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AssertionError #43

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orubaba opened this issue Jul 17, 2022 · 12 comments
Open

AssertionError #43

orubaba opened this issue Jul 17, 2022 · 12 comments

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@orubaba
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orubaba commented Jul 17, 2022 •
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Hi gurus,
pls, I need your help. I am trying to run the get-vocab.py on my small dataset around 100. but keep getting this error as shown below:
Is there a way to go around this. the reference for the error is to the mol_graph.py line82:
"assert n - m <= 1 #must be connected"
image
@max-unfried
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I'm having the exact same issue - any idea why this is?

@NiharikaVadlamudi
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@wengong-jin Can you please suggest a solution for this ? Thanks

@max-unfried
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Anything that you could suggest - still hung up on it?

@AdamIzdebski
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+1

@marshallcase
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Can you post a picture of your molecule / encoded graph? In my experience you get n-m > 1 when there's atoms that aren't connected to the rest of the molecule. This could be because the cluster generation process in find_clusters() wasn't built for a particular combination of rings / bonds

@JonathanBroadbent
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JonathanBroadbent commented Sep 27, 2023 •
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Hi, reopening this as I am currently experiencing the same problem.
It says the issue occurs in tree_decomp line 82

Has anybody found a fix yet?

@orubaba
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orubaba commented Sep 28, 2023 via email

@JonathanBroadbent
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JonathanBroadbent commented Sep 28, 2023 via email

@orubaba
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orubaba commented Sep 29, 2023 via email

@JonathanBroadbent
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JonathanBroadbent commented Sep 29, 2023 via email

@orubaba
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orubaba commented Sep 30, 2023

import sys
import argparse
from hgraph import *
from rdkit import Chem
from multiprocessing.dummy import Pool

def process(data):
vocab = set()
for line in data:
s = line.strip("\r\n ")
hmol = MolGraph(s)
for node,attr in hmol.mol_tree.nodes(data=True):
smiles = attr['smiles']
vocab.add( attr['label'] )
for i,s in attr['inter_label']:
vocab.add( (smiles, s) )
return vocab

if name == "main":

parser = argparse.ArgumentParser()
parser.add_argument('--ncpu', type=int, default=1)
args = parser.parse_args()

data = [mol for line in sys.stdin for mol in line.split()[:2]]
data = list(set(data))

batch_size = len(data) // args.ncpu + 1
batches = [data[i : i + batch_size] for i in range(0, len(data), batch_size)]

with Pool(args.ncpu) as pool:
    vocab_list = pool.map(process, batches, chunksize=1)
    vocab = [(x,y) for vocab in vocab_list for x,y in vocab]

@orubaba
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orubaba commented Sep 30, 2023

Interestingly, I removed all contents from line 34 downwards (I don't know why that should solve the problem for me) and it ran well. sorry you couldn't get the img. I was responding within my mail. let's see if it works. btw, chatgpt was really helpful with the error clearings.

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6 participants
@AdamIzdebski @marshallcase @max-unfried @NiharikaVadlamudi @orubaba @JonathanBroadbent