ProSHADE.h

Go to the documentation of this file.

//============================================ Apply -pedantic and -Wshadow to my code only (some of the dependencies fill not compile if this is allowed for all)
//#define __PROSHADE_DEVEL_CODE__

//============================================ Include once
#ifndef __PROSHADE_LIBRARY__
#define __PROSHADE_LIBRARY__

//============================================ Standard library
#include <iostream>
#include <fstream>
#include <sstream>
#include <iterator>
#include <string>
#include <vector>
#include <array>
#include <numeric>
#include <functional>
#include <algorithm>
#include <ctime>
#include <chrono>
#include <memory>
#include <exception>
#include <getopt.h>
#include <limits>
#include <string.h>
#include <cmath>
#include <sys/stat.h>

//============================================ Development compilation pragmas
#ifdef __PROSHADE_DEVEL_CODE__
#pragma GCC diagnostic error "-Wshadow"
#pragma GCC diagnostic error "-Wpedantic"
#endif

typedef double fftw_complex[2];

namespace ProSHADE
{
    //======================================== The Task data type
    enum Task { NA, Symmetry, Distances, DistancesFrag, Features, BuildDB, HalfMaps, RotateMap, OverlayMap, SimpleRebox };
    
    class ProSHADE_settings
    {
    public:
        //==================================== Settings regarding resolutions
        double                                mapResolution;                       
        bool                                  wasResolutionGiven;                  
        unsigned int                          bandwidth;                           
        bool                                  wasBandGiven;                        
        unsigned int                          glIntegOrder;                        
        unsigned int                          theta;                               
        unsigned int                          phi;                                 
        bool                                  mapResDefault;                       
        
        //==================================== Settings regarding B factors
        double                                bFactorValue;                        
        double                                bFactorChange;                       
        bool                                  wasBChangeGiven;                     
        
        //==================================== Setting regarding maps and removing noise
        double                                noIQRsFromMap;                       
        
        //==================================== Settings regarding concentric shells
        double                                shellSpacing;                        
        bool                                  wasShellSpacingGiven;                
        unsigned int                          manualShells;                        
        
        //==================================== Settings regarding phase
        bool                                  usePhase;                            
        bool                                  saveWithAndWithout;                  
        
        //==================================== Settings regarding map with phases
        bool                                  useCOM;                              
        bool                                  firstLineCOM;                        
        
        //==================================== Settings regarding space around the structure in lattice
        double                                extraSpace;                          
        bool                                  wasExtraSpaceGiven;                  
        
        //==================================== Settings regarding weighting the distances
        double                                alpha;                               
        double                                mPower;                              
        
        //==================================== Settings regarding bands to ignore
        std::vector<int>                      ignoreLs;                            
        
        //==================================== Settings regarding the structures to use
        std::vector <std::string>             structFiles;                         
        
        //==================================== Settings regarding peak finding
        double                                peakHeightNoIQRs;                    
        double                                peakDistanceForReal;                 
        int                                   peakSurroundingPoints;               
        
        //==================================== Settings regarding axis and angle error tolerance
        double                                aaErrorTolerance;                    
        double                                symGapTolerance;                     
        
        //==================================== Settings regarding which distances to compute
        bool                                  energyLevelDist;                     
        bool                                  traceSigmaDist;                      
        bool                                  fullRotFnDist;                       
        
        //==================================== Settings regarding thresholds for hierarchical distance computation
        double                                enLevelsThreshold;                   
        double                                trSigmaThreshold;                    
        
        //==================================== Settings regarding which of the task to perform
        Task                                  taskToPerform;                       
        
        //==================================== Settings regarding where and if to save the clear map
        std::string                           clearMapFile;                        
        bool                                  useCubicMaps;                        
        bool                                  clearMapData;                        
        double                                maskBlurFactor;                      
        bool                                  maskBlurFactorGiven;                 
        
        //==================================== Settings regarding map fragmentation
        double                                mapFragBoxSize;                      
        std::string                           mapFragName;                         
        double                                mapFragBoxFraction;                  
        
        //==================================== Settings regarding structure database
        std::string                           databaseName;                        
        double                                databaseMinVolume;                   
        double                                databaseMaxVolume;                   
        double                                volumeTolerance;                     
        
        //==================================== Settings regarding the symmetry type required
        unsigned int                          symmetryFold;                        
        std::string                           symmetryType;                        
        
        //==================================== Settings regarding the map rotation mode
        double                                rotAngle;                            
        double                                rotXAxis;                            
        double                                rotYAxis;                            
        double                                rotZAxis;                            
        bool                                  rotChangeDefault;                    
        double                                xTranslation;                        
        double                                yTranslation;                        
        double                                zTranslation;                        
        
        //==================================== Settings regarding the map overlay mode
        bool                                  overlayDefaults;                     
        bool                                  dbDistOverlay;                       
        bool                                  resizeMovingStructure;
        unsigned int                          maxRotError;                         
        std::vector<std::string>              deleteModels;                        
        
        //==================================== Settings regarding the map saving mode
        std::string                           axisOrder;                           
        
        //==================================== Settings regarding verbosity of the program
        bool                                  htmlReport;                          
        int                                   htmlReportLine;                      
        int                                   htmlReportLineProgress;              
        int                                   verbose;                             
        
    public:
        //==================================== Public functions available to user: Constructor and destructor
        ProSHADE_settings                                                ( );
        
        //==================================== Public functions available to user: Pecularities
        void                                  printSettings              ( );
        void                                  getCommandLineParams       ( int argc, char* argv[] );
        void                                  ignoreLsAddValuePy         ( const int val );
        void                                  appendStructure            ( std::string str );
    };
    
    class ProSHADE
    {
        //==================================== Friends
        friend class ProSHADE_settings;
        
    private:
        //==================================== Keep settings object
        ProSHADE_settings*                    settings;                          
        
        //==================================== Decision bools
        bool                                  distancesAvailable;                
        bool                                  symmetriesAvailable;               
        bool                                  fragmentsAvailable;                
        
        //==================================== Values from the ProSHADE run
        std::vector<double>                   crossCorrDists;                    
        std::vector<double>                   traceSigmaDists;                   
        std::vector<double>                   rotFunctionDists;                  
        std::vector< std::array<double,5> >   cyclicSymmetries;                  
        std::vector< std::array<double,5> >   cyclicSymmetriesClear;             
        std::vector< std::vector< std::array<double,6> > > dihedralSymmetries;   
        std::vector< std::vector< std::array<double,6> > > dihedralSymmetriesClear; 
        std::vector< std::array<double,5> >   tetrahedralSymmetry;               
        std::vector< std::array<double,5> >   octahedralSymmetry;                
        std::vector< std::array<double,5> >   icosahedralSymmetry;               
        std::vector< std::string >            fragmentList;                      
        
    public:
        //==================================== Public functions available to user: Constructor and destructor
        ProSHADE                                                         ( ProSHADE_settings *settings );
        ~ProSHADE                                                        ( void );
        
        //==================================== Public functions available to user: Accessor functions for distances
        std::vector<double>                   getCrossCorrDists          ( void );
        std::vector<double>                   getTraceSigmaDists         ( void );
        std::vector<double>                   getRotFunctionDists        ( void );
        
        //==================================== Public functions available to user: Accessor functions for symmetries (C++)
        std::vector< std::array<double,5> >   getCyclicSymmetries        ( void );
        std::vector< std::array<double,5> >   getClearCyclicSymmetries   ( void );
        std::vector< std::vector<std::array< double,6> > > getDihedralSymmetries ( void );
        std::vector< std::vector<std::array< double,6> > > getClearDihedralSymmetries ( void );
        std::vector< std::array<double,5> >   getTetrahedralSymmetries   ( void );
        std::vector< std::array<double,5> >   getOctahedralSymmetries    ( void );
        std::vector< std::array<double,5> >   getIcosahedralSymmetries   ( void );
        std::vector< std::array<double,5> >   getRecommendedSymmetry     ( void );
        std::vector< std::array<double,5> >   getSpecificSymmetryElements ( std::string symType, int symFold = 0 );
        
        //==================================== Public functions available to user: Accessor functions for symmetries (Python)
        std::vector< double >                 getCyclicSymmetriesPy      ( void );
        std::vector< double >                 getDihedralSymmetriesPy    ( void );
        std::vector< double >                 getTetrahedralSymmetriesPy ( void );
        std::vector< double >                 getOctahedralSymmetriesPy  ( void );
        std::vector< double >                 getIcosahedralSymmetriesPy ( void );
        std::vector< double >                 getRecommendedSymmetryElementsPy ( void );
        std::vector< double >                 getSpecificSymmetryElementsPy ( std::string symType, int symFold = 0 );
        
        //==================================== Public functions available to user: Accessor functions for fragmentation
        std::vector< std::string >            getMapFragments            ( void );
        
        //==================================== Public functions available to user: Miscellaneous
        std::string                           getProSHADEVersion         ( void );
    };
}

//============================================ END
#endif