diff --git a/alphafold_casp13/README.md b/alphafold_casp13/README.md index 191626e..690a6d6 100644 --- a/alphafold_casp13/README.md +++ b/alphafold_casp13/README.md @@ -34,6 +34,10 @@ pip install wheel pip install -r alphafold_casp13/requirements.txt ``` +Alternatively, you can just use the `run_eval.sh` script provided which runs +these commands for you, see the section on running the system below for more +details. + ## Data While the code is licensed under the Apache License, the AlphaFold weights and @@ -54,12 +58,7 @@ Once you have obtained access, you can download the data from The dataset to reproduce AlphaFold's CASP13 results can be downloaded from [Google Cloud Storage](https://console.cloud.google.com/storage/browser/alphafold_casp13_data). - -Download it e.g. using `wget` (the file is about 43.5 GB): - -```shell -wget https://storage.googleapis.com/alphafold_casp13_data/casp13_data.zip -``` +The dataset is in a file called `casp13_data.zip` which has about **43.5 GB**. The zip file contains 1 directory for each CASP13 target and a `LICENSE.md` file. Each target directory contains the following files: @@ -86,12 +85,8 @@ targets to get the contact map. The model checkpoints can be downloaded from [Google Cloud Storage](https://console.cloud.google.com/storage/browser/alphafold_casp13_data). - -Download them e.g. using `wget` (the file is about 210 MB): - -```shell -wget https://storage.googleapis.com/alphafold_casp13_data/alphafold_casp13_weights.zip -``` +The model checkpoints are in a file called `alphafold_casp13_weights.zip` which +has about **210 MB**. The zip file contains: diff --git a/alphafold_casp13/run_eval.sh b/alphafold_casp13/run_eval.sh index 3d93db0..5de18e6 100755 --- a/alphafold_casp13/run_eval.sh +++ b/alphafold_casp13/run_eval.sh @@ -27,6 +27,7 @@ TARGET_PATH="alphafold_casp13/${TARGET}" # Path to the directory with the targe # Set up the virtual environment and install dependencies. python3 -m venv alphafold_venv source alphafold_venv/bin/activate +pip install wheel pip install -r alphafold_casp13/requirements.txt # Create the output directory.