Detect_ATP_sites module - README

data/

	ATP_ff/ : FEATURE vectors of training and test datasets
	ATP_PDB/: PDB files of train and test structures
	ptf/: Location of train and test sites in PDB structures
	pytables_atp/: pytables of extracted local protein boxes in voxel representation for training and evaluation


code/
	
	Data processing
		store_pytable.py

	Models
		3DCNN_atp_drop.py  
		FEATURE_SVM_atp.py   
		Voxel_SVM_atp.py 
		layers.py          
	
	Evaluation

		Evaluate probability scores of each test site using the trained 3DCNN model
			post_train_eval_3DCNN_drop.py  

		Evaluate precision, recall, specificity, accuracy, MCC, AUC and RE scores
			eval_prediction_metrics.py 

		Generate PDB files with detection probability scores of each residue written in the B-factor field:
	    	visualize_true_ATP_sites.py
			visualize_detected_ATP_sites_FEATURE.py  
			visualize_detected_ATP_sites_Voxel.py           
	
results/

	prob_scores/: Predicted probability scores of test sites
	test_detect/: PDB files with detected probability scores of each residue written in the B-factor field
	weights/: Trained model weights