ProSHADE  0.7.5.4 (MAR 2021)
Protein Shape Detection
ProSHADE_data.cpp File Reference

This is the source file containing internal data representation and manipulation structures and functions. More...

#include "ProSHADE_data.hpp"
#include <gemmi/to_pdb.hpp>

Go to the source code of this file.

Functions

void axesToGroupTypeSanityCheck (proshade_unsign requiredAxes, proshade_unsign obtainedAxes, std::string groupType)
 This function checks that the required and obtained numbers of axes are correct, printing error if they are not. More...
 
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. More...
 
bool checkElementsFormGroup (std::vector< std::vector< proshade_double > > *elements, proshade_double matrixTolerance)
 This function checks if all group element products produce another group element. More...
 

Detailed Description

This is the source file containing internal data representation and manipulation structures and functions.

This source file contains the ProSHADE_data class definitions as well as the code for simple manipulations with the data (more complex manipulations are done in dedicated source files) and caller functions for the more complex manipulations. The class described here is how ProSHADE stores the structural data internally; however, the user should not need to access any of this code manually, as changes to this structure may have large consequences unforseen by the user.

Copyright by Michal Tykac and individual contributors. All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1) Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2) Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3) Neither the name of Michal Tykac nor the names of this code's contributors may be used to endorse or promote products derived from this software without specific prior written permission.

This software is provided by the copyright holders and contributors "as is" and any express or implied warranties, including, but not limitted to, the implied warranties of merchantibility and fitness for a particular purpose are disclaimed. In no event shall the copyright owner or the contributors be liable for any direct, indirect, incidental, special, exemplary, or consequential damages (including, but not limitted to, procurement of substitute goods or services, loss of use, data or profits, or business interuption) however caused and on any theory of liability, whether in contract, strict liability or tort (including negligence or otherwise) arising in any way out of the use of this software, even if advised of the possibility of such damage.

Author
Michal Tykac
Garib N. Murshudov
Version
0.7.5.4
Date
MAR 2021

Definition in file ProSHADE_data.cpp.

Function Documentation

◆ axesToGroupTypeSanityCheck()

void axesToGroupTypeSanityCheck ( proshade_unsign  requiredAxes,
proshade_unsign  obtainedAxes,
std::string  groupType 
)

This function checks that the required and obtained numbers of axes are correct, printing error if they are not.

Parameters
[in]requiredAxesNumber of axes that are required by the symmetry type.
[in]obtainedAxesNumber of axes given.
[in]groupTypeA string specifying for which symmetry type the group elements are to be computed.

Definition at line 2397 of file ProSHADE_data.cpp.

2398 {
2399  //================================================ Sanity check
2400  if ( obtainedAxes != requiredAxes )
2401  {
2402  std::stringstream hlpSS;
2403  hlpSS << "The supplied number of axes for group element\n : detection ( >" << obtainedAxes << "< ) does not match the group type ( >" << groupType << "< ).";
2404  throw ProSHADE_exception ( "Mismatch between supplied number of axes and\n : symmetry type.", "ES00059", __FILE__, __LINE__, __func__, hlpSS.str() );
2405  }
2406 
2407  //================================================ Done
2408  return ;
2409 
2410 }

◆ 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.

Parameters
[in]elementsVector containing all group elements.
[in]elemA single element which should already be in the list.
[in]matrixToleranceThe maximum allowed trace error on rotation matrices to be still considered the same.
[out]elementFoundA boolean value stating if the element was found int the elements list or not.

Definition at line 2419 of file ProSHADE_data.cpp.

2420 {
2421  //================================================ Initialise variables
2422  bool elementFound = false;
2423 
2424  //================================================ For each existing element
2425  for ( proshade_unsign elIt = 0; elIt < static_cast<proshade_unsign> ( elements->size() ); elIt++ )
2426  {
2427  if ( ProSHADE_internal_maths::rotationMatrixSimilarity ( &elements->at(elIt), elem, matrixTolerance ) )
2428  {
2429  elementFound = true;
2430  break;
2431  }
2432  }
2433 
2434  //================================================ Done
2435  return ( elementFound );
2436 
2437 }

◆ checkElementsFormGroup()

bool checkElementsFormGroup ( std::vector< std::vector< proshade_double > > *  elements,
proshade_double  matrixTolerance 
)

This function checks if all group element products produce another group element.

Parameters
[in]elementsVector containing all group elements.
[in]matrixToleranceThe maximum trace error for the matrices to be still considered the same.
[out]isGroupA boolean value stating if all group element products for another group element.

Definition at line 2445 of file ProSHADE_data.cpp.

2446 {
2447  //================================================ Initialise variables
2448  bool isGroup = true;
2449 
2450  //================================================ Multiply all group element pairs
2451  for ( proshade_unsign gr1 = 0; gr1 < static_cast<proshade_unsign> ( elements->size() ); gr1++ )
2452  {
2453  for ( proshade_unsign gr2 = 1; gr2 < static_cast<proshade_unsign> ( elements->size() ); gr2++ )
2454  {
2455  //======================================== Use unique pairs only
2456  if ( gr1 >= gr2 ) { continue; }
2457 
2458  //======================================== Multiply the two rotation matrices
2459  std::vector< proshade_double > product = ProSHADE_internal_maths::multiplyGroupElementMatrices ( &elements->at(gr1), &elements->at(gr2) );
2460 
2461  //======================================== Check the group already contains the produces as an element
2462  if ( !checkElementAlreadyExists ( elements, &product, matrixTolerance ) )
2463  {
2464  isGroup = false;
2465  break;
2466  }
2467  }
2468 
2469  //============================================ Stop if problem was found
2470  if ( !isGroup ) { break; }
2471  }
2472 
2473  //================================================ Done
2474  return ( isGroup );
2475 
2476 }
ProSHADE_exception
This class is the representation of ProSHADE exception.
Definition: ProSHADE_exceptions.hpp:37
ProSHADE_internal_maths::rotationMatrixSimilarity
bool rotationMatrixSimilarity(std::vector< proshade_double > *mat1, std::vector< proshade_double > *mat2, proshade_double tolerance=0.1)
This function compares the distance between two rotation matrices and decides if they are similar usi...
Definition: ProSHADE_maths.cpp:2195
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