esm_embedding.sh is missing

[kenken28]

I am trying to retrain SurfDock by following section 6 of the README file, but the esm_embedding.sh script for preparing the ESM embedding is missing. I tried running the train_SurfDock.sh script without preparing the ESM embeddings, but I ran into the following error:

Traceback (most recent call last):
File "/t9k/mnt/.pycharm_helpers/pydev/pydevd.py", line 1570, in _exec
pydev_imports.execfile(file, globals, locals) # execute the script
File "/t9k/mnt/.pycharm_helpers/pydev/_pydev_imps/_pydev_execfile.py", line 18, in execfile
exec(compile(contents+"\n", file, 'exec'), glob, loc)
File "/t9k/mnt/projects/SurfDock/train_accelarete.py", line 234, in
main_function()
File "/t9k/mnt/projects/SurfDock/train_accelarete.py", line 186, in main_function
train_loader, val_loader = construct_loader(args, t_to_sigma)
File "/t9k/mnt/projects/SurfDock/datasets/pdbbind.py", line 590, in construct_loader
train_dataset = PDBBind(cache_path=args.cache_path, split_path=args.split_train, keep_original=True,
File "/t9k/mnt/projects/SurfDock/datasets/pdbbind.py", line 179, in init
self.preprocessing()
File "/t9k/mnt/projects/SurfDock/datasets/pdbbind.py", line 261, in preprocessing
id_to_embeddings = torch.load(self.esm_embeddings_path)
File "/t9k/mnt/.conda/envs/SurfDock/lib/python3.10/site-packages/torch/serialization.py", line 998, in load
with _open_file_like(f, 'rb') as opened_file:
File "/t9k/mnt/.conda/envs/SurfDock/lib/python3.10/site-packages/torch/serialization.py", line 445, in _open_file_like
return _open_file(name_or_buffer, mode)
File "/t9k/mnt/.conda/envs/SurfDock/lib/python3.10/site-packages/torch/serialization.py", line 426, in init
super().init(open(name, mode))
FileNotFoundError: [Errno 2] No such file or directory: './PDBBIND/esm_embedding/esm_embedding_pocket_for_train/esm2_3billion_embeddings.pt'