ProSHADE  0.7.5.3 (FEB 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 2268 of file ProSHADE_data.cpp.

2269 {
2270  //================================================ Initialise variables
2271  std::vector< proshade_double > angList;
2272  std::vector<std::vector< proshade_double > > ret;
2273 
2274  //================================================ Allocate memory
2275  proshade_double* rotMat = new proshade_double[9];
2276  ProSHADE_internal_misc::checkMemoryAllocation ( rotMat, __FILE__, __LINE__, __func__ );
2277 
2278 
2279  //================================================ Normalise the axis to have magnitude of 1.0
2280  proshade_double normF = std::sqrt( std::pow ( xAx, 2.0 ) + std::pow ( yAx, 2.0 ) + std::pow ( zAx, 2.0 ) );
2281  xAx /= normF;
2282  yAx /= normF;
2283  zAx /= normF;
2284 
2285  //================================================ Determine the list of angles
2286  if ( fold % 2 == 0 )
2287  {
2288  //============================================ If fold is even, add the negative angles
2289  for ( proshade_double iter = static_cast < proshade_double > ( -( ( fold / 2 ) - 1 ) ); iter <= static_cast < proshade_double > ( fold / 2 ); iter++ )
2290  {
2291  ProSHADE_internal_misc::addToDoubleVector ( &angList, ( ( 2.0 * M_PI ) / static_cast<proshade_double> ( fold ) ) * iter );
2292  }
2293  }
2294  else
2295  {
2296  //============================================ If fold is odd, do the same as for even, but start one index earlier
2297  for ( proshade_double iter = static_cast < proshade_double > ( -fold / 2 ); iter <= static_cast < proshade_double > ( fold / 2 ); iter++ )
2298  {
2299  ProSHADE_internal_misc::addToDoubleVector ( &angList, ( ( 2.0 * M_PI ) / static_cast<proshade_double> ( fold ) ) * iter );
2300  }
2301  }
2302 
2303  //================================================ For each detected angle
2304  for ( proshade_unsign iter = 0; iter < static_cast < proshade_unsign > ( angList.size() ); iter++ )
2305  {
2306  //============================================ Compute the rotation matrix
2307  ProSHADE_internal_maths::getRotationMatrixFromAngleAxis ( rotMat, xAx, yAx, zAx, angList.at(iter) );
2308 
2309  //============================================ Convert to vector of vectors of doubles and save to ret
2310  std::vector < proshade_double > retEl;
2311  for ( proshade_unsign matIt = 0; matIt < 9; matIt++ )
2312  {
2313  ProSHADE_internal_misc::addToDoubleVector ( &retEl, rotMat[matIt] );
2314  }
2316  }
2317 
2318  //================================================ Release memory
2319  delete[] rotMat;
2320 
2321  //================================================ Done
2322  return ( ret );
2323 
2324 }

◆ 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 2421 of file ProSHADE_data.cpp.

2422 {
2423  //================================================ Initialise variables
2424  std::vector< std::vector< proshade_double > > ret;
2425 
2426  //================================================ Add the first list to ret, checking for uniqueness
2427  for ( proshade_unsign elIt = 0; elIt < static_cast<proshade_unsign> ( first->size() ); elIt++ )
2428  {
2429  if ( !checkElementAlreadyExists( &ret, &first->at(elIt), matrixTolerance ) )
2430  {
2431  ProSHADE_internal_misc::addToDoubleVectorVector ( &ret, first->at(elIt) );
2432  }
2433  }
2434 
2435  //================================================ Add the second list to ret, checking for uniqueness
2436  for ( proshade_unsign elIt = 0; elIt < static_cast<proshade_unsign> ( second->size() ); elIt++ )
2437  {
2438  if ( !checkElementAlreadyExists( &ret, &second->at(elIt), matrixTolerance ) )
2439  {
2440  ProSHADE_internal_misc::addToDoubleVectorVector ( &ret, second->at(elIt) );
2441  }
2442  }
2443 
2444  //================================================ Multiply all combinations of first and second and check for uniqueness
2445  if ( combine )
2446  {
2447  for ( proshade_unsign gr1 = 0; gr1 < static_cast<proshade_unsign> ( first->size() ); gr1++ )
2448  {
2449  for ( proshade_unsign gr2 = 0; gr2 < static_cast<proshade_unsign> ( second->size() ); gr2++ )
2450  {
2451  //==================================== Multiply the two rotation matrices
2452  std::vector< proshade_double > product = ProSHADE_internal_maths::multiplyGroupElementMatrices ( &first->at(gr1), &second->at(gr2) );
2453 
2454  //==================================== Add
2455  if ( !checkElementAlreadyExists( &ret, &product, matrixTolerance ) )
2456  {
2458  }
2459 
2460  }
2461  }
2462  }
2463 
2464  //================================================ Done
2465  return ( ret );
2466 
2467 }
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:1343
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:65
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:210
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:2141
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:2354