ProSHADE  0.7.6.6 (JUL 2022)
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 2911 of file ProSHADE_data.cpp.

2912 {
2913  //================================================ Initialise variables
2914  std::vector< proshade_double > angList;
2915  std::vector<std::vector< proshade_double > > ret;
2916 
2917  //================================================ Allocate memory
2918  proshade_double* rotMat = new proshade_double[9];
2919  ProSHADE_internal_misc::checkMemoryAllocation ( rotMat, __FILE__, __LINE__, __func__ );
2920 
2921 
2922  //================================================ Normalise the axis to have magnitude of 1.0
2923  proshade_double normF = std::sqrt( std::pow ( xAx, 2.0 ) + std::pow ( yAx, 2.0 ) + std::pow ( zAx, 2.0 ) );
2924  xAx /= normF;
2925  yAx /= normF;
2926  zAx /= normF;
2927 
2928  //================================================ Determine the list of angles
2929  if ( fold % 2 == 0 )
2930  {
2931  //============================================ If fold is even, add the negative angles
2932  for ( proshade_double iter = static_cast < proshade_double > ( -( ( fold / 2 ) - 1 ) ); iter <= static_cast < proshade_double > ( fold / 2 ); iter++ )
2933  {
2934  ProSHADE_internal_misc::addToDoubleVector ( &angList, ( ( 2.0 * M_PI ) / static_cast<proshade_double> ( fold ) ) * iter );
2935  }
2936  }
2937  else
2938  {
2939  //============================================ If fold is odd, do the same as for even, but start one index earlier
2940  for ( proshade_double iter = static_cast < proshade_double > ( -fold / 2 ); iter <= static_cast < proshade_double > ( fold / 2 ); iter++ )
2941  {
2942  ProSHADE_internal_misc::addToDoubleVector ( &angList, ( ( 2.0 * M_PI ) / static_cast<proshade_double> ( fold ) ) * iter );
2943  }
2944  }
2945 
2946  //================================================ For each detected angle
2947  for ( proshade_unsign iter = 0; iter < static_cast < proshade_unsign > ( angList.size() ); iter++ )
2948  {
2949  //============================================ Compute the rotation matrix
2950  ProSHADE_internal_maths::getRotationMatrixFromAngleAxis ( rotMat, xAx, yAx, zAx, angList.at(iter) );
2951 
2952  //============================================ Convert to vector of vectors of doubles and save to ret
2953  std::vector < proshade_double > retEl;
2954  for ( proshade_unsign matIt = 0; matIt < 9; matIt++ )
2955  {
2956  ProSHADE_internal_misc::addToDoubleVector ( &retEl, rotMat[matIt] );
2957  }
2959  }
2960 
2961  //================================================ Release memory
2962  delete[] rotMat;
2963 
2964  //================================================ Done
2965  return ( ret );
2966 
2967 }

◆ 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 3064 of file ProSHADE_data.cpp.

3065 {
3066  //================================================ Initialise variables
3067  std::vector< std::vector< proshade_double > > ret;
3068 
3069  //================================================ Add the first list to ret, checking for uniqueness
3070  for ( proshade_unsign elIt = 0; elIt < static_cast<proshade_unsign> ( first->size() ); elIt++ )
3071  {
3072  if ( !checkElementAlreadyExists( &ret, &first->at(elIt), matrixTolerance ) )
3073  {
3074  ProSHADE_internal_misc::addToDoubleVectorVector ( &ret, first->at(elIt) );
3075  }
3076  }
3077 
3078  //================================================ Add the second list to ret, checking for uniqueness
3079  for ( proshade_unsign elIt = 0; elIt < static_cast<proshade_unsign> ( second->size() ); elIt++ )
3080  {
3081  if ( !checkElementAlreadyExists( &ret, &second->at(elIt), matrixTolerance ) )
3082  {
3083  ProSHADE_internal_misc::addToDoubleVectorVector ( &ret, second->at(elIt) );
3084  }
3085  }
3086 
3087  //================================================ Multiply all combinations of first and second and check for uniqueness
3088  if ( combine )
3089  {
3090  for ( proshade_unsign gr1 = 0; gr1 < static_cast<proshade_unsign> ( first->size() ); gr1++ )
3091  {
3092  for ( proshade_unsign gr2 = 0; gr2 < static_cast<proshade_unsign> ( second->size() ); gr2++ )
3093  {
3094  //==================================== Multiply the two rotation matrices
3095  std::vector< proshade_double > product = ProSHADE_internal_maths::multiplyGroupElementMatrices ( &first->at(gr1), &second->at(gr2) );
3096 
3097  //==================================== Add
3098  if ( !checkElementAlreadyExists( &ret, &product, matrixTolerance ) )
3099  {
3101  }
3102 
3103  }
3104  }
3105  }
3106 
3107  //================================================ Done
3108  return ( ret );
3109 
3110 }
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:1458
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:73
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:2523
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:2997