mofid_wrapper

A pip-installable wrapper around MOFid for rapid identification and analysis of metal-organic frameworks.

Prebuilt release wheels for Linux x86_64 include the required native binaries (Open Babel and MOFid's CLI tools). Installing one of these wheels does not require a C/C++ compiler and does not build Open Babel from source.

This is the recommended installation method.

pip install https://github.com/ComPlat/mofid_wrapper/releases/download/<VERSION>/<WHEEL_FILE>.whl

For example:

pip install https://github.com/ComPlat/mofid_wrapper/releases/download/v0.1.0/mofid_wrapper-0.1.0-py3-none-manylinux_2_28_x86_64.whl

The wheel is built beforehand by GitHub Actions and already contains the required Open Babel and MOFid binaries. No local C/C++ compilation is performed during installation.

Download the appropriate .whl file from the GitHub Releases page and then install it with:

pip install ./mofid_wrapper-0.1.0-py3-none-manylinux_2_28_x86_64.whl

This is equivalent to installing the wheel directly from its GitHub release URL. The native binaries are already included, so no local compiler is required.

If you clone the repository instead of installing a prebuilt wheel, the vendored native binaries are not present in the Git repository and must be built locally first.

git clone https://github.com/ComPlat/mofid_wrapper.git
cd mofid_wrapper

./ci/build_binaries.sh
pip install .

ci/build_binaries.sh builds Open Babel and the required MOFid CLI tools and places them into the package's _vendor directory. pip install . then builds and installs the Python package using these locally built binaries.

This installation method therefore requires the necessary C/C++ compiler and build dependencies.

Running only:

git clone https://github.com/ComPlat/mofid_wrapper.git
cd mofid_wrapper
pip install .

is not sufficient, because pip install . does not automatically run ci/build_binaries.sh and the native Open Babel/MOFid binaries are not stored in the Git repository.

from mofid_wrapper import cif2mofid

result = cif2mofid("my_mof.cif", output_path="Output")
print(result["mofid"])
print(result["mofkey"])

• Linux, x86_64.
• A Java runtime (java on PATH), used for the topology step (Systre). E.g. apt install default-jre-headless on Debian/Ubuntu. This is checked lazily -- only raised when you actually compute topology, not on import.

This wraps the parts of upstream mofid that only shell out to compiled executables and java. Three upstream modules that depend on Open Babel's SWIG Python bindings (pybel) -- a separate, heavier build path not produced by this package's build -- are not included: old_cheminformatics.py, extract_metals.py, remove_metals.py.

See ci/build_binaries.sh. In short: a pinned upstream mofid commit is built inside a manylinux_2_28_x86_64 container, with a small patch (ci/patches/0001-babel-env-no-overwrite.patch) applied first -- upstream's sbu/sobgrep/tsfm_smiles/compare/searchdb binaries call setenv("BABEL_DATADIR"/"BABEL_LIBDIR", ..., 1) with overwrite=1, which unconditionally clobbers the environment variables this package needs to set for the binaries to find their bundled data/plugins on someone else's machine.

The resulting binaries + Open Babel's data/plugins + the InChI shared library

• the Systre jar + the RCSR net archive are bundled as package data and shipped as a manylinux_2_28_x86_64-tagged wheel.

mofid_wrapper's own code is GPL-2.0-or-later. See LICENSE.

The wheel redistributes precompiled binaries and data files that are the work of others. NOTICE (repo root, also installed with the package) lists every bundled component with its license and a pointer to its corresponding source; full license texts are in THIRD_PARTY_LICENSES/:

The copyleft components (MOFid, Open Babel, InChI) require their corresponding source to be available. It is not shipped in the wheel but is fully specified by ci/build_binaries.sh, which pins every upstream revision and records the toolchain; see NOTICE for details.