├── README.md ├── architecture ├── EGNN_Block.py ├── GVP_Block.py ├── Gate_Block.py ├── GraphTransformer_Block.py ├── MDN_Block.py ├── Net_architecture.py └── __pycache__ │ ├── EGNN_Block.cpython-38.pyc │ ├── EGNN_Block.cpython-39.pyc │ ├── GVP_Block.cpython-38.pyc │ ├── GVP_Block.cpython-39.pyc │ ├── Gate_Block.cpython-38.pyc │ ├── Gate_Block.cpython-39.pyc │ ├── GraphTransformer_Block.cpython-38.pyc │ ├── GraphTransformer_Block.cpython-39.pyc │ ├── MDN_Block.cpython-38.pyc │ ├── MDN_Block.cpython-39.pyc │ ├── Net_architecture.cpython-38.pyc │ └── Net_architecture.cpython-39.pyc ├── clean_example.sh ├── dataset ├── __pycache__ │ ├── dataloader_obj.cpython-38.pyc │ ├── dataloader_obj.cpython-39.pyc │ ├── graph_obj.cpython-310.pyc │ ├── graph_obj.cpython-38.pyc │ ├── graph_obj.cpython-39.pyc │ ├── ligand_feature.cpython-38.pyc │ ├── ligand_feature.cpython-39.pyc │ ├── loop_feature.cpython-310.pyc │ ├── loop_feature.cpython-39.pyc │ ├── protein_feature.cpython-310.pyc │ ├── protein_feature.cpython-38.pyc │ └── protein_feature.cpython-39.pyc ├── dataloader_obj.py ├── graph_obj.py ├── loop_feature.py └── protein_feature.py ├── example ├── CASP1314 │ ├── CASP1314.csv │ └── raw │ │ ├── T0950.pdb │ │ ├── T0953s1.pdb │ │ ├── T0954.pdb │ │ ├── T0955.pdb │ │ ├── T0957s1.pdb │ │ ├── T0958.pdb │ │ ├── T0960.pdb │ │ ├── T0963.pdb │ │ ├── T0966.pdb │ │ ├── T0968s2.pdb │ │ ├── T1003.pdb │ │ ├── T1008.pdb │ │ ├── T1011.pdb │ │ ├── T1016.pdb │ │ ├── T1025.pdb │ │ ├── T1026.pdb │ │ ├── T1027.pdb │ │ ├── T1029.pdb │ │ ├── T1030.pdb │ │ ├── T1031.pdb │ │ ├── T1032.pdb │ │ ├── T1033.pdb │ │ ├── T1035.pdb │ │ ├── T1037.pdb │ │ ├── T1038.pdb │ │ ├── T1039.pdb │ │ ├── T1040.pdb │ │ ├── T1042.pdb │ │ ├── T1043.pdb │ │ ├── T1044.pdb │ │ ├── T1049.pdb │ │ ├── T1054.pdb │ │ ├── T1056.pdb │ │ ├── T1067.pdb │ │ ├── T1073.pdb │ │ ├── T1079.pdb │ │ ├── T1080.pdb │ │ ├── T1082.pdb │ │ └── T1099.pdb ├── CASP15 │ ├── CASP15.csv │ └── raw │ │ ├── T1104-D1.pdb │ │ ├── T1106s1-D1.pdb │ │ ├── T1106s2-D1.pdb │ │ ├── T1109-D1.pdb │ │ ├── T1120-D2.pdb │ │ ├── T1121-D1.pdb │ │ ├── T1121-D2.pdb │ │ ├── T1123-D1.pdb │ │ ├── T1124-D1.pdb │ │ ├── T1129s2-D1.pdb │ │ ├── T1137s1-D1.pdb │ │ ├── T1137s1-D2.pdb │ │ ├── T1137s2-D1.pdb │ │ ├── T1137s2-D2.pdb │ │ ├── T1137s3-D1.pdb │ │ ├── T1137s3-D2.pdb │ │ ├── T1137s4-D1.pdb │ │ ├── T1137s4-D2.pdb │ │ ├── T1137s4-D3.pdb │ │ ├── T1137s5-D1.pdb │ │ ├── T1137s5-D2.pdb │ │ ├── T1137s6-D1.pdb │ │ ├── T1137s6-D2.pdb │ │ ├── T1137s7-D1.pdb │ │ ├── T1137s8-D1.pdb │ │ ├── T1137s9-D1.pdb │ │ ├── T1139-D1.pdb │ │ ├── T1145-D1.pdb │ │ ├── T1145-D2.pdb │ │ ├── T1150-D1.pdb │ │ ├── T1157s1-D1.pdb │ │ ├── T1157s1-D2.pdb │ │ ├── T1157s1-D3.pdb │ │ ├── T1157s2-D1.pdb │ │ ├── T1157s2-D2.pdb │ │ ├── T1170-D1.pdb │ │ ├── T1170-D2.pdb │ │ ├── T1180-D1.pdb │ │ ├── T1187-D1.pdb │ │ ├── T1188-D1.pdb │ │ └── T1194-D1.pdb ├── ab_benchmark │ ├── ab_benchmark.csv │ └── raw │ │ ├── 1mim.pdb │ │ ├── 1mlb.pdb │ │ ├── 1mqk.pdb │ │ ├── 1nlb.pdb │ │ ├── 1seq.pdb │ │ ├── 1sy6.pdb │ │ ├── 2adf.pdb │ │ ├── 2d7t.pdb │ │ ├── 2e27.pdb │ │ ├── 2fbj.pdb │ │ ├── 2r8s.pdb │ │ ├── 2v17.pdb │ │ ├── 2w60.pdb │ │ ├── 2xwt.pdb │ │ ├── 3e8u.pdb │ │ ├── 3eo0.pdb │ │ ├── 3eo9.pdb │ │ ├── 3gkw.pdb │ │ ├── 3gnm.pdb │ │ ├── 3go1.pdb │ │ ├── 3hc4.pdb │ │ ├── 3i9g.pdb │ │ ├── 3m8o.pdb │ │ ├── 3mlr.pdb │ │ ├── 3mxw.pdb │ │ ├── 3nfs.pdb │ │ ├── 3nps.pdb │ │ ├── 3p0y.pdb │ │ ├── 3pp3.pdb │ │ ├── 3u0t.pdb │ │ ├── 4cni.pdb │ │ ├── 4g6k.pdb │ │ ├── 4h20.pdb │ │ ├── 4m6n.pdb │ │ ├── 4nyl.pdb │ │ ├── 4nzu.pdb │ │ ├── 4ojf.pdb │ │ ├── 4qxg.pdb │ │ ├── 4x7s.pdb │ │ ├── 4ypg.pdb │ │ ├── 5ggq.pdb │ │ ├── 5kmv.pdb │ │ ├── 5l6y.pdb │ │ ├── 5n2k.pdb │ │ ├── 5nhw.pdb │ │ ├── 5sx4.pdb │ │ ├── 5tru.pdb │ │ ├── 5vh3.pdb │ │ ├── 5xxy.pdb │ │ └── 5y9k.pdb └── single_example │ ├── raw │ ├── T1124-D1.pdb │ ├── T1129s2-D1.pdb │ └── T1145-D2.pdb │ └── single_example.csv ├── karmaloop_env.yml ├── model_pkls └── karmaloop.pkl ├── reproduction.sh ├── utils ├── __pycache__ │ ├── fns.cpython-310.pyc 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