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melihyilmaz avatar melihyilmaz commented on July 23, 2024

Hi Guhan,

I ran inference with pretrained_excl_human.ckpt weights (in addition to few other species) and obtained the QLEQVLAK de novo prediction from the model. Can you check if you're using preprocess_spec=True when running the model on your raw data (it's False by default)?

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guhanrv avatar guhanrv commented on July 23, 2024

Thanks so much for that @melihyilmaz! That worked. :)

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guhanrv avatar guhanrv commented on July 23, 2024

Just a suggestion - you might want to put this in the readme, as it's not clear that this should be done :)

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melihyilmaz avatar melihyilmaz commented on July 23, 2024

I will change the default preprocess_spec=True in the config file. We are planning to create more thorough documentation for Casanovo in the near future. Thank you for your interest!

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