Encountering an error while trying to run the encode_compound.py script for the PubChem23 dataset.

Question

Encountering an error while trying to run the encode_compound.py script for the PubChem23 dataset.

linhduongtuan opened this issue a year ago · comments

Dear Mr. Philipp Seidl,

I appreciate your keen work.
I am encountering an error while trying to run the encode_compound.py script for the PubChem23 dataset. I am not sure if the error is due to the downloaded dataset or if there is a bug in the script. Can you please help me look at the attached file?

Thank you for your time and assistance.
Best regards,
Linh

phseidl · Answer 1 · Tue Sep 05 2023 16:23:51 GMT+0800 (China Standard Time)

Hi Linh,
thanks for your interest in our work.
There seems to be an error parsing one of the assay zip files.
Two things: We will add a try-catch block for invalid zip files, and additionally we will upload a preprocessed version of pubchem23 to make it more comparable.

Best, Philipp

Linh T. Duong · Answer 2 · Tue Sep 05 2023 16:31:14 GMT+0800 (China Standard Time)

Hi Philipp, Thank you for your explanation. I will waiting for your new release. Best, Linh

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On 5 Sep 2023, at 15:24, phseidl ***@***.***> wrote: Hi Linh, thanks for your interest in our work. There seems to be an error parsing one of the assay zip files. Two things: We will add a try-catch block for invalid zip files, and additionally we will upload a preprocessed version of pubchem23 to make it more comparable. Best, Philipp — Reply to this email directly, view it on GitHub <#5 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AFKZ27BMJI7XPHEZC6HDPSLXY3OSDANCNFSM6AAAAAA4KDC2S4>. You are receiving this because you authored the thread.

phseidl · Answer 3 · Tue Sep 05 2023 16:34:18 GMT+0800 (China Standard Time)

Just pushed the changes, please inform us if that resolved the issue.
Best, Philipp