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ProSHADE
0.7.6.2 (DEC 2021)
Protein Shape Detection
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This source file contains all the functions required to detect symmetry axes and types from the inverse SOFT map. More...
#include "ProSHADE_symmetry.hpp"
Go to the source code of this file.
Functions | |
proshade_double | determinePeakThreshold (std::vector< proshade_double > inArr, proshade_double noIQRsFromMedian) |
This function takes a vector of values and determines the threshold for removing noise from it. More... | |
bool | sortProSHADESymmetryByPeak (proshade_double *a, proshade_double *b) |
This function allows using std::sort to sort vectors of ProSHADE symmetry format.. More... | |
std::vector< std::pair< proshade_unsign, proshade_unsign > > | findBestIcosDihedralPair (std::vector< proshade_double * > *CSymList, proshade_double minPeakHeight, proshade_double axErr) |
This function finds all the pairs of axes conforming to the icosahedron dihedral angle. More... | |
std::pair< proshade_unsign, proshade_unsign > | findBestOctaDihedralPair (std::vector< proshade_double * > *CSymList, proshade_double minPeakHeight, proshade_double axErr) |
This function finds the best pair of axes conforming to the octahedron dihedral angle. More... | |
std::pair< proshade_unsign, proshade_unsign > | findBestTetraDihedralPair (std::vector< proshade_double * > *CSymList, proshade_double minPeakHeight, proshade_double axErr) |
This function finds the best pair of axes conforming to the tetrahedron dihedral angle. More... | |
This source file contains all the functions required to detect symmetry axes and types from the inverse SOFT map.
The functions in this source file are required to allow detection of symmetry axes and symmetries from the inverse SOFT map. The currect functionality can detect C, D, T, O and I symmetries with the C and D symmetries having their fold automatically detected as well.
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 holder 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.
Definition in file ProSHADE_symmetry.cpp.
proshade_double determinePeakThreshold | ( | std::vector< proshade_double > | inArr, |
proshade_double | noIQRsFromMedian | ||
) |
This function takes a vector of values and determines the threshold for removing noise from it.
[in] | inArr | A vector of values for which the threshold is to be determined. |
[out] | ret | The threshold. |
Definition at line 71 of file ProSHADE_symmetry.cpp.
std::vector< std::pair< proshade_unsign, proshade_unsign > > findBestIcosDihedralPair | ( | std::vector< proshade_double * > * | CSymList, |
proshade_double | minPeakHeight, | ||
proshade_double | axErr | ||
) |
This function finds all the pairs of axes conforming to the icosahedron dihedral angle.
[in] | CSymList | A vector containing the already detected Cyclic symmetries. |
[in] | minPeakHeight | The minimum average peak height for axis to be considered. |
[in] | axErr | The error tolerance on angle matching. |
[out] | ret | Vector of pairs containing the indices of all axes conforming to the required icosahedron dihedral angle. |
Definition at line 2091 of file ProSHADE_symmetry.cpp.
std::pair< proshade_unsign, proshade_unsign > findBestOctaDihedralPair | ( | std::vector< proshade_double * > * | CSymList, |
proshade_double | minPeakHeight, | ||
proshade_double | axErr | ||
) |
This function finds the best pair of axes conforming to the octahedron dihedral angle.
[in] | CSymList | A vector containing the already detected Cyclic symmetries. |
[in] | minPeakHeight | The minimum average peak height for axis to be considered. |
[in] | axErr | The error tolerance on angle matching. |
[out] | ret | The pair of axes with closest angle to the required icosahedron dihedral angle. |
Definition at line 2270 of file ProSHADE_symmetry.cpp.
std::pair< proshade_unsign, proshade_unsign > findBestTetraDihedralPair | ( | std::vector< proshade_double * > * | CSymList, |
proshade_double | minPeakHeight, | ||
proshade_double | axErr | ||
) |
This function finds the best pair of axes conforming to the tetrahedron dihedral angle.
[in] | CSymList | A vector containing the already detected Cyclic symmetries. |
[in] | minPeakHeight | The minimum average peak height for axis to be considered. |
[in] | axErr | The error tolerance on angle matching. |
[out] | ret | The pair of axes with closest angle to the required icosahedron dihedral angle. |
Definition at line 3444 of file ProSHADE_symmetry.cpp.
bool sortProSHADESymmetryByPeak | ( | proshade_double * | a, |
proshade_double * | b | ||
) |
This function allows using std::sort to sort vectors of ProSHADE symmetry format..
[in] | a | Pointer to a ProSHADE symmetry formatted array. |
[in] | b | Pointer to a ProSHADE symmetry formatted array. |
[out] | X | Boolean whether a is larger than b. |
Definition at line 2886 of file ProSHADE_symmetry.cpp.