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Installation

python -m pip install mmcif-tools

There are no runtime dependencies. For tab completion of the mmcif_* commands, open a new terminal after installing (or run rehash in an open zsh terminal).

The extra tools below are in the repository, not in the package. To install from the repository instead, python tools/smoke_test.py then checks the installation: every command runs, and a few pipelines give the expected results.

git clone https://github.com/matteo-cagiada/mmcif-tools.git
cd mmcif-tools
python -m pip install .
python tools/smoke_test.py

Extra tools

tools/ holds scripts that are not part of mmcif-tools and are not installed with it.

  • tools/check_with_gemmi.py checks CIF files with gemmi, an independent CIF reader: the syntax, and optionally a dictionary such as the PDBx/mmCIF one (--dict). It runs the gemmi program, which you install yourself (e.g. pip install gemmi-program); give its path with --gemmi if it is not on the PATH:
python tools/check_with_gemmi.py --gemmi /path/to/gemmi out.cif
mmcif_selchain -A 1abc.cif | python tools/check_with_gemmi.py --dict mmcif_pdbx_v50.dic -