First of all, thank you for your wonderful research for molecule generation.
I wanted to make vacab for my dataset (from L1000 dataset).
Before vocab generation, I converted my SMILES to canonical SMILES.
However, I got this error continuously when I run vocab.py.
I think there were some problems regarding tree decomposition.
Is there any solution for this error?
I will wait your comment.
Thanks.
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/home/sejeong/anaconda3/envs/PSJ/lib/python3.7/multiprocessing/pool.py", line 121, in worker
result = (True, func(*args, **kwds))
File "/home/sejeong/anaconda3/envs/PSJ/lib/python3.7/multiprocessing/pool.py", line 44, in mapstar
return list(map(*args))
File "get_vocab.py", line 11, in process
hmol = MolGraph(s)
File "/home/sejeong/generative_model/codes/hgraph2graph/hgraph/mol_graph.py", line 22, in __init__
self.mol_tree = self.tree_decomp()
File "/home/sejeong/generative_model/codes/hgraph2graph/hgraph/mol_graph.py", line 83, in tree_decomp
assert n - m <= 1 # must be connected
AssertionError
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "get_vocab.py", line 30, in <module>
vocab_list = pool.map(process, batches)
File "/home/sejeong/anaconda3/envs/PSJ/lib/python3.7/multiprocessing/pool.py", line 268, in map
return self._map_async(func, iterable, mapstar, chunksize).get()
File "/home/sejeong/anaconda3/envs/PSJ/lib/python3.7/multiprocessing/pool.py", line 657, in get
raise self._value
AssertionError
First of all, thank you for your wonderful research for molecule generation. I wanted to make vacab for my dataset (from L1000 dataset). Before vocab generation, I converted my SMILES to canonical SMILES. However, I got this error continuously when I run vocab.py. I think there were some problems regarding tree decomposition. Is there any solution for this error? I will wait your comment. Thanks.