oximachinerunner

Installation

On macOS you need to run brew install libomp first to enable multithreading for the XGBoost library.

Ideally, you install everything in a clean environment, e.g., using conda

conda create -n test_oximachine_runner python=3.7

Confirm with y when asked to do so, then activate with conda activate test_oximachine_runner.

Latest, development, version

pip install git+https://github.com/kjappelbaum/oximachinerunner.git

Latest stable release

pip install oximachinerunner

Note that the installation will require significant (>500 MB) storage space since the ensembles use k-nearest neighbors models.

Usage

Note that since version 1 the models are no longer shipped with the PyPi package. There is a dedicated function to download the models, which has to be run before the first use. Also, in contrast to version 0, the interface is now object-oriented

from oximachinerunner import OximachineRunner
runner = OximachineRunner()
runner.run_oximachine('oximachinerunner/assets/ACODAA.cif')

The function will print for how many sites it will run the model.

It will return a OrderedDict with:

• A list of oxidation state predictions
• A list of indices of the metal sites
• Strings indicating the metal
• The predictions of the base estimators
• The estimated probabilites

The OximachineRunner can be initialized with a modelname. To view which models are available in the current release, use runner.available_models. By default, models will be automatically downloaded if there are not yet in the correct folder. You should output as follows

/Users/kevinmaikjablonka/opt/miniconda3/envs/test_oximachine_runner/lib/python3.7/site-packages/oximachinerunner/assets/all_202000830/classifier.joblib are not exist or md5 is wrong.
Download file from https://www.dropbox.com/s/lc2z4abaycjbbe1/classifier.joblib?dl=1
2.9% of 527.44M

If you want to turn this behavior of, you can set OximachineRunner(automatic_download=False). If you then need a model, you can manually download it using a function from the utils module.

The run_oximachine function accepts pymatgen.Structure, ase.Atoms and str as well as os.PathLike. Latter two are expected to be filepaths to a file that is then parsed with pymatgen.

Reference

Jablonka, Kevin Maik; Ongari, Daniele; Moosavi, Seyed Mohamad; Smit, Berend (2020): Using Collective Knowledge to Assign Oxidation States. ChemRxiv. Preprint. https://doi.org/10.26434/chemrxiv.11604129.v1