├── README.md ├── config.yaml ├── data ├── test_data │ ├── negative │ │ └── README.md │ └── positive │ │ └── README.md └── train_data │ ├── negative │ └── README.md │ └── positive │ └── README.md ├── datasets ├── independent test datasets │ ├── DBAASP │ │ ├── DBAASP_AMP.fasta │ │ └── DBAASP_nonAMP.fasta │ ├── XUAMP │ │ ├── XU_AMP.fasta │ │ └── XU_nonAMP.fasta │ └── other six │ │ ├── APD3_AMP.fasta │ │ ├── APD3_nonAMP.fasta │ │ ├── CAMP_AMP.fasta │ │ ├── CAMP_nonAMP.fasta │ │ ├── DRAMP_AMP.fasta │ │ ├── DRAMP_nonAMP.fasta │ │ ├── LAMP_AMP.fasta │ │ ├── LAMP_nonAMP.fasta │ │ ├── YADAMP_AMP.fasta │ │ ├── YADAMP_nonAMP.fasta │ │ ├── dbAMP_AMP.fasta │ │ ├── dbAMP_nonAMP.fasta │ │ └── non-redundant │ │ ├── AMPfun │ │ ├── APD3_test_neg.fasta │ │ ├── APD3_test_pos.fasta │ │ ├── CAMP_test_neg.fasta │ │ ├── CAMP_test_pos.fasta │ │ ├── DRAMP_test_neg.fasta │ │ ├── DRAMP_test_pos.fasta │ │ ├── LAMP_test_neg.fasta │ │ ├── LAMP_test_pos.fasta │ │ ├── YADAMP_test_neg.fasta │ │ ├── YADAMP_test_pos.fasta │ │ ├── dbAMP_test_neg.fasta │ │ └── dbAMP_test_pos.fasta │ │ ├── AmPEP │ │ ├── APD3_test_neg.fasta │ │ ├── APD3_test_pos.fasta │ │ ├── CAMP_test_neg.fasta │ │ ├── CAMP_test_pos.fasta │ │ ├── DRAMP_test_neg.fasta │ │ ├── DRAMP_test_pos.fasta │ │ ├── LAMP_test_neg.fasta │ │ ├── LAMP_test_pos.fasta │ │ ├── YADAMP_test_neg.fasta │ │ ├── YADAMP_test_pos.fasta │ │ ├── dbAMP_test_neg.fasta │ │ └── dbAMP_test_pos.fasta │ │ └── amPEPpy │ │ ├── APD3_test_neg.fasta │ │ ├── APD3_test_pos.fasta │ │ ├── CAMP_test_neg.fasta │ │ ├── CAMP_test_pos.fasta │ │ ├── DRAMP_test_neg.fasta │ │ ├── DRAMP_test_pos.fasta │ │ ├── LAMP_test_neg.fasta │ │ ├── LAMP_test_pos.fasta │ │ ├── YADAMP_test_neg.fasta │ │ ├── YADAMP_test_pos.fasta │ │ ├── dbAMP_test_neg.fasta │ │ └── dbAMP_test_pos.fasta └── train datasets │ ├── APD3 │ ├── APD3_pretain_train_negative.fasta │ ├── APD3_pretrain_train_positive.fasta │ ├── APD3_pretrain_val_negative.fasta │ ├── APD3_pretrain_val_positive.fasta │ ├── APD3_train_negative.fasta │ ├── APD3_train_positive.fasta │ ├── APD3_val_negative.fasta │ └── APD3_val_positive.fasta │ ├── CAMP │ ├── CAMP_pretain_train_positive.fasta │ ├── CAMP_pretrain_train_negative.fasta │ ├── CAMP_pretrain_val_negative.fasta │ ├── CAMP_pretrain_val_positive.fasta │ ├── CAMP_train_negative.fasta │ ├── CAMP_train_positive.fasta │ ├── CAMP_val_negative.fasta │ └── CAMP_val_positive.fasta │ ├── DBAASP │ ├── DBAASP_pretrain_train_negative.fasta │ ├── DBAASP_pretrain_train_positive.fasta │ ├── DBAASP_pretrain_val_negative.fasta │ ├── DBAASP_pretrain_val_val_positive.fasta │ ├── DBAASP_train_negative.fasta │ ├── DBAASP_train_positive.fasta │ ├── DBAASP_val_negative.fasta │ └── DBAASP_val_positive.fasta │ ├── DRAMP │ ├── DRAMP_pretrain_train_negative.fasta │ ├── DRAMP_pretrain_train_positive.fasta │ ├── DRAMP_pretrain_val_negative.fasta │ ├── DRAMP_pretrain_val_positive.fasta │ ├── DRAMP_train_negative.fasta │ ├── DRAMP_train_positive.fasta │ ├── DRAMP_val_negative.fasta │ └── DRAMP_val_positive.fasta │ ├── LAMP │ ├── LAMP_pretrain_train_negative.fasta │ ├── LAMP_pretrain_train_positive.fasta │ ├── LAMP_pretrain_val_negative.fasta │ ├── LAMP_pretrain_val_positive.fasta │ ├── LAMP_train_negative.fasta │ ├── LAMP_train_positive.fasta │ ├── LAMP_val_negative.fasta │ └── LAMP_val_positive.fasta │ ├── XUAMP │ ├── XU_pretrain_train_negative.fasta │ ├── XU_pretrain_train_positive.fasta │ ├── XU_pretrain_val_negative.fasta │ ├── XU_pretrain_val_positive.fasta │ ├── XU_train_negative.fasta │ ├── XU_train_positive.fasta │ ├── XU_val_negative.fasta │ └── XU_val_positive.fasta │ ├── YADAMP │ ├── YADAMP_pretrain_train_negative.fasta │ ├── YADAMP_pretrain_val_negative.fasta │ ├── YADAMP_pretrain_val_positive.fasta │ ├── YADAMP_pretraintrain_positive.fasta │ ├── YADAMP_train_negative.fasta │ ├── YADAMP_train_positive.fasta │ ├── YADAMP_val_negative.fasta │ └── YADAMP_val_positive.fasta │ └── dbAMP │ ├── dbAMP_pretrain_train_negative.fasta │ ├── dbAMP_pretrain_train_positive.fasta │ ├── dbAMP_pretrain_val_negative.fasta │ ├── dbAMP_pretrain_val_positive.fasta │ ├── dbAMP_train_negative.fasta │ ├── dbAMP_train_positive.fasta │ ├── dbAMP_val_negative.fasta │ └── dbAMP_val_positive.fasta ├── example ├── negative │ ├── a3m │ │ ├── seq3.a3m │ │ ├── seq4.a3m │ │ ├── seq5.a3m │ │ └── tmp.hhr │ ├── example_neg.fasta │ ├── hhm │ │ └── output │ │ │ ├── seq3.hhm │ │ │ ├── seq4.hhm │ │ │ └── seq5.hhm │ ├── npz │ │ ├── seq3.npz │ │ ├── seq4.npz │ │ └── seq5.npz │ └── pssm │ │ └── output │ │ ├── seq3.pssm │ │ ├── seq4.pssm │ │ └── seq5.pssm └── positive │ ├── a3m │ ├── seq0.a3m │ ├── seq1.a3m │ ├── seq2.a3m │ └── tmp.hhr │ ├── example_pos.fasta │ ├── hhm │ └── output │ │ ├── seq0.hhm │ │ ├── seq1.hhm │ │ └── seq2.hhm │ ├── npz │ ├── seq0.npz │ ├── seq1.npz │ └── seq2.npz │ └── pssm │ └── output │ ├── seq0.pssm │ ├── seq1.pssm │ └── seq2.pssm ├── generate_features.py ├── generate_features_example.sh ├── models ├── GAT.py └── __init__.py 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