Add demo data file #11

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1. jusjosgra commented on Jun 24, 2023

   

   jusjosgra

   on Jun 24, 2023

   Last edited by jusjosgra

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   I am able to initiate infilling with the following fasta file and command

   fasta

   >1JPT_1
   DIQMTQSPSSLSASVGDRVTITCRASRDIKSYLNWYQQKPGKAPKVLIYYATSLAEGVPSRFSGSGSGTDYTLTISSLQPEDFATYYCLQHGESPWTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
   >1JPT_2
   EVQLVESGGGLVQPGGSLRLSCAASGFNIKEYYMHWVRQAPGKGLEWVGLIDPEQGNTIYDPKFQDRATISADNSKNTAYLQMNSLRAEDTAVYYCARDTAAYFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT
   

   command
   iglm_infill data/antibodies/rcsb_pdb_1JPT.fasta 1JPT_2 98 106 --chain_token [HEAVY] --species_token [HUMAN] --num_seqs 100

   However this results in the following error (seemingly produced in an infinite loop)

   Input length of input_ids is 221, but `max_length` is set to 150. This can lead to unexpected behavior. You should consider increasing `max_new_tokens`.
   Input length of input_ids is 221, but `max_length` is set to 150. This can lead to unexpected behavior. You should consider increasing `max_new_tokens`.
   Input length of input_ids is 221, but `max_length` is set to 150. This can lead to unexpected behavior. You should consider increasing `max_new_tokens`.
   

   I have tried updating max_length to 300 but this had no effect.
2. jusjosgra commented on Jun 24, 2023

   

   jusjosgra

   on Jun 24, 2023

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   I was able to successfully run CDR infill by truncating the length of the input sequence however this is not really a solution, in particular since I am working with the example PDB you provide. Could you advise how I should use this with Ab sequences that are longer than 150 amino acids?