DOI: 10.5281/zenodo.14880578
title: Code and raw data for 'Robot-assisted mapping of chemical reaction hyperspaces and networks'

description: Code and data supporting the article 'Robot-assisted mapping of chemical reaction hyperspaces and networks'

This repository contains the code and data supporting the research article "Robot-assisted mapping of chemical reaction hyperspaces and networks" byYankai Jia, Rafał Frydrych, Yaroslav I. Sobolev, Wai-Shing Wong, Bibek Prajapati, Daniel Matuszczyk, Yasemin Bilgi, Louis Gadina, Juan Carlos Ahumada, Galymzhan Moldagulov, Namhun Kim, Eric Larsen, Maxence Deschamps, Yanqiu Jiang, Bartosz A. Grzybowski.

There are four ZIP files here:



github-code-repository.zip  is the copy of Github repository (https://github.com/yaroslavsobolev/robowski-maps), which contains all code and some of the data. Typical install time on a "normal" desktop computer: 30 minutes. Run time for worked example of spectral unmixing workflow (notebooks/spectral_unmixing_tutorial.ipynb) is 10 minutes.

data.zip contains all the raw data that was not included into the Github repository github-code-repository.zip. The /mechanical_designs subdirectory of this archive contains the CAD files (technical drawings) of parts designed for the automation hardware. The archive data.zip is roughly 19 Gb when unzipped. 

HyperspaceViewer_with_manual_and_datasets.zip  contains the compiled build from the source code, along with the dataset used in the paper (in CSV format) and a user manual (in PDF format) explaining how to use the tool.

HyperspaceViewer_source_code-0.7.6.zip is the souce code for the software HyperspaceViewer, and it is the copy of the Gitlab repository (https://gitlab.com/az-steak/hyperspace_viewer)


If you are only looking for the final datasets of reaction yields

The final reaction yield datasets are tables in CSV format located in the summary_of_reaction_yield_data folder inside the github-code-repository.zipSee the README.md file in that folder for more details.

Extracting all the raw data to be accessible by Python scripts

The ZIP file containing all the raw data is named data.zip, it is 6.8 Gb, and 19 Gb when unzipped. Unzip it to any folder of your choosing, and then list the path to that folder in your operating system's "environment variable" named ROBOCHEM_DATA_PATH. This environment variable will be used by the Python scripts to locate the data files.

Code description and functionalities

All the Python scripts used in this work are contained in the github-code-repository.zip. Description of the code, alond with requirements and instructions for running it can be found in the in the README.md file in the root of the github-code-repository.zip. That README.md file also describes how to reproduce the article's figures from the raw data. The following functionalities are covered by the supplied scripts:



Automation of pipetting and NanoDrop spectrophotometer measurement

Automatic washing of vial plates

Automation of CRAIC microspectrometer

Spectral unmixing of the UV-Vis absorption spectra

3D visualization of the yield maps

Outlier filtration and interpolation in Ugi reaction data

Fitting the kinetic models to the data

Calculating proton exchange equilibrium in a complex mixture

Numerical exploration of the smoothness of the yield maps of reaction networks

Calculation of theoretical light absorption spectra from TD-DFT