Cannot Find exs.sabdab and exs.scalop Modules

[clear1111]

Hi, great work! I have questions about the code!
I am currently trying to run the script generate_data.py and generate_data_summary.py located in the directory src/abodybuilder3/stages/data/. However, I am encountering an issue where the module exs.sabdab, exs.scalop and some other modules cannot be found. Could you kindly provide some guidance on how to resolve this issue?

[henrykenlay]

Thanks @clear1111! Unfortunately, this code would need some refactoring to work. Data from Sabdab with IMGT numbering can be downloaded from https://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/sabdab. Similarly, a version of SCALOP can be found here https://github.com/oxpig/SCALOP (alternatively, it can be removed from the code as it's not too important).

[clear1111]

Thank you for your previous reply and the provided links. I was wondering if there is any relevant code regarding "exs.sabdab"? If so, would it be possible for you to share it with me?
Thanks a lot in advance!

[fdreyer]

Unfortunately we will not be able to share the internal sabdab code that we use at Exscientia, so the data processing steps would have to be adapted manually if you want to prepare a new dataset. The training data used to train the model in our paper is available on zenodo at https://zenodo.org/records/11354577