ProSHADE  0.7.6.2 (DEC 2021)
Protein Shape Detection
ProSHADE_internal_data Namespace Reference

This namespace contains the structure and functions required for data reading and storing their derivates. More...

Classes

class  ProSHADE_data
 This class contains all inputed and derived data for a single structure. More...
 

Functions

std::vector< std::vector< proshade_double > > computeGroupElementsForGroup (proshade_double xAx, proshade_double yAx, proshade_double zAx, proshade_signed fold)
 This function computes the group elements as rotation matrices (except for the identity element) for any cyclic point group given as axis and fold. More...
 
std::vector< std::vector< proshade_double > > joinElementsFromDifferentGroups (std::vector< std::vector< proshade_double > > *first, std::vector< std::vector< proshade_double > > *second, proshade_double matrixTolerance, bool combine)
 This function joins two group element lists using only unique elements. More...
 

Detailed Description

This namespace contains the structure and functions required for data reading and storing their derivates.

The ProSHADE_internal_data namespace contains the data structure. It also has the data derivates storing variables, but it does not provide the computation code except for the forward declarations. The user should not need to access this namespace when using the library.

Function Documentation

◆ computeGroupElementsForGroup()

std::vector< std::vector< proshade_double > > ProSHADE_internal_data::computeGroupElementsForGroup ( proshade_double  xAx,
proshade_double  yAx,
proshade_double  zAx,
proshade_signed  fold 
)

This function computes the group elements as rotation matrices (except for the identity element) for any cyclic point group given as axis and fold.

Parameters
[in]xAxThe x-axis element of the axis vector of the point group axis.
[in]yAxThe y-axis element of the axis vector of the point group axis.
[in]zAxThe z-axis element of the axis vector of the point group axis.
[in]foldThe fold of the point group.
[out]valA vector containing vectors of 9 (rotation matrix) for each group element for the requested group, except for the identity element.

Definition at line 2939 of file ProSHADE_data.cpp.

2940 {
2941  //================================================ Initialise variables
2942  std::vector< proshade_double > angList;
2943  std::vector<std::vector< proshade_double > > ret;
2944 
2945  //================================================ Allocate memory
2946  proshade_double* rotMat = new proshade_double[9];
2947  ProSHADE_internal_misc::checkMemoryAllocation ( rotMat, __FILE__, __LINE__, __func__ );
2948 
2949 
2950  //================================================ Normalise the axis to have magnitude of 1.0
2951  proshade_double normF = std::sqrt( std::pow ( xAx, 2.0 ) + std::pow ( yAx, 2.0 ) + std::pow ( zAx, 2.0 ) );
2952  xAx /= normF;
2953  yAx /= normF;
2954  zAx /= normF;
2955 
2956  //================================================ Determine the list of angles
2957  if ( fold % 2 == 0 )
2958  {
2959  //============================================ If fold is even, add the negative angles
2960  for ( proshade_double iter = static_cast < proshade_double > ( -( ( fold / 2 ) - 1 ) ); iter <= static_cast < proshade_double > ( fold / 2 ); iter++ )
2961  {
2962  ProSHADE_internal_misc::addToDoubleVector ( &angList, ( ( 2.0 * M_PI ) / static_cast<proshade_double> ( fold ) ) * iter );
2963  }
2964  }
2965  else
2966  {
2967  //============================================ If fold is odd, do the same as for even, but start one index earlier
2968  for ( proshade_double iter = static_cast < proshade_double > ( -fold / 2 ); iter <= static_cast < proshade_double > ( fold / 2 ); iter++ )
2969  {
2970  ProSHADE_internal_misc::addToDoubleVector ( &angList, ( ( 2.0 * M_PI ) / static_cast<proshade_double> ( fold ) ) * iter );
2971  }
2972  }
2973 
2974  //================================================ For each detected angle
2975  for ( proshade_unsign iter = 0; iter < static_cast < proshade_unsign > ( angList.size() ); iter++ )
2976  {
2977  //============================================ Compute the rotation matrix
2978  ProSHADE_internal_maths::getRotationMatrixFromAngleAxis ( rotMat, xAx, yAx, zAx, angList.at(iter) );
2979 
2980  //============================================ Convert to vector of vectors of doubles and save to ret
2981  std::vector < proshade_double > retEl;
2982  for ( proshade_unsign matIt = 0; matIt < 9; matIt++ )
2983  {
2984  ProSHADE_internal_misc::addToDoubleVector ( &retEl, rotMat[matIt] );
2985  }
2987  }
2988 
2989  //================================================ Release memory
2990  delete[] rotMat;
2991 
2992  //================================================ Done
2993  return ( ret );
2994 
2995 }

◆ joinElementsFromDifferentGroups()

std::vector< std::vector< proshade_double > > ProSHADE_internal_data::joinElementsFromDifferentGroups ( std::vector< std::vector< proshade_double > > *  first,
std::vector< std::vector< proshade_double > > *  second,
proshade_double  matrixTolerance,
bool  combine 
)

This function joins two group element lists using only unique elements.

Parameters
[in]firstVector of group elements.
[in]secondVector of group elements.
[in]matrixToleranceThe maximum trace error for rotation matrices to be still considered the same.
[in]combineShould the element combinations be added as well?
[out]retA vector of group elements containing all unique elements from both input element groups.

Definition at line 3092 of file ProSHADE_data.cpp.

3093 {
3094  //================================================ Initialise variables
3095  std::vector< std::vector< proshade_double > > ret;
3096 
3097  //================================================ Add the first list to ret, checking for uniqueness
3098  for ( proshade_unsign elIt = 0; elIt < static_cast<proshade_unsign> ( first->size() ); elIt++ )
3099  {
3100  if ( !checkElementAlreadyExists( &ret, &first->at(elIt), matrixTolerance ) )
3101  {
3102  ProSHADE_internal_misc::addToDoubleVectorVector ( &ret, first->at(elIt) );
3103  }
3104  }
3105 
3106  //================================================ Add the second list to ret, checking for uniqueness
3107  for ( proshade_unsign elIt = 0; elIt < static_cast<proshade_unsign> ( second->size() ); elIt++ )
3108  {
3109  if ( !checkElementAlreadyExists( &ret, &second->at(elIt), matrixTolerance ) )
3110  {
3111  ProSHADE_internal_misc::addToDoubleVectorVector ( &ret, second->at(elIt) );
3112  }
3113  }
3114 
3115  //================================================ Multiply all combinations of first and second and check for uniqueness
3116  if ( combine )
3117  {
3118  for ( proshade_unsign gr1 = 0; gr1 < static_cast<proshade_unsign> ( first->size() ); gr1++ )
3119  {
3120  for ( proshade_unsign gr2 = 0; gr2 < static_cast<proshade_unsign> ( second->size() ); gr2++ )
3121  {
3122  //==================================== Multiply the two rotation matrices
3123  std::vector< proshade_double > product = ProSHADE_internal_maths::multiplyGroupElementMatrices ( &first->at(gr1), &second->at(gr2) );
3124 
3125  //==================================== Add
3126  if ( !checkElementAlreadyExists( &ret, &product, matrixTolerance ) )
3127  {
3129  }
3130 
3131  }
3132  }
3133  }
3134 
3135  //================================================ Done
3136  return ( ret );
3137 
3138 }
ProSHADE_internal_misc::addToDoubleVector
void addToDoubleVector(std::vector< proshade_double > *vecToAddTo, proshade_double elementToAdd)
Adds the element to the vector.
Definition: ProSHADE_misc.cpp:77
ProSHADE_internal_maths::getRotationMatrixFromAngleAxis
void getRotationMatrixFromAngleAxis(proshade_double *rotMat, proshade_double x, proshade_double y, proshade_double z, proshade_double ang)
This function converts the axis-angle representation to the rotation matrix representation.
Definition: ProSHADE_maths.cpp:1459
ProSHADE_internal_misc::checkMemoryAllocation
void checkMemoryAllocation(chVar checkVar, std::string fileP, unsigned int lineP, std::string funcP, std::string infoP="This error may occurs when ProSHADE requests memory to be\n : allocated to it and this operation fails. This could\n : happen when not enough memory is available, either due to\n : other processes using a lot of memory, or when the machine\n : does not have sufficient memory available. Re-run to see\n : if this problem persists.")
Checks if memory was allocated properly.
Definition: ProSHADE_misc.hpp:68
ProSHADE_internal_misc::addToDoubleVectorVector
void addToDoubleVectorVector(std::vector< std::vector< proshade_double > > *vecToAddTo, std::vector< proshade_double > elementToAdd)
Adds the element to the vector of vectors.
Definition: ProSHADE_misc.cpp:233
ProSHADE_internal_maths::multiplyGroupElementMatrices
std::vector< proshade_double > multiplyGroupElementMatrices(std::vector< proshade_double > *el1, std::vector< proshade_double > *el2)
This function computes matrix multiplication using the ProSHADE group element matrix format as input ...
Definition: ProSHADE_maths.cpp:2499
checkElementAlreadyExists
bool checkElementAlreadyExists(std::vector< std::vector< proshade_double > > *elements, std::vector< proshade_double > *elem, proshade_double matrixTolerance)
This function checks if the element list already contains a given matrix.
Definition: ProSHADE_data.cpp:3025