TP_predict/782f6e99f685master
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readme.md
TP_predict - Predict TPs and create suspect lists
This collection of scripts allows the user to reproduce the TP prediction and data analyses presented in the following publication:
Trostel, L. & Coll, C., Fenner, K., Hafner, J. Synergy of predictive and analytical methods advances elucidating biotransformation processes in activated sludge, 2023. [insert DOI]
The tools can further be used to perform the same predictions and analyses on a different set of compounds.
Content
- TP_prediction: Script to predict TPs and corresponding biodegradation pathways
- File_conversion: Conversion of prediction output to input for suspect screening tools
- Prediction_output_to_mass_list
- SMILES_to_mass_and_inclusion_list
- Additional_analyses
- Compare_methods
- Analyse_cutoff_thresholds
Specific user guidance can be found in the README.md files of the content folders.
How to
To fetch the code from the git repository, open a terminal and run:
$ git clone [insert link]
To install the dependencies, go to the nicepath directory and run:
$ cd TP_predict $ make
Installation and requirements
The scripts requires rdkit for python, which is easiest installed in a conda environment. All scripts have been developed and tested in Python 3.6 and higher.
Anaconda: Step by step guide for non-python users:
- Download Anaconda and install it, then run Anaconda Navigator
- create new environment under the Environment tab, select python version 3.6.13
- go to environments, click play button on newly created environment, open Terminal
- run following lines individually (need to confirm: type y and press enter)(might take a while): conda install -c rdkit rdkit and pip install pubchempy
- check if pandas is installed and active according to this Tutorial
- open Anaconda Navigator, go to Home tab, check if Applications on is set to the new environment
- click gear icon on Spyder > install specific version > 5.0.5 and wait for installation to finish
- click launch button below Spyder