labdao / diffdock Goto Github PK

Precomputing and saving to cache SO(3) distribution table
Precomputing and saving to cache torus distribution table
100%|██████████| 201/201 [01:37<00:00,  2.07it/s]
100%|██████████| 201/201 [01:55<00:00,  1.75it/s]
/root/utils/torus.py:39: RuntimeWarning: invalid value encountered in divide
  score_ = grad(x, sigma[:, None], N=100) / p_
Reading molecules and generating local structures with RDKit (unless --keep_local_structures is turned on).
1it [00:00, 2113.00it/s]
Traceback (most recent call last):
  File "/opt/conda/envs/DiffDock/lib/python3.9/runpy.py", line 197, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "/opt/conda/envs/DiffDock/lib/python3.9/runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "/root/inference.py", line 81, in <module>
    test_dataset = PDBBind(transform=None, root='', protein_path_list=protein_path_list, ligand_descriptions=ligand_descriptions,
  File "/root/datasets/pdbbind.py", line 102, in __init__
    self.inference_preprocessing()
  File "/root/datasets/pdbbind.py", line 227, in inference_preprocessing
    if not os.path.exists(self.esm_embeddings_path): raise Exception('ESM embeddings path does not exist: ',self.esm_embeddings_path)
Exception: ('ESM embeddings path does not exist: ', 'data/esm2_output')
Failed to read molecule  /test/test.sdf  We are skipping it. The reason is the exception:  File error: Bad input file /test/test.sdf
Reading language model embeddings.

Processing 1 of 1 batches (2 sequences)
Traceback (most recent call last):
  File "/opt/conda/envs/DiffDock/lib/python3.9/runpy.py", line 197, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "/opt/conda/envs/DiffDock/lib/python3.9/runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "/root/inference.py", line 16, in <module>
    from datasets.pdbbind import PDBBind
  File "/root/datasets/pdbbind.py", line 22, in <module>
    from utils.utils import read_strings_from_txt
  File "/root/utils/utils.py", line 12, in <module>
    from torch_geometric.nn.data_parallel import DataParallel
  File "/opt/conda/envs/DiffDock/lib/python3.9/site-packages/torch_geometric/nn/__init__.py", line 3, in <module>
    from .sequential import Sequential
  File "/opt/conda/envs/DiffDock/lib/python3.9/site-packages/torch_geometric/nn/sequential.py", line 8, in <module>
    from torch_geometric.nn.conv.utils.jit import class_from_module_repr
  File "/opt/conda/envs/DiffDock/lib/python3.9/site-packages/torch_geometric/nn/conv/__init__.py", line 25, in <module>
    from .spline_conv import SplineConv
  File "/opt/conda/envs/DiffDock/lib/python3.9/site-packages/torch_geometric/nn/conv/spline_conv.py", line 16, in <module>
    from torch_spline_conv import spline_basis, spline_weighting
  File "/opt/conda/envs/DiffDock/lib/python3.9/site-packages/torch_spline_conv/__init__.py", line 11, in <module>
    torch.ops.load_library(importlib.machinery.PathFinder().find_spec(
AttributeError: 'NoneType' object has no attribute 'origin'

[ 86%] Built target obconformer
Scanning dependencies of target bindings_python
make[2]: *** No rule to make target '/opt/conda/lib/libpython3.10.so', needed by 'lib/_openbabel.so'.  Stop.
make[2]: *** Waiting for unfinished jobs....
[ 86%] Building CXX object scripts/CMakeFiles/bindings_python.dir/python/openbabel/openbabel-python.cpp.o
/root/openbabel-3.1.1/scripts/python/openbabel/openbabel-python.cpp:177:11: fatal error: Python.h: No such file or directory
  177 | # include <Python.h>
      |           ^~~~~~~~~~
compilation terminated.
make[2]: *** [scripts/CMakeFiles/bindings_python.dir/build.make:70: scripts/CMakeFiles/bindings_python.dir/python/openbabel/openbabel-python.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:5563: scripts/CMakeFiles/bindings_python.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[ 86%] Building CXX object test/CMakeFiles/test_runner.dir/aliastest.cpp.o
...