ProSHADE  0.7.5.4 (MAR 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 2333 of file ProSHADE_data.cpp.

2334 {
2335  //================================================ Initialise variables
2336  std::vector< proshade_double > angList;
2337  std::vector<std::vector< proshade_double > > ret;
2338 
2339  //================================================ Allocate memory
2340  proshade_double* rotMat = new proshade_double[9];
2341  ProSHADE_internal_misc::checkMemoryAllocation ( rotMat, __FILE__, __LINE__, __func__ );
2342 
2343 
2344  //================================================ Normalise the axis to have magnitude of 1.0
2345  proshade_double normF = std::sqrt( std::pow ( xAx, 2.0 ) + std::pow ( yAx, 2.0 ) + std::pow ( zAx, 2.0 ) );
2346  xAx /= normF;
2347  yAx /= normF;
2348  zAx /= normF;
2349 
2350  //================================================ Determine the list of angles
2351  if ( fold % 2 == 0 )
2352  {
2353  //============================================ If fold is even, add the negative angles
2354  for ( proshade_double iter = static_cast < proshade_double > ( -( ( fold / 2 ) - 1 ) ); iter <= static_cast < proshade_double > ( fold / 2 ); iter++ )
2355  {
2356  ProSHADE_internal_misc::addToDoubleVector ( &angList, ( ( 2.0 * M_PI ) / static_cast<proshade_double> ( fold ) ) * iter );
2357  }
2358  }
2359  else
2360  {
2361  //============================================ If fold is odd, do the same as for even, but start one index earlier
2362  for ( proshade_double iter = static_cast < proshade_double > ( -fold / 2 ); iter <= static_cast < proshade_double > ( fold / 2 ); iter++ )
2363  {
2364  ProSHADE_internal_misc::addToDoubleVector ( &angList, ( ( 2.0 * M_PI ) / static_cast<proshade_double> ( fold ) ) * iter );
2365  }
2366  }
2367 
2368  //================================================ For each detected angle
2369  for ( proshade_unsign iter = 0; iter < static_cast < proshade_unsign > ( angList.size() ); iter++ )
2370  {
2371  //============================================ Compute the rotation matrix
2372  ProSHADE_internal_maths::getRotationMatrixFromAngleAxis ( rotMat, xAx, yAx, zAx, angList.at(iter) );
2373 
2374  //============================================ Convert to vector of vectors of doubles and save to ret
2375  std::vector < proshade_double > retEl;
2376  for ( proshade_unsign matIt = 0; matIt < 9; matIt++ )
2377  {
2378  ProSHADE_internal_misc::addToDoubleVector ( &retEl, rotMat[matIt] );
2379  }
2381  }
2382 
2383  //================================================ Release memory
2384  delete[] rotMat;
2385 
2386  //================================================ Done
2387  return ( ret );
2388 
2389 }

◆ 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 2486 of file ProSHADE_data.cpp.

2487 {
2488  //================================================ Initialise variables
2489  std::vector< std::vector< proshade_double > > ret;
2490 
2491  //================================================ Add the first list to ret, checking for uniqueness
2492  for ( proshade_unsign elIt = 0; elIt < static_cast<proshade_unsign> ( first->size() ); elIt++ )
2493  {
2494  if ( !checkElementAlreadyExists( &ret, &first->at(elIt), matrixTolerance ) )
2495  {
2496  ProSHADE_internal_misc::addToDoubleVectorVector ( &ret, first->at(elIt) );
2497  }
2498  }
2499 
2500  //================================================ Add the second list to ret, checking for uniqueness
2501  for ( proshade_unsign elIt = 0; elIt < static_cast<proshade_unsign> ( second->size() ); elIt++ )
2502  {
2503  if ( !checkElementAlreadyExists( &ret, &second->at(elIt), matrixTolerance ) )
2504  {
2505  ProSHADE_internal_misc::addToDoubleVectorVector ( &ret, second->at(elIt) );
2506  }
2507  }
2508 
2509  //================================================ Multiply all combinations of first and second and check for uniqueness
2510  if ( combine )
2511  {
2512  for ( proshade_unsign gr1 = 0; gr1 < static_cast<proshade_unsign> ( first->size() ); gr1++ )
2513  {
2514  for ( proshade_unsign gr2 = 0; gr2 < static_cast<proshade_unsign> ( second->size() ); gr2++ )
2515  {
2516  //==================================== Multiply the two rotation matrices
2517  std::vector< proshade_double > product = ProSHADE_internal_maths::multiplyGroupElementMatrices ( &first->at(gr1), &second->at(gr2) );
2518 
2519  //==================================== Add
2520  if ( !checkElementAlreadyExists( &ret, &product, matrixTolerance ) )
2521  {
2523  }
2524 
2525  }
2526  }
2527  }
2528 
2529  //================================================ Done
2530  return ( ret );
2531 
2532 }
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:2419