void mirrors() {
setStyle();
init_parameters();
write_parameters();
simulateResponse();
TControlBar* bar =
new TControlBar("vertical", "LTCC Segments by Maurizio Ungaro");
bar->AddButton("", "");
bar->AddButton("Show Photon Yield", "draw_W()");
bar->AddButton("", "");
bar->AddButton("Show refractive index of C4F10", "draw_c4f10n()");
bar->AddButton("Show quantum efficiencies", "draw_qes()");
bar->AddButton("Show reflectivities", "draw_reflectivities()");
bar->AddButton("Show wc reflectivities", "draw_wcreflectivities()");
bar->AddButton("Show Window Gains", "draw_window_gain()");
bar->AddButton("", "");
bar->AddButton("Integrate Yield", "integrate_yield()");
bar->AddButton("Plot Yields", "plot_yields()");
bar->AddButton("Plot Ratios", "normalized_yields_mirrors()");
bar->AddButton("", "");
bar->AddButton("Change particle", "change_particle()");
bar->AddButton("Change mirror", "change_mirror()");
bar->AddButton("Change gas", "change_gas()");
bar->AddButton("Change pmt", "change_pmt()");
bar->AddButton("Change WC", "change_WC()");
bar->AddButton("", "");
bar->AddButton("Simulate Response", "simulateResponse()");
bar->AddButton("", "");
bar->AddButton("Write Parameters", "write_parameters()");
bar->AddButton("", "");
bar->Show();
// that's all!
}
static void *logwriter_thread(void *arg)
{
/* set name */
prctl(PR_SET_NAME, "sdlog2_writer", 0);
int log_fd = open_log_file();
if (log_fd < 0) {
return NULL;
}
struct logbuffer_s *logbuf = (struct logbuffer_s *)arg;
/* write log messages formats, version and parameters */
log_bytes_written += write_formats(log_fd);
log_bytes_written += write_version(log_fd);
log_bytes_written += write_parameters(log_fd);
fsync(log_fd);
int poll_count = 0;
void *read_ptr;
int n = 0;
bool should_wait = false;
bool is_part = false;
while (true) {
/* make sure threads are synchronized */
pthread_mutex_lock(&logbuffer_mutex);
/* update read pointer if needed */
if (n > 0) {
logbuffer_mark_read(&lb, n);
}
/* only wait if no data is available to process */
if (should_wait && !logwriter_should_exit) {
/* blocking wait for new data at this line */
pthread_cond_wait(&logbuffer_cond, &logbuffer_mutex);
}
/* only get pointer to thread-safe data, do heavy I/O a few lines down */
int available = logbuffer_get_ptr(logbuf, &read_ptr, &is_part);
/* continue */
pthread_mutex_unlock(&logbuffer_mutex);
if (available > 0) {
/* do heavy IO here */
if (available > MAX_WRITE_CHUNK) {
n = MAX_WRITE_CHUNK;
} else {
n = available;
}
n = write(log_fd, read_ptr, n);
should_wait = (n == available) && !is_part;
if (n < 0) {
main_thread_should_exit = true;
err(1, "error writing log file");
}
if (n > 0) {
log_bytes_written += n;
}
} else {
n = 0;
/* exit only with empty buffer */
if (main_thread_should_exit || logwriter_should_exit) {
break;
}
should_wait = true;
}
if (++poll_count == 10) {
fsync(log_fd);
poll_count = 0;
}
}
fsync(log_fd);
close(log_fd);
return NULL;
}
static void
checkargs (int argc, char **argv, char const ***image_template,
char **wfa_name, float *quality, fiasco_c_options_t **options)
/*
* Check validness of command line parameters and of the parameter files.
*
* Return value:
* 1 on success
* 0 otherwise
*
*
* Side effects:
* 'image_template', 'wfa_name', 'quality' and 'options' are set.
*/
{
int optind; /* last processed commandline param */
char *image_name; /* filename given by option '--input_name' */
int i; /* counter */
optind = parseargs (params, argc, argv,
"Compress raw PPM/PGM image FILEs to a FIASCO file.",
"With no image FILE, or if FILE is -, "
"read standard input.\n"
"FILE must be either a filename"
" or an image template of the form:\n"
"`prefix[start-end{+,-}step]suffix'\n"
"e.g., img0[12-01-1].pgm is substituted by"
" img012.pgm ... img001.pgm\n\n"
"Environment:\n"
"FIASCO_DATA Search and save path for FIASCO files. "
"Default: ./\n"
"FIASCO_IMAGES Search path for image files. "
"Default: ./", " [FILE]...",
FIASCO_SHARE, "system.fiascorc", ".fiascorc");
/*
* Default options ...
*/
image_name = (char *) parameter_value (params, "image-name");
*wfa_name = (char *) parameter_value (params, "output-name");
for (;;)
{
*quality = * (float *) parameter_value (params, "quality");
if (*quality > 100)
fprintf (stderr, "Typical range of quality: (0,100].\n"
"Expect some trouble on slow machines.\n");
if (*quality > 0)
break;
ask_and_set (params, "quality",
"Please enter coding quality 'q' ('q' > 0): ");
}
if (optind < argc) /* Additional command line param */
{
if (image_name)
error ("Multiple image_template arguments."
"\nOption --input-name %s already specified!", image_name);
*image_template = calloc (argc - optind + 1, sizeof (char *));
if (!*image_template)
error ("Out of memory.");
for (i = 0; optind < argc; i++, optind++)
(*image_template) [i] = argv [optind];
(*image_template) [i] = NULL;
}
else /* option -i image_name */
{
*image_template = calloc (2, sizeof (char *));
if (!*image_template)
error ("Out of memory.");
(*image_template) [0] = image_name;
(*image_template) [1] = NULL;
}
/*
* Additional options ... (have to be set with the fiasco_set_... methods)
*/
{
*options = fiasco_c_options_new ();
{
char *pattern = (char *) parameter_value (params, "pattern");
if (!fiasco_c_options_set_frame_pattern (*options, pattern))
error (fiasco_get_error_message ());
}
{
char *basis = (char *) parameter_value (params, "basis-name");
if (!fiasco_c_options_set_basisfile (*options, basis))
error (fiasco_get_error_message ());
}
{
int n = * (int *) parameter_value (params, "chroma-dictionary");
float q = * (float *) parameter_value (params, "chroma-qfactor");
if (!fiasco_c_options_set_chroma_quality (*options, q, MAX(0, n)))
error (fiasco_get_error_message ());
}
{
int n = *((int *) parameter_value (params, "smooth"));
if (!fiasco_c_options_set_smoothing (*options, MAX(0, n)))
error (fiasco_get_error_message ());
}
{
int n = * (int *) parameter_value (params, "progress-meter");
fiasco_progress_e type = (n < 0) ?
FIASCO_PROGRESS_NONE : (fiasco_progress_e) n;
if (!fiasco_c_options_set_progress_meter (*options, type))
error (fiasco_get_error_message ());
}
{
char *t = (char *) parameter_value (params, "title");
if (strlen (t) > 0 && !fiasco_c_options_set_title (*options, t))
error (fiasco_get_error_message ());
}
{
char *c = (char *) parameter_value (params, "comment");
if (strlen (c) > 0 && !fiasco_c_options_set_comment (*options, c))
error (fiasco_get_error_message ());
}
{
fiasco_tiling_e method = FIASCO_TILING_VARIANCE_DSC;
int e = * (int *) parameter_value (params, "tiling-exponent");
char *m = (char *) parameter_value (params, "tiling-method");
if (strcaseeq (m, "desc-variance"))
method = FIASCO_TILING_VARIANCE_DSC;
else if (strcaseeq (m, "asc-variance"))
method = FIASCO_TILING_VARIANCE_ASC;
else if (strcaseeq (m, "asc-spiral"))
method = FIASCO_TILING_SPIRAL_ASC;
else if (strcaseeq (m, "dsc-spiral"))
method = FIASCO_TILING_SPIRAL_DSC;
else
error (_("Invalid tiling method `%s' specified."), m);
if (!fiasco_c_options_set_tiling (*options, method, MAX(0, e)))
error (fiasco_get_error_message ());
}
{
int M/* = * (int *) parameter_value (params, "max-level") */;
int m/* = * (int *) parameter_value (params, "min-level") */;
int N/* = * (int *) parameter_value (params, "max-elements") */;
int D = * (int *) parameter_value (params, "dictionary-size");
int o = * (int *) parameter_value (params, "optimize");
if (o <= 0)
{
o = 0;
M = 10;
m = 6;
N = 3;
}
else
{
o -= 1;
M = 12;
m = 4;
N = 5;
}
if (!fiasco_c_options_set_optimizations (*options, m, M, N,
MAX(0, D), o))
error (fiasco_get_error_message ());
}
{
int M = * (int *) parameter_value (params, "max-level");
int m = * (int *) parameter_value (params, "min-level");
int p = * (int *) parameter_value (params, "prediction");
if (!fiasco_c_options_set_prediction (*options,
p, MAX(0, m), MAX(0, M)))
error (fiasco_get_error_message ());
}
{
float r = * (float *)parameter_value(params, "rpf-range");
float dc_r = * (float *)parameter_value(params, "dc-rpf-range");
int m = * (int *) parameter_value(params, "rpf-mantissa");
int dc_m = * (int *) parameter_value(params, "dc-rpf-mantissa");
fiasco_rpf_range_e range, dc_range;
if (r < 1)
range = FIASCO_RPF_RANGE_0_75;
else if (r < 1.5)
range = FIASCO_RPF_RANGE_1_00;
else if (r < 2.0)
range = FIASCO_RPF_RANGE_1_50;
else
range = FIASCO_RPF_RANGE_2_00;
if (dc_r < 1)
dc_range = FIASCO_RPF_RANGE_0_75;
else if (dc_r < 1.5)
dc_range = FIASCO_RPF_RANGE_1_00;
else if (dc_r < 2.0)
dc_range = FIASCO_RPF_RANGE_1_50;
else
dc_range = FIASCO_RPF_RANGE_2_00;
if (!fiasco_c_options_set_quantization (*options,
MAX(0, m), range,
MAX(0, dc_m), dc_range))
error (fiasco_get_error_message ());
}
if (fiasco_get_verbosity () == FIASCO_ULTIMATE_VERBOSITY)
write_parameters (params, stderr);
}
}
DockWidget::DockWidget(PARSER *Input, QTextEdit* Ed)
{
this->Inp = Input;
this->Editor = Ed;
mainLayout = new QVBoxLayout(this);
editLayout = new QGridLayout;
buttonLayout = new QHBoxLayout;
messageLayout = new QHBoxLayout;
progress_layout = new QVBoxLayout;
mainLayout->addLayout(editLayout);
mainLayout->addStretch();
mainLayout->addLayout(buttonLayout);
mainLayout->setSizeConstraint(QLayout::SetFixedSize);
rec_mol2 = new QPushButton(tr("Receptor MOL2 file:"));
choose_rec_mol2 = new QLineEdit(tr("Choose file..."));
lig_mol2 = new QPushButton(tr("Ligand MOL2 file:"));
choose_lig_mol2 = new QLineEdit(tr("Choose file..."));
reflig_mol2 = new QPushButton(tr("Reference MOl2 file:"));
choose_reflig_mol2 = new QLineEdit(tr("Choose file..."));
docking_mol2 = new QPushButton(tr("Docking Molecules (MOL2 File): "));
choose_docking_mol2 = new QLineEdit(tr("Choose files..."));
mol2_aa = new QComboBox;
mol2_aa->addItem("False"); // 0
mol2_aa->addItem("True"); // 1
mol2_aa->setCurrentIndex(0);
mol2_aa_lab = new QLabel(tr("MOL2 File has Amber Atom Types? "));
scoring_function = new QComboBox;
scoring_function->addItem("Amber Softcore + Desolvation"); //0
scoring_function->addItem("Amber Softcore"); //1
scoring_function->addItem("Amber FF + Desolvation"); //2
scoring_function->addItem("Amber FF"); //3
scoring_function->setCurrentIndex(2);
scoring_function_lab = new QLabel(tr("Scoring function: "));
diel = new QDoubleSpinBox;
diel->setMaximum(80.0);
diel->setMinimum(1.0);
diel->setDecimals(1);
diel->setSingleStep(1.0);
diel->setValue(Inp->diel);
diel_lab = new QLabel(tr("Dieletric constant: "));
dielectric_model = new QComboBox;
dielectric_model->addItem("constant"); //0
dielectric_model->addItem("r"); //1
dielectric_model->setCurrentIndex(1);
dielectric_model_lab = new QLabel(tr("Dielectric Model: "));
sigma = new QDoubleSpinBox;
sigma->setDecimals(1);
sigma->setSingleStep(0.1);
sigma->setValue(Inp->sigma);
sigma->setMinimum(1.0);
sigma_lab = new QLabel(tr("Solvation sigma: "));
alpha = new QDoubleSpinBox;
alpha->setDecimals(2);
alpha->setSingleStep(0.01);
alpha->setValue(Inp->solvation_alpha);
alpha->setMinimum(0.01);
alpha_lab = new QLabel(tr("Alpha Solvation Parameter: "));
beta = new QDoubleSpinBox;
beta->setDecimals(3);
beta->setMinimum(-10.000);
beta->setSingleStep(0.001);
beta->setValue(Inp->solvation_beta);
beta_lab = new QLabel(tr("Beta Solvation Parameter: "));
deltaij_vdw = new QDoubleSpinBox;
deltaij_vdw->setMaximum(10.0);
deltaij_vdw->setMinimum(0.0);
deltaij_vdw->setValue(2.75);
deltaij_vdw->setSingleStep(0.25);
deltaij_vdw->setDecimals(2);
deltaij_vdw_lab = new QLabel(tr("Softcore delta for VDW term: "));
deltaij_elec = new QDoubleSpinBox;
deltaij_elec->setMaximum(10.0);
deltaij_elec->setMinimum(0.0);
deltaij_elec->setValue(1.75);
deltaij_elec->setSingleStep(0.25);
deltaij_elec->setDecimals(2);
deltaij_elec_lab = new QLabel(tr("Softcore delta for electrostatic term: "));
vdw_scale = new QDoubleSpinBox;
vdw_scale->setMaximum(100.0);
vdw_scale->setMinimum(0.0);
vdw_scale->setDecimals(1);
vdw_scale->setSingleStep(1.0);
vdw_scale->setValue(Inp->vdw_scale);
vdw_scale_lab = new QLabel(tr("Scale for VDW term in overlay optimization: "));
elec_scale = new QDoubleSpinBox;
elec_scale->setMaximum(100.0);
elec_scale->setMinimum(0.0);
elec_scale->setDecimals(1);
elec_scale->setSingleStep(1.0);
elec_scale->setValue(Inp->elec_scale);
elec_scale_lab = new QLabel(tr("Scale for electrostatic term in overlay optimization: "));
box_size = new QDoubleSpinBox;
box_size->setMinimum(0.1);
box_size->setMaximum(50.0);
box_size->setSingleStep(0.1);
box_size->setDecimals(1);
box_size->setValue(Inp->search_box_x);
box_size_lab = new QLabel(tr("Search Box : "));
min_delta = new QDoubleSpinBox;
min_delta->setMinimum(1E-10);
min_delta->setMaximum(1.0);
min_delta->setDecimals(10);
min_delta->setSingleStep(0.0000000001);
min_delta->setValue(Inp->min_delta);
min_delta_lab = new QLabel(tr("Minimization step: "));
min_tol = new QDoubleSpinBox;
min_tol->setMinimum(1e-10);
min_tol->setMaximum(1.0);
min_tol->setDecimals(10);
min_tol->setSingleStep(0.0000000001);
min_tol->setValue(Inp->min_tol);
min_tol_lab = new QLabel(tr("Minimization tolerance: "));
min_timeout = new QSpinBox;
min_timeout->setMinimum(1);
min_timeout->setMaximum(120);
min_timeout->setSingleStep(1);
min_timeout->setValue(Inp->min_timeout);
min_timeout_lab = new QLabel(tr("Minimization timeout: "));
overlay_optimizer = new QComboBox;
overlay_optimizer->addItem("COBYLA"); //0
overlay_optimizer->addItem("AUGLAG (Gradient-free)"); //1
overlay_optimizer->addItem("AUGLAG"); //2
overlay_optimizer->addItem("LBFGS"); //3
overlay_optimizer->addItem("MMA"); //4
overlay_optimizer->addItem("SUBPLEX"); //5
overlay_optimizer->addItem("DIRECT"); //6
overlay_optimizer->setCurrentIndex(1);
overlay_optimizer_lab = new QLabel(tr("Overlay optimizer: "));
energy_optimizer = new QComboBox;
energy_optimizer->addItem("COBYLA"); //0
energy_optimizer->addItem("AUGLAG (Gradient-free)"); //1
energy_optimizer->addItem("AUGLAG"); //2
energy_optimizer->addItem("LBFGS"); //3
energy_optimizer->addItem("MMA"); //4
energy_optimizer->addItem("SUBPLEX"); //5
energy_optimizer->addItem("SIMPLEX"); //6
energy_optimizer->addItem("DIRECT"); //7
energy_optimizer->addItem("CRS"); //8
energy_optimizer->addItem("NONE");
energy_optimizer->setCurrentIndex(7);
energy_optimizer_lab = new QLabel(tr("Binding energy optimizer: "));
output_prefix = new QLineEdit(tr("iMcLiBELa"));
output_prefix_lab = new QLabel(tr("Output prefix: "));
write_mol2 = new QCheckBox (tr("Write Mol2 file? "), this);
write_mol2->setChecked(Inp->write_mol2);
use_grids = new QCheckBox(tr("Use grids?"), this);
use_grids->setChecked(Inp->use_grids);
grid_spacing = new QDoubleSpinBox;
grid_spacing->setValue(Inp->grid_spacing);
grid_spacing->setDecimals(3);
grid_spacing->setMinimum(0.01);
grid_spacing->setMaximum(0.5);
grid_spacing_lab = new QLabel(tr("Grid spacing: "));
load_write_file = new QComboBox;
load_write_file->addItem("Choose an option: ");
load_write_file->addItem("Load File");
load_write_file->addItem("Write File");
grid_file = new QLineEdit;
grid_file->setText("McGrid.grid");
grid_box = new QDoubleSpinBox;
grid_box->setValue(30.0);
grid_box->setDecimals(1);
grid_box->setMinimum(15.0);
grid_box->setSingleStep(1.0);
grid_box_lab = new QLabel(tr("Grid box: "));
progressbar = new QProgressBar;
progressbar->setRange(0, 100);
progressbar->setValue(0);
progress_label = new QLabel(tr("<h2>Progress</h2>"));
progress_label->setAlignment(Qt::AlignHCenter);
advanced_settings = new QCheckBox(tr("&Advanced settings"), this);
dock_no_h = new QCheckBox(tr("Ignore hydrogens"), this);
dock_no_h->setChecked(false);
generate_conformers = new QCheckBox (tr("Generate conformers? "), this);
generate_conformers->setChecked(Inp->generate_conformers);
conformers_lab = new QLabel(tr("Number of conformers: "));
conformers = new QSpinBox;
conformers->setValue(Inp->lig_conformers);
conformers->setSingleStep(1);
conformers->setMinimum(1);
conformers_to_evaluate_lab = new QLabel(tr("Conformers to optimize: "));
conformers_to_evaluate = new QSpinBox;
conformers_to_evaluate->setValue(Inp->conformers_to_evaluate);
conformers_to_evaluate->setMinimum(1);
conformer_generator_lab = new QLabel(tr("Conformer Generator: "));
conformer_generator = new QComboBox;
conformer_generator->addItem("GA");
conformer_generator->addItem("WRS");
conformer_generator->setCurrentIndex(0);
dock_min_tol_lab = new QLabel(tr("Docking tolerance: "));
dock_min_tol = new QDoubleSpinBox;
dock_min_tol->setDecimals(10);
dock_min_tol->setValue(Inp->dock_min_tol);
dock_timeout_lab = new QLabel(tr("Docking timeout: "));
dock_timeout = new QSpinBox;
dock_timeout->setValue(Inp->min_timeout);
parallel = new QCheckBox (tr("Parallel execution? "), this);
parallel_jobs_lab = new QLabel(tr("Parallel jobs: "));
parallel_jobs = new QSpinBox;
parallel_jobs->setValue(1);
parallel_jobs->setMinimum(1);
files_label = new QLabel(tr("<h2>Input Files</h2>"));
editLayout->addWidget(files_label, 0, 0);
editLayout->addWidget(rec_mol2, 1, 0);
editLayout->addWidget(choose_rec_mol2, 1, 1);
editLayout->addWidget(reflig_mol2, 2, 0);
editLayout->addWidget(choose_reflig_mol2, 2, 1);
editLayout->addWidget(docking_mol2, 3, 0);
editLayout->addWidget(choose_docking_mol2, 3, 1);
editLayout->addWidget(mol2_aa_lab, 4, 0);
editLayout->addWidget(mol2_aa, 4, 1);
output_label = new QLabel(tr("<h2>Output Files</h2>"));
editLayout->addWidget(output_label, 5, 0);
editLayout->addWidget(output_prefix_lab, 6, 0);
editLayout->addWidget(output_prefix, 6, 1);
editLayout->addWidget(write_mol2, 7,0);
sf_input = new QLabel(tr("<h2>Scoring options</h2>"));
editLayout->addWidget(sf_input, 8, 0);
editLayout->addWidget(scoring_function_lab, 9, 0);
editLayout->addWidget(scoring_function, 9, 1);
editLayout->addWidget(box_size_lab, 10, 0);
editLayout->addWidget(box_size, 10, 1);
editLayout->addWidget(diel_lab, 11, 0);
editLayout->addWidget(diel, 11, 1);
editLayout->addWidget(dielectric_model_lab, 12, 0);
editLayout->addWidget(dielectric_model, 12, 1);
editLayout->addWidget(sigma_lab, 13, 0);
editLayout->addWidget(sigma, 13, 1);
editLayout->addWidget(alpha_lab, 14, 0);
editLayout->addWidget(alpha, 14, 1);
editLayout->addWidget(beta_lab, 15, 0);
editLayout->addWidget(beta, 15, 1);
editLayout->addWidget(deltaij_vdw_lab, 16, 0);
editLayout->addWidget(deltaij_vdw, 16, 1);
editLayout->addWidget(deltaij_elec_lab, 17, 0);
editLayout->addWidget(deltaij_elec, 17, 1);
editLayout->addWidget(vdw_scale_lab, 18, 0);
editLayout->addWidget(vdw_scale, 18, 1);
editLayout->addWidget(elec_scale_lab, 19, 0);
editLayout->addWidget(elec_scale, 19, 1);
opt_input = new QLabel(tr("<h2>Optimization options</h2>"));
editLayout->addWidget(opt_input, 20, 0);
editLayout->addWidget(min_delta_lab, 21, 0);
editLayout->addWidget(min_delta, 21, 1);
editLayout->addWidget(min_tol_lab, 22, 0);
editLayout->addWidget(min_tol, 22, 1);
editLayout->addWidget(dock_min_tol_lab, 23, 0);
editLayout->addWidget(dock_min_tol, 23, 1);
editLayout->addWidget(min_timeout_lab, 24, 0);
editLayout->addWidget(min_timeout, 24, 1);
editLayout->addWidget(dock_timeout_lab, 25, 0);
editLayout->addWidget(dock_timeout, 25, 1);
editLayout->addWidget(overlay_optimizer_lab, 26, 0);
editLayout->addWidget(overlay_optimizer, 26, 1);
editLayout->addWidget(energy_optimizer_lab, 27, 0);
editLayout->addWidget(energy_optimizer, 27, 1);
editLayout->addWidget(box_size_lab, 28, 0);
editLayout->addWidget(box_size, 28, 1);
editLayout->addWidget(dock_no_h, 29, 0);
conf_input = new QLabel(tr("<h2>Conformer options</h2>"));
editLayout->addWidget(conf_input, 30, 0);
editLayout->addWidget(generate_conformers, 31, 0);
editLayout->addWidget(conformers_lab, 32, 0);
editLayout->addWidget(conformers, 32, 1);
editLayout->addWidget(conformers_to_evaluate_lab, 33, 0);
editLayout->addWidget(conformers_to_evaluate, 33, 1);
editLayout->addWidget(conformer_generator_lab, 34, 0);
editLayout->addWidget(conformer_generator, 34, 1);
parallel_label = new QLabel(tr("<h2>Parallel execution</h2>"));
editLayout->addWidget(parallel_label, 35, 0);
editLayout->addWidget(parallel, 36, 0);
editLayout->addWidget(parallel_jobs_lab, 37, 0);
editLayout->addWidget(parallel_jobs, 37, 1);
grid_label = new QLabel(tr("<h2>Grid Potentials</h2>"));
editLayout->addWidget(grid_label, 38, 0);
editLayout->addWidget(use_grids, 39,0);
editLayout->addWidget(grid_spacing_lab, 40,0);
editLayout->addWidget(grid_spacing, 40,1);
editLayout->addWidget(load_write_file, 41, 0);
editLayout->addWidget(grid_file, 41, 1);
editLayout->addWidget(grid_box_lab, 42, 0);
editLayout->addWidget(grid_box, 42, 1);
progress_layout->addWidget(advanced_settings);
progress_layout->addWidget(progress_label, Qt::AlignCenter);
progress_layout->addWidget(progressbar);
mainLayout->addStretch();
mainLayout->addLayout(progress_layout);
mainLayout->addStretch();
Run = new QPushButton(tr("Run!"));
WriteButton = new QPushButton(tr("Write parameter file"));
buttonLayout->addStretch();
buttonLayout->addWidget(WriteButton, Qt::AlignHCenter);
buttonLayout->addWidget(Run, Qt::AlignHCenter);
Run->setDefault(true);
setWindowTitle(tr("iMcLiBEla by Alessandro Nascimento"));
connect(rec_mol2, SIGNAL(clicked()), this, SLOT(choose_rec_file()));
connect(reflig_mol2, SIGNAL(clicked()), this, SLOT(choose_reflig_file()));
connect(docking_mol2, SIGNAL(clicked()), this, SLOT(choose_docking_mol2_files()));
connect(advanced_settings, SIGNAL(toggled(bool)), this, SLOT(show_advanced_setttings(bool)));
connect(Run, SIGNAL(clicked()), this, SLOT(Start()));
connect(WriteButton, SIGNAL(clicked()), this, SLOT(write_parameters()));
connect(scoring_function, SIGNAL(currentIndexChanged(int)), this, SLOT(show_scoring_function_options(int)));
connect(write_mol2, SIGNAL(stateChanged(int)), this, SLOT(slot_write_mol2(int)));
connect(dock_no_h, SIGNAL(stateChanged(int)), this, SLOT(slot_ignore_h(int)));
connect(generate_conformers, SIGNAL(stateChanged(int)), this, SLOT(slot_generate_conformers(int)));
// connect(parallel, SIGNAL(stateChanged(int)), this, SLOT(slot_parallel(int)));
connect(parallel_jobs, SIGNAL(valueChanged(int)), this, SLOT(slot_parallel(int)));
connect(load_write_file, SIGNAL(currentIndexChanged(int)), this, SLOT(slot_grid_file(int)));
connect(use_grids, SIGNAL(stateChanged(int)), this, SLOT(slot_use_grids(int)));
this->set_initial_parameters();
this->hide_advanced_options();
}