Hi gurus, pls, I need your help. I am trying to run the get-vocab.py on my small d

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AssertionError,about wengong-jin/hgraph2graph

max-unfried commented on September 10, 2024

I'm having the exact same issue - any idea why this is?

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NiharikaVadlamudi commented on September 10, 2024

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

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max-unfried commented on September 10, 2024

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

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AdamIzdebski commented on September 10, 2024

+1

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marshallcase commented on September 10, 2024

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

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JonathanBroadbent commented on September 10, 2024

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?

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orubaba commented on September 10, 2024

Hi, check out this code and correct your get_vocal.py. let's see if it works. this is what i adjusted. [image: image.png]

…

On Wed, Sep 27, 2023 at 9:32 PM JonathanBroadbent ***@***.***> wrote: Hi, reopening this as I am currently experiencing the same problem. It says the issue occurs in tree_decomp line 82 — Reply to this email directly, view it on GitHub <#43 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AVBVXE34PIUE4MT7NVBFVRLX4R5OTANCNFSM53ZE4TNQ> . You are receiving this because you authored the thread.Message ID: ***@***.***>

-- Regards, Adeshina

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JonathanBroadbent commented on September 10, 2024

HI Adeshina, Thanks for the response, the image you attached only shows alt text. Can you resend it to me? Jonathan From: Adeshina John Orubuloye ***@***.***> Date: Wednesday, September 27, 2023 at 9:56 PM To: wengong-jin/hgraph2graph ***@***.***> Cc: Broadbent, Jonathan /CA ***@***.***>, Comment ***@***.***> Subject: Re: [wengong-jin/hgraph2graph] AssertionError (Issue #43) Hi, check out this code and correct your get_vocal.py. let's see if it works. this is what i adjusted. [image: image.png]

…

On Wed, Sep 27, 2023 at 9:32 PM JonathanBroadbent ***@***.***> wrote: Hi, reopening this as I am currently experiencing the same problem. It says the issue occurs in tree_decomp line 82 — Reply to this email directly, view it on GitHub <#43 (comment)<https://github.com/wengong-jin/hgraph2graph/issues/43#issuecomment-1737964626>>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AVBVXE34PIUE4MT7NVBFVRLX4R5OTANCNFSM53ZE4TNQ<https://github.com/notifications/unsubscribe-auth/AVBVXE34PIUE4MT7NVBFVRLX4R5OTANCNFSM53ZE4TNQ>> . You are receiving this because you authored the thread.Message ID: ***@***.***>

-- Regards, Adeshina — Reply to this email directly, view it on GitHub<#43 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BAGO4OZUGGJCB4MEE3VS6N3X4TKMXANCNFSM53ZE4TNQ>. You are receiving this because you commented.Message ID: ***@***.***>

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orubaba commented on September 10, 2024

Hi, sorry for that. hope this works this time. On Thu, Sep 28, 2023 at 7:12 PM JonathanBroadbent ***@***.***> wrote:

…

HI Adeshina, Thanks for the response, the image you attached only shows alt text. Can you resend it to me? Jonathan From: Adeshina John Orubuloye ***@***.***> Date: Wednesday, September 27, 2023 at 9:56 PM To: wengong-jin/hgraph2graph ***@***.***> Cc: Broadbent, Jonathan /CA ***@***.***>, Comment ***@***.***> Subject: Re: [wengong-jin/hgraph2graph] AssertionError (Issue #43) Hi, check out this code and correct your get_vocal.py. let's see if it works. this is what i adjusted. [image: image.png] On Wed, Sep 27, 2023 at 9:32 PM JonathanBroadbent ***@***.***> wrote: > Hi, reopening this as I am currently experiencing the same problem. > It says the issue occurs in tree_decomp line 82 > > — > Reply to this email directly, view it on GitHub > < #43 (comment) < #43 (comment)>>, > or unsubscribe > < https://github.com/notifications/unsubscribe-auth/AVBVXE34PIUE4MT7NVBFVRLX4R5OTANCNFSM53ZE4TNQ < https://github.com/notifications/unsubscribe-auth/AVBVXE34PIUE4MT7NVBFVRLX4R5OTANCNFSM53ZE4TNQ>> > . > You are receiving this because you authored the thread.Message ID: > ***@***.***> > -- Regards, Adeshina — Reply to this email directly, view it on GitHub< #43 (comment)>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/BAGO4OZUGGJCB4MEE3VS6N3X4TKMXANCNFSM53ZE4TNQ>. You are receiving this because you commented.Message ID: ***@***.***> — Reply to this email directly, view it on GitHub <#43 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AVBVXE7VJCH4TH4QNAHXB6DX4WVZXANCNFSM53ZE4TNQ> . You are receiving this because you authored the thread.Message ID: ***@***.***>

-- Regards, Adeshina

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JonathanBroadbent commented on September 10, 2024

Hi Adeshina, Sorry, I still do not see any image. Perhaps you could upload it by replying directly on github? Or email me directly? ***@***.***) Jonathan From: Adeshina John Orubuloye ***@***.***> Date: Friday, September 29, 2023 at 12:37 AM To: wengong-jin/hgraph2graph ***@***.***> Cc: Broadbent, Jonathan /CA ***@***.***>, Comment ***@***.***> Subject: Re: [wengong-jin/hgraph2graph] AssertionError (Issue #43) Hi, sorry for that. hope this works this time. On Thu, Sep 28, 2023 at 7:12 PM JonathanBroadbent ***@***.***> wrote:

…

HI Adeshina, Thanks for the response, the image you attached only shows alt text. Can you resend it to me? Jonathan From: Adeshina John Orubuloye ***@***.***> Date: Wednesday, September 27, 2023 at 9:56 PM To: wengong-jin/hgraph2graph ***@***.***> Cc: Broadbent, Jonathan /CA ***@***.***>, Comment ***@***.***> Subject: Re: [wengong-jin/hgraph2graph] AssertionError (Issue #43) Hi, check out this code and correct your get_vocal.py. let's see if it works. this is what i adjusted. [image: image.png] On Wed, Sep 27, 2023 at 9:32 PM JonathanBroadbent ***@***.***> wrote: > Hi, reopening this as I am currently experiencing the same problem. > It says the issue occurs in tree_decomp line 82 > > — > Reply to this email directly, view it on GitHub > < #43 (comment)<https://github.com/wengong-jin/hgraph2graph/issues/43#issuecomment-1737964626> < #43 (comment)<https://github.com/wengong-jin/hgraph2graph/issues/43#issuecomment-1737964626>>>, > or unsubscribe > < https://github.com/notifications/unsubscribe-auth/AVBVXE34PIUE4MT7NVBFVRLX4R5OTANCNFSM53ZE4TNQ<https://github.com/notifications/unsubscribe-auth/AVBVXE34PIUE4MT7NVBFVRLX4R5OTANCNFSM53ZE4TNQ> < https://github.com/notifications/unsubscribe-auth/AVBVXE34PIUE4MT7NVBFVRLX4R5OTANCNFSM53ZE4TNQ<https://github.com/notifications/unsubscribe-auth/AVBVXE34PIUE4MT7NVBFVRLX4R5OTANCNFSM53ZE4TNQ>>> > . > You are receiving this because you authored the thread.Message ID: > ***@***.***> > -- Regards, Adeshina — Reply to this email directly, view it on GitHub< #43 (comment)<https://github.com/wengong-jin/hgraph2graph/issues/43#issuecomment-1738330411>>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/BAGO4OZUGGJCB4MEE3VS6N3X4TKMXANCNFSM53ZE4TNQ<https://github.com/notifications/unsubscribe-auth/BAGO4OZUGGJCB4MEE3VS6N3X4TKMXANCNFSM53ZE4TNQ>>. You are receiving this because you commented.Message ID: ***@***.***> — Reply to this email directly, view it on GitHub <#43 (comment)<https://github.com/wengong-jin/hgraph2graph/issues/43#issuecomment-1739718579>>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AVBVXE7VJCH4TH4QNAHXB6DX4WVZXANCNFSM53ZE4TNQ<https://github.com/notifications/unsubscribe-auth/AVBVXE7VJCH4TH4QNAHXB6DX4WVZXANCNFSM53ZE4TNQ>> . You are receiving this because you authored the thread.Message ID: ***@***.***>

-- Regards, Adeshina — Reply to this email directly, view it on GitHub<#43 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BAGO4O462PX5P5JZVCVEDATX4ZGBTANCNFSM53ZE4TNQ>. You are receiving this because you commented.Message ID: ***@***.***>

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orubaba commented on September 10, 2024

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]

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orubaba commented on September 10, 2024

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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