AttributeError: 'int' object has no attribute 'shape'

[EsToHi]

Hi dear,

I used alphafold's pdb as input but I ended up with following error.
That's the line 68 in Data.py happened in seq_emb = np.tile(seq_emb,(atom_emb.shape[0],1))
Then I added print command to know exactly why the error happened : print("Shape of seq_emb:", seq_emb.shape)
print("Shape of atom_emb:", atom_emb.shape)

• This suggests that atom_emb is not being assigned the expected array-like object, but rather an integer value.

The error message :
2024-03-21 06:41:59.870582: I tensorflow/core/platform/cpu_feature_guard.cc:210] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: AVX2 FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
WARNING:root:Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
Global seed set to 4022849662
2024-03-21 06:42:01.931396: E external/org_tensorflow/tensorflow/compiler/xla/stream_executor/cuda/cuda_driver.cc:267] failed call to cuInit: CUDA_ERROR_NO_DEVICE: no CUDA-capable device is detected
WARNING:jax._src.lib.xla_bridge:No GPU/TPU found, falling back to CPU. (Set TF_CPP_MIN_LOG_LEVEL=0 and rerun for more info.)
/data/sharedData/ATOMRefine/amber/stereo_chemical_props.txt
/data/sharedData/Post-modeling/Refined2/Vdp236.pdb
[['/data/sharedData/Post-modeling/Refined2/Vdp236.pdb', '/data/sharedData/Post-modeling/Refined2/Vdp236.pdb']]
Start prediction ...Predict each model may take 4 or 5 mins...In total, 5 models will be generated....
Shape of seq_emb: (21,)
Shape of atom_emb: (6, 40)
Shape of seq_emb: (21,)
Shape of atom_emb: (4, 40)
Shape of seq_emb: (21,)
Shape of atom_emb: (6, 40)
Shape of seq_emb: (21,)
Shape of atom_emb: (9, 40)
Shape of seq_emb: (21,)
Shape of atom_emb: (6, 40)
Shape of seq_emb: (21,)
Shape of atom_emb: (4, 40)
Shape of seq_emb: (21,)
Shape of atom_emb: (10, 40)
Shape of seq_emb: (21,)
Traceback (most recent call last):
File "/data/sharedData/ATOMRefine/predict.py", line 196, in
for batch in test_loader:
File "/data/sharedData/colabfold/localcolabfold/colabfold-conda/lib/python3.10/site-packages/torch/utils/data/dataloader.py", line 631, in next
data = self._next_data()
File "/data/sharedData/colabfold/localcolabfold/colabfold-conda/lib/python3.10/site-packages/torch/utils/data/dataloader.py", line 1346, in _next_data
return self._process_data(data)
File "/data/sharedData/colabfold/localcolabfold/colabfold-conda/lib/python3.10/site-packages/torch/utils/data/dataloader.py", line 1372, in _process_data
data.reraise()
File "/data/sharedData/colabfold/localcolabfold/colabfold-conda/lib/python3.10/site-packages/torch/_utils.py", line 722, in reraise
raise exception
AttributeError: Caught AttributeError in DataLoader worker process 0.
Original Traceback (most recent call last):
File "/data/sharedData/colabfold/localcolabfold/colabfold-conda/lib/python3.10/site-packages/torch/utils/data/_utils/worker.py", line 308, in _worker_loop
data = fetcher.fetch(index)
File "/data/sharedData/colabfold/localcolabfold/colabfold-conda/lib/python3.10/site-packages/torch/utils/data/_utils/fetch.py", line 51, in fetch
data = [self.dataset[idx] for idx in possibly_batched_index]
File "/data/sharedData/colabfold/localcolabfold/colabfold-conda/lib/python3.10/site-packages/torch/utils/data/_utils/fetch.py", line 51, in
data = [self.dataset[idx] for idx in possibly_batched_index]
File "/data/sharedData/ATOMRefine/Data.py", line 69, in getitem
print("Shape of atom_emb:", atom_emb.shape)
AttributeError: 'int' object has no attribute 'shape'