bin.cpp

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/*======================== DOxygen main page specifications ===============*/
//============================================ ProSHADE
#include "../proshade/ProSHADE.h"

//============================================ Main
int main ( int argc, char **argv )
{
    //======================================== Default settings
    ProSHADE::ProSHADE_settings* setUp        = new ProSHADE::ProSHADE_settings ( );

    // ... Settings regarding resolutions
    setUp->mapResolution                      = 8.0;
    setUp->wasResolutionGiven                 = false;
    setUp->bandwidth                          = 0;
    setUp->wasBandGiven                       = false;
    setUp->glIntegOrder                       = 0;
    setUp->theta                              = 0;
    setUp->phi                                = 0;
    setUp->mapResDefault                      = true;

    // ... Settings regarding B factors
    setUp->bFactorValue                       = 80.0;
    setUp->bFactorChange                      = 0.0;
    setUp->wasBChangeGiven                    = false;

    // ... Setting regarding maps and removing noise
    setUp->noIQRsFromMap                      = 4.0;

    // Settings regarding concentric shells
    setUp->shellSpacing                       = 0.0;
    setUp->wasShellSpacingGiven               = false;
    setUp->manualShells                       = 0;
    
    // ... Settings regarding phase
    setUp->usePhase                           = true;

    // ... Settings regarding map with phases
    setUp->useCOM                             = true;
    setUp->firstLineCOM                       = false;

    // ... Settings regarding space around the structure in lattice
    setUp->extraSpace                         = 8.0;
    setUp->wasExtraSpaceGiven                 = false;

    // ... Settings regarding weighting the distances
    setUp->alpha                              = 1.0;
    setUp->mPower                             = 1.0;
    
    // ... Settings regarding bands to be ignored
    std::vector<int> lsToIgnore;
    lsToIgnore.emplace_back ( 0 );
    setUp->ignoreLs                           = lsToIgnore;

    // ... Settings regarding the map masking threshold
    setUp->noIQRsFromMap                      = 4.0;
    
    // ... Settings regarding peak detection
    setUp->peakHeightNoIQRs                   = 3.0;
    setUp->peakDistanceForReal                = 0.20;
    setUp->peakSurroundingPoints              = 1;
    
    // ... Settings regarding tolerances
    setUp->aaErrorTolerance                   = 0.1;
    setUp->symGapTolerance                    = 0.2;

    // ... Settings regarding which distances to compute
    setUp->energyLevelDist                    = true;
    setUp->traceSigmaDist                     = true;
    setUp->fullRotFnDist                      = true;

    // ... Settings regarding hierarchical distance computation
    setUp->enLevelsThreshold                  = -999.9;
    setUp->trSigmaThreshold                   = -999.9;
    
    // ... Settings regarding the task
    setUp->taskToPerform                      = ProSHADE::NA;
    
    // ... Settings regarding where and if to save the clear map
    setUp->clearMapFile                       = "";
    setUp->useCubicMaps                       = false;
    setUp->clearMapData                       = false;
    setUp->maskBlurFactor                     = 500.0;
    setUp->maskBlurFactorGiven                = false;
    
    // ... Settings regarding map fragmentation
    setUp->mapFragBoxSize                     = 0.0;
    setUp->mapFragName                        = "./mapFrag";
    setUp->mapFragBoxFraction                 = 0.5;
    
    // ... Settings regarding the database
    setUp->databaseName                       = "";
    setUp->volumeTolerance                    = 0.2;
    
    // ... Settings regarding the symmetry type required
    setUp->symmetryFold                       = 0;
    setUp->symmetryType                       = "";
    
    // ... Settings regarding the map rotation mode
    setUp->rotAngle                           = 0.0;
    setUp->rotXAxis                           = 0.0;
    setUp->rotYAxis                           = 0.0;
    setUp->rotZAxis                           = 0.0;
    setUp->rotChangeDefault                   = false;
    setUp->xTranslation                       = 0.0;
    setUp->yTranslation                       = 0.0;
    setUp->zTranslation                       = 0.0;
    
    // ... Settings regarding the map overlay mode
    setUp->overlayDefaults                    = false;
    setUp->maxRotError                        = 0;
    
    // ... Settings regarding the map saving mode
    setUp->axisOrder                          = "xyz";
    
    // ... Settings regarding the verbosity of the program
    setUp->verbose                            = 1;

    //======================================== Parse command line arguments
    setUp->getCommandLineParams               ( argc, argv );
    
    ProSHADE::ProSHADE *proshadeObj           = new ProSHADE::ProSHADE ( setUp );
    
    delete proshadeObj;
    delete setUp;

    //======================================== DONE
    return 0;
}