zrqiao / NeuralPLexer

NeuralPLexer: State-specific protein-ligand complex structure prediction with a multi-scale deep generative model
https://doi.org/10.1038/s42256-024-00792-z
BSD 3-Clause Clear License
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AttributeError: 'NoneType' object has no attribute 'origin' #36

Open cyangNYU opened 4 months ago

cyangNYU commented 4 months ago

I have run the following command:

neuralplexer-inference --task=batched_structure_sampling \
                                     --input-receptor /data/NeuralPLexer_pred/protein.pdb \
                                     --input-ligand /data/NeuralPLexer_pred/HJX_ideal.sdf \
                                     --out-path outdir \
                                     --model-checkpoint complex_structure_prediction.ckpt \
                                      --n-samples 16 --chunk-size 4 --num-steps=40 \
                                      --cuda --sampler=langevin_simulated_annealing

Got this error:

__init__.py 14 <module>
f'{library}_{suffix}', [osp.dirname(__file__)]).origin)

AttributeError:
'NoneType' object has no attribute 'origin'

----------------------------------------------------------------------------------------------------------------
neuralplexer-inference 33 <module>
sys.exit(load_entry_point('neuralplexer', 'console_scripts', 'neuralplexer-inference')())

neuralplexer-inference 25 importlib_load_entry_point
return next(matches).load()

__init__.py 171 load
module = import_module(match.group('module'))

__init__.py 126 import_module
return _bootstrap._gcd_import(name[level:], package, level)

<frozen importlib._bootstrap> 1050 _gcd_import

<frozen importlib._bootstrap> 1027 _find_and_load

<frozen importlib._bootstrap> 1006 _find_and_load_unlocked

<frozen importlib._bootstrap> 688 _load_unlocked

<frozen importlib._bootstrap_external> 883 exec_module

<frozen importlib._bootstrap> 241 _call_with_frames_removed

inference.py 30 <module>
from neuralplexer.model.wrappers import NeuralPlexer

wrappers.py 11 <module>
from neuralplexer.model.cpm import BindingFormer, ProtFormer

cpm.py 6 <module>
from neuralplexer.model.common import GELUMLP

common.py 4 <module>
from torch_scatter import scatter_max, scatter_min

__init__.py 17 <module>
raise AttributeError(e)

AttributeError:
'NoneType' object has no attribute 'origin'

Any suggestions here?

chixinglong commented 4 months ago

maybe you need to download the correct version of torch-scatter and others ,then install them using pip