Hi, I'm sorry to bother you, but while running the program, I found that the Kiba data set worked fine, but using the Davis data set, I found the following error, and there was no ADCK in the original prot. PDB files, and Davis has 442 PDB files, should be a complete data set, please ask this how to deal with it？
Epoch 0: 75%|▊| 11344/15101 [31:02<10:16, 6.09it/s, loss=0.801, v_num=59, lossTraceback (most recent call last):
File "/home/lq/Ligand_Generation-main/train_binding_affinity.py", line 109, in
trainer.fit(model, train_loader, val_loader)
File "/root/anaconda3/envs/cold/lib/python3.7/site-packages/pytorch_lightning/trainer/trainer.py", line 609, in fit
self, self._fit_impl, model, train_dataloaders, val_dataloaders, datamodule, ckpt_path
File "/root/anaconda3/envs/cold/lib/python3.7/site-packages/pytorch_lightning/trainer/call.py", line 38, in _call_and_handle_interrupt
return trainer_fn(*args, kwargs)
File "/root/anaconda3/envs/cold/lib/python3.7/site-packages/pytorch_lightning/trainer/trainer.py", line 650, in _fit_impl
self._run(model, ckpt_path=self.ckpt_path)
File "/root/anaconda3/envs/cold/lib/python3.7/site-packages/pytorch_lightning/trainer/trainer.py", line 1112, in _run
results = self._run_stage()
File "/root/anaconda3/envs/cold/lib/python3.7/site-packages/pytorch_lightning/trainer/trainer.py", line 1191, in _run_stage
self._run_train()
File "/root/anaconda3/envs/cold/lib/python3.7/site-packages/pytorch_lightning/trainer/trainer.py", line 1214, in _run_train
self.fit_loop.run()
File "/root/anaconda3/envs/cold/lib/python3.7/site-packages/pytorch_lightning/loops/loop.py", line 199, in run
self.advance(*args, *kwargs)
File "/root/anaconda3/envs/cold/lib/python3.7/site-packages/pytorch_lightning/loops/fit_loop.py", line 267, in advance
self._outputs = self.epoch_loop.run(self._data_fetcher)
File "/root/anaconda3/envs/cold/lib/python3.7/site-packages/pytorch_lightning/loops/loop.py", line 199, in run
self.advance(args, kwargs)
File "/root/anaconda3/envs/cold/lib/python3.7/site-packages/pytorch_lightning/loops/epoch/training_epoch_loop.py", line 187, in advance
batch = next(data_fetcher)
File "/root/anaconda3/envs/cold/lib/python3.7/site-packages/pytorch_lightning/utilities/fetching.py", line 184, in next
return self.fetching_function()
File "/root/anaconda3/envs/cold/lib/python3.7/site-packages/pytorch_lightning/utilities/fetching.py", line 265, in fetching_function
self._fetch_next_batch(self.dataloader_iter)
File "/root/anaconda3/envs/cold/lib/python3.7/site-packages/pytorch_lightning/utilities/fetching.py", line 280, in _fetch_next_batch
batch = next(iterator)
File "/root/anaconda3/envs/cold/lib/python3.7/site-packages/pytorch_lightning/trainer/supporters.py", line 571, in next
return self.request_next_batch(self.loader_iters)
File "/root/anaconda3/envs/cold/lib/python3.7/site-packages/pytorch_lightning/trainer/supporters.py", line 583, in request_next_batch
return apply_to_collection(loader_iters, Iterator, next)
File "/root/anaconda3/envs/cold/lib/python3.7/site-packages/lightning_utilities/core/apply_func.py", line 51, in apply_to_collection
return function(data, *args, **kwargs)
File "/root/anaconda3/envs/cold/lib/python3.7/site-packages/torch/utils/data/dataloader.py", line 628, in next
data = self._next_data()
File "/root/anaconda3/envs/cold/lib/python3.7/site-packages/torch/utils/data/dataloader.py", line 671, in _next_data
data = self._dataset_fetcher.fetch(index) # may raise StopIteration
File "/root/anaconda3/envs/cold/lib/python3.7/site-packages/torch/utils/data/_utils/fetch.py", line 58, in fetch
data = [self.dataset[idx] for idx in possibly_batched_index]
File "/root/anaconda3/envs/cold/lib/python3.7/site-packages/torch/utils/data/_utils/fetch.py", line 58, in
data = [self.dataset[idx] for idx in possibly_batched_index]
File "/home/lq/Ligand_Generation-main/binding_data.py", line 33, in getitem
protein_graph = torch.load(protein_file, map_location="cpu")
File "/root/anaconda3/envs/cold/lib/python3.7/site-packages/torch/serialization.py", line 771, in load
with _open_file_like(f, 'rb') as opened_file:
File "/root/anaconda3/envs/cold/lib/python3.7/site-packages/torch/serialization.py", line 270, in _open_file_like
return _open_file(name_or_buffer, mode)
File "/root/anaconda3/envs/cold/lib/python3.7/site-packages/torch/serialization.py", line 251, in init
super(_open_file, self).init(open(name, mode))
FileNotFoundError: [Errno 2] No such file or directory: 'data/davis/prot_3d_for_Davis/res_graph/ADCK.pdb.pt'
Hi, I'm sorry to bother you, but while running the program, I found that the Kiba data set worked fine, but using the Davis data set, I found the following error, and there was no ADCK in the original prot. PDB files, and Davis has 442 PDB files, should be a complete data set, please ask this how to deal with it？ Epoch 0: 75%|▊| 11344/15101 [31:02<10:16, 6.09it/s, loss=0.801, v_num=59, lossTraceback (most recent call last): File "/home/lq/Ligand_Generation-main/train_binding_affinity.py", line 109, in
trainer.fit(model, train_loader, val_loader)
File "/root/anaconda3/envs/cold/lib/python3.7/site-packages/pytorch_lightning/trainer/trainer.py", line 609, in fit
self, self._fit_impl, model, train_dataloaders, val_dataloaders, datamodule, ckpt_path
File "/root/anaconda3/envs/cold/lib/python3.7/site-packages/pytorch_lightning/trainer/call.py", line 38, in _call_and_handle_interrupt
return trainer_fn(*args, kwargs)
File "/root/anaconda3/envs/cold/lib/python3.7/site-packages/pytorch_lightning/trainer/trainer.py", line 650, in _fit_impl
self._run(model, ckpt_path=self.ckpt_path)
File "/root/anaconda3/envs/cold/lib/python3.7/site-packages/pytorch_lightning/trainer/trainer.py", line 1112, in _run
results = self._run_stage()
File "/root/anaconda3/envs/cold/lib/python3.7/site-packages/pytorch_lightning/trainer/trainer.py", line 1191, in _run_stage
self._run_train()
File "/root/anaconda3/envs/cold/lib/python3.7/site-packages/pytorch_lightning/trainer/trainer.py", line 1214, in _run_train
self.fit_loop.run()
File "/root/anaconda3/envs/cold/lib/python3.7/site-packages/pytorch_lightning/loops/loop.py", line 199, in run
self.advance(*args, *kwargs)
File "/root/anaconda3/envs/cold/lib/python3.7/site-packages/pytorch_lightning/loops/fit_loop.py", line 267, in advance
self._outputs = self.epoch_loop.run(self._data_fetcher)
File "/root/anaconda3/envs/cold/lib/python3.7/site-packages/pytorch_lightning/loops/loop.py", line 199, in run
self.advance(args, kwargs)
File "/root/anaconda3/envs/cold/lib/python3.7/site-packages/pytorch_lightning/loops/epoch/training_epoch_loop.py", line 187, in advance
batch = next(data_fetcher)
File "/root/anaconda3/envs/cold/lib/python3.7/site-packages/pytorch_lightning/utilities/fetching.py", line 184, in next
return self.fetching_function()
File "/root/anaconda3/envs/cold/lib/python3.7/site-packages/pytorch_lightning/utilities/fetching.py", line 265, in fetching_function
self._fetch_next_batch(self.dataloader_iter)
File "/root/anaconda3/envs/cold/lib/python3.7/site-packages/pytorch_lightning/utilities/fetching.py", line 280, in _fetch_next_batch
batch = next(iterator)
File "/root/anaconda3/envs/cold/lib/python3.7/site-packages/pytorch_lightning/trainer/supporters.py", line 571, in next
return self.request_next_batch(self.loader_iters)
File "/root/anaconda3/envs/cold/lib/python3.7/site-packages/pytorch_lightning/trainer/supporters.py", line 583, in request_next_batch
return apply_to_collection(loader_iters, Iterator, next)
File "/root/anaconda3/envs/cold/lib/python3.7/site-packages/lightning_utilities/core/apply_func.py", line 51, in apply_to_collection
return function(data, *args, **kwargs)
File "/root/anaconda3/envs/cold/lib/python3.7/site-packages/torch/utils/data/dataloader.py", line 628, in next
data = self._next_data()
File "/root/anaconda3/envs/cold/lib/python3.7/site-packages/torch/utils/data/dataloader.py", line 671, in _next_data
data = self._dataset_fetcher.fetch(index) # may raise StopIteration
File "/root/anaconda3/envs/cold/lib/python3.7/site-packages/torch/utils/data/_utils/fetch.py", line 58, in fetch
data = [self.dataset[idx] for idx in possibly_batched_index]
File "/root/anaconda3/envs/cold/lib/python3.7/site-packages/torch/utils/data/_utils/fetch.py", line 58, in
data = [self.dataset[idx] for idx in possibly_batched_index]
File "/home/lq/Ligand_Generation-main/binding_data.py", line 33, in getitem
protein_graph = torch.load(protein_file, map_location="cpu")
File "/root/anaconda3/envs/cold/lib/python3.7/site-packages/torch/serialization.py", line 771, in load
with _open_file_like(f, 'rb') as opened_file:
File "/root/anaconda3/envs/cold/lib/python3.7/site-packages/torch/serialization.py", line 270, in _open_file_like
return _open_file(name_or_buffer, mode)
File "/root/anaconda3/envs/cold/lib/python3.7/site-packages/torch/serialization.py", line 251, in init
super(_open_file, self).init(open(name, mode))
FileNotFoundError: [Errno 2] No such file or directory: 'data/davis/prot_3d_for_Davis/res_graph/ADCK.pdb.pt'