This is the Snakemake workflow for reproducing the data analysis of our paper on a quantum definition of molecular structure.

In order to execute the workflow, you need to have Julia with the MolStructSampling.jl, NPZ.jl, and ProgressBars.jl packages installed and Snakemake as well as Apptainer in your path.

Once you have Julia, you can install the required packages via starting the Julia REPL by typing julia in a terminal, then entering Pkg mode by pressing the ] key and entering the following commands:

• add https://github.com/LucasLang/MolStructSampling.jl.git
• add ProgressBars
• add NPZ

In order to install Snakemake, you can e.g. enter the following commands (requires conda, e.g. through a Miniconda or Anaconda installation):

conda config --set channel_priority strict
conda create --name snakemake python=3.11
conda activate snakemake
conda install -c conda-forge -c bioconda snakemake

Basic settings for the sampling and analysis can be set in config/config.yaml.

Usage:

cd workflow
snakemake -c1 --use-conda --conda-frontend conda