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Docker

The initial containerization experiments for MOFid used Docker. Installation instructions for Docker are highly system-dependent and beyond the scope of this document. For example, Windows users may need to set up WSL2 or VirtualBox. Two potentially helpful links for Linux include the installation and configuration docs.

Installation

  1. Once Docker is set up, clone the MOFid repository.
  2. Build the container by running docker build -t mofid path_to_mofid_repo

Usage

To start a shell within the Docker container, run docker run -it mofid /bin/bash

To analyze a single MOF crystal structure:

# Configure paths in the first two lines, then run this block
MOFID_IN_FILENAME="P1-Cu-BTC.cif"
MOFID_IN_DIR="$PWD"  # absolute path to parent directory, e.g. current directory via $PWD

docker run \
    --mount type=bind,source="$MOFID_IN_DIR",target="$MOFID_IN_DIR",readonly \
    mofid \
    python /mofid/Python/run_mofid.py "$MOFID_IN_DIR/$MOFID_IN_FILENAME" /mofid/TempOutput json

Or, for analyzing an entire folder:

# Configure the paths in the first two lines, then run this block
MOFID_IN_DIR="$PWD/Resources/TestCIFs"
MOFID_OUT_DIR="$PWD/mofid_output"

mkdir -p "$MOFID_OUT_DIR"
docker run \
    --mount type=bind,source="$MOFID_IN_DIR",target=/data,readonly \
    --mount type=bind,source="$MOFID_OUT_DIR",target=/out \
    mofid \
    Scripts/run_folder.sh /data /out