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ProSHADE
0.7.6.0 (JUL 2021)
Protein Shape Detection
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This class provides the access point to the library. More...
#include <ProSHADE.hpp>
Public Member Functions | |
ProSHADE_run (ProSHADE_settings *settings) | |
Contructor for the ProSHADE_run class. More... | |
~ProSHADE_run (void) | |
Destructor for the ProSHADE class. More... | |
proshade_unsign | getNoStructures (void) |
This function returns the number of structures used. More... | |
proshade_signed | getVerbose (void) |
This function returns the verbose value. More... | |
proshade_unsign | getNoRecommendedSymmetryAxes (void) |
This function returns the number of detected recommended symmetry axes. More... | |
proshade_unsign | getNoSymmetryAxes (void) |
This function returns the number of detected recommended symmetry axes. More... | |
std::vector< proshade_double > | getEnergyLevelsVector (void) |
This function returns the energy level distances vector from the first to all other structures. More... | |
std::vector< proshade_double > | getTraceSigmaVector (void) |
This function returns the trace sigma distances vector from the first to all other structures. More... | |
std::vector< proshade_double > | getRotationFunctionVector (void) |
This function returns the full rotation function distances vector from the first to all other structures. More... | |
std::string | getSymmetryType (void) |
This is the main accessor function for the user to get to know what symmetry type ProSHADE has detected and recommends. More... | |
proshade_unsign | getSymmetryFold (void) |
This is the main accessor function for the user to get to know what symmetry fold ProSHADE has detected and recommends. More... | |
std::vector< std::string > | getSymmetryAxis (proshade_unsign axisNo) |
This function returns a single symmetry axis as a vector of strings from the recommended symmetry axes list. More... | |
std::vector< std::vector< proshade_double > > | getAllCSyms (void) |
This function returns a all symmetry axes as a vector of vectors of doubles. More... | |
std::vector< proshade_double > | getMapCOMProcessChange (void) |
This function returns the internal map COM shift. More... | |
std::vector< proshade_signed > | getOriginalBounds (proshade_unsign strNo) |
This function returns a specific structure original bounds. More... | |
std::vector< proshade_signed > | getReBoxedBounds (proshade_unsign strNo) |
This function returns a specific structure re-boxed bounds. More... | |
proshade_double | getMapValue (proshade_unsign strNo, proshade_unsign mapIndex) |
This function returns a single, specific structure map value. More... | |
std::vector< proshade_double > | getEulerAngles (void) |
This function returns the vector of Euler angles with best overlay correlation. More... | |
std::vector< proshade_double > | getOptimalRotMat (void) |
This function returns the vector forming rotation matrix (rows first) with best overlay correlation. More... | |
std::vector< proshade_double > | getTranslationToOrigin (void) |
This function returns the negative values of the position of the rotation centre (the point about which the rotation should be done). More... | |
std::vector< proshade_double > | getOriginToOverlayTranslation (void) |
This function returns the translation required to move the structure from origin to optimal overlay. More... | |
This class provides the access point to the library.
This class codes the object that the user of the library needs to create (and presumably delete) in order to get access to the ProSHADE library.
Definition at line 38 of file ProSHADE.hpp.
ProSHADE_run::ProSHADE_run | ( | ProSHADE_settings * | settings | ) |
Contructor for the ProSHADE_run class.
This is where all the decisions regarding what should be done are made. It takes the settings and based on them, it decides what to do and how to report the results.
[in] | settings | ProSHADE_settings object specifying what should be done. |
Definition at line 1664 of file ProSHADE.cpp.
ProSHADE_run::~ProSHADE_run | ( | void | ) |
Destructor for the ProSHADE class.
This destructor is responsible for releasing all memory used by the executing object
Definition at line 1762 of file ProSHADE.cpp.
std::vector< std::vector< proshade_double > > ProSHADE_run::getAllCSyms | ( | void | ) |
This function returns a all symmetry axes as a vector of vectors of doubles.
[out] | val | A vector of vectors of doubles containing all the symmetries axis fold, x, y, z axis element, angle and peak height in this order. |
Definition at line 2882 of file ProSHADE.cpp.
std::vector< proshade_double > ProSHADE_run::getEnergyLevelsVector | ( | void | ) |
This function returns the energy level distances vector from the first to all other structures.
[out] | enLevs | Vector of doubles of the distances. |
Definition at line 2744 of file ProSHADE.cpp.
std::vector< proshade_double > ProSHADE_run::getEulerAngles | ( | void | ) |
This function returns the vector of Euler angles with best overlay correlation.
[out] | ret | Vector of Euler angles (ZXZ convention) which lead to the globally best overlay correlation. |
Definition at line 3023 of file ProSHADE.cpp.
std::vector< proshade_double > ProSHADE_run::getMapCOMProcessChange | ( | void | ) |
This function returns the internal map COM shift.
[out] | val | The shift used to centre the internal map COM to the centre of the box. |
Definition at line 2897 of file ProSHADE.cpp.
proshade_double ProSHADE_run::getMapValue | ( | proshade_unsign | strNo, |
proshade_unsign | mapIndex | ||
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This function returns a single, specific structure map value.
[in] | strNo | The index of the structure for which the map value is to be returned. |
[in] | mapIndex | The map array index of which the value is returned. |
[out] | val | The map density value for the particular mapIndex position. |
Definition at line 2978 of file ProSHADE.cpp.
proshade_unsign ProSHADE_run::getNoRecommendedSymmetryAxes | ( | void | ) |
This function returns the number of detected recommended symmetry axes.
[out] | val | The length of the recommended symmetry axes vector. |
Definition at line 2813 of file ProSHADE.cpp.
proshade_unsign ProSHADE_run::getNoStructures | ( | void | ) |
This function returns the number of structures used.
[in] | noStructures | Number of structures supplied to the settings object. |
Definition at line 2783 of file ProSHADE.cpp.
proshade_unsign ProSHADE_run::getNoSymmetryAxes | ( | void | ) |
This function returns the number of detected recommended symmetry axes.
[out] | val | The length of the recommended symmetry axes vector. |
Definition at line 2803 of file ProSHADE.cpp.
std::vector< proshade_double > ProSHADE_run::getOptimalRotMat | ( | void | ) |
This function returns the vector forming rotation matrix (rows first) with best overlay correlation.
[out] | ret | Vector forming rotation matrix (rows first) which lead to the globally best overlay correlation. |
Definition at line 3045 of file ProSHADE.cpp.
std::vector< proshade_signed > ProSHADE_run::getOriginalBounds | ( | proshade_unsign | strNo | ) |
This function returns a specific structure original bounds.
[in] | strNo | The index of the structure for which the bounds are to be returned. |
Definition at line 2912 of file ProSHADE.cpp.
std::vector< proshade_double > ProSHADE_run::getOriginToOverlayTranslation | ( | void | ) |
This function returns the translation required to move the structure from origin to optimal overlay.
[out] | ret | Translation required to move structure from origin to optimal overlay. |
Definition at line 3107 of file ProSHADE.cpp.
std::vector< proshade_signed > ProSHADE_run::getReBoxedBounds | ( | proshade_unsign | strNo | ) |
This function returns a specific structure re-boxed bounds.
[in] | strNo | The index of the structure for which the bounds are to be returned. |
Definition at line 2944 of file ProSHADE.cpp.
std::vector< proshade_double > ProSHADE_run::getRotationFunctionVector | ( | void | ) |
This function returns the full rotation function distances vector from the first to all other structures.
[out] | rotFun | Vector of doubles of the distances. |
Definition at line 2772 of file ProSHADE.cpp.
std::vector< std::string > ProSHADE_run::getSymmetryAxis | ( | proshade_unsign | axisNo | ) |
This function returns a single symmetry axis as a vector of strings from the recommended symmetry axes list.
[in] | axisNo | The index of the axis to be returned. |
[out] | val | A vector of strings containing the symmetry axis fold, x, y, z axis element, angle and peak height in this order. |
Definition at line 2827 of file ProSHADE.cpp.
proshade_unsign ProSHADE_run::getSymmetryFold | ( | void | ) |
This is the main accessor function for the user to get to know what symmetry fold ProSHADE has detected and recommends.
[out] | symRecommFold | This is the fold of ProSHADE detected and recommended symmetry (C and D symmetry types only). |
Definition at line 1811 of file ProSHADE.cpp.
std::string ProSHADE_run::getSymmetryType | ( | void | ) |
This is the main accessor function for the user to get to know what symmetry type ProSHADE has detected and recommends.
[out] | symRecommType | This is the value ( ""=None, C=cyclic, D=Dihedral, T=Tetrahedral, O=Octahedral or I=Icosahedral) of ProSHADE detected and recommended symmetry. |
Definition at line 1796 of file ProSHADE.cpp.
std::vector< proshade_double > ProSHADE_run::getTraceSigmaVector | ( | void | ) |
This function returns the trace sigma distances vector from the first to all other structures.
[out] | trSigm | Vector of doubles of the distances. |
Definition at line 2758 of file ProSHADE.cpp.
std::vector< proshade_double > ProSHADE_run::getTranslationToOrigin | ( | void | ) |
This function returns the negative values of the position of the rotation centre (the point about which the rotation should be done).
[out] | ret | Vector specifying the negative values of the rotation centre - i.e. the translation of the rotation centre to the origin. |
Definition at line 3079 of file ProSHADE.cpp.
proshade_signed ProSHADE_run::getVerbose | ( | void | ) |
This function returns the verbose value.
[in] | verbose | How loud the run should be? |
Definition at line 2793 of file ProSHADE.cpp.