The code in this repository demonstrates the Multi-Generation Evaluation approach documented in Holistic Evaluation of Biodegradation Pathway Prediction: Assessing Multi-Step Reactions and Intermediate Products.
The repository also contains two files, TRAIN_SOIL_PW.csv and TEST_SOIL_PW.csv. They each contain a list of pathway names included respectively in the TRAIN_SOIL and TEST_SOIL packages, which were used in the experiment.
The code is intended to be used with Python 3.5.3 or later versions. Other required libraries are listed in requirements.txt and can be installed using the package manager pip.
pip install -r requirements.txtSimply run this in the terminal
python main.pyafter parameters such as obsPathwayQuery and predPathwayQuery are configured at the bottom of the code script