PAE output data

[hlasimpk]

I've been running openfold3 with pae_enabled set to true in config yaml, but looking at the output and also having had a glance through writer.py, this seems to only outputs the PAE confidence scores in the confidences_aggregated.json file.

Meanwhile in the confidences.json file I am getting the PDE scores, but these don't work with some downstream tools I'm using that require PAE (e.g. ipSAE).

Is there an option to output the PAE data that I'm missing? Or would it be possible to add an option to output it?

[jnwei]

Hi @hlasimpk thank you for the suggestion and interest in OpenFold3!

Could you elaborate a bit more about the form of the PAE score you are looking for? We follow the AlphaFold3 SI Section 4.3.2, so our PAE has the form of

Is the form you are looking for the same as the PDE output, which is a tokenwise pair matrix?

[hlasimpk]

Hi @jnwei,

Yes, it's the tokenwise pair matrix that I'm after. Is there a way to get this already built in to OpenFold3?

[jnwei]

Not yet, but now it will be added to the full confidence outputs in #142