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Sure! I think the easiest way to do this is with a slight modification of the Colab notebook that is linked in the README. There's a function in that notebook called _get_score under the "Import Libraries" header. If you replace that with this very slightly modified version:
then the full PAE matrix will be part of the output. The only modification here is in the second-to-last line. Then, after running the rest of the notebook, the SCORES variable will have pae_full as one of its features, which you can use however you want. Let me know if that helps!
Hi,
Nice work! Would it be possible to also return the PAE matrix for each decoy?
Thank you!
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