This thesis was carried out at UniFr in the COMMONS Lab https://www.unifr.ch/bio/en/groups/allard/. For six months, I immersed myself in chemical structure expansion using Pickaxe. In this repository, I have collected all the important scripts from this journey.
All scripts relevant to the MSc thesis ‘Expanded natural product chemspace’ can be found here.
More details about the scripts can be found in the jupyter-lab files.
(expanded-naturalproduct-chemspace/*)
LOTUS overview:
Read in the data from LOTUS (the file has some errors, why there is a specific way).
MINES Input:
Analyzing the Inputdata from Lotus and reaction rules.
MINES lists:
Script for getting columns of interest. Specifically reactions.
MINES validation:
scripts for validate SMILES in PubChem. (Didn't work with a big dataset)
MINES taxonomy search:
Lot of different scripts. Annotating the LOTUS db with the output from pickaxe.
Plots:
Creating the plots for the master thesis can be found here.