RosettaCommons
AF2 Model Parameters Download for af2_metrics.py
Hi RFDesign team,
I've been trying to run the af2_metrics.py program and after solving issue #26, I found that the model 4 parameters for AF2 weren't downloaded:
File "/home/ec2-user/RFDesign/scripts/../hallucination/models/alphafold/alphafold/model/data.py", line 36, in get_model_haiku_params with open(path, 'rb') as f: FileNotFoundError: [Errno 2] No such file or directory: '/software/mlfold/alphafold-data/params/params_model_4.npz'
I looked into how to download them by looking at the alphafold repo that is cloned into hallucination/models/alphafold. The readme explains that there is a script in hallucination/models/alphafold/scripts called download_alphafold_params.sh to do this. af2_metrics.py tries to get the model parameters from /software/mlfold/alphafold-data/params/ This doesn't exist on my machine but I thought about creating this folder using mkdir and then running download_alphafold_params.sh to this directory. Alternatively, I also tried creating a folder called hallucination/models/alphafold/alphafold-data/params/ and installing to here. Then I changed the code in the af2_metrics.py command so that it could find the model parameters. Running download_alphafold_params.sh also required aria2 to be installed (sudo apt install aria2 or yum install aria2 or conda install aria2) (however, I am currently stuck here on my machine because there are some inconsistencies between aria2 and the version of openssl/libssl that my machine is running :( )
Would you have any other suggestions for how to install the model 4 parameters? Perhaps you would be able to design a way as part of the workflow of af2_metrics.py to install the af2 model 4 parameters to a place that af2_metrics can easily call from whatever machine is running the af2_metrics?
With Kind Regards, Adam
Sorry we didn't explain this more clearly in the README. We provided alphafold code but not weights, so you need to install those yourself. I think the best option is to go to the alphafold repo and follow their instructions for downloading the weights, and then edit our code (line 243 of af2_metrics.py) to point to where you've installed them.
On Mon, Sep 19, 2022 at 4:52 AM Germanki @.***> wrote:
Hi RFDesign team,
I've been trying to run the af2_metrics.py program and after solving issue #26 https://github.com/RosettaCommons/RFDesign/issues/26, I found that the model 4 parameters for AF2 weren't downloaded: File "/home/ec2-user/RFDesign/scripts/../hallucination/models/alphafold/alphafold/model/data.py", line 36, in get_model_haiku_params with open(path, 'rb') as f: FileNotFoundError: [Errno 2] No such file or directory: '/software/mlfold/alphafold-data/params/params_model_4.npz'
I looked into how to download them by looking at the alphafold repo that is cloned into hallucination/models/alphafold. The readme explains that there is a script in hallucination/models/alphafold/scripts called download_alphafold_params.sh to do this. af2_metrics.py tries to get the model parameters from /software/mlfold/alphafold-data/params/ This doesn't exist on my machine but I thought about creating this folder using mkdir and then running download_alphafold_params.sh to this directory. Alternatively, I also tried creating a folder called hallucination/models/alphafold/alphafold-data/params/ and installing to here. Then I changed the code in the af2_metrics.py command so that it could find the model parameters. Running download_alphafold_params.sh also required aria2 to be installed (sudo apt install aria2 or yum install aria2 or conda install aria2) (however, I am currently stuck here on my machine because there are some inconsistencies between aria2 and the version of openssl/libssl that my machine is running :( )
Would you have any other suggestions for how to install the model 4 parameters? Perhaps you would be able to design a way as part of the workflow of af2_metrics.py to install the af2 model 4 parameters to a place that af2_metrics can easily call from whatever machine is running the af2_metrics?
With Kind Regards, Adam
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