU binary and Systre that assemble the MOFid and MOFkey.
• Tests: contains intermediate and integration test scripts.

Background and Troubleshooting

Please read this page for a detailed background and for important tips and tricks in troubleshooting problematic scenarios.

Credits

This work is supported by the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences through the Nanoporous Materials Genome Center under award DE-FG02-17ER16362.

The MOFid command line and web tools are built on top of other open-source software projects.

• Open Babel cheminformatics toolkit
• Eigen as a dependency for Open Babel
• GoogleTest C++ testing framework
• Make, CMake, Node.js, and Emscripten for build infrastructure
• Systre and webGavrog to analyze crystal graph data and assign RCSR topology symbols for MOFs
• NGL Viewer to visualize MOF structures and components on the website
• Kekule.js to draw molecule substructure queries in the SearchDB web tool

You can find the source code for Jekyll at GitHub: jekyll / jekyll