int main(int argc, char *argv[]){
input_parameters_t *in_para;
in_para = (input_parameters_t *)malloc(sizeof(input_parameters_t));
display_msg("Reading the configure file \n");
load_parameters_from_file(in_para,argv[1]);
char *crossover_file_name = NULL;
int ind, ind_ref_1, ind_ref_2, cros_choose;
//Setting crossover file name
crossover_file_name = Malloc(char, MAX_FILE_NAME);
strcpy(crossover_file_name, "pop_crossover.pdb");
primary_seq_t *primary_sequence; // Primary Sequence of Protein
protein_t *population_p; // main population
protein_t *new_population; // main population
//Loading Fasta file
primary_sequence = _load_amino_seq(in_para->seq_protein_file_name);
//Allocating PDB ATOMS of population_p
population_p = allocateProtein(&in_para->size_population);
new_population = allocateProtein(&in_para->size_population);
//Loading initial population and allocating atom and topology
load_initial_population_file(population_p, &in_para->size_population,
in_para->path_local_execute,in_para->initial_pop_file_name,
primary_sequence);
//Only to initialize new_population
load_initial_population_file(new_population, &in_para->size_population,
in_para->path_local_execute,in_para->initial_pop_file_name,
primary_sequence);
initialize_protein_population_atoms(new_population, &in_para->size_population);
//Checking what crossover will be applied
cros_choose = 0;
while ( (cros_choose <= 0) || (cros_choose > MAX_CROS)){
printf ("Enter type of crossover 1 - 1-Point ");
scanf ("%d",&cros_choose);
}
for (ind = 0; ind < in_para->size_population; ind++){
ind_ref_1 = 0;
ind_ref_2 = 1;
if (cros_choose == 1){
crossover_one_point(&new_population[ind], &population_p[ind_ref_1], &population_p[ind_ref_2]);
}
}
save_population_file(new_population, in_para->path_local_execute, crossover_file_name, &in_para->size_population);
deAllocateload_parameters(in_para);
display_msg("Done 2PG Crossover \n");
return 0;
}
int main(int argc, char *argv[]) {
input_parameters_t in_param;
display_msg("Reading the configure file \n");
load_parameters_from_file(&in_param,argv[1]);
build_initial_population(&in_param);
deAllocateload_parameters(&in_param);
display_msg("Done Build Initial Population !!! \n");
return 0;
}
int main(int argc, char *argv[]){
input_parameters_t in_param;
display_msg("Reading the configure file \n");
load_parameters_from_file(&in_param,argv[1]);
if (in_param.number_fitness == 1){
ea_mono(&in_param);
}else{
fatal_error("In mono-objective, NumberObjective option must be 1. Please, check it. \n");
}
deAllocateload_parameters(&in_param);
display_msg("Done EA Mono !!! \n");
return 0;
}
int main(int argc, char *argv[]){
input_parameters_t in_param;
display_msg("Reading the configure file \n");
load_parameters_from_file(&in_param,argv[1]);
/*Represents extension of files that will be looked in directory*/
char *ext = NULL;
/*Represents how many files there is in directory*/
int num_files;
/*Represents file names that are in directory and have target extension*/
owner_file_t *file_names = NULL;
protein_t *population_p= NULL; // main population of protein
solution_t *solutions_p= NULL; // main solution
dominance_t *dominance= NULL; // main of dominance
ea_nsga2_t *nsga2_solutions_p= NULL; // main of front
/**************** START GETTING FILE NAMES *************************/
ext = Malloc(char, 4);
strcpy(ext, "pdb");
num_files = how_many_files_directory_by_extension(in_param.path_local_execute, ext);
file_names = allocate_file_t(&num_files, &in_param.number_fitness);
insert_files_directory_by_extension(file_names, in_param.path_local_execute, ext);
free(ext);
/**************** FINISHED GETTING FILE NAMES *************************/
/**************** START GETTING THE OBJECTIVES *************************/
init_gromacs_execution();
/*
// RUN PDB2GMX IN ALL FILES FOR PATTERN OF ATOM NAMES
display_msg("Run of pdb2gmx for pattern of atom names\n");
for (int ind = 0; ind < num_files; ind ++){
call_pdb2gmx_for_pattern_atom_names(file_names[ind].file_name, in_param.path_local_execute, in_param.path_gromacs_programs, in_param.force_field);
clean_gromacs_simulation(in_param.path_local_execute);
}
// FINISHED RUN PDB2GMX
*/
population_p = allocateProtein(&num_files);
solutions_p = allocate_solution(&num_files, &in_param.number_fitness);
for (int ind = 0; ind < num_files; ind ++){
printf("Computing Objectives of %s\n", file_names[ind].file_name);
char *path_PDB_file_name = path_join_file(in_param.path_local_execute, file_names[ind].file_name);
int num_atom = get_num_atom(path_PDB_file_name);
population_p[ind].p_atoms = allocate_pdbatom(&num_atom);
load_pdb_file_without_num_atom(population_p[ind].p_atoms, NULL, path_PDB_file_name);
int num_res = get_number_residues_from_atom(population_p[ind].p_atoms, &num_atom);
population_p[ind].p_topol = allocateTop_Global(&num_res, &num_atom);
renumerate_residue_number(population_p[ind].p_atoms, &num_atom);
build_topology_individual(&population_p[ind]);
solutions_p[ind].representation = &population_p[ind];
get_gromacs_objectives_of_solution(&solutions_p[ind], &in_param, &ind);
desAllocateTop_Global(population_p[ind].p_topol);
desAllocate_pdbatom(population_p[ind].p_atoms);
free(path_PDB_file_name);
}
finish_gromacs_execution();
//Deleting temporary files
system("rm PROT_IND_*.pdb");
/**************** FINISHED GETTING THE OBJECTIVES *************************/
/**************** START GETTING FRONT *************************/
in_param.size_population = num_files;
nsga2_solutions_p = allocate_nsga2_without_allocation_of_representation(&in_param);
//Setting identification
for (int i = 0; i < num_files; i++){
nsga2_solutions_p[i].sol->ID = i+1;
}
//Setting dominance
dominance = allocate_dominance(&num_files);
set_dominance(dominance, solutions_p, &num_files);
//Coping values of dominance
for (int ind = 0; ind < num_files; ind++){
// Indicates number of solutions that are dominated by me
file_names[ind].number_solutions_are_dominated = dominance[ind].max_dominated;
}
//Coping values of objective
for (int ind = 0; ind < num_files; ind++){
for (int ob = 0; ob < in_param.number_fitness; ob++)
nsga2_solutions_p[ind].sol->obj_values[ob] = solutions_p[ind].obj_values[ob];
}
//Setting front based on dominance concept
compute_fronts(nsga2_solutions_p, dominance, &num_files);
//Coping values from nsga2_solutions_p to owner_file_t
for (int ind = 0; ind < num_files; ind++){
//Coping objectives
for (int ob = 0; ob < in_param.number_fitness; ob++){
file_names[ind].obj_values[ob] = nsga2_solutions_p[ind].sol->obj_values[ob];
}
file_names[ind].front = nsga2_solutions_p[ind].front;
}
desallocate_dominance(dominance, &num_files);
desallocate_solution_nsga2(nsga2_solutions_p, &num_files);
/**************** FINISHED GETTING FRONT *************************/
/**************** START GETTING FINAL RESULTS *************************/
//Sorting solutions
sorting_solutions_by_front_dominance(file_names, &num_files, &in_param.number_fitness);
//Saving file
save_analysis_files(file_names, &num_files, &in_param.number_fitness, in_param.fitness_energies);
/**************** FINISHED FINAL RESULTS *************************/
desalocate_file_t(file_names, &num_files);
desallocate_solution(solutions_p, &num_files);
desallocateProtein(population_p, &num_files);
deAllocateload_parameters(&in_param);
display_msg("Done !!! \n");
return 0;
}
int main(int argc, char *argv[]){
input_parameters_t *in_para;
in_para = (input_parameters_t *)malloc(sizeof(input_parameters_t));
display_msg("Reading the configure file \n");
load_parameters_from_file(in_para,argv[1]);
FILE *f_angle = NULL;
primary_seq_t *primary_sequence; // Primary Sequence of Protein
protein_t *population_p = NULL;
float angle, angle_d;
int num_res_first, chi, max_chi;
int num_residue_choose_2;
char *file_name, *file_name_aux;
int num_frame, num_rotacoes, p, r, one;
int kind_of_rotation;
char *name_kid_of_rotation;
protein_t *frame_rot; //frame for rotation
protein_t *rotated_frames; //frames that were rotated
//Allocating variables
file_name = Malloc(char, 600);
file_name_aux = Malloc(char, 600);
name_kid_of_rotation = Malloc(char, 15);
//Assing varible using for allocating
one = 1;
num_frame = 1;
//Loading Fasta file
primary_sequence = _load_amino_seq(in_para->seq_protein_file_name);
//Allocating PDB ATOMS of population_p
population_p = allocateProtein(&one);
//Loading initial population and allocating atom and topology
load_initial_population_file(population_p, &one,
in_para->path_local_execute,in_para->initial_pop_file_name,
primary_sequence);
//Allocating frame
frame_rot = allocateProtein(&num_frame);
frame_rot->p_atoms = allocate_pdbatom(&population_p[0].p_topol->numatom);
copy_protein(frame_rot, &population_p[0]);
//Getting data to rotate
printf ("Enter number of rotation: ");
scanf ("%d",&num_rotacoes);
num_res_first = 0;
while ( (num_res_first <= 0) || (num_res_first > population_p[0].p_topol->numres)){
printf ("Enter number of residue for rotating: 1 to %d ", population_p[0].p_topol->numres);
scanf ("%d",&num_res_first);
}
angle_d = 0;
while ( (angle_d <= 0) || (angle_d > 360)){
printf ("Enter value of angle for rotating: 0 to 360 (degree) ");
scanf ("%f",&angle_d);
}
angle = degree2radians(&angle_d);
kind_of_rotation = 0;
while ( (kind_of_rotation <= 0) || (kind_of_rotation > 4)){
printf ("Enter kid of rotating: 1 - PHI 2 - PSI 3 - OMEGA 4 - Side Chain ");
scanf ("%d",&kind_of_rotation);
}
//Assing name of kind of rotation
if (kind_of_rotation == 1){
strcpy(name_kid_of_rotation, "PHI");
}else if (kind_of_rotation == 2){
strcpy(name_kid_of_rotation, "PSI");
}else if (kind_of_rotation == 3){
strcpy(name_kid_of_rotation, "OMEGA");
}if (kind_of_rotation == 4){
strcpy(name_kid_of_rotation, "Side_Chain");
}
//Checking side chain rotation
if (kind_of_rotation == 4){
char *res_name;
res_name = Malloc(char, MAX_CHI);
get_res_name_from_res_num(res_name, &num_res_first, population_p[0].p_atoms, &population_p[0].p_topol->numatom);
max_chi = get_number_chi(res_name);
chi = 0;
if (max_chi > 0){
//Choose a chi of residue. It must be started 1 untill number of residue
if (max_chi == 1){
chi = 1;
}else{
while ( (chi <= 0) || (chi > max_chi) ){
printf ("Enter Side Chain 1 to %d ", max_chi);
scanf ("%d",&chi);
}
}
}else{
printf("No side chain for your selected residue (Name %s Number %i). Please choose another residue\n",res_name, num_res_first);
exit(1);
}
free(res_name);
}
