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HelloJocelynLu / t5chem

Transformer-based model for chemical reactions
MIT License
62 stars 15 forks source link

ModuleNotFoundError: No module named 'rdkit' #7

Closed yxnyu closed 2 years ago

yxnyu commented 2 years ago

The Colab environment seems that rdkit and transformer do not well perform

HelloJocelynLu commented 2 years ago

Based on the error message, it seems that rdkit is not successfully installed... rdkit is a pain for google colab. I will work on this. Meanwhile, would you mind trying condacolab? I find an examples on installing rdkit here and here

yxnyu commented 2 years ago

Dear Jocelyn

Yes. Sorry for responsing so later. I am trying to rebuild the rdkit in my environment and I realize my supervisor permit the NYU-HPC account and I am learning about the HPC knowledge while I just know how to use the server in the group .

Condacolab is a new to me but I would like to use it. I will reach out to you once the trying is done.

Best, Yuzhi

On Wed, Jul 20, 2022 at 7:54 AM Jocelyn @.***> wrote:

Based on the error message, it seems that rdkit is not successfully installed... rdkit is a pain for google colab. I will work on this. Meanwhile, would you mind trying condacolab? I find an examples on installing rdkit here https://urldefense.com/v3/__https://iwatobipen.wordpress.com/2018/11/01/run-rdkit-and-deep-learning-on-google-colab-rdkit/__;!!BhJSzQqDqA!TubnQrcqa6jWmvuGEWqHgJihd4j5345B7pcw8n6xfW9ALHccfjbtQVbqLmTCiA6JpnJXIii4_SHdqFtJVwwzmNT5MAI$ and here https://urldefense.com/v3/__https://colab.research.google.com/gist/iwatobipen/2ec7faeafe5974501e69fcc98c122922/pymol.ipynb*scrollTo=xIYbBtkjgEfU__;Iw!!BhJSzQqDqA!TubnQrcqa6jWmvuGEWqHgJihd4j5345B7pcw8n6xfW9ALHccfjbtQVbqLmTCiA6JpnJXIii4_SHdqFtJVwwzDM5BgRk$

— Reply to this email directly, view it on GitHub https://urldefense.com/v3/__https://github.com/HelloJocelynLu/t5chem/issues/7*issuecomment-1189658505__;Iw!!BhJSzQqDqA!TubnQrcqa6jWmvuGEWqHgJihd4j5345B7pcw8n6xfW9ALHccfjbtQVbqLmTCiA6JpnJXIii4_SHdqFtJVwwzoHslwSg$, or unsubscribe https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AZ26DYMXO26PF3VIAK33N23VU452ZANCNFSM532VH3PA__;!!BhJSzQqDqA!TubnQrcqa6jWmvuGEWqHgJihd4j5345B7pcw8n6xfW9ALHccfjbtQVbqLmTCiA6JpnJXIii4_SHdqFtJVwwzd7eeRoM$ . You are receiving this because you authored the thread.Message ID: @.***>

HelloJocelynLu commented 2 years ago

Hi, I've updated the google colabs and successfully ran it on Google cloud. Free feel to try it!

yxnyu commented 2 years ago

Dear Jocelyn

Awesome, thanks! I will try it, and I am in NYC taking the course and are you still in the NYC?

Best, Yuzhi

On Tue, Aug 30, 2022 at 4:14 PM Jocelyn @.***> wrote:

Hi, I've updated the google colabs and successfully ran it on Google cloud. Free feel to try it!

— Reply to this email directly, view it on GitHub https://urldefense.com/v3/__https://github.com/HelloJocelynLu/t5chem/issues/7*issuecomment-1232119375__;Iw!!BhJSzQqDqA!XW8xf3HlYIhoDGB5rV0Od5GUa14FOM3k6p6YF8AOPFYpwoMoFooLsL77TWKr2AWNekDiVHkh6sXMHaD_bcFQ2z6ECrU$, or unsubscribe https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AZ26DYLSN3CLSKYIT6MZ4HLV3ZTQNANCNFSM532VH3PA__;!!BhJSzQqDqA!XW8xf3HlYIhoDGB5rV0Od5GUa14FOM3k6p6YF8AOPFYpwoMoFooLsL77TWKr2AWNekDiVHkh6sXMHaD_bcFQfXYyr6o$ . You are receiving this because you authored the thread.Message ID: @.***>

HelloJocelynLu commented 2 years ago

Hi Yuzhi,

I replied your message via email.

Best, Jocelyn