Comments (6)
I'm still getting the same issue too - getting the modules as close to the version Wengong was using as in issue #20 as follows:
rdkit 2019.03.4.0 py37hc20afe1_1
python 3.7.6 h0371630_2
pytorch 1.12.0 py3.7_cuda11.6_cudnn8.3.2_0
numpy 1.21.5 py37h6c91a56_3
still gives me the following issue:
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/home/marcase/.conda/envs/hgraph-rdkit/lib/python3.7/multiprocessing/pool.py", line 121, in worker
result = (True, func(*args, **kwds))
File "/home/marcase/.conda/envs/hgraph-rdkit/lib/python3.7/multiprocessing/pool.py", line 44, in mapstar
return list(map(*args))
File "preprocess.py", line 19, in tensorize
x = MolGraph.tensorize(mol_batch, vocab, common_atom_vocab)
File "/home/marcase/hgraph2graph/hgraph/mol_graph.py", line 153, in tensorize
tree_tensors, tree_batchG = MolGraph.tensorize_graph([x.mol_tree for x in mol_batch], vocab)
File "/home/marcase/hgraph2graph/hgraph/mol_graph.py", line 194, in tensorize_graph
fnode[v] = vocab[attr]
File "/home/marcase/hgraph2graph/hgraph/vocab.py", line 43, in __getitem__
return self.hmap[x[0]], self.vmap[x]
KeyError: 'C1=CNN=C1'
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "preprocess.py", line 106, in <module>
all_data = pool.map(func, batches)
File "/home/marcase/.conda/envs/hgraph-rdkit/lib/python3.7/multiprocessing/pool.py", line 268, in map
return self._map_async(func, iterable, mapstar, chunksize).get()
File "/home/marcase/.conda/envs/hgraph-rdkit/lib/python3.7/multiprocessing/pool.py", line 657, in get
raise self._value
KeyError: 'C1=CNN=C1'
from hgraph2graph.
I also had this issue (see #20). It might help to try rerunning with the vocab and preprocessing using rdkit=2019.03.4.0
from hgraph2graph.
Hey, where you able to solve the issue? I'm having similar issue now. kindly share your solution if any!
from hgraph2graph.
I solved this problem by regenerating the vocab.txt (use get_vocab.py), because this bug seems to occur when the drug can't tensorize by the vocab list.
from hgraph2graph.
I solved this problem by regenerating the vocab.txt (use get_vocab.py), because this bug seems to occur when the drug can't tensorize by the vocab list.
Can you elaborate more on how you solved it?
from hgraph2graph.
I solved this problem by regenerating the vocab.txt (use get_vocab.py), because this bug seems to occur when the drug can't tensorize by the vocab list.
Can you elaborate more on how you solved it?
I mean, if we want to preprocess a list of SMILES, it's necessary to first run the get_vocab.py file to create a customized vocab.txt. Then, we can replace the given vocab.txt in the preprocess.py file with the one we have created. The author might have included differences in his version of vocab.txt, so we could regenerate the vocab.txt file to solve the issue.
from hgraph2graph.
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from hgraph2graph.