Aravinda Munasinghe

Results 8 comments of Aravinda Munasinghe

Information on split_folder command

Ah! Thanks a lot! I was running it outside the jupyter notebook and was thinking it as an executable! Should have noticed the cell!!!!!! Anyway, appreciate the prompt response! :)

Issue with alphafold-complex predication with initial guess of binder position

Did you find a solution for this? I am having the same issue and I wonder if you found a solution.

Error while running af2_interface_metrics.py

ah! I didnt see this. Did you find a solution for this? :)

Error while running af2_interface_metrics.py

Thanks for the update! Yes, I just saw the RFDiffusion code. We will try designs from both tools! absolutely amazing work from the team and thanks a lot for getting...

Type Error with af2_interface_metrics.py

okay, after reading a little bit of the model.py prediction_result = jax.vmap(model_runner.apply, in_axes=(None,None,0,0))(model_runner.params, jax.random.PRNGKey(0), processed_feature_dict, processed_initial_guess_dict) module.AlphaFold is compiled by jax's jit, and the batch should be a dictionary with...

Type Error with af2_interface_metrics.py

I didn't see that #48 #38 were basically the same issue as this.

Add Ligand Bond Order Information to PDB output

I tried this fix for the following ligand as it keeps giving me incorrect bond order at the inference. O=C(N1)CCCC1=O And it always dumps a planer IMiD. However, when I...

Add Ligand Bond Order Information to PDB output

ah! my bad. I thought the fix reads the bond order from the input and overwrites the inferred bond order. I see, this is to retain information when writing the...