#20, merge rmsd solution into fastergrad

README.md

@@ -98,6 +98,7 @@ By default the output log file is written in the current working folder. Example
 | -lsrat   | Local-search rate                | 6 (%)         |
 | -trat    | Tournament rate                  | 60 (%)        |
 | -resnam  | Name for docking output log      | _"docking"_   |
+| -hsym    | Handle symmetry in RMSD calc.    | 1             |
 
 For a complete list of available arguments and their default values, check: [getparameters.cpp](host/src/getparameters.cpp).
 

doc/readme/readme_users.md

@@ -75,6 +75,7 @@ By default the output log file is written in the current working folder. Example
 | -lsrat   | Local-search rate            | 6 (%)         |
 | -trat    | Tournament rate              | 60 (%)        |
 | -resnam  | Name for docking output log  | "docking"     |
+| -hsym    | Handle symmetry in RMSD calc.| 1             |
 
 For a complete list of available arguments and their default values, check: [getparameters.cpp](host/src/getparameters.cpp).
 

host/inc/getparameters.h

@@ -67,6 +67,8 @@ typedef struct
 		char  gen_pdbs;
 		char  fldfile [128];
 		char  ligandfile [128];
+		char  xrayligandfile [128];
+		bool  given_xrayligandfile;
 		float ref_ori_angles [3];
 	unsigned long num_of_runs;
 		char  reflig_en_reqired;

host/inc/performdocking.h

@@ -67,13 +67,14 @@ typedef struct {
 } Gradientparameters;
 #endif
 
-int docking_with_gpu(const Gridinfo* 	mygrid,
-         	     /*const*/ float* 	cpu_floatgrids,
-		           Dockpars*	mypars,
-		     const Liganddata* 	myligand_init,
-		     const int* 	argc,
-		     char**		argv,
-		           clock_t 	clock_start_program);
+int docking_with_gpu(const Gridinfo* 		mygrid,
+         	     /*const*/ float* 		cpu_floatgrids,
+		           Dockpars*		mypars,
+		     const Liganddata* 	 	myligand_init,
+		     const Liganddata* 		myxrayligand,
+		     const int* 		argc,
+		     char**			argv,
+		           clock_t 		clock_start_program);
 
 double check_progress(int* evals_of_runs,
 		      int generation_cnt,

host/inc/processresult.h

@@ -73,6 +73,7 @@ void make_resfiles(	      float* final_population,
 		   	      float* energies,
 		   const Liganddata* ligand_ref,
                    const Liganddata* ligand_from_pdb,
+		   const Liganddata* ligand_xray,
 		   const Dockpars*   mypars,
 		   		int  evals_performed,
                    		int  generations_used,

host/src/getparameters.cpp

@@ -167,12 +167,14 @@ void get_commandpars(const int* argc,
 	mypars->reflig_en_reqired   = 0;
 				    // char unbound_model
 				    // AD4_free_energy_coeffs coeffs
-	mypars->handle_symmetry     = 0;
+	mypars->handle_symmetry     = 1;
 	mypars->gen_finalpop        = 0;
 	mypars->gen_best            = 0;
 	strcpy(mypars->resname, "docking");
 	mypars->qasp 		    = 0.01097f;
-	mypars->rmsd_tolerance      = 2.0;		//2 Angström
+	mypars->rmsd_tolerance      = 2.0;			//2 Angström	
+	strcpy(mypars->xrayligandfile, mypars->ligandfile);	// By default xray-ligand file is the same as the randomized input ligand
+	mypars->given_xrayligandfile      = false;		// That is, not given (explicitly by the user)
 	// ------------------------------------------
 
 	//overwriting values which were defined as a command line argument
@@ -574,9 +576,20 @@ void get_commandpars(const int* argc,
 			else
 				printf("Warning: value of -rmstol argument ignored. Value must be a double greater than 0.\n");
 		}
+
+		// ----------------------------------
+		//Argument: ligand xray pdbqt file name
+		if (strcmp("-xraylfile", argv[i]) == 0)
+		{
+			arg_recognized = 1;
+			strcpy(mypars->xrayligandfile, argv[i+1]);
+			mypars->given_xrayligandfile = true;
+			printf("Info: using -xraylfile value as X-ray ligand.");
+		}
+		// ----------------------------------
+
 		if (arg_recognized != 1)
 			printf("Warning: unknown argument '%s'.\n", argv [i]);
-
 	}
 
 	//validating some settings

host/src/main.cpp

@@ -92,6 +92,17 @@ int main(int argc, char* argv[])
 	//------------------------------------------------------------
 	get_commandpars(&argc, argv, &(mygrid.spacing), &mypars);
 
+	Liganddata myxrayligand;
+	Gridinfo   mydummygrid;
+	// if -lxrayfile provided, then read xray ligand data
+	if (mypars.given_xrayligandfile == true) {
+			if (init_liganddata(mypars.xrayligandfile, &myxrayligand, &mydummygrid) != 0)
+				return 1;
+
+			if (get_liganddata(mypars.xrayligandfile, &myxrayligand, mypars.coeffs.AD4_coeff_vdW, mypars.coeffs.AD4_coeff_hb) != 0)
+				return 1;
+	}
+
 	//------------------------------------------------------------
 	// Calculating energies of reference ligand if required
 	//------------------------------------------------------------
@@ -114,9 +125,7 @@ int main(int argc, char* argv[])
 	// Starting Docking
 	//------------------------------------------------------------
 
-	printf("\nOCLADock version: %s\n", VERSION);
-
-	if (docking_with_gpu(&mygrid, floatgrids, &mypars, &myligand_init, &argc, argv, clock_start_program) != 0)
+	if (docking_with_gpu(&mygrid, floatgrids, &mypars, &myligand_init, &myxrayligand, &argc, argv, clock_start_program) != 0)
 		return 1;
 
 	free(floatgrids);

host/src/performdocking.cpp

@@ -93,13 +93,14 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
 #include "stringify.h"
 #include "correct_grad_axisangle.h"
 
-int docking_with_gpu(const Gridinfo*   mygrid,
-	         /*const*/ float*      cpu_floatgrids,
-                           Dockpars*   mypars,
-		     const Liganddata* myligand_init,
-		     const int*        argc,
-		           char**      argv,
-		           clock_t     clock_start_program)
+int docking_with_gpu(const Gridinfo*  	 	mygrid,
+	         /*const*/ float*      		cpu_floatgrids,
+                           Dockpars*   		mypars,
+		     const Liganddata* 		myligand_init,
+		     const Liganddata* 		myxrayligand,
+		     const int*        		argc,
+		           char**      		argv,
+		           clock_t     		clock_start_program)
 /* The function performs the docking algorithm and generates the corresponding result files.
 parameter mygrid:
 		describes the grid
@@ -113,6 +114,9 @@ parameter mypars:
 parameter myligand_init:
 		describes the ligands
 		filled with get_liganddata()
+parameter myxrayligand:
+		describes the xray ligand
+		filled with get_xrayliganddata()
 parameters argc and argv:
 		are the corresponding command line arguments parameter clock_start_program:
 		contains the state of the clock tick counter at the beginning of the program
@@ -1116,8 +1120,10 @@ filled with clock() */
 		arrange_result(cpu_final_populations+run_cnt*mypars->pop_size*GENOTYPE_LENGTH_IN_GLOBMEM, cpu_energies+run_cnt*mypars->pop_size, mypars->pop_size);
 
 		make_resfiles(cpu_final_populations+run_cnt*mypars->pop_size*GENOTYPE_LENGTH_IN_GLOBMEM, 
-			      cpu_energies+run_cnt*mypars->pop_size, &myligand_reference,
-			      myligand_init, 
+			      cpu_energies+run_cnt*mypars->pop_size, 
+			      &myligand_reference,
+			      myligand_init,
+			      myxrayligand, 
 			      mypars, 
 			      cpu_evals_of_runs[run_cnt], 
 			      generation_cnt, 

host/src/processresult.cpp

@@ -232,9 +232,22 @@ void write_basic_info_dlg(FILE* fp, const Liganddata* ligand_ref, const Dockpars
 	fprintf(fp, "DPF> move %s\n\n\n", mypars->ligandfile);
 }
 
-void make_resfiles(float* final_population, float* energies, const Liganddata* ligand_ref,
-				   const Liganddata* ligand_from_pdb, const Dockpars* mypars, int evals_performed, int generations_used, const Gridinfo* mygrid, const float* grids,
-				   float* cpu_ref_ori_angles, const int* argc, char** argv, int debug, int run_cnt, Ligandresult* best_result)
+void make_resfiles(float* final_population, 
+		   float* energies, 
+		   const Liganddata* ligand_ref,
+		   const Liganddata* ligand_from_pdb,
+		   const Liganddata* ligand_xray,
+		   const Dockpars* mypars, 
+		         int evals_performed, 
+			 int generations_used, 
+		   const Gridinfo* mygrid, 
+		   const float* grids,
+		   float* cpu_ref_ori_angles, 
+		   const int* argc, 
+		   char** argv, 
+		   int debug, 
+		   int run_cnt, 
+		   Ligandresult* best_result)
 //The function writes out final_population generated by get_result
 //as well as different parameters about the docking, the receptor and the ligand to a file called fdock_report.txt in a
 //readable and understandable format. The ligand_from_pdb parametere must be the Liganddata which includes the original
@@ -309,7 +322,12 @@ void make_resfiles(float* final_population, float* energies, const Liganddata* l
 			accurate_intraE[i] = calc_intraE_f(&temp_docked, 8, mypars->smooth, 0, mypars->coeffs.scaled_AD4_coeff_elec, mypars->coeffs.AD4_coeff_desolv, mypars->qasp, debug);
 
 		move_ligand(&temp_docked, mygrid->origo_real_xyz);				//moving it according to grid location
-		entity_rmsds [i] = calc_rmsd(ligand_from_pdb, &temp_docked, mypars->handle_symmetry);	//calculating rmds compared to original pdb file
+		if (mypars->given_xrayligandfile == true) {
+			entity_rmsds [i] = calc_rmsd(ligand_xray, &temp_docked, mypars->handle_symmetry);	//calculating rmds compared to original xray file
+		}
+		else {
+			entity_rmsds [i] = calc_rmsd(ligand_from_pdb, &temp_docked, mypars->handle_symmetry);	//calculating rmds compared to original pdb file
+		}
 
 		//copying best result to output parameter
 		if (i == 0)		//assuming this is the best one (final_population is arranged), however,