User test module - README

data/
	
	pdb/: User input structures in pdb format
	ptf/: Store extracted positions of test sites centered around targeted residue type(s) 
		The targeted residue type(s) is determined by the specified functional site of interest.
			- Specified conserved residue for PROSITE functional families
			- CYS, ARG, TRP and GLU for NOS site 
			- HIS and SER for TRYPSIN_like enzyme detection
			- All residues for ATP binding residue detection
	numpy/: numpy arrays of extracted local protein boxes in voxel representation
	
code/
	
	main.py ---- The main file that the users will interact with to perform the detection tests
		Usage:

			THEANO_FLAGS=floatX=float32 python main.py module_name site_name PDB_list

			- module_name : Can be one of "PROSITE", "TRYPSIN_like", "NOS" or "ATP"
			- site_name   : Use to specify functional site within the 10 PROSITE families for test 

				If the chosen module_name is "PROSITE", please input any of the below 10 functional families

					'EGF_1.10'
					'IG_MHC.3'
					'EF_HAND_1.1'
					'RNASE_PANCREATIC.2'
					'INSULIN.2'
					'PROTEIN_KINASE_ST.5'
					'PROTEIN_KINASE_TYR.5'
					'TRYPSIN_HIS.5'
					'TRYPSIN_SER.6'
					'ADH_SHORT.5'
					
				If the chosen module_name is "TRYPSIN_like", "NOS" or "ATP", please repeat the module_name as site_name

			- PDB_list    : A list of user input PDB structures. Please put the PDB files and PDB under the directory data/pdb.				Example PDB list can be found in the data/pdb directory (IG_FN.list, TRYPSIN.list, NOS.list, ATP_PDB.list)


		Example: (example PDB structures and PDB list are provided under the data/pdb directory)

			THEANO_FLAGS=floatX=float32 python main.py PROSITE IG_MHC.3 IG_FN.list

			THEANO_FLAGS=floatX=float32 python main.py TRYPSIN_like TRYPSIN_like TRYPSIN.list

			THEANO_FLAGS=floatX=float32 python main.py NOS NOS NOS.list

			THEANO_FLAGS=floatX=float32 python main.py ATP ATP ATP_PDB.list



	Code files that will be called by main.py to perform individual tasks:

		Data processing
			Extract positions of test sites centered around targeted residue type, write positions in ptf files
				extract_all_res_defined_AA_type.py

			Extract positions of test sites centered around all residues, write positions in ptf files
				extract_all_res.py

			Extract local boxes around specified positions in the correpsonding pdb files
				cut_box_site_test_pdb.py

		Evaluate probability scores of each test site using trained 3DCNN models
			eval_ATP_3DCNN.py
			eval_NOS_3DCNN.py
			eval_PROSITE_3DCNN.py
			eval_TRYPSIN_3DCNN.py
			layers.py

		Record representative probabilty score for each site
			detection_summary.py

		Generate PDB files with representative probability scores of each examined site written in the B-factor field:
			visualize_detected_sites.py
	 
results/

	prob_score/: Predicted probability scores of test sites
	summary/: Recorded representative probabilty score for each site
	pdb_detect/: PDB files with representative probability score of each examined site written in the B-factor field