Tutorial of the Open Bidentate Ligand eXplorer (OBeLiX) workflow

The tutorial consists of 3 parts in which we will start with generating structures of homogeneous catalysts from scratch and move towards the calculation of physical-chemical descriptors. Each folder contains a Jupyter notebook (and sometimes a Python script for people that hate Jupyter notebooks) with explanations and example code.

Installation instructions

The OBeLiX code requires Anaconda/Miniconda and a Unix operating system due to a dependency on the xtb-python package. You can still run parts of this tutorial on a Windows system, but slight modifications are needed. I will mention this in the instructions below.

The repository of obelix is included in this tutorial as a submodule, meaning that is a Github repository within this Github repository. This makes it easier to install everything at once.

Clone this repository and the code for all included submodules to your pc:

git clone https://github.com/EPiCs-group/obelix-tutorial --recurse-submodules

Navigate to the newly created folder on your pc:

cd obelix-tutorial

Create the conda environment with all dependencies for the OBeLiX code:
Note for if you run this tutorial on a Windows system: before running the conda env create command you need to put a # before the line with - xtb-python in the environment.yml file such that it is ignored.

cd obelix
conda env create -f environment.yml

This installs a conda environment named 'obelix', which we have to activate:

conda activate obelix

Since we want to run Jupyter notebooks, we have to install the notebook package in this environment:

pip install notebook

And finally we install the code of OBeLiX as a package in this environment:

pip install -e .

Now we can move one folder up towards the root folder of this repository (obelix-tutorial) and run Jupyter:

cd ..
jupyter notebook

Now you should be ready to go through the tutorial! Feel free to create issues in this repository if you have any questions/comments/improvements.

Contents

• 1_MACE
  • Generate structures from the SMILES of metal and ligands (generate_structures.ipynb)
• 2_ChemSpaX
  • Replace dummy atoms on a chemical scaffold in 3D with a functional group (functionalize_skeleton.ipynb)
• 3_OBeLiX
  • Automate the usage of MACE and ChemSpaX for high-throughput generation of homogeneous catalysts with bidentate ligands (structure_generation/structure_generation_workflow.ipynb)
  • Automate the calculation of different types of descriptors for different filetypes, allowing to create a ML-ready representation of homogeneous catalysts with bidentate ligands (calculate_descriptors.ipynb)
    • Note: DFT_descriptors.csv and xyz_descriptors.csv have been provided for people that are working on a Windows system and are thus unable to run the descriptor calculation on their system.