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Commit 1354f05c authored by Leonardo Solis's avatar Leonardo Solis
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corrected grid forces for ligand with rotbond

parent 1948124e
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.gitignore
View file @ 1354f05c
...@@ -4,6 +4,7 @@ initpop.txt ...@@ -4,6 +4,7 @@ initpop.txt
*.xml *.xml
input/albumin_dock/ input/albumin_dock/
ocladock.wiki/ ocladock.wiki/
bin/
final_population_run* final_population_run*
device/stringify_tmp device/stringify_tmp
KernelProgramBuildInfo.txt KernelProgramBuildInfo.txt
......
Makefile
View file @ 1354f05c
...@@ -197,7 +197,11 @@ odock: check-env-all stringify $(SRC) ...@@ -197,7 +197,11 @@ odock: check-env-all stringify $(SRC)
# Example # Example
PDB := 1ac8 # 1ac8: for testing gradients of translation and rotation genes
# 7cpa: for testing gradients of torsion genes (15 torsions)
# 3tmn: for testing gradients of torsion genes (1 torsion)
PDB := 3tmn
NRUN := 1 NRUN := 1
POPSIZE := 10 POPSIZE := 10
TESTNAME:= test TESTNAME:= test
......
device/calcenergy.cl
View file @ 1354f05c
...@@ -22,6 +22,9 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. ...@@ -22,6 +22,9 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
*/ */
#define DEBUG_ENERGY
#include "calcenergy_basic.h" #include "calcenergy_basic.h"
// All related pragmas are in defines.h (accesible by host and device code) // All related pragmas are in defines.h (accesible by host and device code)
...@@ -53,6 +56,11 @@ void gpu_calc_energy( ...@@ -53,6 +56,11 @@ void gpu_calc_energy(
__local float* calc_coords_z, __local float* calc_coords_z,
__local float* partial_energies, __local float* partial_energies,
#if defined (DEBUG_ENERGY)
__local float* partial_interE,
__local float* partial_intraE,
#endif
__constant float* atom_charges_const, __constant float* atom_charges_const,
__constant char* atom_types_const, __constant char* atom_types_const,
__constant char* intraE_contributors_const, __constant char* intraE_contributors_const,
...@@ -76,6 +84,12 @@ void gpu_calc_energy( ...@@ -76,6 +84,12 @@ void gpu_calc_energy(
{ {
partial_energies[get_local_id(0)] = 0.0f; partial_energies[get_local_id(0)] = 0.0f;
#if defined (DEBUG_ENERGY)
partial_interE[get_local_id(0)] = 0.0f;
partial_intraE[get_local_id(0)] = 0.0f;
#endif
#if defined (IMPROVE_GRID) #if defined (IMPROVE_GRID)
// INTERMOLECULAR for-loop (intermediate results) // INTERMOLECULAR for-loop (intermediate results)
// It stores a product of two chars // It stores a product of two chars
...@@ -276,6 +290,10 @@ void gpu_calc_energy( ...@@ -276,6 +290,10 @@ void gpu_calc_energy(
|| (y >= dockpars_gridsize_y-1) || (y >= dockpars_gridsize_y-1)
|| (z >= dockpars_gridsize_z-1)){ || (z >= dockpars_gridsize_z-1)){
partial_energies[get_local_id(0)] += 16777216.0f; //100000.0f; partial_energies[get_local_id(0)] += 16777216.0f; //100000.0f;
#if defined (DEBUG_ENERGY)
partial_interE[get_local_id(0)] += 16777216.0f;
#endif
} }
else else
{ {
...@@ -380,6 +398,10 @@ void gpu_calc_energy( ...@@ -380,6 +398,10 @@ void gpu_calc_energy(
// Calculating affinity energy // Calculating affinity energy
partial_energies[get_local_id(0)] += TRILININTERPOL(cube, weights); partial_energies[get_local_id(0)] += TRILININTERPOL(cube, weights);
#if defined (DEBUG_ENERGY)
partial_interE[get_local_id(0)] += TRILININTERPOL(cube, weights);
#endif
// Capturing electrostatic values // Capturing electrostatic values
atom_typeid = dockpars_num_of_atypes; atom_typeid = dockpars_num_of_atypes;
...@@ -444,6 +466,10 @@ void gpu_calc_energy( ...@@ -444,6 +466,10 @@ void gpu_calc_energy(
// Calculating electrosatic energy // Calculating electrosatic energy
partial_energies[get_local_id(0)] += q * TRILININTERPOL(cube, weights); partial_energies[get_local_id(0)] += q * TRILININTERPOL(cube, weights);
#if defined (DEBUG_ENERGY)
partial_interE[get_local_id(0)] += q * TRILININTERPOL(cube, weights);
#endif
// Capturing desolvation values // Capturing desolvation values
atom_typeid = dockpars_num_of_atypes+1; atom_typeid = dockpars_num_of_atypes+1;
...@@ -507,10 +533,36 @@ void gpu_calc_energy( ...@@ -507,10 +533,36 @@ void gpu_calc_energy(
// Calculating desolvation energy // Calculating desolvation energy
partial_energies[get_local_id(0)] += fabs(q) * TRILININTERPOL(cube, weights); partial_energies[get_local_id(0)] += fabs(q) * TRILININTERPOL(cube, weights);
#if defined (DEBUG_ENERGY)
partial_interE[get_local_id(0)] += fabs(q) * TRILININTERPOL(cube, weights);
#endif
} }
} // End atom_id for-loop (INTERMOLECULAR ENERGY) } // End atom_id for-loop (INTERMOLECULAR ENERGY)
#if defined (DEBUG_ENERGY)
barrier(CLK_LOCAL_MEM_FENCE);
if (get_local_id(0) == 0)
{
float energy_interE = partial_interE[0];
for (uint contributor_counter=1;
contributor_counter<NUM_OF_THREADS_PER_BLOCK;
contributor_counter++)
{
energy_interE += partial_interE[contributor_counter];
}
partial_interE[0] = energy_interE;
//printf("%-20s %-10.8f\n", "energy_interE: ", energy_interE);
}
barrier(CLK_LOCAL_MEM_FENCE);
#endif
// In paper: intermolecular and internal energy calculation // In paper: intermolecular and internal energy calculation
// are independent from each other, -> NO BARRIER NEEDED // are independent from each other, -> NO BARRIER NEEDED
// but require different operations, // but require different operations,
...@@ -559,33 +611,49 @@ void gpu_calc_energy( ...@@ -559,33 +611,49 @@ void gpu_calc_energy(
// Calculating van der Waals / hydrogen bond term // Calculating van der Waals / hydrogen bond term
#if defined (NATIVE_PRECISION) #if defined (NATIVE_PRECISION)
partial_energies[get_local_id(0)] += native_divide(VWpars_AC_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],native_powr(atomic_distance,12)); partial_energies[get_local_id(0)] += native_divide(VWpars_AC_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],native_powr(atomic_distance,12));
#if defined (DEBUG_ENERGY)
partial_intraE[get_local_id(0)] += native_divide(VWpars_AC_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],native_powr(atomic_distance,12));
#endif
#elif defined (HALF_PRECISION) #elif defined (HALF_PRECISION)
pfor (uint rotation_counter = get_local_id(0); for (uint rotation_counter = get_local_id(0);
rotation_counter < dockpars_rotbondlist_length; rotation_counter < dockpars_rotbondlist_length;
rotation_counter+=NUM_OF_THREADS_PER_BLOCK) rotation_counter+=NUM_OF_THREADS_PER_BLOCK)
{artial_energies[get_local_id(0)] += half_divide(VWpars_AC_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],half_powr(atomic_distance,12)); {partial_energies[get_local_id(0)] += half_divide(VWpars_AC_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],half_powr(atomic_distance,12));
#else // Full precision #else // Full precision
partial_energies[get_local_id(0)] += VWpars_AC_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid]/powr(atomic_distance,12); partial_energies[get_local_id(0)] += VWpars_AC_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid]/powr(atomic_distance,12);
#endif #endif
if (intraE_contributors_const[3*contributor_counter+2] == 1) //H-bond if (intraE_contributors_const[3*contributor_counter+2] == 1) { //H-bond
#if defined (NATIVE_PRECISION) #if defined (NATIVE_PRECISION)
partial_energies[get_local_id(0)] -= native_divide(VWpars_BD_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],native_powr(atomic_distance,10)); partial_energies[get_local_id(0)] -= native_divide(VWpars_BD_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],native_powr(atomic_distance,10));
#if defined (DEBUG_ENERGY)
partial_intraE[get_local_id(0)] -= native_divide(VWpars_BD_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],native_powr(atomic_distance,10));
#endif
#elif defined (HALF_PRECISION) #elif defined (HALF_PRECISION)
partial_energies[get_local_id(0)] -= half_divide(VWpars_BD_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],half_powr(atomic_distance,10)); partial_energies[get_local_id(0)] -= half_divide(VWpars_BD_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],half_powr(atomic_distance,10));
#else // Full precision #else // Full precision
partial_energies[get_local_id(0)] -= VWpars_BD_const[atom1_typeid*dockpars_num_of_atypes+atom2_typeid]/powr(atomic_distance,10); partial_energies[get_local_id(0)] -= VWpars_BD_const[atom1_typeid*dockpars_num_of_atypes+atom2_typeid]/powr(atomic_distance,10);
#endif #endif
}
else //van der Waals else { //van der Waals
#if defined (NATIVE_PRECISION) #if defined (NATIVE_PRECISION)
partial_energies[get_local_id(0)] -= native_divide(VWpars_BD_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],native_powr(atomic_distance,6)); partial_energies[get_local_id(0)] -= native_divide(VWpars_BD_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],native_powr(atomic_distance,6));
#if defined (DEBUG_ENERGY)
partial_intraE[get_local_id(0)] -= native_divide(VWpars_BD_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],native_powr(atomic_distance,6));
#endif
#elif defined (HALF_PRECISION) #elif defined (HALF_PRECISION)
partial_energies[get_local_id(0)] -= half_divide(VWpars_BD_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],half_powr(atomic_distance,6)); partial_energies[get_local_id(0)] -= half_divide(VWpars_BD_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],half_powr(atomic_distance,6));
#else // Full precision #else // Full precision
partial_energies[get_local_id(0)] -= VWpars_BD_const[atom1_typeid*dockpars_num_of_atypes+atom2_typeid]/powr(atomic_distance,6); partial_energies[get_local_id(0)] -= VWpars_BD_const[atom1_typeid*dockpars_num_of_atypes+atom2_typeid]/powr(atomic_distance,6);
#endif #endif
}
// Calculating electrostatic term // Calculating electrostatic term
/* /*
...@@ -600,7 +668,24 @@ void gpu_calc_energy( ...@@ -600,7 +668,24 @@ void gpu_calc_energy(
atomic_distance * (-8.5525f + half_divide(86.9525f,(1.0f + 7.7839f*half_exp(-0.3154f*atomic_distance)))) atomic_distance * (-8.5525f + half_divide(86.9525f,(1.0f + 7.7839f*half_exp(-0.3154f*atomic_distance))))
); );
#else // Full precision #else // Full precision
partial_energies[get_local_id(0)] += dockpars_coeff_elec*atom_charges_const[atom1_id]*atom_charges_const[atom2_id]/ partial_energies[get_local_ #if defined (DEBUG_ENERGY)
barrier(CLK_LOCAL_MEM_FENCE);
if (get_local_id(0) == 0)
{
float energy_interE = partial_interE[0];
for (uint contributor_counter=1;
contributor_counter<NUM_OF_THREADS_PER_BLOCK;
contributor_counter++)
{
energy_interE += partial_interE[contributor_counter];
}
}
printf("%-20s %-10.8f\n", "energy_interE: ", energy_interE);
barrier(CLK_LOCAL_MEM_FENCE);
#endifid(0)] += dockpars_coeff_elec*atom_charges_const[atom1_id]*atom_charges_const[atom2_id]/
(atomic_distance*(-8.5525f + 86.9525f/(1.0f + 7.7839f*exp(-0.3154f*atomic_distance)))); (atomic_distance*(-8.5525f + 86.9525f/(1.0f + 7.7839f*exp(-0.3154f*atomic_distance))));
#endif #endif
*/ */
...@@ -611,6 +696,15 @@ void gpu_calc_energy( ...@@ -611,6 +696,15 @@ void gpu_calc_energy(
dockpars_coeff_elec * atom_charges_const[atom1_id] * atom_charges_const[atom2_id], dockpars_coeff_elec * atom_charges_const[atom1_id] * atom_charges_const[atom2_id],
atomic_distance * (DIEL_A + native_divide(DIEL_B,(1.0f + DIEL_K*native_exp(-DIEL_B_TIMES_H*atomic_distance)))) atomic_distance * (DIEL_A + native_divide(DIEL_B,(1.0f + DIEL_K*native_exp(-DIEL_B_TIMES_H*atomic_distance))))
); );
#if defined (DEBUG_ENERGY)
partial_intraE[get_local_id(0)] += native_divide (
dockpars_coeff_elec * atom_charges_const[atom1_id] * atom_charges_const[atom2_id],
atomic_distance * (DIEL_A + native_divide(DIEL_B,(1.0f + DIEL_K*native_exp(-DIEL_B_TIMES_H*atomic_distance))))
);
#endif
#elif defined (HALF_PRECISION) #elif defined (HALF_PRECISION)
partial_energies[get_local_id(0)] += half_divide ( partial_energies[get_local_id(0)] += half_divide (
dockpars_coeff_elec * atom_charges_const[atom1_id] * atom_charges_const[atom2_id], dockpars_coeff_elec * atom_charges_const[atom1_id] * atom_charges_const[atom2_id],
...@@ -635,6 +729,15 @@ void gpu_calc_energy( ...@@ -635,6 +729,15 @@ void gpu_calc_energy(
(dspars_S_const[atom2_typeid] + (dspars_S_const[atom2_typeid] +
dockpars_qasp*fabs(atom_charges_const[atom2_id]))*dspars_V_const[atom1_typeid]) * dockpars_qasp*fabs(atom_charges_const[atom2_id]))*dspars_V_const[atom1_typeid]) *
dockpars_coeff_desolv*native_exp(-atomic_distance*native_divide(atomic_distance,25.92f)); dockpars_coeff_desolv*native_exp(-atomic_distance*native_divide(atomic_distance,25.92f));
#if defined (DEBUG_ENERGY)
partial_intraE[get_local_id(0)] += ((dspars_S_const[atom1_typeid] +
dockpars_qasp*fabs(atom_charges_const[atom1_id]))*dspars_V_const[atom2_typeid] +
(dspars_S_const[atom2_typeid] +
dockpars_qasp*fabs(atom_charges_const[atom2_id]))*dspars_V_const[atom1_typeid]) *
dockpars_coeff_desolv*native_exp(-atomic_distance*native_divide(atomic_distance,25.92f));
#endif
#elif defined (HALF_PRECISION) #elif defined (HALF_PRECISION)
partial_energies[get_local_id(0)] += ((dspars_S_const[atom1_typeid] + partial_energies[get_local_id(0)] += ((dspars_S_const[atom1_typeid] +
dockpars_qasp*fabs(atom_charges_const[atom1_id]))*dspars_V_const[atom2_typeid] + dockpars_qasp*fabs(atom_charges_const[atom1_id]))*dspars_V_const[atom2_typeid] +
...@@ -666,6 +769,26 @@ void gpu_calc_energy( ...@@ -666,6 +769,26 @@ void gpu_calc_energy(
} }
} }
#if defined (DEBUG_ENERGY)
barrier(CLK_LOCAL_MEM_FENCE);
if (get_local_id(0) == 0)
{
float energy_intraE = partial_intraE[0];
for (uint contributor_counter=1;
contributor_counter<NUM_OF_THREADS_PER_BLOCK;
contributor_counter++)
{
energy_intraE += partial_intraE[contributor_counter];
}
partial_intraE[0] = energy_intraE;
//printf("%-20s %-10.8f\n", "energy_intraE: ", energy_intraE);
}
barrier(CLK_LOCAL_MEM_FENCE);
#endif
} }
#include "kernel1.cl" #include "kernel1.cl"
......
device/calcgradient.cl
View file @ 1354f05c
This diff is collapsed.
device/kernel1.cl
View file @ 1354f05c
...@@ -67,6 +67,10 @@ gpu_calc_initpop( ...@@ -67,6 +67,10 @@ gpu_calc_initpop(
__local float calc_coords_y[MAX_NUM_OF_ATOMS]; __local float calc_coords_y[MAX_NUM_OF_ATOMS];
__local float calc_coords_z[MAX_NUM_OF_ATOMS]; __local float calc_coords_z[MAX_NUM_OF_ATOMS];
__local float partial_energies[NUM_OF_THREADS_PER_BLOCK]; __local float partial_energies[NUM_OF_THREADS_PER_BLOCK];
#if defined (DEBUG_ENERGY)
__local float partial_interE [NUM_OF_THREADS_PER_BLOCK];
__local float partial_intraE [NUM_OF_THREADS_PER_BLOCK];
#endif
// Copying genotype from global memory // Copying genotype from global memory
event_t ev = async_work_group_copy(genotype, event_t ev = async_work_group_copy(genotype,
...@@ -105,6 +109,10 @@ gpu_calc_initpop( ...@@ -105,6 +109,10 @@ gpu_calc_initpop(
calc_coords_y, calc_coords_y,
calc_coords_z, calc_coords_z,
partial_energies, partial_energies,
#if defined (DEBUG_ENERGY)
partial_interE,
partial_intraE,
#endif
atom_charges_const, atom_charges_const,
atom_types_const, atom_types_const,
......
device/kernel3.cl
View file @ 1354f05c
...@@ -97,6 +97,11 @@ perform_LS( ...@@ -97,6 +97,11 @@ perform_LS(
__local float calc_coords_z[MAX_NUM_OF_ATOMS]; __local float calc_coords_z[MAX_NUM_OF_ATOMS];
__local float partial_energies[NUM_OF_THREADS_PER_BLOCK]; __local float partial_energies[NUM_OF_THREADS_PER_BLOCK];
#if defined (DEBUG_ENERGY)
__local float partial_interE [NUM_OF_THREADS_PER_BLOCK];
__local float partial_intraE [NUM_OF_THREADS_PER_BLOCK];
#endif
// Determining run ID and entity ID // Determining run ID and entity ID
// Initializing offspring genotype // Initializing offspring genotype
if (get_local_id(0) == 0) if (get_local_id(0) == 0)
...@@ -204,6 +209,10 @@ perform_LS( ...@@ -204,6 +209,10 @@ perform_LS(
calc_coords_y, calc_coords_y,
calc_coords_z, calc_coords_z,
partial_energies, partial_energies,
#if defined (DEBUG_ENERGY)
partial_interE,
partial_intraE,
#endif
atom_charges_const, atom_charges_const,
atom_types_const, atom_types_const,
...@@ -298,6 +307,10 @@ perform_LS( ...@@ -298,6 +307,10 @@ perform_LS(
calc_coords_y, calc_coords_y,
calc_coords_z, calc_coords_z,
partial_energies, partial_energies,
#if defined (DEBUG_ENERGY)
partial_interE,
partial_intraE,
#endif
atom_charges_const, atom_charges_const,
atom_types_const, atom_types_const,
......
device/kernel4.cl
View file @ 1354f05c
...@@ -89,6 +89,10 @@ gpu_gen_and_eval_newpops( ...@@ -89,6 +89,10 @@ gpu_gen_and_eval_newpops(
__local float calc_coords_y[MAX_NUM_OF_ATOMS]; __local float calc_coords_y[MAX_NUM_OF_ATOMS];
__local float calc_coords_z[MAX_NUM_OF_ATOMS]; __local float calc_coords_z[MAX_NUM_OF_ATOMS];
__local float partial_energies[NUM_OF_THREADS_PER_BLOCK]; __local float partial_energies[NUM_OF_THREADS_PER_BLOCK];
#if defined (DEBUG_ENERGY)
__local float partial_interE [NUM_OF_THREADS_PER_BLOCK];
__local float partial_intraE [NUM_OF_THREADS_PER_BLOCK];
#endif
// In this case this compute-unit is responsible for elitist selection // In this case this compute-unit is responsible for elitist selection
if ((get_group_id(0) % dockpars_pop_size) == 0) { if ((get_group_id(0) % dockpars_pop_size) == 0) {
...@@ -255,6 +259,10 @@ gpu_gen_and_eval_newpops( ...@@ -255,6 +259,10 @@ gpu_gen_and_eval_newpops(
calc_coords_y, calc_coords_y,
calc_coords_z, calc_coords_z,
partial_energies, partial_energies,
#if defined (DEBUG_ENERGY)
partial_interE,
partial_intraE,
#endif
atom_charges_const, atom_charges_const,
atom_types_const, atom_types_const,
......
device/kernel_gradient.cl
View file @ 1354f05c
...@@ -45,6 +45,9 @@ gradient_minimizer( ...@@ -45,6 +45,9 @@ gradient_minimizer(
__constant float* rotbonds_moving_vectors_const, __constant float* rotbonds_moving_vectors_const,
__constant float* rotbonds_unit_vectors_const, __constant float* rotbonds_unit_vectors_const,
__constant float* ref_orientation_quats_const, __constant float* ref_orientation_quats_const,
__constant int* rotbonds_const,
__constant int* rotbonds_atoms_const,
__constant int* num_rotating_atoms_per_rotbond_const,
// Specific gradient-minimizer args // Specific gradient-minimizer args
// __global float* restrict dockpars_conformations_next, // initial population // __global float* restrict dockpars_conformations_next, // initial population
// whose (some) entities (genotypes) are to be minimized // whose (some) entities (genotypes) are to be minimized
...@@ -199,23 +202,67 @@ gradient_minimizer( ...@@ -199,23 +202,67 @@ gradient_minimizer(
__local float calc_coords_z[MAX_NUM_OF_ATOMS]; __local float calc_coords_z[MAX_NUM_OF_ATOMS];
__local float partial_energies[NUM_OF_THREADS_PER_BLOCK]; __local float partial_energies[NUM_OF_THREADS_PER_BLOCK];
#if defined (DEBUG_ENERGY)
__local float partial_interE [NUM_OF_THREADS_PER_BLOCK];
__local float partial_intraE [NUM_OF_THREADS_PER_BLOCK];
#endif
// ----------------------------------------------------------------------------- // -----------------------------------------------------------------------------
// Perform gradient-descent iterations // Perform gradient-descent iterations
float grid_center_x = 52.340;
float grid_center_y = 15.029;
float grid_center_z = -2.932;
float ligand_center_x = 52.22740741;
float ligand_center_y = 15.51751852;
float ligand_center_z = -2.40896296;
do { do {
///* /*
// Specific input genotypes for a ligand with no rotatable bonds (1ac8). // Specific input genotypes for a ligand with no rotatable bonds (1ac8).
// Translation genes must be expressed in grids in OCLADock (local_genotype [0|1|2]). // Translation genes must be expressed in grids in OCLADock (local_genotype [0|1|2]).
// However, for testing purposes, // However, for testing purposes,
// we start using translation values in real space (Angstrom): {31.79575, 93.743875, 47.699875} // we start using translation values in real space (Angstrom): {31.79575, 93.743875, 47.699875}
// Rotation genes are expresed in the Shoemake space: local_genotype [3|4|5] // Rotation genes are exp5.96902604 / (2*math.pi)
resed in the Shoemake space: local_genotype [3|4|5]
// xyz_gene_gridspace = gridcenter_gridspace + (input_gene_realspace - gridcenter_realspace)/gridsize // xyz_gene_gridspace = gridcenter_gridspace + (input_gene_realspace - gridcenter_realspace)/gridsize
// 1ac8
local_genotype[0] = 30 + (31.79575 - 31.924) / 0.375; local_genotype[0] = 30 + (31.79575 - 31.924) / 0.375;
local_genotype[1] = 30 + (93.743875 - 93.444) / 0.375; local_genotype[1] = 30 + (93.743875 - 93.444) / 0.375;
local_genotype[2] = 30 + (47.699875 - 47.924) / 0.375; local_genotype[2] = 30 + (47.699875 - 47.924) / 0.375;
local_genotype[3] = 0.1f; local_genotype[3] = 0.1f;
local_genotype[4] = 0.5f; local_genotype[4] = 0.5f;
local_genotype[5] = 0.9f; local_genotype[5] = 0.9f;
//*/ */
///*
// 3tmn
local_genotype[0] = 30 + (ligand_center_x - grid_center_x) / 0.375;
local_genotype[1] = 30 + (ligand_center_y - grid_center_y) / 0.375;
local_genotype[2] = 30 + (ligand_center_z - grid_center_z) / 0.375;
local_genotype[3] = 0.02000000f;
local_genotype[4] = 1.44513262f / PI_TIMES_2;
local_genotype[5] = 5.96902604f / PI_TIMES_2;
local_genotype[6] = 0.0f;
local_genotype[7] = 0.0f;
local_genotype[8] = 0.0f;
local_genotype[9] = 0.0f;
local_genotype[10] = 0.0f;
local_genotype[11] = 0.0f;
local_genotype[12] = 0.0f;
local_genotype[13] = 0.0f;
local_genotype[14] = 0.0f;
local_genotype[15] = 0.0f;
local_genotype[16] = 0.0f;
local_genotype[17] = 0.0f;
local_genotype[18] = 0.0f;
local_genotype[19] = 0.0f;
local_genotype[20] = 0.0f;
//*/
// Calculating gradient // Calculating gradient
// ============================================================= // =============================================================
gpu_calc_gradient( gpu_calc_gradient(
...@@ -255,7 +302,10 @@ gradient_minimizer( ...@@ -255,7 +302,10 @@ gradient_minimizer(
ref_coords_z_const, ref_coords_z_const,
rotbonds_moving_vectors_const, rotbonds_moving_vectors_const,
rotbonds_unit_vectors_const, rotbonds_unit_vectors_const,
ref_orientation_quats_const ref_orientation_quats_const,
rotbonds_const,
rotbonds_atoms_const,
num_rotating_atoms_per_rotbond_const
// Gradient-related arguments // Gradient-related arguments
// Calculate gradients (forces) for intermolecular energy // Calculate gradients (forces) for intermolecular energy
// Derived from autodockdev/maps.py // Derived from autodockdev/maps.py
...@@ -346,15 +396,41 @@ gradient_minimizer( ...@@ -346,15 +396,41 @@ gradient_minimizer(
// ----------------------------------------------------------------------------- // -----------------------------------------------------------------------------
///* /*
// 1ac8
local_genotype[0] = 30 + (31.79575 - 31.924) / 0.375; local_genotype[0] = 30 + (31.79575 - 31.924) / 0.375;
local_genotype[1] = 30 + (93.743875 - 93.444) / 0.375; local_genotype[1] = 30 + (93.743875 - 93.444) / 0.375;
local_genotype[2] = 30 + (47.699875 - 47.924) / 0.375; local_genotype[2] = 30 + (47.699875 - 47.924) / 0.375;
local_genotype[3] = 0.1f; local_genotype[3] = 0.1f;
local_genotype[4] = 0.5f; local_genotype[4] = 0.5f;
local_genotype[5] = 0.9f; local_genotype[5] = 0.9f;
//*/ */
///*
// 7cpa
local_genotype[0] = 30 + (ligand_center_x - grid_center_x) / 0.375;
local_genotype[1] = 30 + (ligand_center_y - grid_center_y) / 0.375;
local_genotype[2] = 30 + (ligand_center_z - grid_center_z) / 0.375;
local_genotype[3] = 0.02000000f;
local_genotype[4] = 1.44513262f / PI_TIMES_2;
local_genotype[5] = 5.96902604f / PI_TIMES_2;
local_genotype[6] = 0.0f;
local_genotype[7] = 0.0f;