├── .gitignore ├── LICENSE ├── README.md ├── bionoi ├── README.md ├── alignment.py ├── bionoi.py ├── cmaps │ ├── atom_cmap.csv │ └── res_hydro_cmap.csv ├── colorscale.py ├── dependency │ └── environment.yml ├── example_output │ ├── 5iunE00_atom_type_XOY+_r0_OO.png │ ├── 5iunE00_binding_prob_XOY+_r0_OO.png │ ├── 5iunE00_blended_XOY+_r0_OO.png │ ├── 5iunE00_center_dist_XOY+_r0_OO.png │ ├── 5iunE00_charge_XOY+_r0_OO.png │ ├── 5iunE00_hydrophobicity_XOY+_r0_OO.png │ ├── 5iunE00_residue_type_XOY+_r0_OO.png │ ├── 5iunE00_sasa_XOY+_r0_OO.png │ ├── 5iunE00_seq_entropy_XOY+_r0_OO.png │ └── flowchart.png ├── img_gen.sh ├── legacy │ ├── img_gen.py │ ├── info_gen.py │ ├── overlay.py │ ├── overlay_folder.py │ ├── pocket_visual.py │ ├── split_folder.py │ └── split_folder_cv.py ├── log │ ├── bionoi_atom_type.o742767 │ ├── bionoi_atom_type.o743228 │ ├── bionoi_binding_prob.o742774 │ ├── bionoi_binding_prob.o743232 │ ├── bionoi_blended.o742775 │ ├── bionoi_blended.o743314 │ ├── bionoi_blended.o743782 │ ├── bionoi_center_dist.o742770 │ ├── bionoi_center_dist.o743234 │ ├── bionoi_charge.o742769 │ ├── bionoi_charge.o743231 │ ├── bionoi_hydrophobicity.o742772 │ ├── bionoi_hydrophobicity.o743230 │ ├── bionoi_residue_type.o742768 │ ├── bionoi_residue_type.o743229 │ ├── bionoi_sasa.o742771 │ ├── bionoi_sasa.o743235 │ ├── bionoi_seq_entropy.o742773 │ └── bionoi_seq_entropy.o743236 ├── output │ ├── 1dflA00-1_XOY+_r0_OO.png │ ├── 1fdhB00-1_XOY+_r0_OO.png │ ├── 1u0jA00-1_XOY+_r0_OO.png │ ├── 2ra5A00-1_XOY+_r0_OO.png │ ├── 2uw1A00-1_XOY+_r0_OO.png │ ├── 3j9lG00-1_XOY+_r0_OO.png │ ├── 4qreA01-1_XOY+_r0_OO.png │ └── 5iunE00_XOY+_r0_OO.png └── testfiles │ ├── .DS_Store │ ├── mol2 │ ├── .DS_Store │ ├── 1dflA00-1.mol2 │ ├── 1fdhB00-1.mol2 │ ├── 1u0jA00-1.mol2 │ ├── 2ra5A00-1.mol2 │ ├── 2uw1A00-1.mol2 │ ├── 3i5rA00.mol2 │ ├── 3j9lG00-1.mol2 │ ├── 4qreA01-1.mol2 │ ├── 5iunE00.mol2 │ ├── E361110.mol2 │ ├── E374447.mol2 │ └── E406084.mol2 │ ├── popsa │ ├── .DS_Store │ ├── 1dflA.out │ ├── 1fdhB.out │ ├── 1u0jA.out │ ├── 2ra5A.out │ ├── 2uw1A.out │ ├── 3i5rA.out │ ├── 3j9lG.out │ ├── 4qreA.out │ ├── 5iunE.out │ ├── E361110.out │ ├── E374447.out │ └── E406084.out │ └── profile │ ├── .DS_Store │ ├── 1dflA.profile │ ├── 1fdhB.profile │ ├── 1u0jA.profile │ ├── 2ra5A.profile │ ├── 2uw1A.profile │ ├── 3i5rA.profile │ ├── 3j9lG.profile │ ├── 4qreA.profile │ ├── 5iunE.profile │ ├── E361110.profile │ ├── E374447-pruned.profile │ ├── E374447.profile │ └── E406084.profile ├── bionoi_autoencoder ├── README.md ├── autoencoder_general.py ├── dataset_statistics.py ├── feature_gen.py ├── feature_gen_bionoi.py ├── feature_gen_foldloop.py ├── helper.py ├── hpc_documentation.md ├── reconstruct.py ├── reconstructed_imgs │ ├── reconstructed_0.png │ ├── reconstructed_1.png │ ├── reconstructed_2.png │ ├── reconstructed_3.png │ ├── reconstructed_4.png │ ├── reconstructed_5.png │ ├── reconstructed_6.png │ ├── reconstructed_7.png │ ├── reconstructed_8.png │ ├── reconstructed_9.png │ └── rmse.png ├── trained_model │ ├── conv1x1-4M-batch512.pt │ └── loss.png ├── utils.py └── verify_loss.py ├── bionoi_cnn_homology_reduced ├── homology_reduced_cnn_cv_resnet18.py ├── log │ ├── control_vs_heme_res18_10th_run.log │ ├── control_vs_heme_res18_11th_run.log │ ├── control_vs_heme_res18_12th_run.log │ ├── control_vs_heme_res18_1th_run.log │ ├── control_vs_heme_res18_2th_run.log │ ├── control_vs_heme_res18_3th_run.log │ ├── control_vs_heme_res18_4th_run.log │ ├── control_vs_heme_res18_5th_run.log │ ├── control_vs_heme_res18_6th_run.log │ ├── control_vs_heme_res18_7th_run.log │ ├── control_vs_heme_res18_8th_run.log │ ├── control_vs_heme_res18_9th_run.log │ ├── control_vs_heme_res18_atom_type.log │ ├── control_vs_heme_res18_binding_prob.log │ ├── control_vs_heme_res18_blended.log │ ├── control_vs_heme_res18_center_dist.log │ ├── control_vs_heme_res18_charge.log │ ├── control_vs_heme_res18_hydrophobicity.log │ ├── control_vs_heme_res18_residue_type.log │ ├── control_vs_heme_res18_sasa.log │ ├── control_vs_heme_res18_seq_entropy.log │ ├── control_vs_nucleotide_res18_10th_run.log │ ├── control_vs_nucleotide_res18_11th_run.log │ ├── control_vs_nucleotide_res18_12th_run.log │ ├── control_vs_nucleotide_res18_13th_run.log │ ├── control_vs_nucleotide_res18_14th_run.log │ ├── control_vs_nucleotide_res18_15th_run.log │ ├── control_vs_nucleotide_res18_16th_run.log │ ├── control_vs_nucleotide_res18_1th.log │ ├── control_vs_nucleotide_res18_2th_run.log │ ├── control_vs_nucleotide_res18_3th_run.log │ ├── control_vs_nucleotide_res18_4th_run.log │ ├── control_vs_nucleotide_res18_5th_run.log │ ├── control_vs_nucleotide_res18_6th_run.log │ ├── control_vs_nucleotide_res18_7th_run.log │ ├── control_vs_nucleotide_res18_8th_run.log │ ├── control_vs_nucleotide_res18_9th_run.log │ ├── control_vs_nucleotide_res18_atom_type.log │ ├── control_vs_nucleotide_res18_binding_prob.log │ ├── control_vs_nucleotide_res18_blended.log │ ├── control_vs_nucleotide_res18_center_dist.log │ ├── control_vs_nucleotide_res18_charge.log │ ├── control_vs_nucleotide_res18_hydrophobicity.log │ ├── control_vs_nucleotide_res18_residue_type.log │ ├── control_vs_nucleotide_res18_sasa.log │ ├── control_vs_nucleotide_res18_seq_entropy.log │ ├── control_vs_nucleotide_res50.log │ └── heme_vs_nucleotide_res18_1th_run.log ├── resnet18.sh └── results │ ├── control_vs_heme_cv_10thrun.json │ ├── control_vs_heme_cv_11thrun.json │ ├── control_vs_heme_cv_12thrun.json │ ├── control_vs_heme_cv_1thrun.json │ ├── control_vs_heme_cv_2thrun.json │ ├── control_vs_heme_cv_3thrun.json │ ├── control_vs_heme_cv_4thrun.json │ ├── control_vs_heme_cv_5thrun.json │ ├── control_vs_heme_cv_6thrun.json │ ├── control_vs_heme_cv_7thrun.json │ ├── control_vs_heme_cv_8thrun.json │ ├── control_vs_heme_cv_9thrun.json │ ├── control_vs_heme_cv_atom_type.json │ ├── control_vs_heme_cv_binding_prob.json │ ├── control_vs_heme_cv_blended.json │ ├── control_vs_heme_cv_center_dist.json │ ├── control_vs_heme_cv_charge.json │ ├── control_vs_heme_cv_hydrophobicity.json │ ├── control_vs_heme_cv_residue_type.json │ ├── control_vs_heme_cv_sasa.json │ ├── control_vs_heme_cv_seq_entropy.json │ ├── control_vs_nucleotide_cv_10thrun.json │ ├── control_vs_nucleotide_cv_11thrun.json │ ├── control_vs_nucleotide_cv_12thrun.json │ ├── control_vs_nucleotide_cv_13thrun.json │ ├── control_vs_nucleotide_cv_14thrun.json │ ├── control_vs_nucleotide_cv_15thrun.json │ ├── control_vs_nucleotide_cv_16thrun.json │ ├── control_vs_nucleotide_cv_5thrun.json │ ├── control_vs_nucleotide_cv_6thrun.json │ ├── control_vs_nucleotide_cv_7thrun.json │ ├── control_vs_nucleotide_cv_8thrun.json │ ├── control_vs_nucleotide_cv_9thrun.json │ ├── control_vs_nucleotide_cv_atom_type.json │ ├── control_vs_nucleotide_cv_binding_prob.json │ ├── control_vs_nucleotide_cv_blended.json │ ├── control_vs_nucleotide_cv_center_dist.json │ ├── control_vs_nucleotide_cv_charge.json │ ├── control_vs_nucleotide_cv_hydrophobicity.json │ ├── control_vs_nucleotide_cv_residue_type.json │ ├── control_vs_nucleotide_cv_sasa.json │ ├── control_vs_nucleotide_cv_seq_entropy.json │ └── heme_vs_nucleotide_cv_1thrun.json ├── dependency └── environment.yml ├── figures └── BionoiNet.PNG ├── homology_reduced_folds ├── atp-0.2-folds ├── control-folds ├── folds_gen.py ├── folds_gen_autoencoder_vec.py ├── heme-0.2-folds └── mols.zip └── legacy ├── bionoi_ml_homology_reduced ├── mlp_autoencoder_vec.py ├── mlp_autoencoder_vec.sh ├── mlp_autoencoder_vec_log │ ├── control_vs_heme_mlp_autoencoder_1th_run.log │ └── control_vs_nucleotide_mlp_autoencoder_1th_run.log ├── mlp_autoencoder_vec_result │ ├── control_vs_heme_cv_1th_run.json │ └── control_vs_nucleotide_cv_1th_run.json ├── mlp_img.py ├── mlp_img.sh ├── mlp_img_log │ ├── control_vs_heme_mlp_1th_run.log │ └── control_vs_nucleotide_mlp_img_1th_run.log ├── mlp_img_result │ ├── control_vs_heme_cv_1th_run.json │ └── control_vs_nucleotide_cv_1th_run.json ├── rf_autoencoder_vec.py ├── rf_autoencoder_vec.sh ├── rf_autoencoder_vec_log │ ├── control_vs_heme_rf_autoencoder_1th_run.log │ ├── control_vs_heme_rf_autoencoder_2th_run.log │ ├── control_vs_heme_rf_autoencoder_3th_run.log │ ├── control_vs_heme_rf_autoencoder_4th_run.log │ ├── control_vs_heme_rf_autoencoder_5th_run.log │ ├── control_vs_heme_rf_autoencoder_6th_run.log │ ├── control_vs_heme_rf_autoencoder_7th_run.log │ ├── control_vs_nucleotide_rf_autoencoder_1th_run.log │ ├── control_vs_nucleotide_rf_autoencoder_2th_run.log │ ├── control_vs_nucleotide_rf_autoencoder_3th_run.log │ ├── control_vs_nucleotide_rf_autoencoder_4th_run.log │ ├── control_vs_nucleotide_rf_autoencoder_5th_run.log │ ├── control_vs_nucleotide_rf_autoencoder_6th_run.log │ └── control_vs_nucleotide_rf_autoencoder_7th_run.log └── rf_autoencoder_vec_result │ ├── control_vs_heme_cv_1th_run.json │ ├── control_vs_heme_cv_2th_run.json │ ├── control_vs_heme_cv_3th_run.json │ ├── control_vs_heme_cv_4th_run.json │ ├── control_vs_heme_cv_5th_run.json │ 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