├── CODE_OF_CONDUCT.md ├── Dockerfile ├── EvoDiff_modelcard.md ├── LICENSE ├── MANIFEST.in ├── README.md ├── SECURITY.md ├── SUPPORT.md ├── analysis ├── calc_aafreq_train_valid_test.py ├── calc_fid.py ├── calc_kl_ss.py ├── calc_nearestseq_hamming.py ├── downstream_bash_scripts │ ├── get_TMscore.sh │ ├── iterate_alphafold.sh │ ├── iterate_esmif.sh │ ├── iterate_mpnn.sh │ ├── prep_alphafold.sh │ ├── sample_sequences.py │ └── score_log_likelihoods.py ├── gen-analysis.py ├── msa_perp.py ├── percent_similarity_msa.py ├── rmsd_analysis.py ├── self_consistency_analysis.py └── sequence_perp.py ├── config ├── __init__.py ├── config38M.json ├── config640M.json ├── configMSA-600M.json └── configMSA.json ├── data ├── blosum62-special-MSA.mat ├── human_idr_alignments │ ├── human_idr_boundaries.tsv │ └── human_idr_boundaries_gap.tsv ├── openfold │ ├── openfold_depths.npz │ ├── openfold_gap_depths.npz │ └── openfold_lengths.npz ├── train_msas.csv ├── uniref50_aa_ref_test.csv └── valid_msas.csv ├── environment.yml ├── evodiff ├── __init__.py ├── collaters.py ├── conditional_generation.py ├── conditional_generation_msa.py ├── constants.py ├── data.py ├── generate.py ├── generate_msa.py ├── losses.py ├── metrics.py ├── model.py ├── plot.py ├── pretrained.py └── utils.py ├── examples ├── README.md ├── evodiff.ipynb ├── evodiff_Azure_AI_Foundry.ipynb ├── example_files │ └── bfd_uniclust_hits.a3m ├── scaffolding-msas │ ├── 1bcf.a3m │ ├── 1prw.a3m │ ├── 1qjg.a3m │ ├── 1ycr.a3m │ ├── 2kl8.a3m │ ├── 3ixt.a3m │ ├── 4jhw.a3m │ ├── 4zyp.a3m │ ├── 5ius.a3m │ ├── 5tpn.a3m │ ├── 5trv.a3m │ ├── 5wn9.a3m │ ├── 5yui.a3m │ ├── 6e6r.a3m │ ├── 6exz.a3m │ ├── 6vw1.a3m │ └── 7mrx.a3m └── scaffolding-pdbs │ ├── 1bcf.fasta │ ├── 1bcf.pdb │ ├── 1bcf_clean.pdb │ ├── 1bcf_reference.pdb │ ├── 1bcf_reres.pdb │ ├── 1prw.fasta │ ├── 1prw.pdb │ ├── 1prw_clean.pdb │ ├── 1prw_reres.pdb │ ├── 1qjg.fasta │ ├── 1qjg.pdb │ ├── 1qjg_clean.pdb │ ├── 1qjg_reference.pdb │ ├── 1qjg_reres.pdb │ ├── 1ycr.fasta │ ├── 1ycr.pdb │ ├── 1ycr_clean.pdb │ ├── 1ycr_reference.pdb │ ├── 1ycr_reres.pdb │ ├── 2kl8.fasta │ ├── 2kl8.pdb │ ├── 2kl8_clean.pdb │ ├── 2kl8_reres.pdb │ ├── 3ixt.fasta │ ├── 3ixt.pdb │ ├── 3ixt_clean.pdb │ ├── 3ixt_reference.pdb │ ├── 3ixt_reres.pdb │ ├── 4jhw.fasta │ ├── 4jhw.pdb │ ├── 4jhw_clean.pdb │ ├── 4jhw_reference.pdb │ ├── 4jhw_reres.pdb │ ├── 4zyp.fasta │ ├── 4zyp.pdb │ ├── 4zyp_clean.pdb │ ├── 4zyp_reres.pdb │ ├── 5ius.fasta │ ├── 5ius.pdb │ ├── 5ius_clean.pdb │ ├── 5ius_reference.pdb │ ├── 5ius_reres.pdb │ ├── 5tpn.fasta │ ├── 5tpn.pdb │ ├── 5tpn_clean.pdb │ ├── 5tpn_reference.pdb │ ├── 5tpn_reres.pdb │ ├── 5trv.fasta │ ├── 5trv.pdb │ ├── 5trv_clean.pdb │ ├── 5trv_reres.pdb │ ├── 5wn9.fasta │ ├── 5wn9.pdb │ ├── 5wn9_clean.pdb │ ├── 5wn9_reres.pdb │ ├── 5yui.fasta │ ├── 5yui.pdb │ ├── 5yui_clean.pdb │ ├── 5yui_reres.pdb │ ├── 6e6r.fasta │ ├── 6e6r.pdb │ ├── 6e6r_clean.pdb │ ├── 6e6r_reference.pdb │ ├── 6e6r_reres.pdb │ ├── 6exz.fasta │ ├── 6exz.pdb │ ├── 6exz_clean.pdb │ ├── 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