evodiff
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microsoft
Generation of protein sequences and evolutionary alignments via discrete diffusion models
I was trying to run the IDR inpainting task and faced some issues: ### Issue 1: On running the example given on the GitHub: `python evodiff/conditional_generation_msa.py --model-type msa_oa_ar_maxsub --cond-task idr...
I used conditional sequence generation via evodiff.ipynb with my own MSA file. However it came with a amino acid sequence containing un-natural amino acid codes such as "Z" and "B"...
I've been having trouble with getting the conda environment to work properly, so this may be exacerbating the issue below. ``` (evodiff3) ubuntu@209-20-159-77:~/evodiff_repo$ python evodiff/generate.py --model-type oa_dm_38M --num-seqs 100 Traceback...
I played with evo-diff on msa conditional generation. Structures of query and generated are not as similar as I expected. Actually many times they are quite different. Below is a...
Hello, I am experiencing a key error attempting to use the code 1 for 1 from the example notebook for conditional generation: https://github.com/microsoft/evodiff/blob/main/examples/evodiff.ipynb from evodiff.pretrained import MSA_OA_DM_MAXSUB from evodiff.generate_msa import...
Hi, I'm trying to run the example command for 1PRW in the README. ```bash python evodiff/conditional_generation_msa.py --model-type msa_oa_ar_maxsub --cond-task scaffold --pdb 1prw --start-idxs 15 --end-idxs 34 --start-idxs 51 --end-idxs 70...
Hi, I try to run script `python evodiff/generate-msa.py --model-type msa_oa_dm_maxsub --batch-size 1 --n-sequences 64 --n-sequences 256 --subsampling MaxHamming --start-query` But it seems couldn't find this file human_idr_alignments/human_protein_alignments. Also, could put...
