├── .gitattributes ├── 2FYD.pdb ├── GPDL_colab.ipynb ├── LICENSE ├── README.md ├── data ├── esm_pdb_denovo │ ├── 1QYS.pdb │ ├── 2KL8.pdb │ ├── 2KPO.pdb │ ├── 2LN3.pdb │ ├── 2LTA.pdb │ ├── 2LVB.pdb │ ├── 2N2T.pdb │ ├── 2N2U.pdb │ ├── 2N3Z.pdb │ ├── 2N76.pdb │ ├── 4KY3.pdb │ ├── 4KYZ.pdb │ ├── 5CW9.pdb │ ├── 5KPE.pdb │ ├── 5KPH.pdb │ ├── 5L33.pdb │ ├── 5TPJ.pdb │ ├── 5TRV.pdb │ ├── 6CZG.pdb │ ├── 6CZH.pdb │ ├── 6CZI.pdb │ ├── 6CZJ.pdb │ ├── 6D0T.pdb │ ├── 6DG6.pdb │ ├── 6DKM_A.pdb │ ├── 6DKM_B.pdb │ ├── 6DLM_A.pdb │ ├── 6DLM_B.pdb │ ├── 6E5C.pdb │ ├── 6LLQ.pdb │ ├── 6MRR.pdb │ ├── 6MRS.pdb │ ├── 6MSP.pdb │ ├── 6NUK.pdb │ ├── 6W3F.pdb │ ├── 6W3W.pdb │ ├── 6WI5.pdb │ ├── 6WVS.pdb │ └── 7MCD.pdb ├── esm_pdb_fasta │ ├── 1QYS.fasta │ ├── 2KL8.fasta │ ├── 2KPO.fasta │ ├── 2LN3.fasta │ ├── 2LTA.fasta │ ├── 2LVB.fasta │ ├── 2N2T.fasta │ ├── 2N2U.fasta │ ├── 2N3Z.fasta │ ├── 2N76.fasta │ ├── 4KY3.fasta │ ├── 4KYZ.fasta │ ├── 5CW9.fasta │ ├── 5KPE.fasta │ ├── 5KPH.fasta │ ├── 5L33.fasta │ ├── 5TPJ.fasta │ ├── 5TRV.fasta │ ├── 6CZG.fasta │ ├── 6CZH.fasta │ ├── 6CZI.fasta │ ├── 6CZJ.fasta │ ├── 6D0T.fasta │ ├── 6DG6.fasta │ ├── 6DKM_A.fasta │ ├── 6DKM_B.fasta │ ├── 6DLM_A.fasta │ ├── 6DLM_B.fasta │ ├── 6E5C.fasta │ ├── 6LLQ.fasta │ ├── 6MRR.fasta │ ├── 6MRS.fasta │ ├── 6MSP.fasta │ ├── 6NUK.fasta │ ├── 6W3F.fasta │ ├── 6W3W.fasta │ ├── 6WI5.fasta │ ├── 6WVS.fasta │ └── 7MCD.fasta ├── fasta │ ├── 1QYS.fasta │ ├── 2KL8.fasta │ ├── 2KPO.fasta │ ├── 2LN3.fasta │ ├── 2LTA.fasta │ ├── 2LVB.fasta │ ├── 2N2T.fasta │ ├── 2N2U.fasta │ ├── 2N3Z.fasta │ ├── 2N76.fasta │ ├── 4KY3.fasta │ ├── 4KYZ.fasta │ ├── 5CW9.fasta │ ├── 5KPE.fasta │ ├── 5KPH.fasta │ ├── 5L33.fasta │ ├── 5TPJ.fasta │ ├── 5TRV.fasta │ ├── 6CZG.fasta │ ├── 6CZH.fasta │ ├── 6CZI.fasta │ ├── 6CZJ.fasta │ ├── 6D0T.fasta │ ├── 6DG6.fasta │ ├── 6DKM.fasta │ ├── 6DLM.fasta │ ├── 6E5C.fasta │ ├── 6LLQ.fasta │ ├── 6MRR.fasta │ ├── 6MRS.fasta │ ├── 6MSP.fasta │ ├── 6NUK.fasta │ ├── 6W3F.fasta │ ├── 6W3W.fasta │ ├── 6WI5.fasta │ ├── 6WVS.fasta │ └── 7MCD.fasta └── pdb │ ├── 1QYS.pdb │ ├── 2KL8.pdb │ ├── 2KPO.pdb │ ├── 2LN3.pdb │ ├── 2LTA.pdb │ ├── 2LVB.pdb │ ├── 2N2T.pdb │ ├── 2N2U.pdb │ ├── 2N3Z.pdb │ ├── 2N76.pdb │ ├── 4KY3.pdb │ ├── 4KYZ.pdb │ ├── 5CW9.pdb │ ├── 5KPE.pdb │ ├── 5KPH.pdb │ ├── 5L33.pdb │ ├── 5TPJ.pdb │ ├── 5TRV.pdb │ ├── 6CZG.pdb │ ├── 6CZH.pdb │ ├── 6CZI.pdb │ ├── 6CZJ.pdb │ ├── 6D0T.pdb │ ├── 6DG6.pdb │ ├── 6DKM.pdb │ ├── 6DLM.pdb │ ├── 6E5C.pdb │ ├── 6LLQ.pdb │ ├── 6MRR.pdb │ ├── 6MRS.pdb │ ├── 6MSP.pdb │ ├── 6NUK.pdb │ ├── 6W3F.pdb │ ├── 6W3W.pdb │ ├── 6WI5.pdb │ ├── 6WVS.pdb │ └── 7MCD.pdb ├── example.sh ├── filtering_scripts ├── Add_ChainID.py ├── alphafold │ ├── alphafold.slurm │ ├── cpu_alphafold.slurm │ └── extract_pdbs.py ├── fast_relax.py ├── fasta_rename.py ├── filter │ ├── motif_rmsd.py │ ├── net_charge.py │ ├── polar_score.py │ ├── recovery.py │ ├── rg.py │ ├── rmsd.py │ ├── sap.py │ └── scRMSD.py └── sequences_extract │ ├── folder_seperate.py │ └── sequence_extract.py ├── gpdl_hallucination ├── __pycache__ │ ├── inference_v1.cpython-38.pyc │ ├── loss.cpython-38.pyc │ └── mutate.cpython-38.pyc ├── hallucination.py ├── inference_v1.py ├── inference_v2.py ├── loss.py └── mutate.py ├── gpdl_inpainting ├── benchmark.ipynb ├── benchmark_set │ ├── 1BCF.pdb │ ├── 1PRW.pdb │ ├── 1QJG.pdb │ ├── 1YCR.pdb │ ├── 2KL8.pdb │ ├── 3IXT.pdb │ ├── 4JHW.pdb │ ├── 4ZYP.pdb │ ├── 5IUS.pdb │ ├── 5TPN.pdb │ ├── 5TRV.pdb │ ├── 5WN9.pdb │ ├── 5YUI.pdb │ ├── 6E6R.pdb │ ├── 6EXZ.pdb │ ├── 6VW1.pdb │ ├── 7MRX.pdb │ └── 7r8f.pdb ├── checkpoints │ └── inpaint_weight_11.pt ├── customize_data.py ├── esm │ ├── __init__.py │ ├── axial_attention.py │ ├── constants.py │ ├── data.py │ ├── esmfold │ │ └── v1 │ │ │ ├── __init__.py │ │ │ ├── categorical_mixture.py │ │ │ ├── esmfold.py │ │ │ ├── misc.py │ │ │ ├── pretrained.py │ │ │ ├── tri_self_attn_block.py │ │ │ └── trunk.py │ ├── inverse_folding │ │ ├── __init__.py │ │ ├── features.py │ │ ├── gvp_encoder.py │ │ ├── gvp_modules.py │ │ ├── gvp_transformer.py │ │ ├── gvp_transformer_encoder.py │ │ ├── gvp_utils.py │ │ ├── multichain_util.py │ │ ├── transformer_decoder.py │ │ ├── transformer_layer.py │ │ └── util.py │ ├── model │ │ ├── esm1.py │ │ ├── esm2.py │ │ └── msa_transformer.py │ ├── modules.py │ ├── multihead_attention.py │ ├── pretrained.py │ ├── rotary_embedding.py │ └── version.py ├── esm_inference.py ├── modules.py ├── train_poc.py ├── train_poc.sh ├── utils.py └── utils_seq.py ├── gpdl_sample ├── sub_2KL8.sh ├── sub_7MRX_128.sh ├── sub_7MRX_60.sh └── sub_7MRX_85.sh ├── img └── img.png ├── sample_sequences.py └── scripts ├── diffusion_loss.py ├── fape_loss.py ├── ipa_module.py └── rigid_utils.py /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sirius777coder/GPDL/HEAD/.gitattributes -------------------------------------------------------------------------------- /2FYD.pdb: 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