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ml-jku / clamp

Code for the paper Enhancing Activity Prediction Models in Drug Discovery with the Ability to Understand Human Language
https://arxiv.org/abs/2303.03363
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Encountering an error while trying to run the encode_compound.py script for the PubChem23 dataset. #5

Closed linhduongtuan closed 1 year ago

linhduongtuan commented 1 year ago

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 Untitled

phseidl commented 1 year ago

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

linhduongtuan commented 1 year ago

Hi Philipp, Thank you for your explanation.

I will waiting for your new release.

Best, Linh

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 https://github.com/ml-jku/clamp/issues/5#issuecomment-1706164689, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFKZ27BMJI7XPHEZC6HDPSLXY3OSDANCNFSM6AAAAAA4KDC2S4. You are receiving this because you authored the thread.

phseidl commented 1 year ago

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