Error When Executing the code from instructions

[Harshitasahni]

Sampling geometries

Traceback (most recent call last):
File "inference.py", line 275, in
run_cv(params)
File "inference.py", line 178, in run_cv
gen_xyzs = sample_ic_backmap(testloader, device, model, atomic_nums, n_cgs, info_dict=info_dict)
File "/users/hsahni/data_genz/GenZProt/scripts/sampling.py", line 505, in sample_ic_backmap
for batch in loader:
File "/users/hsahni/.conda/envs/genzprot_new/lib/python3.8/site-packages/torch/utils/data/dataloader.py", line 681, in next
data = self._next_data()
File "/users/hsahni/.conda/envs/genzprot_new/lib/python3.8/site-packages/torch/utils/data/dataloader.py", line 721, in _next_data
data = self._dataset_fetcher.fetch(index) # may raise StopIteration
File "/users/hsahni/.conda/envs/genzprot_new/lib/python3.8/site-packages/torch/utils/data/_utils/fetch.py", line 52, in fetch
return self.collate_fn(data)
File "/users/hsahni/data_genz/GenZProt/scripts/../GenZProt/data.py", line 224, in CG_collate_inf
cumulative_atoms = np.cumsum([0] + [d['num_atoms'] for d in dicts])[:-1]
File "<array_function internals>", line 200, in cumsum
File "/users/hsahni/.conda/envs/genzprot_new/lib/python3.8/site-packages/numpy/core/fromnumeric.py", line 2597, in cumsum
return _wrapfunc(a, 'cumsum', axis=axis, dtype=dtype, out=out)
File "/users/hsahni/.conda/envs/genzprot_new/lib/python3.8/site-packages/numpy/core/fromnumeric.py", line 54, in _wrapfunc
return _wrapit(obj, method, *args, **kwds)
File "/users/hsahni/.conda/envs/genzprot_new/lib/python3.8/site-packages/numpy/core/fromnumeric.py", line 43, in _wrapit
result = getattr(asarray(obj), method)(*args, **kwds)

ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 1 dimensions. The detected shape was (5,) + inhomogeneous part.

[SoojungYang]

Hi Harshitasahni, thank you for your interest in using our code. Could you provide us with your input files (both all atom topology file (${top_path}) and coarse-grained pdb file ($ca_trace_path)) so that we can look into the issue?

[lfkrapp]

Following the example from "Backmapping C_alpha traces into all-atom structures" doesn't work.

input:
python inference.py -load_model_path ../ckpt/model_seed_12345 -ca_trace_path ../data/PED00055_CA_trace.pdb -topology_path ../data/PED00055.pdb

output:
Sampling Task
traj has 1 chains
generate mask: 100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 85/85 [00:00<00:00, 5233.80it/s]
building CG nbr list: 100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 55/55 [00:00<00:00, 2496.37it/s]
finished creating dataset
model loaded successfully
Sampling geometries
0%| | 0/1 [00:00<?, ?it/s]
Traceback (most recent call last):
File "/home/khaos/syncfolder/phd/projects/mdapi/opt/GenZProt/scripts/inference.py", line 349, in
run_cv(params)
File "/home/khaos/syncfolder/phd/projects/mdapi/opt/GenZProt/scripts/inference.py", line 242, in run_cv
gen_xyzs = sample_ic_backmap(
^^^^^^^^^^^^^^^^^^
File "/home/khaos/syncfolder/phd/projects/mdapi/opt/GenZProt/scripts/sampling.py", line 625, in sample_ic_backmap
for batch in loader:
File "/home/khaos/syncfolder/phd/projects/mdapi/opt/GenZProt/.venv/lib/python3.12/site-packages/tqdm/std.py", line 1181, in iter
for obj in iterable:
File "/home/khaos/syncfolder/phd/projects/mdapi/opt/GenZProt/.venv/lib/python3.12/site-packages/torch/utils/data/dataloader.py", line 631, in next
data = self._next_data()
^^^^^^^^^^^^^^^^^
File "/home/khaos/syncfolder/phd/projects/mdapi/opt/GenZProt/.venv/lib/python3.12/site-packages/torch/utils/data/dataloader.py", line 675, in _next_data
data = self._dataset_fetcher.fetch(index) # may raise StopIteration
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/khaos/syncfolder/phd/projects/mdapi/opt/GenZProt/.venv/lib/python3.12/site-packages/torch/utils/data/_utils/fetch.py", line 54, in fetch
return self.collate_fn(data)
^^^^^^^^^^^^^^^^^^^^^
File "/home/khaos/syncfolder/phd/projects/mdapi/opt/GenZProt/.venv/lib/python3.12/site-packages/GenZProt-0.1-py3.12.egg/GenZProt/data.py", line 224, in CG_collate_inf
File "/home/khaos/syncfolder/phd/projects/mdapi/opt/GenZProt/.venv/lib/python3.12/site-packages/numpy/core/fromnumeric.py", line 2586, in cumsum
return _wrapfunc(a, 'cumsum', axis=axis, dtype=dtype, out=out)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/khaos/syncfolder/phd/projects/mdapi/opt/GenZProt/.venv/lib/python3.12/site-packages/numpy/core/fromnumeric.py", line 56, in _wrapfunc
return _wrapit(obj, method, *args, **kwds)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/khaos/syncfolder/phd/projects/mdapi/opt/GenZProt/.venv/lib/python3.12/site-packages/numpy/core/fromnumeric.py", line 45, in _wrapit
result = getattr(asarray(obj), method)(*args, **kwds)
^^^^^^^^^^^^
ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 1 dimensions. The detected shape was (56,) + inhomogeneous part.