ProSHADE_run Class Reference

This class provides the access point to the library. More...

#include <ProSHADE.hpp>

Public Member Functions
	ProSHADE_run (ProSHADE_settings *settings)
	Contructor for the ProSHADE_run class. More...
	~ProSHADE_run (void)
	Destructor for the ProSHADE class. More...
proshade_unsign	getNoStructures (void)
	This function returns the number of structures used. More...
proshade_signed	getVerbose (void)
	This function returns the verbose value. More...
proshade_unsign	getNoRecommendedSymmetryAxes (void)
	This function returns the number of detected recommended symmetry axes. More...
proshade_unsign	getNoSymmetryAxes (void)
	This function returns the number of detected recommended symmetry axes. More...
std::vector< proshade_double >	getEnergyLevelsVector (void)
	This function returns the energy level distances vector from the first to all other structures. More...
std::vector< proshade_double >	getTraceSigmaVector (void)
	This function returns the trace sigma distances vector from the first to all other structures. More...
std::vector< proshade_double >	getRotationFunctionVector (void)
	This function returns the full rotation function distances vector from the first to all other structures. More...
std::string	getSymmetryType (void)
	This is the main accessor function for the user to get to know what symmetry type ProSHADE has detected and recommends. More...
proshade_unsign	getSymmetryFold (void)
	This is the main accessor function for the user to get to know what symmetry fold ProSHADE has detected and recommends. More...
std::vector< std::string >	getSymmetryAxis (proshade_unsign axisNo)
	This function returns a single symmetry axis as a vector of strings from the recommended symmetry axes list. More...
std::vector< std::vector< proshade_double > >	getAllCSyms (void)
	This function returns a all symmetry axes as a vector of vectors of doubles. More...
std::vector< proshade_double >	getMapCOMProcessChange (void)
	This function returns the internal map COM shift. More...
std::vector< proshade_signed >	getOriginalBounds (proshade_unsign strNo)
	This function returns a specific structure original bounds. More...
std::vector< proshade_signed >	getReBoxedBounds (proshade_unsign strNo)
	This function returns a specific structure re-boxed bounds. More...
proshade_double	getMapValue (proshade_unsign strNo, proshade_unsign mapIndex)
	This function returns a single, specific structure map value. More...
std::vector< proshade_double >	getEulerAngles (void)
	This function returns the vector of Euler angles with best overlay correlation. More...
std::vector< proshade_double >	getOptimalRotMat (void)
	This function returns the vector forming rotation matrix (rows first) with best overlay correlation. More...
std::vector< proshade_double >	getTranslationToOrigin (void)
	This function returns the negative values of the position of the rotation centre (the point about which the rotation should be done). More...
std::vector< proshade_double >	getOriginToOverlayTranslation (void)
	This function returns the translation required to move the structure from origin to optimal overlay. More...

Detailed Description

This class provides the access point to the library.

This class codes the object that the user of the library needs to create (and presumably delete) in order to get access to the ProSHADE library.

Definition at line 38 of file ProSHADE.hpp.

Constructor & Destructor Documentation

ProSHADE_run()

ProSHADE_run::ProSHADE_run

(

ProSHADE_settings *

settings

)

Contructor for the ProSHADE_run class.

This is where all the decisions regarding what should be done are made. It takes the settings and based on them, it decides what to do and how to report the results.

Parameters

[in]

settings

ProSHADE_settings object specifying what should be done.

Definition at line 1900 of file ProSHADE.cpp.

{
    //================================================ Wellcome message if required
    ProSHADE_internal_messages::printWellcomeMessage  ( settings->verbose );
    
    //================================================ Save the general information
    this->noStructures                                = static_cast<proshade_unsign> ( settings->inputFiles.size() );
    this->verbose                                     = static_cast<proshade_signed> ( settings->verbose );
    
    //================================================ Try to run ProSHADE
    try
    {
        //============================================ Depending on task, switch to correct function to call
        switch ( settings->task )
        {
            case NA:
                throw ProSHADE_exception ( "No task has been specified.", "E000001", __FILE__, __LINE__, __func__, "ProSHADE requires to be told which particular functiona-\n                    : lity (task) is requested from it. In order to do so, the\n                    : command line arguments specifying task need to be used\n                    : (if used from command line), or the ProSHADE_settings\n                    : object needs to have the member variable \'Task\' set to\n                    : one of the following values: Distances, Symmetry,\n                    : OverlayMap or MapManip." );
                
            case Symmetry:
                ProSHADE_internal_tasks::SymmetryDetectionTask ( settings, &this->mapCOMShift, &this->symRecommType, &this->symRecommFold, &this->RecomSymAxes, &this->allCSymAxes );
                
                break;
                
            case Distances:
                ProSHADE_internal_tasks::DistancesComputationTask ( settings, &this->enLevs, &this->trSigm, &this->rotFun );
                break;
                
            case OverlayMap:
                ProSHADE_internal_tasks::MapOverlayTask ( settings, &this->coordRotationCentre, &this->eulerAngles, &this->overlayTranslation );
                break;
                
            case MapManip:
                ProSHADE_internal_tasks::MapManipulationTask ( settings, &this->originalBounds, &this->reboxedBounds, &this->manipulatedMaps );
                break;
        }
    }
    
    //================================================ If this is ProSHADE exception, give all available info and terminate gracefully :-)
    catch ( ProSHADE_exception& err )
    {
        std::cerr << std::endl << "=====================" << std::endl << "!! ProSHADE ERROR !!" << std::endl << "=====================" << std::endl << std::flush;
        std::cerr << "Error Code          : " << err.get_errc() << std::endl << std::flush;
        std::cerr << "ProSHADE version    : " << PROSHADE_VERSION << std::endl << std::flush;
        std::cerr << "File                : " << err.get_file() << std::endl << std::flush;
        std::cerr << "Line                : " << err.get_line() << std::endl << std::flush;
        std::cerr << "Function            : " << err.get_func() << std::endl << std::flush;
        std::cerr << "Message             : " << err.what() << std::endl << std::flush;
        std::cerr << "Further information : " << err.get_info() << std::endl << std::endl << std::flush;
        
        //============================================ Done
        ProSHADE_internal_messages::printTerminateMessage ( settings->verbose );
        exit                                          ( EXIT_FAILURE );
    }
    
    //================================================ Well, give all there is and just end
    catch ( ... )
    {
        std::cerr << std::endl << "=====================" << std::endl << "!! ProSHADE ERROR !!" << std::endl << "=====================" << std::endl << std::flush;
        
        //============================================ Try to find out more
#if __cplusplus >= 201103L
            std::exception_ptr exc                    = std::current_exception();
            try
            {
                if (exc)
                {
                    std::rethrow_exception            ( exc );
                }
            }
            catch ( const std::exception& e )
            {
                std::cerr << "Caught unknown exception with following information: " << e.what() << std::endl << std::flush;
            }
#else
            std::cerr << "Unknown error with no further explanation available. Please contact the author for help." << std::endl << std::flush;
#endif
        std::cerr << "Terminating..." << std::endl << std::endl << std::flush;
        
        //============================================ Done
        ProSHADE_internal_messages::printTerminateMessage ( settings->verbose );
        exit                                          ( EXIT_FAILURE );
    }
    
    //================================================ Terminating message
    ProSHADE_internal_messages::printTerminateMessage ( settings->verbose );
    
    //================================================ Done
    
}

~ProSHADE_run()

ProSHADE_run::~ProSHADE_run

(

void

)

Destructor for the ProSHADE class.

This destructor is responsible for releasing all memory used by the executing object

Definition at line 1998 of file ProSHADE.cpp.

{
    //================================================ Release reboxing pointers
    if ( this->originalBounds.size() > 0 ) { for ( proshade_unsign iter = 0; iter < static_cast<proshade_unsign> ( this->originalBounds.size() ); iter++ ) { delete[] this->originalBounds.at(iter); } }
    if ( this->reboxedBounds.size()  > 0 ) { for ( proshade_unsign iter = 0; iter < static_cast<proshade_unsign> ( this->reboxedBounds.size()  ); iter++ ) { delete[] this->reboxedBounds.at(iter); } }
    if ( this->manipulatedMaps.size() > 0 ) { for ( proshade_unsign iter = 0; iter < static_cast<proshade_unsign> ( this->manipulatedMaps.size() ); iter++ ) { delete[] this->manipulatedMaps.at(iter); } }
    
    //================================================ Clear vectors
    this->enLevs.clear                                ( );
    this->trSigm.clear                                ( );
    this->rotFun.clear                                ( );
    
    //================================================ Delete symmetry axes memory
    if ( this->RecomSymAxes.size() > 0 )
    {
        for ( size_t iter = 0; iter < this->RecomSymAxes.size(); iter++ )
        {
            delete[] this->RecomSymAxes.at(iter);
        }
        this->RecomSymAxes.clear                      ( );
    }
    
    //================================================ Done
    
}

Member Function Documentation

getAllCSyms()

std::vector< std::vector< proshade_double > > ProSHADE_run::getAllCSyms

(

void

)

This function returns a all symmetry axes as a vector of vectors of doubles.

Parameters

[out]

val

A vector of vectors of doubles containing all the symmetries axis fold, x, y, z axis element, angle and peak height in this order.

Definition at line 3154 of file ProSHADE.cpp.

{
    //================================================ Done
    return                                            ( this->allCSymAxes );
    
}

getEnergyLevelsVector()

std::vector< proshade_double > ProSHADE_run::getEnergyLevelsVector

(

void

)

This function returns the energy level distances vector from the first to all other structures.

Parameters

[out]

enLevs

Vector of doubles of the distances.

Definition at line 3016 of file ProSHADE.cpp.

{
    //================================================ Return the value
    return                                            ( this->enLevs );
}

getEulerAngles()

std::vector< proshade_double > ProSHADE_run::getEulerAngles

(

void

)

This function returns the vector of Euler angles with best overlay correlation.

Parameters

[out]

ret

Vector of Euler angles (ZYZ convention) which lead to the globally best overlay correlation.

Definition at line 3295 of file ProSHADE.cpp.

{
    //================================================ Sanity check
    if ( this->eulerAngles.size() != 3 )
    {
        ProSHADE_internal_messages::printWarningMessage ( this->verbose, "!!! ProSHADE WARNING !!! Requested rotation/translation values for Overlay functionality without having successfully computed it. Please check the correct task was used and no other warnings/errors were obtained.", "WO00042" );
        return                                        ( std::vector< proshade_double > ( ) );
    }
    
    //================================================ Return required value
    return                                            ( this->eulerAngles );
    
}

getMapCOMProcessChange()

std::vector< proshade_double > ProSHADE_run::getMapCOMProcessChange

(

void

)

This function returns the internal map COM shift.

Parameters

[out]

val

The shift used to centre the internal map COM to the centre of the box.

Definition at line 3169 of file ProSHADE.cpp.

{
    //================================================ Done
    return                                            ( this->mapCOMShift );
    
}

getMapValue()

proshade_double ProSHADE_run::getMapValue	(	proshade_unsign	strNo,
		proshade_unsign	mapIndex
	)

This function returns a single, specific structure map value.

Parameters

[in]	strNo	The index of the structure for which the map value is to be returned.
[in]	mapIndex	The map array index of which the value is returned.
[out]	val	The map density value for the particular mapIndex position.

Definition at line 3250 of file ProSHADE.cpp.

{
    //================================================ Return the value
    return                                            ( this->manipulatedMaps.at(strNo)[mapIndex] );
}

getNoRecommendedSymmetryAxes()

proshade_unsign ProSHADE_run::getNoRecommendedSymmetryAxes

(

void

)

This function returns the number of detected recommended symmetry axes.

Parameters

[out]

val

The length of the recommended symmetry axes vector.

Definition at line 3085 of file ProSHADE.cpp.

{
    //================================================ Return the value
    return                                            ( static_cast<proshade_unsign> ( this->RecomSymAxes.size() ) );
}

getNoStructures()

proshade_unsign ProSHADE_run::getNoStructures

(

void

)

This function returns the number of structures used.

Parameters

[in]

noStructures

Number of structures supplied to the settings object.

Definition at line 3055 of file ProSHADE.cpp.

{
    //================================================ Return the value
    return                                            ( this->noStructures );
}

getNoSymmetryAxes()

proshade_unsign ProSHADE_run::getNoSymmetryAxes

(

void

)

This function returns the number of detected recommended symmetry axes.

Parameters

[out]

val

The length of the recommended symmetry axes vector.

Definition at line 3075 of file ProSHADE.cpp.

{
    //================================================ Return the value
    return                                            ( static_cast<proshade_unsign> ( this->RecomSymAxes.size() ) );
}

getOptimalRotMat()

std::vector< proshade_double > ProSHADE_run::getOptimalRotMat

(

void

)

This function returns the vector forming rotation matrix (rows first) with best overlay correlation.

Parameters

[out]

ret

Vector forming rotation matrix (rows first) which lead to the globally best overlay correlation.

Definition at line 3317 of file ProSHADE.cpp.

{
    //================================================ Sanity check
    if ( this->eulerAngles.size() != 3 )
    {
        ProSHADE_internal_messages::printWarningMessage ( this->verbose, "!!! ProSHADE WARNING !!! Requested rotation/translation values for Overlay functionality without having successfully computed it. Please check the correct task was used and no other warnings/errors were obtained.", "WO00042" );
        return                                        ( std::vector< proshade_double > ( ) );
    }
    
    //================================================ Obtain the optimal rotation matrix
    proshade_double* rotMat                           = new proshade_double[9];
    ProSHADE_internal_misc::checkMemoryAllocation     ( rotMat, __FILE__, __LINE__, __func__ );
    ProSHADE_internal_maths::getRotationMatrixFromEulerZYZAngles ( this->eulerAngles.at(0), this->eulerAngles.at(1), this->eulerAngles.at(2), rotMat );
    
    //================================================ Copy to the output variable
    std::vector< proshade_double > ret;
    for ( proshade_unsign iter = 0; iter < 9; iter++ ) { ProSHADE_internal_misc::addToDoubleVector ( &ret, rotMat[iter] ); }
    
    //================================================ Release the memory
    delete[] rotMat;
    
    //================================================ Return required value
    return                                            ( ret );
    
}

getOriginalBounds()

std::vector< proshade_signed > ProSHADE_run::getOriginalBounds

(

proshade_unsign

strNo

)

This function returns a specific structure original bounds.

Parameters

[in]

strNo

The index of the structure for which the bounds are to be returned.

Definition at line 3184 of file ProSHADE.cpp.

{
    //================================================ Sanity checks
    if ( noStructures <= strNo )
    {
        ProSHADE_internal_messages::printWarningMessage ( this->verbose, "!!! ProSHADE WARNING !!! Requested bounds for structure index which does not exist. Returning empty vector.", "WB00041" );
        return                                        ( std::vector< proshade_signed > ( ) );
    }
    
    //================================================ Initialise local variables
    std::vector< proshade_signed > ret;
    
    //================================================ Input the axis data as strings
    ProSHADE_internal_misc::addToSignedVector         ( &ret, this->originalBounds.at( strNo )[0] );
    ProSHADE_internal_misc::addToSignedVector         ( &ret, this->originalBounds.at( strNo )[1] );
    ProSHADE_internal_misc::addToSignedVector         ( &ret, this->originalBounds.at( strNo )[2] );
    ProSHADE_internal_misc::addToSignedVector         ( &ret, this->originalBounds.at( strNo )[3] );
    ProSHADE_internal_misc::addToSignedVector         ( &ret, this->originalBounds.at( strNo )[4] );
    ProSHADE_internal_misc::addToSignedVector         ( &ret, this->originalBounds.at( strNo )[5] );
    
    //================================================ Done
    return                                            ( ret );
}

getOriginToOverlayTranslation()

std::vector< proshade_double > ProSHADE_run::getOriginToOverlayTranslation

(

void

)

This function returns the translation required to move the structure from origin to optimal overlay.

Parameters

[out]

ret

Translation required to move structure from origin to optimal overlay.

Definition at line 3379 of file ProSHADE.cpp.

{
    //================================================ Sanity check
    if ( this->overlayTranslation.size() != 3 )
    {
        ProSHADE_internal_messages::printWarningMessage ( this->verbose, "!!! ProSHADE WARNING !!! Requested rotation/translation values for Overlay functionality without having successfully computed it. Please check the correct task was used and no other warnings/errors were obtained.", "WO00042" );
        return                                        ( std::vector< proshade_double > ( ) );
    }
    
    //================================================ Return required value
    return                                            ( this->overlayTranslation );
    
}

getReBoxedBounds()

std::vector< proshade_signed > ProSHADE_run::getReBoxedBounds

(

proshade_unsign

strNo

)

This function returns a specific structure re-boxed bounds.

Parameters

[in]

strNo

The index of the structure for which the bounds are to be returned.

Definition at line 3216 of file ProSHADE.cpp.

{
    //================================================ Sanity checks
    if ( noStructures <= strNo )
    {
        ProSHADE_internal_messages::printWarningMessage ( this->verbose, "!!! ProSHADE WARNING !!! Requested bounds for structure index which does not exist. Returning empty vector.", "WB00041" );
        return                                        ( std::vector< proshade_signed > ( ) );
    }
    
    //================================================ Initialise local variables
    std::vector< proshade_signed > ret;
    
    //================================================ Input the axis data as strings
    ProSHADE_internal_misc::addToSignedVector         ( &ret, this->reboxedBounds.at( strNo )[0] );
    ProSHADE_internal_misc::addToSignedVector         ( &ret, this->reboxedBounds.at( strNo )[1] );
    ProSHADE_internal_misc::addToSignedVector         ( &ret, this->reboxedBounds.at( strNo )[2] );
    ProSHADE_internal_misc::addToSignedVector         ( &ret, this->reboxedBounds.at( strNo )[3] );
    ProSHADE_internal_misc::addToSignedVector         ( &ret, this->reboxedBounds.at( strNo )[4] );
    ProSHADE_internal_misc::addToSignedVector         ( &ret, this->reboxedBounds.at( strNo )[5] );
    
    //================================================ Done
    return                                            ( ret );
}

getRotationFunctionVector()

std::vector< proshade_double > ProSHADE_run::getRotationFunctionVector

(

void

)

This function returns the full rotation function distances vector from the first to all other structures.

Parameters

[out]

rotFun

Vector of doubles of the distances.

Definition at line 3044 of file ProSHADE.cpp.

{
    //================================================ Return the value
    return                                            ( this->rotFun );
}

getSymmetryAxis()

std::vector< std::string > ProSHADE_run::getSymmetryAxis

(

proshade_unsign

axisNo

)

This function returns a single symmetry axis as a vector of strings from the recommended symmetry axes list.

Parameters

[in]	axisNo	The index of the axis to be returned.
[out]	val	A vector of strings containing the symmetry axis fold, x, y, z axis element, angle and peak height in this order.

Definition at line 3099 of file ProSHADE.cpp.

{
    //================================================ Sanity checks
    if ( static_cast<proshade_unsign> ( this->RecomSymAxes.size() ) <= axisNo )
    {
        ProSHADE_internal_messages::printWarningMessage ( this->verbose, "!!! ProSHADE WARNING !!! Requested symmetry index does not exist. Returning empty vector.", "WS00039" );
        return                                        ( std::vector< std::string > ( ) );
    }
    
    //================================================ Initialise local variables
    std::vector< std::string > ret;
    
    //================================================ Input the axis data as strings
    std::stringstream ssHlp;
    ssHlp << this->RecomSymAxes.at(axisNo)[0];
    ProSHADE_internal_misc::addToStringVector         ( &ret, ssHlp.str() );
    ssHlp.str                                         ( "" );
    
    ssHlp << this->RecomSymAxes.at(axisNo)[1];
    ProSHADE_internal_misc::addToStringVector         ( &ret, ssHlp.str() );
    ssHlp.str                                         ( "" );
            
    ssHlp << this->RecomSymAxes.at(axisNo)[2];
    ProSHADE_internal_misc::addToStringVector         ( &ret, ssHlp.str() );
    ssHlp.str                                         ( "" );
            
    ssHlp << this->RecomSymAxes.at(axisNo)[3];
    ProSHADE_internal_misc::addToStringVector         ( &ret, ssHlp.str() );
    ssHlp.str                                         ( "" );
            
    ssHlp << this->RecomSymAxes.at(axisNo)[4];
    ProSHADE_internal_misc::addToStringVector         ( &ret, ssHlp.str() );
    ssHlp.str                                         ( "" );
            
    ssHlp << this->RecomSymAxes.at(axisNo)[5];
    ProSHADE_internal_misc::addToStringVector         ( &ret, ssHlp.str() );
    ssHlp.str                                         ( "" );
    
    ssHlp << this->RecomSymAxes.at(axisNo)[6];
    ProSHADE_internal_misc::addToStringVector         ( &ret, ssHlp.str() );
    ssHlp.str                                         ( "" );
    
    //================================================ Done
    return                                            ( ret );
    
}

getSymmetryFold()

proshade_unsign ProSHADE_run::getSymmetryFold

(

void

)

This is the main accessor function for the user to get to know what symmetry fold ProSHADE has detected and recommends.

Parameters

[out]

symRecommFold

This is the fold of ProSHADE detected and recommended symmetry (C and D symmetry types only).

Definition at line 2047 of file ProSHADE.cpp.

{
    //================================================ Return the value
    return                                            ( this->symRecommFold );
}

getSymmetryType()

std::string ProSHADE_run::getSymmetryType

(

void

)

This is the main accessor function for the user to get to know what symmetry type ProSHADE has detected and recommends.

Parameters

[out]

symRecommType

This is the value ( ""=None, C=cyclic, D=Dihedral, T=Tetrahedral, O=Octahedral or I=Icosahedral) of ProSHADE detected and recommended symmetry.

Definition at line 2032 of file ProSHADE.cpp.

{
    //================================================ Return the value
    return                                            ( this->symRecommType );
}

getTraceSigmaVector()

std::vector< proshade_double > ProSHADE_run::getTraceSigmaVector

(

void

)

This function returns the trace sigma distances vector from the first to all other structures.

Parameters

[out]

trSigm

Vector of doubles of the distances.

Definition at line 3030 of file ProSHADE.cpp.

{
    //================================================ Return the value
    return                                            ( this->trSigm );
}

getTranslationToOrigin()

std::vector< proshade_double > ProSHADE_run::getTranslationToOrigin

(

void

)

This function returns the negative values of the position of the rotation centre (the point about which the rotation should be done).

Parameters

[out]

ret

Vector specifying the negative values of the rotation centre - i.e. the translation of the rotation centre to the origin.

Definition at line 3351 of file ProSHADE.cpp.

{
    //================================================ Sanity check
    if ( this->coordRotationCentre.size() != 3 )
    {
        ProSHADE_internal_messages::printWarningMessage ( this->verbose, "!!! ProSHADE WARNING !!! Requested rotation/translation values for Overlay functionality without having successfully computed it. Please check the correct task was used and no other warnings/errors were obtained.", "WO00042" );
        return                                        ( std::vector< proshade_double > ( ) );
    }
    
    //================================================ Create return variable with negative values of the internal varariable
    std::vector < proshade_double > ret;
    ProSHADE_internal_misc::addToDoubleVector         ( &ret, -this->coordRotationCentre.at(0) );
    ProSHADE_internal_misc::addToDoubleVector         ( &ret, -this->coordRotationCentre.at(1) );
    ProSHADE_internal_misc::addToDoubleVector         ( &ret, -this->coordRotationCentre.at(2) );
    
    //================================================ Return required value
    return                                            ( ret );
    
}

getVerbose()

proshade_signed ProSHADE_run::getVerbose

(

void

)

This function returns the verbose value.

Parameters

[in]

verbose

How loud the run should be?

Definition at line 3065 of file ProSHADE.cpp.

{
    //================================================ Return the value
    return                                            ( this->verbose );
}

---

The documentation for this class was generated from the following files:

• src/proshade/ProSHADE.hpp
• src/proshade/ProSHADE.cpp