zeobind

This repository contains code for the computational screening workflow used in the paper "Exhaustive mapping of the zeolite-template chemical space" by Xie et. al. If you use our code and data, please cite our paper: [TODO insert paper citation]

Installation

To install the code, clone the repository and install the dependencies using the following commands:

mamba create -f environment.yml
mamba activate zeobind

The data used in the paper, dataset of hypothetical molecules, as well as predictions across all the IZA framework - hypothetical molecule chemical space, can be found at Materials Data Facility. Download the data and place it in the zeobind/data directory.

Usage

Screening molecules from predictions

We provide a bash script for screening for molecules for a targeted framework using the pre-generated predictions stored inside data/predictions.

Example bash scripts, which are also the ones used in the paper's CHA and ERI case studies, can be found at run_scripts/inference/screen_{cha,eri}.sh. Run

bash run_scripts/inference/screen_cha.sh

Predicting on new molecules

If you have a new set of molecules you would like to predict on, an example bash script can be found at run_scripts/predict.sh.

bash run_scripts/inference/predict.sh

Training models

To train models, template bash scripts can be found at run_scripts/training/.

# example
bash run_scripts/training/binary/template.sh

Reproducing results and figures

The notebooks in the notebooks directory generate metrics and figures reported in the paper.