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Singularity

Installation

If you have access to a Linux system or high-performance computing cluster, it may be possible to run the MOFid code via singularity, which packages the MOFid installer into a portable, reproducible environment. To get started, refer to documentation from your university or computing center (example) for help on singularity. There may be setup instructions specific to your compute environment. (For example, you may need to load modules or bind paths to set up singularity.)

  1. Download the pre-compiled singularity container (mofid.sif) from the most recent release.
  2. Test your installation using singularity test mofid.sif. Your installation is successful if you receive the message Results: 0 errors in 28 MOFs at the end of the run.

Alternatively, if you wish to use Docker see docker.md.

Usage

The singularity container wraps all of the MOFid software into a single package.

As a command line tool:

# Analyzing a single MOF crystal structure
./mofid.sif file path_to_mof.cif
# alternatively: singularity run mofid.sif file path_to_mof.cif

# Analyzing a folder
./mofid.sif folder path_to_input_cif_folder path_to_mofid_output
# By default, path_to_mofid_output is set to "Output/" in your current directory

Or, as part of a Python script:

import json
import sys

import subprocess

MOFID_SIF = "path_to_mofid.sif"
MOF_CIF_TO_ANALYZE = "path_to_mof.cif"
mofid_cmd = ["singularity", "run", MOFID_SIF, "file", MOF_CIF_TO_ANALYZE]
mofid_run = subprocess.run(mofid_cmd, universal_newlines=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
sys.stderr.write(mofid_run.stderr)  # Re-forwarding C++ errors
mofid_output = json.loads(mofid_run.stdout)

The mofid_output variable above is a dictionary containing eight entries: the MOFid (mofid), MOFkey (mofkey), SMILES string (smiles, smiles_nodes, or smiles_linkers), topology (topology), catenation (cat), and basename of the CIF (cifname).