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Commit 6d8cf12e authored by Leonardo Solis's avatar Leonardo Solis
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first version in Shoemake-space for rotation genes, works nrun=5, popsize=10

parent d3275d6f
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Makefile
View file @ 6d8cf12e
......@@ -197,11 +197,12 @@ odock: check-env-all stringify $(SRC)
# Example
PDB := 3ce3
NRUN := 100
NRUN := 5
POPSIZE := 10
TESTNAME:= test
test: odock
$(BIN_DIR)/$(TARGET) -ffile ./input/$(PDB)/derived/$(PDB)_protein.maps.fld -lfile ./input/$(PDB)/derived/$(PDB)_ligand.pdbqt -nrun $(NRUN) -resnam $(TESTNAME) -gfpop 1
$(BIN_DIR)/$(TARGET) -ffile ./input/$(PDB)/derived/$(PDB)_protein.maps.fld -lfile ./input/$(PDB)/derived/$(PDB)_ligand.pdbqt -nrun $(NRUN) -psize $(POPSIZE) -resnam $(TESTNAME) -gfpop 1
clean:
rm -f $(BIN_DIR)/* initpop.txt
device/calcenergy.cl
View file @ 6d8cf12e
......@@ -88,8 +88,32 @@ void gpu_calc_energy( int dockpars_rotbondlist_length,
float weights[2][2][2];
int x_low, x_high, y_low, y_high, z_low, z_high;
// -------------------------------------------------------------------
// L30nardoSV
// Replacing rotation genes: from spherical space to Shoemake space
// gene [0:2]: translation -> kept as original x, y, z
// gene [3:5]: rotation -> transformed into Shoemake (u1: adimensional, u2&u3: sexagesimal)
// gene [6:N]: torsions -> kept as original angles (all in sexagesimal)
// Shoemake ranges:
// u1: [0, 1]
// u2: [0: 2PI] or [0: 360]
// Random generator in the host is changed:
// LCG (original, myrand()) -> CPP std (rand())
// -------------------------------------------------------------------
// Original code commented out
/*
float phi, theta, genrotangle, rotation_angle, sin_angle;
float genrot_unitvec[3], rotation_unitvec[3], rotation_movingvec[3];
*/
float rotation_angle, sin_angle;
float rotation_unitvec[3], rotation_movingvec[3];
int rotation_counter, rotation_list_element;
float atom_to_rotate[3];
int atom_id, rotbond_id;
......@@ -107,13 +131,53 @@ void gpu_calc_energy( int dockpars_rotbondlist_length,
//CALCULATE CONFORMATION
// -------------------------------------------------------------------
// L30nardoSV
// Replacing rotation genes: from spherical space to Shoemake space
// gene [0:2]: translation -> kept as original x, y, z
// gene [3:5]: rotation -> transformed into Shoemake (u1: adimensional, u2&u3: sexagesimal)
// gene [6:N]: torsions -> kept as original angles (all in sexagesimal)
// Shoemake ranges:
// u1: [0, 1]
// u2: [0: 2PI] or [0: 360]
// Random generator in the host is changed:
// LCG (original, myrand()) -> CPP std (rand())
// -------------------------------------------------------------------
/*
//calculate vectors for general rotation
phi = genotype[3]*DEG_TO_RAD;
theta = genotype[4]*DEG_TO_RAD;
genrotangle = genotype[5]*DEG_TO_RAD;
*/
// Rotational genes in the Shoemake space expressed in radians
float u1, u2, u3;
u1 = genotype[3];
u2 = genotype[4]*DEG_TO_RAD;
u3 = genotype[5]*DEG_TO_RAD;
#if defined (IMPROVE_GRID)
#if defined (IMPROVE_GRID)
// -------------------------------------------------------------------
// L30nardoSV
// Replacing rotation genes: from spherical space to Shoemake space
// gene [0:2]: translation -> kept as original x, y, z
// gene [3:5]: rotation -> transformed into Shoemake (u1: adimensional, u2&u3: sexagesimal)
// gene [6:N]: torsions -> kept as original angles (all in sexagesimal)
// Shoemake ranges:
// u1: [0, 1]
// u2: [0: 2PI] or [0: 360]
// Random generator in the host is changed:
// LCG (original, myrand()) -> CPP std (rand())
// -------------------------------------------------------------------
// Original code is commented out
/*
#if defined (NATIVE_PRECISION)
sin_angle = native_sin(theta);
genrot_unitvec [0] = sin_angle*native_cos(phi);
......@@ -130,6 +194,7 @@ void gpu_calc_energy( int dockpars_rotbondlist_length,
genrot_unitvec [1] = sin_angle*sin(phi);
genrot_unitvec [2] = cos(theta);
#endif
*/
// INTERMOLECULAR for-loop (intermediate results)
// It stores a product of two chars
......@@ -137,25 +202,43 @@ void gpu_calc_energy( int dockpars_rotbondlist_length,
unsigned char g1 = dockpars_gridsize_x;
unsigned int g2 = dockpars_gridsize_x * dockpars_gridsize_y;
unsigned int g3 = dockpars_gridsize_x * dockpars_gridsize_y * dockpars_gridsize_z;
unsigned int g3 = dockpars_gridsize_x * dockpars_gridsize_y * dockpars_gridsize_z;
unsigned int ylow_times_g1, yhigh_times_g1;
unsigned int zlow_times_g2, zhigh_times_g2;
unsigned int cube_000;
unsigned int cube_100;
unsigned int cube_010;
unsigned int cube_010;
unsigned int cube_110;
unsigned int cube_001;
unsigned int cube_101;
unsigned int cube_011;
unsigned int cube_111;
unsigned int cube_101;
unsigned int cube_011;
unsigned int cube_111;
#else
// -------------------------------------------------------------------
// L30nardoSV
// Replacing rotation genes: from spherical space to Shoemake space
// gene [0:2]: translation -> kept as original x, y, z
// gene [3:5]: rotation -> transformed into Shoemake (u1: adimensional, u2&u3: sexagesimal)
// gene [6:N]: torsions -> kept as original angles (all in sexagesimal)
// Shoemake ranges:
// u1: [0, 1]
// u2: [0: 2PI] or [0: 360]
// Random generator in the host is changed:
// LCG (original, myrand()) -> CPP std (rand())
// -------------------------------------------------------------------
// Original code commented out
/*
sin_angle = sin(theta);
genrot_unitvec [0] = sin_angle*cos(phi);
genrot_unitvec [1] = sin_angle*sin(phi);
genrot_unitvec [2] = cos(theta);
*/
#endif
// ================================================
......@@ -188,12 +271,36 @@ void gpu_calc_energy( int dockpars_rotbondlist_length,
//capturing rotation vectors and angle
if ((rotation_list_element & RLIST_GENROT_MASK) != 0) //if general rotation
{
// -------------------------------------------------------------------
// L30nardoSV
// Replacing rotation genes: from spherical space to Shoemake space
// gene [0:2]: translation -> kept as original x, y, z
// gene [3:5]: rotation -> transformed into Shoemake (u1: adimensional, u2&u3: sexagesimal)
// gene [6:N]: torsions -> kept as original angles (all in sexagesimal)
// Shoemake ranges:
// u1: [0, 1]
// u2: [0: 2PI] or [0: 360]
// Random generator in the host is changed:
// LCG (original, myrand()) -> CPP std (rand())
// -------------------------------------------------------------------
/*
rotation_unitvec[0] = genrot_unitvec[0];
rotation_unitvec[1] = genrot_unitvec[1];
rotation_unitvec[2] = genrot_unitvec[2];
rotation_angle = genrotangle;
rotation_angle = genrotangle;rotation_unitvec
*/
// Moved back in here
// Transforming Shoemake (u1, u2, u3) into quaternions
// FIXME: add precision choices with preprocessor directives:
// NATIVE_PRECISION, HALF_PRECISION, Full precision
quatrot_left_q = sqrt(1 - u1) * sin(u2);
quatrot_left_x = sqrt(1 - u1) * cos(u2);
quatrot_left_y = sqrt(u1) * sin(u3);
quatrot_left_z = sqrt(u1) * cos(u3);
// Kept as the original
rotation_movingvec[0] = genotype[0];
rotation_movingvec[1] = genotype[1];
rotation_movingvec[2] = genotype[2];
......@@ -215,26 +322,82 @@ void gpu_calc_energy( int dockpars_rotbondlist_length,
atom_to_rotate[0] -= rotation_movingvec[0];
atom_to_rotate[1] -= rotation_movingvec[1];
atom_to_rotate[2] -= rotation_movingvec[2];
// -------------------------------------------------------------------
// L30nardoSV
// Replacing rotation genes: from spherical space to Shoemake space
// gene [0:2]: translation -> kept as original x, y, z
// gene [3:5]: rotation -> transformed into Shoemake (u1: adimensional, u2&u3: sexagesimal)
// gene [6:N]: torsions -> kept as original angles (all in sexagesimal)
// Shoemake ranges:
// u1: [0, 1]
// u2: [0: 2PI] or [0: 360]
// Random generator in the host is changed:
// LCG (original, myrand()) -> CPP std (rand())
// -------------------------------------------------------------------
// Moved back in here
// Transforming torsion angles into quaternions
// FIXME: add precision choices with preprocessor directives:
// NATIVE_PRECISION, HALF_PRECISION, Full precision
rotation_angle = rotation_angle/2;
quatrot_left_q = cos(rotation_angle);
sin_angle = sin(rotation_angle);
quatrot_left_x = sin_angle*rotation_unitvec[0];
quatrot_left_y = sin_angle*rotation_unitvec[1];
quatrot_left_z = sin_angle*rotation_unitvec[2];
}
//performing rotation
// -------------------------------------------------------------------
// L30nardoSV
// Replacing rotation genes: from spherical space to Shoemake space
// gene [0:2]: translation -> kept as original x, y, z
// gene [3:5]: rotation -> transformed into Shoemake (u1: adimensional, u2&u3: sexagesimal)
// gene [6:N]: torsions -> kept as original angles (all in sexagesimal)
// Shoemake ranges:
// u1: [0, 1]
// u2: [0: 2PI] or [0: 360]
// Random generator in the host is changed:
// LCG (original, myrand()) -> CPP std (rand())
// -------------------------------------------------------------------
// Original code is commented out
// The purpose of this block of code is to ultimately
// calculate quatrot_left_q, quatrot_left_x, quatrot_left_y, quatrot_left_z.
// The calculation of these is moved to each respective case:
// a) if generarl rotation, b) if rotating around rotatable bond
/*
#if defined (NATIVE_PRECISION)
rotation_angle = native_divide(rotation_angle,2);
quatrot_left_q = native_cos(rotation_angle);
sin_angle = native_sin(rotation_angle);
sin_angle = native_sin(rotation_angle);
#elif defined (HALF_PRECISION)
rotation_angle = half_divide(rotation_angle,2);
quatrot_left_q = half_cos(rotation_angle);
sin_angle = half_sin(rotation_angle);
sin_angle = half_sin(rotation_angle);
#else // Full precision
rotation_angle = rotation_angle/2;
quatrot_left_q = cos(rotation_angle);
sin_angle = sin(rotation_angle);
sin_angle = sin(rotation_angle);
#endif
quatrot_left_x = sin_angle*rotation_unitvec[0];
quatrot_left_y = sin_angle*rotation_unitvec[1];
quatrot_left_z = sin_angle*rotation_unitvec[2];
*/
if ((rotation_list_element & RLIST_GENROT_MASK) != 0) // if general rotation,
// two rotations should be performed
......@@ -248,53 +411,53 @@ void gpu_calc_energy( int dockpars_rotbondlist_length,
quatrot_temp_z = quatrot_left_z;
quatrot_left_q = quatrot_temp_q*ref_orientation_quats_const[4*(*run_id)]-
quatrot_temp_x*ref_orientation_quats_const[4*(*run_id)+1]-
quatrot_temp_y*ref_orientation_quats_const[4*(*run_id)+2]-
quatrot_temp_z*ref_orientation_quats_const[4*(*run_id)+3];
quatrot_temp_x*ref_orientation_quats_const[4*(*run_id)+1]-
quatrot_temp_y*ref_orientation_quats_const[4*(*run_id)+2]-
quatrot_temp_z*ref_orientation_quats_const[4*(*run_id)+3];
quatrot_left_x = quatrot_temp_q*ref_orientation_quats_const[4*(*run_id)+1]+
ref_orientation_quats_const[4*(*run_id)]*quatrot_temp_x+
quatrot_temp_y*ref_orientation_quats_const[4*(*run_id)+3]-
ref_orientation_quats_const[4*(*run_id)+2]*quatrot_temp_z;
ref_orientation_quats_const[4*(*run_id)]*quatrot_temp_x+
quatrot_temp_y*ref_orientation_quats_const[4*(*run_id)+3]-
ref_orientation_quats_const[4*(*run_id)+2]*quatrot_temp_z;
quatrot_left_y = quatrot_temp_q*ref_orientation_quats_const[4*(*run_id)+2]+
ref_orientation_quats_const[4*(*run_id)]*quatrot_temp_y+
ref_orientation_quats_const[4*(*run_id)+1]*quatrot_temp_z-
quatrot_temp_x*ref_orientation_quats_const[4*(*run_id)+3];
ref_orientation_quats_const[4*(*run_id)]*quatrot_temp_y+
ref_orientation_quats_const[4*(*run_id)+1]*quatrot_temp_z-
quatrot_temp_x*ref_orientation_quats_const[4*(*run_id)+3];
quatrot_left_z = quatrot_temp_q*ref_orientation_quats_const[4*(*run_id)+3]+
ref_orientation_quats_const[4*(*run_id)]*quatrot_temp_z+
quatrot_temp_x*ref_orientation_quats_const[4*(*run_id)+2]-
ref_orientation_quats_const[4*(*run_id)+1]*quatrot_temp_y;
ref_orientation_quats_const[4*(*run_id)]*quatrot_temp_z+
quatrot_temp_x*ref_orientation_quats_const[4*(*run_id)+2]-
ref_orientation_quats_const[4*(*run_id)+1]*quatrot_temp_y;
}
quatrot_temp_q = 0 -
quatrot_left_x*atom_to_rotate [0] -
quatrot_left_y*atom_to_rotate [1] -
quatrot_left_z*atom_to_rotate [2];
quatrot_left_x*atom_to_rotate [0] -
quatrot_left_y*atom_to_rotate [1] -
quatrot_left_z*atom_to_rotate [2];
quatrot_temp_x = quatrot_left_q*atom_to_rotate [0] +
quatrot_left_y*atom_to_rotate [2] -
quatrot_left_z*atom_to_rotate [1];
quatrot_left_y*atom_to_rotate [2] -
quatrot_left_z*atom_to_rotate [1];
quatrot_temp_y = quatrot_left_q*atom_to_rotate [1] -
quatrot_left_x*atom_to_rotate [2] +
quatrot_left_z*atom_to_rotate [0];
quatrot_left_x*atom_to_rotate [2] +
quatrot_left_z*atom_to_rotate [0];
quatrot_temp_z = quatrot_left_q*atom_to_rotate [2] +
quatrot_left_x*atom_to_rotate [1] -
quatrot_left_y*atom_to_rotate [0];
quatrot_left_x*atom_to_rotate [1] -
quatrot_left_y*atom_to_rotate [0];
atom_to_rotate [0] = 0 -
quatrot_temp_q*quatrot_left_x +
quatrot_temp_x*quatrot_left_q -
quatrot_temp_y*quatrot_left_z +
quatrot_temp_z*quatrot_left_y;
quatrot_temp_q*quatrot_left_x +
quatrot_temp_x*quatrot_left_q -
quatrot_temp_y*quatrot_left_z +
quatrot_temp_z*quatrot_left_y;
atom_to_rotate [1] = 0 -
quatrot_temp_q*quatrot_left_y +
quatrot_temp_x*quatrot_left_z +
quatrot_temp_y*quatrot_left_q -
quatrot_temp_z*quatrot_left_x;
quatrot_temp_q*quatrot_left_y +
quatrot_temp_x*quatrot_left_z +
quatrot_temp_y*quatrot_left_q -
quatrot_temp_z*quatrot_left_x;
atom_to_rotate [2] = 0 -
quatrot_temp_q*quatrot_left_z -
quatrot_temp_x*quatrot_left_y +
quatrot_temp_y*quatrot_left_x +
quatrot_temp_z*quatrot_left_q;
quatrot_temp_q*quatrot_left_z -
quatrot_temp_x*quatrot_left_y +
quatrot_temp_y*quatrot_left_x +
quatrot_temp_z*quatrot_left_q;
//performing final movement and storing values
calc_coords_x[atom_id] = atom_to_rotate [0] + rotation_movingvec[0];
......@@ -321,8 +484,8 @@ void gpu_calc_energy( int dockpars_rotbondlist_length,
q = atom_charges_const[atom1_id];
if ((x < 0) || (y < 0) || (z < 0) || (x >= dockpars_gridsize_x-1)
|| (y >= dockpars_gridsize_y-1)
|| (z >= dockpars_gridsize_z-1)){
|| (y >= dockpars_gridsize_y-1)
|| (z >= dockpars_gridsize_z-1)){
partial_energies[get_local_id(0)] += 16777216.0f; //100000.0f;
}
else
......
device/kernel3.cl
View file @ 6d8cf12e
......@@ -162,10 +162,38 @@ perform_LS( char dockpars_num_of_atoms,
{
genotype_deviate[gene_counter] = rho*(2*gpu_randf(dockpars_prng_states)-1);
// -------------------------------------------------------------------
// L30nardoSV
// Replacing rotation genes: from spherical space to Shoemake space
// gene [0:2]: translation -> kept as original x, y, z
// gene [3:5]: rotation -> transformed into Shoemake (u1: adimensional, u2&u3: sexagesimal)
// gene [6:N]: torsions -> kept as original angles (all in sexagesimal)
// Shoemake ranges:
// u1: [0, 1]
// u2: [0: 2PI] or [0: 360]
// Random generator in the host is changed:
// LCG (original, myrand()) -> CPP std (rand())
// -------------------------------------------------------------------
// Original code is commented out
/*
if (gene_counter < 3)
genotype_deviate[gene_counter] *= dockpars_base_dmov_mul_sqrt3;
else
genotype_deviate[gene_counter] *= dockpars_base_dang_mul_sqrt3;
*/
if (gene_counter < 3)
genotype_deviate[gene_counter] *= dockpars_base_dmov_mul_sqrt3;
else if (gene_counter == 3) // u1, FIXME: hardcoded
genotype_deviate[gene_counter] *= 0.2f;
else if (gene_counter < 6) // u2&u3, FIXME: harcoded
genotype_deviate[gene_counter] *= 90.0f;
else
genotype_deviate[gene_counter] *= dockpars_base_dang_mul_sqrt3;
}
//generating new genotype candidate
......@@ -370,11 +398,33 @@ perform_LS( char dockpars_num_of_atoms,
}
//mapping angles
// -------------------------------------------------------------------
// L30nardoSV
// Replacing rotation genes: from spherical space to Shoemake space
// gene [0:2]: translation -> kept as original x, y, z
// gene [3:5]: rotation -> transformed into Shoemake (u1: adimensional, u2&u3: sexagesimal)
// gene [6:N]: torsions -> kept as original angles (all in sexagesimal)
// Shoemake ranges:
// u1: [0, 1]
// u2: [0: 2PI] or [0: 360]
// Random generator in the host is changed:
// LCG (original, myrand()) -> CPP std (rand())
// -------------------------------------------------------------------
/*
for (gene_counter=get_local_id(0);
gene_counter<dockpars_num_of_genes;
gene_counter+=NUM_OF_THREADS_PER_BLOCK)
if (gene_counter >= 3)
map_angle(&(offspring_genotype[gene_counter]));
*/
for (gene_counter=get_local_id(0);
gene_counter<dockpars_num_of_genes;
gene_counter+=NUM_OF_THREADS_PER_BLOCK)
if (gene_counter >= 4)
map_angle(&(offspring_genotype[gene_counter]));
//updating old offspring in population
barrier(CLK_LOCAL_MEM_FENCE);
......
device/kernel4.cl
View file @ 6d8cf12e
......@@ -123,7 +123,8 @@ gpu_gen_and_eval_newpops(char dockpars_num_of_atoms,
best_ID);
else
{
//generating the following random numbers: [0..3] for parent candidates,
//generating the following random numbers:
//[0..3] for parent candidates,
//[4..5] for binary tournaments, [6] for deciding crossover,
//[7..8] for crossover points, [9] for local search
......@@ -222,13 +223,45 @@ gpu_gen_and_eval_newpops(char dockpars_num_of_atoms,
{
if (100.0f*gpu_randf(dockpars_prng_states) < dockpars_mutation_rate)
{
// -------------------------------------------------------------------
// L30nardoSV
// Replacing rotation genes: from spherical space to Shoemake space
// gene [0:2]: translation -> kept as original x, y, z
// gene [3:5]: rotation -> transformed into Shoemake (u1: adimensional, u2&u3: sexagesimal)
// gene [6:N]: torsions -> kept as original angles (all in sexagesimal)
// Shoemake ranges:
// u1: [0, 1]
// u2: [0: 2PI] or [0: 360]
// Random generator in the host is changed:
// LCG (original, myrand()) -> CPP std (rand())
// -------------------------------------------------------------------
// Original code commented out
/*
if (gene_counter < 3)
offspring_genotype[gene_counter] += dockpars_abs_max_dmov*(2*gpu_randf(dockpars_prng_states)-1);
else
{
offspring_genotype[gene_counter] += dockpars_abs_max_dang*(2*gpu_randf(dockpars_prng_states)-1);
map_angle(&(offspring_genotype[gene_counter]));
}
*/
if (gene_counter < 3)
offspring_genotype[gene_counter] += dockpars_abs_max_dmov*(2*gpu_randf(dockpars_prng_states)-1);
else if (gene_counter == 3) // u1, FIXME: hardcoded
offspring_genotype[gene_counter] += 0.2f*(2*gpu_randf(dockpars_prng_states)-1);
else if (gene_counter < 6) { // u2&3, FIXME: hardcoded
offspring_genotype[gene_counter] += 90.0f*(2*gpu_randf(dockpars_prng_states)-1);
map_angle(&(offspring_genotype[gene_counter]));
}
else
{
offspring_genotype[gene_counter] += dockpars_abs_max_dang*(2*gpu_randf(dockpars_prng_states)-1);
map_angle(&(offspring_genotype[gene_counter]));
}
}
}
......
host/inc/miscellaneous.h
View file @ 6d8cf12e
......@@ -66,8 +66,25 @@ double distance(const double [], const double []);
void vec_point2line(const double [], const double [], const double [], double []);
// -------------------------------------------------------------------
// L30nardoSV
// Replacing rotation genes: from spherical space to Shoemake space
// gene [0:2]: translation -> kept as original x, y, z
// gene [3:5]: rotation -> transformed into Shoemake (u1: adimensional, u2&u3: sexagesimal)
// gene [6:N]: torsions -> kept as original angles (all in sexagesimal)
// Shoemake ranges:
// u1: [0, 1]
// u2: [0: 2PI] or [0: 360]
// Random generator in the host is changed:
// LCG (original, myrand()) -> CPP std (rand())
// -------------------------------------------------------------------
void rotate(double [], const double [], const double [], const double*, int);
void rotate_shoemake(double [], const double [], const double [], int);
double angle_of_vectors(const double [], const double []);
void vec_crossprod(const double [], const double [], double []);
......
host/src/calcenergy.cpp
View file @ 6d8cf12e
......@@ -78,7 +78,22 @@ int prepare_const_fields_for_gpu(Liganddata* myligand_reference,
int type_id1, type_id2;
float* floatpoi;
char* charpoi;
float phi, theta, genrotangle;
// -------------------------------------------------------------------
// L30nardoSV
// Replacing rotation genes: from spherical space to Shoemake space
// gene [0:2]: translation -> kept as original x, y, z
// gene [3:5]: rotation -> transformed into Shoemake (all in radians)
// gene [6:N]: torsions -> kept as original angles (all in sexagesimal)
// Shoemake ranges:
// u1: [0, 1]
// u2: [0: 2PI]
// Random generator in the host is changed:
// LCG (original, myrand()) -> CPP std (rand())
// -------------------------------------------------------------------
//float phi, theta, genrotangle;
// ------------------------------
float atom_charges[MAX_NUM_OF_ATOMS];
......@@ -212,6 +227,21 @@ int prepare_const_fields_for_gpu(Liganddata* myligand_reference,
{
//printf("Pregenerated angles for run %d: %f %f %f\n", i, cpu_ref_ori_angles[3*i], cpu_ref_ori_angles[3*i+1], cpu_ref_ori_angles[3*i+2]);
// -------------------------------------------------------------------
// L30nardoSV
// Replacing rotation genes: from spherical space to Shoemake space
// gene [0:2]: translation -> kept as original x, y, z
// gene [3:5]: rotation -> transformed into Shoemake (u1: adimensional, u2&u3: sexagesimal)
// gene [6:N]: torsions -> kept as original angles (all in sexagesimal)
// Shoemake ranges:
// u1: [0, 1]
// u2: [0: 2PI] or [0: 360]
// Random generator in the host is changed:
// LCG (original, myrand()) -> CPP std (rand())
// -------------------------------------------------------------------
/*
phi = cpu_ref_ori_angles[3*i]*DEG_TO_RAD;
theta = cpu_ref_ori_angles[3*i+1]*DEG_TO_RAD;
genrotangle = cpu_ref_ori_angles[3*i+2]*DEG_TO_RAD;
......@@ -220,6 +250,19 @@ int prepare_const_fields_for_gpu(Liganddata* myligand_reference,
ref_orientation_quats[4*i+1] = sinf(genrotangle/2.0f)*sinf(theta)*cosf(phi); //x
ref_orientation_quats[4*i+2] = sinf(genrotangle/2.0f)*sinf(theta)*sinf(phi); //y
ref_orientation_quats[4*i+3] = sinf(genrotangle/2.0f)*cosf(theta); //z
*/
// Shoemake genes
// autodockdev/motions.py
float u1, u2, u3;
u1 = cpu_ref_ori_angles[3*i];
u2 = cpu_ref_ori_angles[3*i+1]*DEG_TO_RAD;
u3 = cpu_ref_ori_angles[3*i+2]*DEG_TO_RAD;
ref_orientation_quats[4*i] = sqrt(1-u1) * sinf(u2); //q
ref_orientation_quats[4*i+1] = sqrt(1-u1) * cosf(u2); //x
ref_orientation_quats[4*i+2] = sqrt(u1) * sinf(u3); //y
ref_orientation_quats[4*i+3] = sqrt(u1) * cosf(u3); //z
//printf("Precalculated quaternion for run %d: %f %f %f %f\n", i, ref_orientation_quats[4*i], ref_orientation_quats[4*i+1], ref_orientation_quats[4*i+2], ref_orientation_quats[4*i+3]);
}
......
host/src/getparameters.cpp
View file @ 6d8cf12e
......@@ -613,12 +613,12 @@ void gen_initpop_and_reflig(Dockpars* mypars,
// L30nardoSV
// Replacing rotation genes: from spherical space to Shoemake space
// gene [0:2]: translation -> kept as original x, y, z
// gene [3:5]: rotation -> transformed into Shoemake (all in radians)
// gene [3:5]: rotation -> transformed into Shoemake (u1: adimensional, u2&u3: sexagesimal)
// gene [6:N]: torsions -> kept as original angles (all in sexagesimal)
// Shoemake ranges:
// u1: [0, 1]
// u2: [0: 2PI]