Created by Leo Trostel on 15.09.2022

This is a READme file for "compare_methods_pps.py"

Purpose:
Compares predictions from EAWAG/BBD-PPS and enviPath with found transformation products (TPs) and calculates precision for each method.
The script uses the output of the script "get_mass_list_from_prediction.py"

Input:
The script uses 2 input files:
o txt file with one SMILES per line of TPs that were found experimentally
o pickle file of combined dictionary with all predictions made by different methods

Output:
The script outputs four files containing information of number of TPs predicted and found.

Note:
The csv and tsv files can be opened in Microsoft Excel and brought to a more readable format.

Step by step guide for non-python users:
1. download Anaconda (link: https://docs.anaconda.com/anaconda/install/index.html) and install it, then run Anaconda Navigator
2. create new environment under the environment tab, select python version 3.6.13
3. you need to install some python packages for this script to work:
3.1. go to environments, click "play button" on newly created environment, open Terminal
3.2. run following lines individually (need to confirm: type "y" and press enter)(might take a while):
conda install -c rdkit rdkit
3.3. check if pandas is installed and active according to: https://docs.anaconda.com/anaconda/navigator/tutorials/pandas/
4. open anaconda navigator, go to home tab, check if "Applications on" is set to the new environment
5. click gear icon on "Spyder" > install specific version > 5.0.5 and wait for installation to finish
6. click launch button below "Spyder"
7. open the script: "compare_methods_pps.py"
8. change the pathway of the input files according to the filepath on your harddrive
9. click somewhere in the left window and press F5 or click "Run File", if Run settings windows appears, click run
10. wait for the script to finish running (you can see the progress in the bottom right window, "Script finished successfully" marks end of script)