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Cannot locate 'rfd3.trainer.rfd3.AADesignTrainer' when running examples or inference

1

## Environment - OS: WSL 2 / Ubuntu - Python: 3.12 - Foundry / RFD3 version: latest commit from https://github.com/RosettaCommons/foundry.git - Dependencies: installed via provided requirements / conda environment ##...

wanzihanhan

This pull request introduces new imports to the `inference_sampler.py` file, preparing the module to support symmetry operations during inference. These changes set up the codebase for future enhancements related to...

Wenzhao-protein

Use for SCFV design?

1

Hello, Thanks for sharing this awesome work. I want to adapt RFD3 for antibody (fab) design in the same way RFAntibody works. Can I follow the same approach as shown...

varunmc92

RFD3

5

Dear Developers, Thank you for open-sourcing such a powerful tool! When I use RFD3 for protein–small-molecule design, I set the hydrogen-bond donors and acceptors, but it seems to have no...

ZhuLvs

Enzyme Design Example

1

I'm consistently seeing issues with strange bonds and disconnected atoms in my RFdiffusion3 outputs for motif scaffolding, particularly around join points and side chains. I'm trying to understand if this...

azam-huss

Instructions for generating MSA

1

Do you have instructions for how to generate the MSAs in some more details or can you refer to other documentation for how to generate it?

fredricj

`models/rfd3/configs/datasets/val/benchmarks` Not Found

3

Hello, When I tried installing using the repository source code, I found that the file mentioned above pointed to a non-public file path. I also noticed that the file was...

hongningzhang-x

I'm wondering if there are plans to implement an option to dump the PAE matrix for a prediction? I'm currently not seeing that as an option. Thanks!

rpavlovicz

Hi all Thank you for your wonderful work. I have been playing around with it for a while and it is super cool, but I wonder whether this model comes...

1326093445a

Using the following json input, I get an error that stems from how modelforge is trying to parse the (DTY) code for D-Tyrosine in my sequence. The error is not...

tsamdin