The code has been tested successfully using Python 3.8; thus we suggest using this version or a later version of Python. A typical process for installing the package dependencies involves creating a new Python virtual environment.
To install the required packages, run the following:
pip install .
The following command downloads the required files, including MSA inputs, predicted structures from Alphafold and Rosetta and ground truth structures.
python download_data.py
Generate processed MSA input data from the current MSA data in txt file format, which consists of the following steps:
- txt to csv
python3 code/MSA_txt_csv.py
- aggergate csv files and match input/output pair
python3 code/MAS_input.py
Generate processed vectors:
python3 code/data_generation.py
train model:
python3 code/training.py
run evaluation on the trained models and reproduce figures:
python3 code/evaluations.py