added smoothing

ofdock_taskpar_alt/Makefile

@@ -741,8 +741,8 @@ $(TARGET_DIR)/$(TARGET) : Makefile $(SRCS) $(INCS) $(TARGET_DIR)
 # Following values are used only for emulation
 # to have a short but still a representative test
 PDB  := 1stp
-NRUN := 10
-NEV  := 50000 
+NRUN := 5
+NEV  := 100000 
 
 # Project name
 PROJECT_NAME := ofdock_taskpar_alt

ofdock_taskpar_alt/device/Krnl_IntraE.cl

@@ -18,6 +18,13 @@ void Krnl_IntraE(
  	     __constant     char*  restrict KerConstStatic_atom_types_const,
 
 	     __global const char3* restrict KerConstStatic_intraE_contributors_const,
+
+			float 				 DockConst_smooth,
+	     __constant     float* restrict KerConstStatic_reqm,
+	     __constant     float* restrict KerConstStatic_reqm_hbond,    
+	     __constant     uint*  restrict KerConstStatic_atom1_types_reqm,
+	     __constant     uint*  restrict KerConstStatic_atom2_types_reqm,   
+
 	     __constant     float* restrict KerConstStatic_VWpars_AC_const,
 	     __constant     float* restrict KerConstStatic_VWpars_BD_const,
 	     __constant     float* restrict KerConstStatic_dspars_S_const,
@@ -112,61 +119,107 @@ while(active) {
 		float suby = loc_coords_atid1.y - loc_coords_atid2.y;
 		float subz = loc_coords_atid1.z - loc_coords_atid2.z;
 
-		//distance_leo = sqrt(subx*subx + suby*suby + subz*subz)*DockConst_grid_spacing;
-		float distance_leo = sqrt_custom(subx*subx + suby*suby + subz*subz)*DockConst_grid_spacing;
+		//atomic_distance = sqrt(subx*subx + suby*suby + subz*subz)*DockConst_grid_spacing;
+		float atomic_distance = sqrt_custom(subx*subx + suby*suby + subz*subz)*DockConst_grid_spacing;
 
-		if (distance_leo < 1.0f) {
+/*
+		if (atomic_distance < 1.0f) {
 			#if defined (DEBUG_KRNL_INTRAE)
-			printf("\n\nToo low distance (%f) between atoms %u and %u\n", distance_leo, atom1_id, atom2_id);
+			printf("\n\nToo low distance (%f) between atoms %u and %u\n", atomic_distance, atom1_id, atom2_id);
 			#endif
 			//return HIGHEST_ENERGY;	// Returning maximal value
-			distance_leo = 1.0f;
+			atomic_distance = 1.0f;
 		}
+*/
 
 		#if defined (DEBUG_KRNL_INTRAE)
 		printf("\n\nCalculating energy contribution of atoms %u and %u\n", atom1_id+1, atom2_id+1);
-		printf("Distance: %f\n", distance_leo);
+		printf("Distance: %f\n", atomic_distance);
 		#endif
 
+/*
 		float partialE1;
 		float partialE2;
 		float partialE3;
 		float partialE4;
+*/
+
+		float partialE1 = 0.0f;
+		float partialE2 = 0.0f;
+		float partialE3 = 0.0f;
+		float partialE4 = 0.0f;
+
+ 		// Getting types ids
+		char atom1_typeid = KerConstStatic_atom_types_const [atom1_id];
+		char atom2_typeid = KerConstStatic_atom_types_const [atom2_id];
+
+		// Getting optimum pair distance (opt_distance) from reqm and reqm_hbond
+		// reqm: equilibrium internuclear separation 
+		//       (sum of the vdW radii of two like atoms (A)) in the case of vdW
+		// reqm_hbond: equilibrium internuclear separation
+		// 	 (sum of the vdW radii of two like atoms (A)) in the case of hbond 
+		float opt_distance;
 
-		// But only if the distance is less than distance cutoff value and 20.48A (because of the tables)
-		//if ((distance_leo < 8.0f) && (distance_leo < 20.48f))
-		if (distance_leo < 8.0f) 
+		uint atom1_type_vdw_hb = KerConstStatic_atom1_types_reqm [atom1_typeid];
+     	        uint atom2_type_vdw_hb = KerConstStatic_atom2_types_reqm [atom2_typeid];
+
+		if (ref_intraE_contributors_const.z == 1)	// H-bond
+		{
+			opt_distance = KerConstStatic_reqm_hbond [atom1_type_vdw_hb] + KerConstStatic_reqm_hbond [atom2_type_vdw_hb];
+		}
+		else	// Van der Waals
 		{
-			float distance_pow_2  = distance_leo*distance_leo; 
-			float inverse_distance_pow_2  = native_divide(1.0f, distance_pow_2);
-			float inverse_distance_pow_4  = inverse_distance_pow_2 * inverse_distance_pow_2;
-			float inverse_distance_pow_6  = inverse_distance_pow_4 * inverse_distance_pow_2;
-			float inverse_distance_pow_10 = inverse_distance_pow_6 * inverse_distance_pow_4;
-			float inverse_distance_pow_12 = inverse_distance_pow_6 * inverse_distance_pow_6;
+			opt_distance = 0.5f*(KerConstStatic_reqm [atom1_type_vdw_hb] + KerConstStatic_reqm [atom2_type_vdw_hb]);
+		}
 
-			char atom1_typeid = KerConstStatic_atom_types_const [atom1_id];
-			char atom2_typeid = KerConstStatic_atom_types_const [atom2_id];
+		// Getting smoothed distance
+		// smoothed_distance = function(atomic_distance, opt_distance)
+		float smoothed_distance;
+		float delta_distance = 0.5f*DockConst_smooth;
 
+		/*printf("delta_distance: %f\n", delta_distance);*/
+
+		if (atomic_distance <= (opt_distance - delta_distance)) {
+			smoothed_distance = atomic_distance + delta_distance;
+		}
+		else if (atomic_distance < (opt_distance + delta_distance)) {
+			smoothed_distance = opt_distance;
+		}
+		else { // else if (atomic_distance >= (opt_distance + delta_distance))
+			smoothed_distance = atomic_distance - delta_distance;
+		}
+
+		float distance_pow_2  = atomic_distance*atomic_distance; 
+
+		float smoothed_distance_pow_2 = smoothed_distance*smoothed_distance; 
+		float inverse_smoothed_distance_pow_2  = native_divide(1.0f, smoothed_distance_pow_2);
+		float inverse_smoothed_distance_pow_4  = inverse_smoothed_distance_pow_2 * inverse_smoothed_distance_pow_2;
+		float inverse_smoothed_distance_pow_6  = inverse_smoothed_distance_pow_4 * inverse_smoothed_distance_pow_2;
+		float inverse_smoothed_distance_pow_10 = inverse_smoothed_distance_pow_6 * inverse_smoothed_distance_pow_4;
+		float inverse_smoothed_distance_pow_12 = inverse_smoothed_distance_pow_6 * inverse_smoothed_distance_pow_6;
+
+		if (atomic_distance < 8.0f) 
+		{
 			// Calculating van der Waals / hydrogen bond term
-			partialE1 = KerConstStatic_VWpars_AC_const [atom1_typeid*DockConst_num_of_atypes+atom2_typeid]*inverse_distance_pow_12;
+			partialE1 = KerConstStatic_VWpars_AC_const [atom1_typeid*DockConst_num_of_atypes+atom2_typeid]*inverse_smoothed_distance_pow_12;
 
 			float tmp_pE2 = KerConstStatic_VWpars_BD_const [atom1_typeid*DockConst_num_of_atypes+atom2_typeid];
 
 			if (ref_intraE_contributors_const.z == 1)	// H-bond
-				partialE2 = tmp_pE2 * inverse_distance_pow_10;
+				partialE2 = tmp_pE2 * inverse_smoothed_distance_pow_10;
 			else	// Van der Waals
-				partialE2 = tmp_pE2 * inverse_distance_pow_6;
+				partialE2 = tmp_pE2 * inverse_smoothed_distance_pow_6;
 
-			// Calculating electrostatic term
-			partialE3 = native_divide(  (DockConst_coeff_elec*KerConstStatic_atom_charges_const[atom1_id]*KerConstStatic_atom_charges_const[atom2_id]) , (distance_leo*(-8.5525f + native_divide(86.9525f, (1.0f + 7.7839f*native_exp(-0.3154f*distance_leo)))))       );
+		} // End of if: if (dist < dcutoff)	
 
-			// Calculating desolvation term
-			partialE4 = (
-				  (KerConstStatic_dspars_S_const [atom1_typeid] + DockConst_qasp*fabs(KerConstStatic_atom_charges_const[atom1_id])) * KerConstStatic_dspars_V_const [atom2_typeid] + 
-				  (KerConstStatic_dspars_S_const [atom2_typeid] + DockConst_qasp*fabs(KerConstStatic_atom_charges_const[atom2_id])) * KerConstStatic_dspars_V_const [atom1_typeid]) * 
-				 DockConst_coeff_desolv*native_exp(-0.0386f*distance_pow_2);
+		// Calculating electrostatic term
+		partialE3 = native_divide(  (DockConst_coeff_elec*KerConstStatic_atom_charges_const[atom1_id]*KerConstStatic_atom_charges_const[atom2_id]) , (atomic_distance*(-8.5525f + native_divide(86.9525f, (1.0f + 7.7839f*native_exp(-0.3154f*atomic_distance)))))       );
 
-		} // End of if: if ((dist < dcutoff) && (dist < 20.48))	
+		// Calculating desolvation term
+		partialE4 = (
+			  (KerConstStatic_dspars_S_const [atom1_typeid] + DockConst_qasp*fabs(KerConstStatic_atom_charges_const[atom1_id])) * KerConstStatic_dspars_V_const [atom2_typeid] + 
+			  (KerConstStatic_dspars_S_const [atom2_typeid] + DockConst_qasp*fabs(KerConstStatic_atom_charges_const[atom2_id])) * KerConstStatic_dspars_V_const [atom1_typeid]) * 
+			 DockConst_coeff_desolv*native_exp(-0.0386f*distance_pow_2);
 	
 		#if defined (FIXED_POINT_INTRAE)
 		//shift_intraE[32] = shift_intraE[0] + partialE1 + partialE2 + partialE3 + partialE4;

ofdock_taskpar_alt/host/inc/calcenergy.h

@@ -59,7 +59,10 @@ typedef struct
 	float  		mutation_rate;
 	float  		abs_max_dmov;
 	float  		abs_max_dang;
-	float  		lsearch_rate;
+	float  		lsearch_rate;
+
+	float 		smooth;
+
 	unsigned int 	num_of_lsentities;
 	float  		rho_lower_bound;
 	float  		base_dmov_mul_sqrt3;
@@ -126,7 +129,12 @@ typedef struct
 /*
        	char  intraE_contributors_const[3*MAX_INTRAE_CONTRIBUTORS]    __attribute__ ((aligned (32768)));
 */
-	cl_char3  intraE_contributors_const[MAX_INTRAE_CONTRIBUTORS]    __attribute__ ((aligned (32768)));
+	cl_char3  intraE_contributors_const[MAX_INTRAE_CONTRIBUTORS]  __attribute__ ((aligned (32768)));
+
+        float reqm_const [ATYPE_NUM]				      __attribute__ ((aligned (64)));
+        float reqm_hbond_const [ATYPE_NUM]			      __attribute__ ((aligned (64)));
+        unsigned int  atom1_types_reqm_const [ATYPE_NUM]	      __attribute__ ((aligned (64)));
+        unsigned int  atom2_types_reqm_const [ATYPE_NUM]	      __attribute__ ((aligned (64)));
 
        	float VWpars_AC_const   [MAX_NUM_OF_ATYPES*MAX_NUM_OF_ATYPES] __attribute__ ((aligned (1024)));
        	float VWpars_BD_const   [MAX_NUM_OF_ATYPES*MAX_NUM_OF_ATYPES] __attribute__ ((aligned (1024)));

ofdock_taskpar_alt/host/inc/getparameters.h

@@ -38,6 +38,9 @@ typedef struct
 		float mutation_rate;
 		float crossover_rate;
 		float lsearch_rate;
+
+		float smooth;
+
 	unsigned long num_of_ls;
 		float tournament_rate;
 		float rho_lower_bound;

ofdock_taskpar_alt/host/inc/processligand.h

@@ -77,6 +77,15 @@ typedef struct
 	int 	atom_rigid_structures [256];
 	char 	bonds [256][256];
 	char 	intraE_contributors [256][256];
+
+	// Sizes are hardcoded, ATYPE_NUM=22 float elements as in
+	// https://git.esa.informatik.tu-darmstadt.de/docking/ocladock/blob/master/host/src/processligand.cpp#L456
+	// See "User Guide AutoDock 4.2" (page 34)
+	double  reqm [ATYPE_NUM];
+	double  reqm_hbond [ATYPE_NUM];
+	unsigned int  atom1_types_reqm [ATYPE_NUM];
+	unsigned int  atom2_types_reqm [ATYPE_NUM];
+
 	double 	VWpars_A [14][14];
 	double	VWpars_B [14][14];
 	double 	VWpars_C [14][14];

ofdock_taskpar_alt/host/src/calcenergy.cpp

@@ -272,6 +272,11 @@ int prepare_conststatic_fields_for_gpu(Liganddata* 	       myligand_reference,
 
 	cl_char3  intraE_contributors[MAX_INTRAE_CONTRIBUTORS];
 
+	float reqm [ATYPE_NUM];
+        float reqm_hbond [ATYPE_NUM];
+	unsigned int atom1_types_reqm [ATYPE_NUM];
+        unsigned int atom2_types_reqm [ATYPE_NUM];
+
 	float VWpars_AC[MAX_NUM_OF_ATYPES*MAX_NUM_OF_ATYPES];
 	float VWpars_BD[MAX_NUM_OF_ATYPES*MAX_NUM_OF_ATYPES];
 	float dspars_S[MAX_NUM_OF_ATYPES];
@@ -341,6 +346,19 @@ int prepare_conststatic_fields_for_gpu(Liganddata* 	       myligand_reference,
 			}
 		}
 
+        // -------------------------------------------
+        // Smoothed pairwise potentials
+        // -------------------------------------------
+	// reqm, reqm_hbond: equilibrium internuclear separation for vdW and hbond
+	for (i= 0; i<ATYPE_NUM/*myligand_reference->num_of_atypes*/; i++) {
+		reqm[i]       = myligand_reference->reqm[i];
+		reqm_hbond[i] = myligand_reference->reqm_hbond[i];
+
+		atom1_types_reqm [i] = myligand_reference->atom1_types_reqm[i];
+        	atom2_types_reqm [i] = myligand_reference->atom2_types_reqm[i];
+	}
+	// -------------------------------------------
+
 	//van der Waals parameters
 	for (i=0; i<myligand_reference->num_of_atypes; i++)
 		for (j=0; j<myligand_reference->num_of_atypes; j++)
@@ -400,8 +418,16 @@ int prepare_conststatic_fields_for_gpu(Liganddata* 	       myligand_reference,
 /*
 	for (m=0;m<3*MAX_INTRAE_CONTRIBUTORS;m++)          { KerConstStatic->intraE_contributors_const[m]   = intraE_contributors[m]; }
 */
-	for (m=0;m<MAX_INTRAE_CONTRIBUTORS;m++)          { KerConstStatic->intraE_contributors_const[m]   = intraE_contributors[m]; }
-
+	for (m=0;m<MAX_INTRAE_CONTRIBUTORS;m++)            { KerConstStatic->intraE_contributors_const[m]   = intraE_contributors[m]; }
+
+	// -------------------------------------------
+        // Smoothed pairwise potentials
+        // -------------------------------------------
+	for (m=0;m<ATYPE_NUM;m++)			   { KerConstStatic->reqm_const[m]             = reqm[m]; }
+	for (m=0;m<ATYPE_NUM;m++)			   { KerConstStatic->reqm_hbond_const[m]       = reqm_hbond[m]; }
+	for (m=0;m<ATYPE_NUM;m++)			   { KerConstStatic->atom1_types_reqm_const[m] = atom1_types_reqm[m]; }
+	for (m=0;m<ATYPE_NUM;m++)                          { KerConstStatic->atom2_types_reqm_const[m] = atom2_types_reqm[m]; }
+	// -------------------------------------------
 
 	for (m=0;m<MAX_NUM_OF_ATYPES*MAX_NUM_OF_ATYPES;m++){ KerConstStatic->VWpars_AC_const[m]    = VWpars_AC[m];    }
 	for (m=0;m<MAX_NUM_OF_ATYPES*MAX_NUM_OF_ATYPES;m++){ KerConstStatic->VWpars_BD_const[m]    = VWpars_BD[m];    }

ofdock_taskpar_alt/host/src/getparameters.cpp

@@ -130,6 +130,8 @@ void get_commandpars(const int* argc,
 	mypars->crossover_rate 	    = 80;		// 80%
 	mypars->lsearch_rate 	    = 6;		// 6%
 				    // unsigned long num_of_ls
+	mypars->smooth              = 0.5f;
+
 	mypars->tournament_rate     = 60;		// 60%
 	mypars->rho_lower_bound     = 0.01;		// 0.01
 	mypars->base_dmov_mul_sqrt3 = 2.0/(*spacing)*sqrt(3.0);	// 2 A
@@ -253,6 +255,24 @@ void get_commandpars(const int* argc,
 		// MISSING: unsigned long num_of_ls
 		// ---------------------------------
 
+		// -------------------------------------------
+		// Smoothed pairwise potentials
+		// -------------------------------------------
+		mypars->smooth              = 0.5f;
+
+		if (strcmp("-smooth", argv [i]) == 0)
+		{
+			arg_recognized = 1;
+			sscanf(argv [i+1], "%f", &tempfloat);
+
+			// smooth is measured in Angstrom
+			if ((tempfloat >= 0.0f) && (tempfloat <= 0.5f))
+				mypars->smooth = tempfloat;
+			else
+				printf("Warning: value of -smooth argument ignored. Value must be a float between 0 and 0.5.\n");
+		}
+		// -------------------------------------------
+
 		//Argument: tournament rate. Must be a float between 50 and 100.
 		//Means the probability that the better entity wins the tournament round during selectin
 		if (strcmp("-trat", argv [i]) == 0)

ofdock_taskpar_alt/host/src/performdocking.cpp

@@ -447,7 +447,13 @@ cl_mem mem_KerConstStatic_fixpt64_atom_charges_const;
 #endif
 cl_mem mem_KerConstStatic_atom_charges_const;
 cl_mem mem_KerConstStatic_atom_types_const;
-cl_mem mem_KerConstStatic_intraE_contributors_const;
+cl_mem mem_KerConstStatic_intraE_contributors_const;
+
+cl_mem mem_KerConstStatic_reqm_const;
+cl_mem mem_KerConstStatic_reqm_hbond_const;
+cl_mem mem_KerConstStatic_atom1_types_reqm_const;
+cl_mem mem_KerConstStatic_atom2_types_reqm_const;
+
 cl_mem mem_KerConstStatic_VWpars_AC_const;
 cl_mem mem_KerConstStatic_VWpars_BD_const;
 cl_mem mem_KerConstStatic_dspars_S_const;
@@ -708,7 +714,8 @@ filled with clock() */
 	dockpars.base_dang_mul_sqrt3 = mypars->base_dang_mul_sqrt3;
 	dockpars.cons_limit        = (unsigned int) mypars->cons_limit;
 	dockpars.max_num_of_iters  = (unsigned int) mypars->max_num_of_iters;
-	dockpars.qasp = mypars->qasp;
+	dockpars.qasp = mypars->qasp;
+	dockpars.smooth = mypars->smooth;
 
 /*
 // passed correctly
@@ -761,8 +768,12 @@ printf("%i %i\n", dockpars.num_of_intraE_contributors, myligand_reference.num_of
 /*
 	mallocBufferObject(context,CL_MEM_READ_ONLY, 3*MAX_INTRAE_CONTRIBUTORS*sizeof(char),            &mem_KerConstStatic_intraE_contributors_const);
 */
-	mallocBufferObject(context,CL_MEM_READ_ONLY, MAX_INTRAE_CONTRIBUTORS*sizeof(cl_char3),            &mem_KerConstStatic_intraE_contributors_const);
-
+	mallocBufferObject(context,CL_MEM_READ_ONLY, MAX_INTRAE_CONTRIBUTORS*sizeof(cl_char3),          &mem_KerConstStatic_intraE_contributors_const);
+
+        mallocBufferObject(context,CL_MEM_READ_ONLY, ATYPE_NUM*sizeof(float),				&mem_KerConstStatic_reqm_const);
+	mallocBufferObject(context,CL_MEM_READ_ONLY, ATYPE_NUM*sizeof(float),				&mem_KerConstStatic_reqm_hbond_const);
+  	mallocBufferObject(context,CL_MEM_READ_ONLY, ATYPE_NUM*sizeof(unsigned int),			&mem_KerConstStatic_atom1_types_reqm_const);
+  	mallocBufferObject(context,CL_MEM_READ_ONLY, ATYPE_NUM*sizeof(unsigned int),                    &mem_KerConstStatic_atom2_types_reqm_const);
 
 	mallocBufferObject(context,CL_MEM_READ_ONLY, MAX_NUM_OF_ATYPES*MAX_NUM_OF_ATYPES*sizeof(float), &mem_KerConstStatic_VWpars_AC_const);
 	mallocBufferObject(context,CL_MEM_READ_ONLY, MAX_NUM_OF_ATYPES*MAX_NUM_OF_ATYPES*sizeof(float), &mem_KerConstStatic_VWpars_BD_const);
@@ -823,6 +834,11 @@ printf("%i %i\n", dockpars.num_of_intraE_contributors, myligand_reference.num_of
 	memcopyBufferObjectToDevice(command_queue1,mem_KerConstStatic_intraE_contributors_const,     &KerConstStatic.intraE_contributors_const[0],     3*MAX_INTRAE_CONTRIBUTORS*sizeof(char));
 */
 	memcopyBufferObjectToDevice(command_queue1,mem_KerConstStatic_intraE_contributors_const,     &KerConstStatic.intraE_contributors_const[0],     MAX_INTRAE_CONTRIBUTORS*sizeof(cl_char3));
+
+	memcopyBufferObjectToDevice(command_queue1,mem_KerConstStatic_reqm_const,         	     &KerConstStatic.reqm_const,           	       ATYPE_NUM*sizeof(float));
+  	memcopyBufferObjectToDevice(command_queue1,mem_KerConstStatic_reqm_hbond_const,              &KerConstStatic.reqm_hbond_const,                 ATYPE_NUM*sizeof(float));
+  	memcopyBufferObjectToDevice(command_queue1,mem_KerConstStatic_atom1_types_reqm_const,        &KerConstStatic.atom1_types_reqm_const,           ATYPE_NUM*sizeof(unsigned int));
+  	memcopyBufferObjectToDevice(command_queue1,mem_KerConstStatic_atom2_types_reqm_const,        &KerConstStatic.atom2_types_reqm_const,           ATYPE_NUM*sizeof(unsigned int));
 
 	memcopyBufferObjectToDevice(command_queue1,mem_KerConstStatic_VWpars_AC_const,               &KerConstStatic.VWpars_AC_const[0],               MAX_NUM_OF_ATYPES*MAX_NUM_OF_ATYPES*sizeof(float));
 	memcopyBufferObjectToDevice(command_queue1,mem_KerConstStatic_VWpars_BD_const,               &KerConstStatic.VWpars_BD_const[0],               MAX_NUM_OF_ATYPES*MAX_NUM_OF_ATYPES*sizeof(float));
@@ -1016,19 +1032,26 @@ printf("%i %i\n", dockpars.num_of_intraE_contributors, myligand_reference.num_of
 #ifdef ENABLE_KERNEL4 // Krnl_IntraE
 	setKernelArg(kernel4,0,  sizeof(mem_KerConstStatic_atom_charges_const),        &mem_KerConstStatic_atom_charges_const);
 	setKernelArg(kernel4,1,  sizeof(mem_KerConstStatic_atom_types_const),          &mem_KerConstStatic_atom_types_const);
-	setKernelArg(kernel4,2/*0*/,  sizeof(mem_KerConstStatic_intraE_contributors_const), &mem_KerConstStatic_intraE_contributors_const);
-	setKernelArg(kernel4,3,  sizeof(mem_KerConstStatic_VWpars_AC_const),           &mem_KerConstStatic_VWpars_AC_const);
-	setKernelArg(kernel4,4,  sizeof(mem_KerConstStatic_VWpars_BD_const),           &mem_KerConstStatic_VWpars_BD_const);
-	setKernelArg(kernel4,5,  sizeof(mem_KerConstStatic_dspars_S_const),            &mem_KerConstStatic_dspars_S_const);
-	setKernelArg(kernel4,6,  sizeof(mem_KerConstStatic_dspars_V_const),            &mem_KerConstStatic_dspars_V_const);
-
-	setKernelArg(kernel4,7 /*1*/, sizeof(unsigned char),                    &dockpars.num_of_atoms);
-	setKernelArg(kernel4,8 /*2*/, sizeof(unsigned int),                     &dockpars.num_of_intraE_contributors);
-	setKernelArg(kernel4,9,  sizeof(float),                          	&dockpars.grid_spacing);
-	setKernelArg(kernel4,10, sizeof(unsigned char),                    	&dockpars.num_of_atypes);
-	setKernelArg(kernel4,11, sizeof(float),                          	&dockpars.coeff_elec);
-	setKernelArg(kernel4,12, sizeof(float),                          	&dockpars.qasp);
-	setKernelArg(kernel4,13, sizeof(float),                          	&dockpars.coeff_desolv);
+	setKernelArg(kernel4,2,  sizeof(mem_KerConstStatic_intraE_contributors_const), &mem_KerConstStatic_intraE_contributors_const);
+
+  	setKernelArg(kernel4,3,  sizeof(dockpars.smooth),                              &dockpars.smooth);
+  	setKernelArg(kernel4,4,  sizeof(mem_KerConstStatic_reqm_const),                &mem_KerConstStatic_reqm_const);
+  	setKernelArg(kernel4,5,  sizeof(mem_KerConstStatic_reqm_hbond_const),          &mem_KerConstStatic_reqm_hbond_const);
+  	setKernelArg(kernel4,6,  sizeof(mem_KerConstStatic_atom1_types_reqm_const),    &mem_KerConstStatic_atom1_types_reqm_const);
+  	setKernelArg(kernel4,7,  sizeof(mem_KerConstStatic_atom2_types_reqm_const),    &mem_KerConstStatic_atom2_types_reqm_const);
+
+	setKernelArg(kernel4,8,  sizeof(mem_KerConstStatic_VWpars_AC_const),           &mem_KerConstStatic_VWpars_AC_const);
+	setKernelArg(kernel4,9,  sizeof(mem_KerConstStatic_VWpars_BD_const),           &mem_KerConstStatic_VWpars_BD_const);
+	setKernelArg(kernel4,10, sizeof(mem_KerConstStatic_dspars_S_const),            &mem_KerConstStatic_dspars_S_const);
+	setKernelArg(kernel4,11, sizeof(mem_KerConstStatic_dspars_V_const),            &mem_KerConstStatic_dspars_V_const);
+
+	setKernelArg(kernel4,12, sizeof(unsigned char),                    	       &dockpars.num_of_atoms);
+	setKernelArg(kernel4,13, sizeof(unsigned int),                     	       &dockpars.num_of_intraE_contributors);
+	setKernelArg(kernel4,14, sizeof(float),                          	       &dockpars.grid_spacing);
+	setKernelArg(kernel4,15, sizeof(unsigned char),                    	       &dockpars.num_of_atypes);
+	setKernelArg(kernel4,16, sizeof(float),                          	       &dockpars.coeff_elec);
+	setKernelArg(kernel4,17, sizeof(float),                          	       &dockpars.qasp);
+	setKernelArg(kernel4,18, sizeof(float),                          	       &dockpars.coeff_desolv);
 /*
 	setKernelArg(kernel4,14, sizeof(unsigned int),                     	&square_num_of_atypes);
 */
@@ -2963,7 +2986,13 @@ void cleanup() {
 #endif
   if(mem_KerConstStatic_atom_charges_const)	  	  {clReleaseMemObject(mem_KerConstStatic_atom_charges_const);}
   if(mem_KerConstStatic_atom_types_const)	   	  {clReleaseMemObject(mem_KerConstStatic_atom_types_const);}
-  if(mem_KerConstStatic_intraE_contributors_const) 	  {clReleaseMemObject(mem_KerConstStatic_intraE_contributors_const);}
+  if(mem_KerConstStatic_intraE_contributors_const) 	  {clReleaseMemObject(mem_KerConstStatic_intraE_contributors_const);}
+
+  if(mem_KerConstStatic_reqm_const) 	  		  {clReleaseMemObject(mem_KerConstStatic_reqm_const);}
+  if(mem_KerConstStatic_reqm_hbond_const) 	  	  {clReleaseMemObject(mem_KerConstStatic_reqm_hbond_const);}
+  if(mem_KerConstStatic_atom1_types_reqm_const) 	  {clReleaseMemObject(mem_KerConstStatic_atom1_types_reqm_const);}
+  if(mem_KerConstStatic_atom2_types_reqm_const)	  	  {clReleaseMemObject(mem_KerConstStatic_atom2_types_reqm_const);}
+
   if(mem_KerConstStatic_VWpars_AC_const)	   	  {clReleaseMemObject(mem_KerConstStatic_VWpars_AC_const);}
   if(mem_KerConstStatic_VWpars_BD_const)	   	  {clReleaseMemObject(mem_KerConstStatic_VWpars_BD_const);}
   if(mem_KerConstStatic_dspars_S_const)		   	  {clReleaseMemObject(mem_KerConstStatic_dspars_S_const);}

ofdock_taskpar_alt/host/src/processligand.cpp

@@ -527,16 +527,28 @@ int get_VWpars(Liganddata* myligand, const double AD4_coeff_vdW, const double AD
 
 			//identifying atom types
 			for (i=0; i<ATYPE_NUM; i++)
-				//L30nardoSV
+/*
+				// OCLADock
 				if (stricmp(atom_names [i], myligand->atom_types [atom_typeid1]) == 0)
 				//if (_stricmp(atom_names[i], myligand->atom_types[atom_typeid1]) == 0)
 					VWid_atype1 = i;
+*/
+				if (stricmp(atom_names [i], myligand->atom_types [atom_typeid1]) == 0) {
+					VWid_atype1 = i;
+					myligand->atom1_types_reqm [atom_typeid1] = VWid_atype1;
+				}
 
 			for (i=0; i<ATYPE_NUM; i++)
-				// L30nardoSV
+/*
+				// OCLADock
 				if (stricmp(atom_names[i], myligand->atom_types[atom_typeid2]) == 0)
 				//if (_stricmp(atom_names[i], myligand->atom_types[atom_typeid2]) == 0)
 					VWid_atype2 = i;
+*/
+				if (stricmp(atom_names[i], myligand->atom_types[atom_typeid2]) == 0) {
+					VWid_atype2 = i;
+					myligand->atom2_types_reqm [atom_typeid2] = VWid_atype2;
+				}
 
 			if (VWid_atype1 == ATYPE_NUM)
 			{
@@ -571,6 +583,11 @@ int get_VWpars(Liganddata* myligand, const double AD4_coeff_vdW, const double AD
 			}
 		}
 
+	for (atom_typeid1 = 0; atom_typeid1 < ATYPE_NUM/*myligand->num_of_atypes*/; atom_typeid1++) {
+		myligand->reqm[atom_typeid1]       = reqm[atom_typeid1];
+		myligand->reqm_hbond[atom_typeid1] = reqm_hbond[atom_typeid1];
+	}
+
 	for (atom_typeid1 = 0; atom_typeid1 < myligand->num_of_atypes; atom_typeid1++)
 	{
 		VWid_atype1 = ATYPE_NUM;

[Leonardo Solis]

Results of FPGA fitting process:

Fitter Status	Successful - Fri Jun 1 23:05:34 2018
Quartus Prime Version	16.0.2 Build 222 07/20/2016 Patches 2.06 SJ Pro Edition
Revision Name	top
Top-level Entity Name	top
Family	Arria 10
Device	10AX115H3F34I2SG
Timing Models	Final
Logic utilization (in ALMs)	226,888 / 427,200 ( 53 % )
Total registers	455472
Total pins	169 / 618 ( 27 % )
Total virtual pins	0
Total block memory bits	24,415,503 / 55,562,240 ( 44 % )
Total RAM Blocks	1,939 / 2,713 ( 71 % )
Total DSP Blocks	670 / 1,518 ( 44 % )
Total HSSI RX channels	8 / 24 ( 33 % )
Total HSSI TX channels	8 / 24 ( 33 % )
Total PLLs	30 / 80 ( 38 % )

	DC4b (FPL/FSP)	This commit (DC4b + smoothing)
Freq	187.5 MHz	190 MHz
	Best E, Best clusterSize, Time	(Kcal/mol), (no units), (sec)
3ptb	-5.53, 66/100, 211	-5.52, 50/100, 213
1stp	-7.76, 69/100, 385	-7.75, 59/100, 377
4hmg	-4.11, 25/100, 623	-3.62, 45/100, 566
3ce3	-10.88, 48/100, 1077	-10.93, 36/100, 1063
3c1x	-12.61, 22/100, 1487	-13.15, 51/100, 1486