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ProSHADE
0.7.5.4 (MAR 2021)
Protein Shape Detection
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This class stores all the settings and is passed to the executive classes instead of a multitude of parameters. More...
#include <ProSHADE_settings.hpp>
Public Member Functions | |
void | determineBandwidthFromAngle (proshade_double uncertainty) |
This function determines the bandwidth for the spherical harmonics computation from the allowed rotation function angle uncertainty. More... | |
void | determineBandwidth (proshade_unsign circumference) |
This function determines the bandwidth for the spherical harmonics computation. More... | |
void | determineSphereDistances (proshade_single maxMapRange) |
This function determines the sphere distances for sphere mapping. More... | |
void | determineIntegrationOrder (proshade_single maxMapRange) |
This function determines the integration order for the between spheres integration. More... | |
void | determineAllSHValues (proshade_unsign xDim, proshade_unsign yDim, proshade_unsign zDim, proshade_double xDimAngs, proshade_double yDimAngs, proshade_double zDimAngs) |
This function determines all the required values for spherical harmonics computation. More... | |
void | setVariablesLeftOnAuto (void) |
Function to determine general values that the user left on auto-determination. | |
ProSHADE_settings (void) | |
Contructor for the ProSHADE_settings class. More... | |
ProSHADE_settings (ProSHADE_Task task) | |
Contructor for the ProSHADE_settings class for particular task. More... | |
~ProSHADE_settings (void) | |
Destructor for the ProSHADE_settings class. More... | |
void | addStructure (std::string structure) |
Adds a structure file name to the appropriate variable. More... | |
void | setResolution (proshade_single resolution) |
Sets the requested resolution in the appropriate variable. More... | |
void | setPDBBFactor (proshade_double newBF) |
Sets the requested B-factor value for PDB files in the appropriate variable. More... | |
void | setNormalisation (bool normalise) |
Sets the requested map normalisation value in the appropriate variable. More... | |
void | setMapInversion (bool mInv) |
Sets the requested map inversion value in the appropriate variable. More... | |
void | setVerbosity (proshade_signed verbosity) |
Sets the requested verbosity in the appropriate variable. More... | |
void | setMaskBlurFactor (proshade_single blurFac) |
Sets the requested map blurring factor in the appropriate variable. More... | |
void | setMaskIQR (proshade_single noIQRs) |
Sets the requested number of IQRs for masking threshold in the appropriate variable. More... | |
void | setMasking (bool mask) |
Sets the requested map masking decision value in the appropriate variable. More... | |
void | setCorrelationMasking (bool corMask) |
Sets the requested map masking type in the appropriate variable. More... | |
void | setTypicalNoiseSize (proshade_single typNoi) |
Sets the requested "fake" half-map kernel in the appropriate variable. More... | |
void | setMinimumMaskSize (proshade_single minMS) |
Sets the requested minimum mask size. More... | |
void | setMaskSaving (bool savMsk) |
Sets whether the mask should be saved. More... | |
void | setMaskFilename (std::string mskFln) |
Sets where the mask should be saved. More... | |
void | setMapReboxing (bool reBx) |
Sets whether re-boxing needs to be done in the appropriate variable. More... | |
void | setBoundsSpace (proshade_single boundsExSp) |
Sets the requested number of angstroms for extra space in re-boxing in the appropriate variable. More... | |
void | setBoundsThreshold (proshade_signed boundsThres) |
Sets the threshold for number of indices difference acceptable to make index sizes same in the appropriate variable. More... | |
void | setSameBoundaries (bool sameB) |
Sets whether same boundaries should be used in the appropriate variable. More... | |
void | setOutputFilename (std::string oFileName) |
Sets the requested output file name in the appropriate variable. More... | |
void | setMapResolutionChange (bool mrChange) |
Sets the requested map resolution change decision in the appropriate variable. More... | |
void | setMapResolutionChangeTriLinear (bool mrChange) |
Sets the requested map resolution change decision using tri-linear interpolation in the appropriate variable. More... | |
void | setMapCentering (bool com) |
Sets the requested map centering decision value in the appropriate variable. More... | |
void | setExtraSpace (proshade_single exSpace) |
Sets the requested map extra space value in the appropriate variable. More... | |
void | setBandwidth (proshade_unsign band) |
Sets the requested spherical harmonics bandwidth in the appropriate variable. More... | |
void | setSphereDistances (proshade_single sphDist) |
Sets the requested distance between spheres in the appropriate variable. More... | |
void | setIntegrationOrder (proshade_unsign intOrd) |
Sets the requested order for the Gauss-Legendre integration in the appropriate variable. More... | |
void | setTaylorSeriesCap (proshade_unsign tayCap) |
Sets the requested Taylor series cap for the Gauss-Legendre integration in the appropriate variable. More... | |
void | setProgressiveSphereMapping (bool progSphMap) |
Sets the requested sphere mapping value settings approach in the appropriate variable. More... | |
void | setEnergyLevelsComputation (bool enLevDesc) |
Sets whether the energy level distance descriptor should be computed. More... | |
void | setTraceSigmaComputation (bool trSigVal) |
Sets whether the trace sigma distance descriptor should be computed. More... | |
void | setRotationFunctionComputation (bool rotfVal) |
Sets whether the rotation function distance descriptor should be computed. More... | |
void | setPeakNeighboursNumber (proshade_unsign pkS) |
Sets the number of neighbour values that have to be smaller for an index to be considered a peak. More... | |
void | setPeakNaiveNoIQR (proshade_double noIQRs) |
Sets the number of IQRs from the median for threshold height a peak needs to be considered a peak. More... | |
void | setPhaseUsage (bool phaseUsage) |
Sets whether the phase information will be used. More... | |
void | setEnLevShellWeight (proshade_double mPower) |
Sets the weight of shell position for the energy levels computation. More... | |
void | setGroupingSmoothingFactor (proshade_double smFact) |
Sets the grouping smoothing factor into the proper variable. More... | |
void | setMissingPeakThreshold (proshade_double mpThres) |
Sets the threshold for starting the missing peaks procedure. More... | |
void | setAxisComparisonThreshold (proshade_double axThres) |
Sets the threshold for matching symmetry axes. More... | |
void | setAxisComparisonThresholdBehaviour (bool behav) |
Sets the automatic symmetry axis tolerance decreasing. More... | |
void | setMinimumPeakForAxis (proshade_double minSP) |
Sets the minimum peak height for symmetry axis to be considered. More... | |
void | setRecommendedSymmetry (std::string val) |
Sets the ProSHADE detected symmetry type. More... | |
void | setRecommendedFold (proshade_unsign val) |
Sets the ProSHADE detected symmetry fold. More... | |
void | setRequestedSymmetry (std::string val) |
Sets the user requested symmetry type. More... | |
void | setRequestedFold (proshade_unsign val) |
Sets the user requested symmetry fold. More... | |
void | setDetectedSymmetry (proshade_double *sym) |
Sets the final detected symmetry axes information. More... | |
void | setOverlaySaveFile (std::string filename) |
Sets the filename to which the overlay structure is to be save into. More... | |
void | setOverlayJsonFile (std::string filename) |
Sets the filename to which the overlay operations are to be save into. More... | |
void | setSymmetryRotFunPeaks (bool rotFunPeaks) |
Sets the symmetry detection algorithm type. More... | |
void | setBicubicInterpolationSearch (bool bicubPeaks) |
Sets the bicubic interpolation on peaks. More... | |
void | setMaxSymmetryFold (proshade_unsign maxFold) |
Sets the maximum symmetry fold (well, the maximum prime symmetry fold). More... | |
void | getCommandLineParams (int argc, char **argv) |
This function parses the command line arguments into the settings object. More... | |
void | printSettings (void) |
This function prints the current values in the settings object. More... | |
Public Attributes | |
ProSHADE_Task | task |
This custom type variable determines which task to perfom (i.e. symmetry detection, distances computation, etc.). | |
std::vector< std::string > | inputFiles |
This vector contains the filenames of all input structure files. | |
bool | forceP1 |
Should the P1 spacegroup be forced on the input PDB files? | |
bool | removeWaters |
Should all waters be removed from input PDB files? | |
bool | firstModelOnly |
Shoud only the first PDB model be used, or should all models be used? | |
proshade_single | requestedResolution |
The resolution to which the calculations are to be done. | |
bool | changeMapResolution |
Should maps be re-sampled to obtain the required resolution? | |
bool | changeMapResolutionTriLinear |
Should maps be re-sampled to obtain the required resolution? | |
proshade_double | pdbBFactorNewVal |
Change all PDB B-factors to this value (for smooth maps). | |
proshade_unsign | maxBandwidth |
The bandwidth of spherical harmonics decomposition for the largest sphere. | |
proshade_double | rotationUncertainty |
Alternative to bandwidth - the angle in degrees to which the rotation function accuracy should be computed. | |
bool | usePhase |
If true, the full data will be used, if false, Patterson maps will be used instead and phased data will be converted to them. Also, only half of the spherical harmonics bands will be necessary as odd bands have to be 0 for Patterson maps. | |
proshade_single | maxSphereDists |
The distance between spheres in spherical mapping for the largest sphere. | |
proshade_unsign | integOrder |
The order required for full Gauss-Legendre integration between the spheres. | |
proshade_unsign | taylorSeriesCap |
The max limit on the Taylor series expansion done for the abscissas of the Gauss-Legendre integration. | |
bool | normaliseMap |
Should the map be normalised to mean 0 sd 1? | |
bool | invertMap |
Should the map be inverted? Only use this if you think you have the wrong hand in your map. | |
proshade_single | blurFactor |
This is the amount by which B-factors should be increased to create the blurred map for masking. | |
proshade_single | maskingThresholdIQRs |
Number of inter-quartile ranges from the median to be used for thresholding the blurred map for masking. | |
bool | maskMap |
Should the map be masked from noise? | |
bool | useCorrelationMasking |
Should the blurring masking (false) or the correlation masking (true) be used? | |
proshade_single | halfMapKernel |
This value in Angstrom will be used as the kernel for the "fake half-map" computation. | |
proshade_single | correlationKernel |
This value in Angstrom will be used as the kernel for the map-FHM correlation computation. | |
bool | saveMask |
Should the mask be saved? | |
std::string | maskFileName |
The filename to which mask should be saved. | |
bool | reBoxMap |
This switch decides whether re-boxing is needed. | |
proshade_single | boundsExtraSpace |
The number of extra angstroms to be added to all re-boxing bounds just for safety. | |
proshade_signed | boundsSimilarityThreshold |
Number of indices which can be added just to make sure same size in indices is achieved. | |
bool | useSameBounds |
Switch to say that the same boundaries as used for the first should be used for all input maps. | |
proshade_signed * | forceBounds |
These will be the boundaries to be forced upon the map. | |
bool | moveToCOM |
Logical value stating whether the structure should be moved to have its Centre Of Mass (COM) in the middle. | |
proshade_single | addExtraSpace |
If this value is non-zero, this many angstroms of empty space will be added to the internal map. | |
bool | progressiveSphereMapping |
If true, each shell will have its own angular resolution dependent on the actual number of map points which are available to it. If false, all shells will have the same settings. | |
std::string | outName |
The file name where the output structure(s) should be saved. | |
bool | computeEnergyLevelsDesc |
If true, the energy levels descriptor will be computed, otherwise all its computations will be omitted. | |
proshade_double | enLevMatrixPowerWeight |
If RRP matrices shell position is to be weighted by putting the position as an exponent, this variable sets the exponent. Set to 0 for no weighting. | |
bool | computeTraceSigmaDesc |
If true, the trace sigma descriptor will be computed, otherwise all its computations will be omitted. | |
bool | computeRotationFuncDesc |
If true, the rotation function descriptor will be computed, otherwise all its computations will be omitted. | |
proshade_unsign | peakNeighbours |
Number of points in any direction that have to be lower than the considered index in order to consider this index a peak. | |
proshade_double | noIQRsFromMedianNaivePeak |
When doing peak searching, how many IQRs from the median the threshold for peak height should be (in terms of median of non-peak values). | |
proshade_double | smoothingFactor |
This factor decides how small the group sizes should be - larger factor means more smaller groups. | |
proshade_double | symMissPeakThres |
Percentage of peaks that could be missing that would warrant starting the missing peaks search procedure. | |
proshade_double | axisErrTolerance |
Allowed error on vector axis in in dot product ( acos ( 1 - axErr ) is the allowed difference in radians ). | |
bool | axisErrToleranceDefault |
proshade_double | minSymPeak |
Minimum average peak for symmetry axis to be considered as "real". | |
std::string | recommendedSymmetryType |
The symmetry type that ProSHADE finds the best fitting for the structure. Possible values are "" for none, "C" for cyclic, "D" for Dihedral, "T" for Tetrahedral, "O" for Octahedral and "I" for Icosahedral. C and D types also have fold value associated. | |
proshade_unsign | recommendedSymmetryFold |
The fold of the recommended symmetry C or D type, 0 otherwise. | |
std::string | requestedSymmetryType |
The symmetry type requested by the user. Allowed values are C, D, T, O and I. | |
proshade_unsign | requestedSymmetryFold |
The fold of the requested symmetry (only applicable to C and D symmetry types). | |
bool | usePeakSearchInRotationFunctionSpace |
This variable switch decides whether symmetry detection will be done using peak search in rotation function or using the angle-axis sperical space. | |
bool | useBiCubicInterpolationOnPeaks |
This variable switch decides whether best symmetry is detected from peak indices, or whether bicubic interpolation is done to seatch for better axis between indices. | |
proshade_unsign | maxSymmetryFold |
The highest symmetry fold to search for. | |
std::string | overlayStructureName |
The filename to which the rotated and translated moving structure is to be saved. | |
std::string | rotTrsJSONFile |
The filename to which the rotation and translation operations are to be saved into. | |
proshade_signed | verbose |
Should the software report on the progress, or just be quiet? Value between -1 (nothing) and 4 (loud) | |
std::vector< proshade_double * > | detectedSymmetry |
The vector of detected symmetry axes. | |
std::vector< std::vector< proshade_double > > | allDetectedCAxes |
The vector of all detected cyclic symmetry axes. | |
std::vector< std::vector< proshade_unsign > > | allDetectedDAxes |
The vector of all detected dihedral symmetry axes indices in allDetectedCAxes. | |
std::vector< proshade_unsign > | allDetectedTAxes |
The vector of all detected tetrahedral symmetry axes indices in allDetectedCAxes. | |
std::vector< proshade_unsign > | allDetectedOAxes |
The vector of all detected octahedral symmetry axes indices in allDetectedCAxes. | |
std::vector< proshade_unsign > | allDetectedIAxes |
The vector of all detected icosahedral symmetry axes indices in allDetectedCAxes. | |
This class stores all the settings and is passed to the executive classes instead of a multitude of parameters.
The ProSHADE_settings class is a simple way of keeping all the settings together and easy to set by the user. Its constructor sets it to the default settings, so that if the user does not want to change these, he just needs to pass the object to the executing class and all is done.
Definition at line 88 of file ProSHADE_settings.hpp.
ProSHADE_settings::ProSHADE_settings | ( | void | ) |
Contructor for the ProSHADE_settings class.
This is the generic constructor used in cases where the settings object will be filled based on run-time determined values. If you know the specific task to be done, it is recommended to use the constructor which takes the task as argument, so that the default values are set specifically for the task at hand.
Definition at line 34 of file ProSHADE.cpp.
ProSHADE_settings::ProSHADE_settings | ( | ProSHADE_Task | taskToPerform | ) |
Contructor for the ProSHADE_settings class for particular task.
This is the generic constructor used in cases where the settings object will be filled based on run-time determined values. If you know the specific task to be done, it is recommended to use the constructor which takes the task as argument, so that the default values are set specifically for the task at hand.
[in] | taskToPerform | The task that should be performed by ProSHADE. |
Definition at line 147 of file ProSHADE.cpp.
ProSHADE_settings::~ProSHADE_settings | ( | void | ) |
Destructor for the ProSHADE_settings class.
This destructor is responsible for releasing all memory used by the settings object
Definition at line 302 of file ProSHADE.cpp.
void ProSHADE_settings::addStructure | ( | std::string | structure | ) |
Adds a structure file name to the appropriate variable.
This function takes a string defining the filename of a structure to be processed and adds it to the list of structures to be processed.
[in] | structure | String file name to be added to the list of structures to process. |
Definition at line 341 of file ProSHADE.cpp.
void ProSHADE_settings::determineAllSHValues | ( | proshade_unsign | xDim, |
proshade_unsign | yDim, | ||
proshade_unsign | zDim, | ||
proshade_double | xDimAngs, | ||
proshade_double | yDimAngs, | ||
proshade_double | zDimAngs | ||
) |
This function determines all the required values for spherical harmonics computation.
This function takes the maximum dimension size (in indices) and uses the settings pre-set by the user to set up the sphherical harmonics bandwidth, sphere sampling, sphere placement and spacing as well as the Gauss-Legendre integration order. This is either done using the user set values (if given), or using automated algorithm which only requires the resolution and max dimension.
Note that this function will use the resolution value to modify the values to be appropriate for the resolution supplied and not necessarily for the map sampling given.
[in] | xDim | The size of the x axis dimension in indices. |
[in] | yDim | The size of the y axis dimension in indices. |
[in] | zDim | The size of the z axis dimension in indices. |
[in] | xDimAngs | The size of the x-axis in Angstroms. |
[in] | yDimAngs | The size of the y-axis in Angstroms. |
[in] | zDimAngs | The size of the z-axis in Angstroms. |
Definition at line 1320 of file ProSHADE.cpp.
void ProSHADE_settings::determineBandwidth | ( | proshade_unsign | circumference | ) |
This function determines the bandwidth for the spherical harmonics computation.
This function is here to automstically determine the bandwidth to which the spherical harmonics computations should be done. It accomplishes this by checking if value is already set, and if not (value is 0), then it sets it to half of the maximum circumference of the map, in indices as recommended by Kostelec and Rockmore (2007).
[in] | circumference | The maximum circumference of the map. |
Definition at line 1180 of file ProSHADE.cpp.
void ProSHADE_settings::determineBandwidthFromAngle | ( | proshade_double | uncertainty | ) |
This function determines the bandwidth for the spherical harmonics computation from the allowed rotation function angle uncertainty.
This function makes use of the fact that the rotation function dimensions will be 2 * bandwidth and that the dimensions will be covering full 360 degrees rotation space. Therefore, by saying what is the maximum allowed angle uncertainty, the minimum required bandwidth value can be determined.
[in] | uncertainty | The maximum allowed uncertainty on the rotation function. |
Definition at line 1212 of file ProSHADE.cpp.
void ProSHADE_settings::determineIntegrationOrder | ( | proshade_single | maxMapRange | ) |
This function determines the integration order for the between spheres integration.
This function determines the order of the Gauss-Legendre integration which needs to be done between the spheres. To do this, it uses the pre-coputed values of maxium distance between integration points for each order and the maxium distance between spheres expressed as a fraction of the total.
[in] | maxMapRange | The maximum diagonal distance of the map in Angstroms. |
Definition at line 1275 of file ProSHADE.cpp.
void ProSHADE_settings::determineSphereDistances | ( | proshade_single | maxMapRange | ) |
This function determines the sphere distances for sphere mapping.
This function determines the distance between two consecutive spheres in the sphere mappin galgorithm. It checks if this values has not been already set and if not, it sets it as the sampling rate (distance between any two map points). It then checks that there will be at least 10 spheres and if not, it changes the sphere distance until at least 10 spheres are to be produced.
[in] | maxMapRange | The maximum diagonal distance of the map in Angstroms. |
Definition at line 1243 of file ProSHADE.cpp.
void ProSHADE_settings::getCommandLineParams | ( | int | argc, |
char ** | argv | ||
) |
This function parses the command line arguments into the settings object.
[in] | argc | The count of the command line arguments (as passed to main function by the system). |
[in] | argv | The string containing the command line arguments (as passed to main function by the system). |
Definition at line 1583 of file ProSHADE.cpp.
void ProSHADE_settings::printSettings | ( | void | ) |
This function prints the current values in the settings object.
Definition at line 2118 of file ProSHADE.cpp.
void ProSHADE_settings::setAxisComparisonThreshold | ( | proshade_double | axThres | ) |
Sets the threshold for matching symmetry axes.
When comparing symmetry axes, there needs to be a threshold allowing for some small error comming from the numberical inaccuracies. This is where you set this threshold.
[in] | axThres | The requested value for the axes comparison threshold. |
Definition at line 955 of file ProSHADE.cpp.
void ProSHADE_settings::setAxisComparisonThresholdBehaviour | ( | bool | behav | ) |
Sets the automatic symmetry axis tolerance decreasing.
When comparing symmetry axes, there needs to be a threshold allowing for some small error comming from the numberical inaccuracies. It turns out that this threshold should take into account the ratio to the next symmetry angles, otherwise it would strongly prefer larger symmetries. This variable decides whether the threshold should be decreased based on the fold of sought åsymmetry or not.
[in] | behav | The requested value for the axes comparison threshold decreasing. |
Definition at line 974 of file ProSHADE.cpp.
void ProSHADE_settings::setBandwidth | ( | proshade_unsign | band | ) |
Sets the requested spherical harmonics bandwidth in the appropriate variable.
This function sets the bandwidth limit for the spherical harmonics computations in the appropriate variable.
[in] | band | The requested value for spherical harmonics bandwidth (0 = AUTOMATIC DETERMINATION). |
Definition at line 732 of file ProSHADE.cpp.
void ProSHADE_settings::setBicubicInterpolationSearch | ( | bool | bicubPeaks | ) |
Sets the bicubic interpolation on peaks.
[in] | bicubPeaks | Should bicubic interpolation be done to search for improved axis in between peak index values (DEFAULT - TRUE)? |
Definition at line 1148 of file ProSHADE.cpp.
void ProSHADE_settings::setBoundsSpace | ( | proshade_single | boundsExSp | ) |
Sets the requested number of angstroms for extra space in re-boxing in the appropriate variable.
This function sets the number of angstroms to be added both before and after the absolute bounds for re-boxing to the correct variable.
[in] | boundsExSp | The requested value for the extra re-boxing space in angstroms. |
Definition at line 586 of file ProSHADE.cpp.
void ProSHADE_settings::setBoundsThreshold | ( | proshade_signed | boundsThres | ) |
Sets the threshold for number of indices difference acceptable to make index sizes same in the appropriate variable.
This function sets the number of indices by which two dimensions can differ for them to be still made the same size.
[in] | boundsThres | The requested value for the bouds difference threhshold. |
Definition at line 602 of file ProSHADE.cpp.
void ProSHADE_settings::setCorrelationMasking | ( | bool | corMask | ) |
Sets the requested map masking type in the appropriate variable.
This function sets the map masking type. If false, the standard map blurring masking will be used, while if true, the new "fake" half-map correlation mask will be used.
[in] | corMask | The requested value for the map masking type. |
Definition at line 487 of file ProSHADE.cpp.
void ProSHADE_settings::setDetectedSymmetry | ( | proshade_double * | sym | ) |
Sets the final detected symmetry axes information.
This function copies (deep copy) the detected and recommended (or requested) symmetry axis information into the settings object variable for further processing. For multiple axes, call this function multiple times - the addition is cumulative.
[in] | sym | A pointer to single symmetry axis constituting the detected symmetry. |
Definition at line 1077 of file ProSHADE.cpp.
void ProSHADE_settings::setEnergyLevelsComputation | ( | bool | enLevDesc | ) |
Sets whether the energy level distance descriptor should be computed.
This function sets the boolean variable deciding whether the RRP matrices and the energy levels descriptor should be computed or not.
[in] | enLevDesc | The requested value for the energy levels descriptor computation switch. |
Definition at line 798 of file ProSHADE.cpp.
void ProSHADE_settings::setEnLevShellWeight | ( | proshade_double | mPower | ) |
Sets the weight of shell position for the energy levels computation.
During the computation of the energy levels descriptor, Pearson's correlation coefficient is computed between different shells with the same band. The shell index can by expanded to its mPower exponential to give higher shells more weight, or vice versa. To do this, set the mPower value as you see fit.
[in] | mPower | The requested value for the shell position exponential. |
Definition at line 903 of file ProSHADE.cpp.
void ProSHADE_settings::setExtraSpace | ( | proshade_single | exSpace | ) |
Sets the requested map extra space value in the appropriate variable.
This function sets the amount of extra space to be added to internal maps in the appropriate variable.
[in] | exSpace | The requested amount of extra space. |
Definition at line 700 of file ProSHADE.cpp.
void ProSHADE_settings::setGroupingSmoothingFactor | ( | proshade_double | smFact | ) |
Sets the grouping smoothing factor into the proper variable.
When detecting symmetry, it is worth grouping the possible rotations by their self-rotation function peak heights. In this process, the distribution of peak heights needs to be smoothen over and this factor decides how smooth it should be. Small value leads to all peaks being in the same group, while large number means each peak will be in its own group.
[in] | smFact | The requested value for the grouping smoothing factor. |
Definition at line 921 of file ProSHADE.cpp.
void ProSHADE_settings::setIntegrationOrder | ( | proshade_unsign | intOrd | ) |
Sets the requested order for the Gauss-Legendre integration in the appropriate variable.
This function sets the Gauss-Legendre integration between the spheres order value in the appropriate variable.
[in] | intOrd | The requested value for the Gauss-Legendre integration order (0 = AUTOMATIC DETERMINATION). |
Definition at line 764 of file ProSHADE.cpp.
void ProSHADE_settings::setMapCentering | ( | bool | com | ) |
Sets the requested map centering decision value in the appropriate variable.
This function sets the map centering using COM between on and off.
[in] | com | The requested value for the map centering (on = true, off = false). |
Definition at line 684 of file ProSHADE.cpp.
void ProSHADE_settings::setMapInversion | ( | bool | mInv | ) |
Sets the requested map inversion value in the appropriate variable.
This function sets the map inversion between on and off.
[in] | mInv | Should the map be inverted? (on = true, off = false). |
Definition at line 405 of file ProSHADE.cpp.
void ProSHADE_settings::setMapReboxing | ( | bool | reBx | ) |
Sets whether re-boxing needs to be done in the appropriate variable.
This function sets the switch as to whether re-boxing needs to be done to the correct variable.
[in] | reBx | The requested value for the re-boxing switch variable. |
Definition at line 569 of file ProSHADE.cpp.
void ProSHADE_settings::setMapResolutionChange | ( | bool | mrChange | ) |
Sets the requested map resolution change decision in the appropriate variable.
This function sets the map resolution change between on and off.
[in] | mrChange | The requested value for the map resolution change (on = true, off = false). |
Definition at line 652 of file ProSHADE.cpp.
void ProSHADE_settings::setMapResolutionChangeTriLinear | ( | bool | mrChange | ) |
Sets the requested map resolution change decision using tri-linear interpolation in the appropriate variable.
This function sets the tri-linear interpolation map resolution change between on and off.
[in] | mrChange | The requested value for the map resolution change (on = true, off = false). |
Definition at line 668 of file ProSHADE.cpp.
void ProSHADE_settings::setMaskBlurFactor | ( | proshade_single | blurFac | ) |
Sets the requested map blurring factor in the appropriate variable.
This function sets the blurring / sharpening factor for map masking in the appropriate variable.
[in] | blurFac | The requested value for the blurring factor. |
Definition at line 437 of file ProSHADE.cpp.
void ProSHADE_settings::setMaskFilename | ( | std::string | mskFln | ) |
Sets where the mask should be saved.
This function sets the the filename to which mask should be saved.
[in] | mskFln | The filename where the mask should be saved. |
Definition at line 553 of file ProSHADE.cpp.
void ProSHADE_settings::setMasking | ( | bool | mask | ) |
Sets the requested map masking decision value in the appropriate variable.
This function sets the map masking between on and off.
[in] | mask | The requested value for the map masking (on = true, off = false). |
Definition at line 470 of file ProSHADE.cpp.
void ProSHADE_settings::setMaskIQR | ( | proshade_single | noIQRs | ) |
Sets the requested number of IQRs for masking threshold in the appropriate variable.
This function sets the number of interquartile ranges from the median to be used for map masking in the correct variable.
[in] | noIQRs | The requested value for the number of IQRs from the median to be used for masking threshold. |
Definition at line 454 of file ProSHADE.cpp.
void ProSHADE_settings::setMaskSaving | ( | bool | savMsk | ) |
Sets whether the mask should be saved.
This function sets the switch variable to whether mask should be saved.
[in] | savMsk | If true, mask will be saved, otherwise it will not be. |
Definition at line 537 of file ProSHADE.cpp.
void ProSHADE_settings::setMaxSymmetryFold | ( | proshade_unsign | maxFold | ) |
Sets the maximum symmetry fold (well, the maximum prime symmetry fold).
[in] | maxFold | Maximum prime number fold that will be searched for. Still its multiples may also be found. |
Definition at line 1162 of file ProSHADE.cpp.
void ProSHADE_settings::setMinimumMaskSize | ( | proshade_single | minMS | ) |
Sets the requested minimum mask size.
This function sets the kernel for the local correlation computation between the "fake half-map" and the original map.
[in] | minMS | The requested value for the minimum mask size in Angstrom. |
Definition at line 521 of file ProSHADE.cpp.
void ProSHADE_settings::setMinimumPeakForAxis | ( | proshade_double | minSP | ) |
Sets the minimum peak height for symmetry axis to be considered.
When considering if a symmetry axis is "real" and should be acted upon, its average peak height will need to be higher than this value.
[in] | minSP | The requested value for the minimum peak height. |
Definition at line 991 of file ProSHADE.cpp.
void ProSHADE_settings::setMissingPeakThreshold | ( | proshade_double | mpThres | ) |
Sets the threshold for starting the missing peaks procedure.
When only mpThres percentage of peaks are missing during symmetry detection, the full missing peak detection procedure will be started. Otherwise, the symmetry will not be detected at all.
[in] | mpThres | The requested value for the missing peaks procedure starting threshold. |
Definition at line 938 of file ProSHADE.cpp.
void ProSHADE_settings::setNormalisation | ( | bool | normalise | ) |
Sets the requested map normalisation value in the appropriate variable.
This function sets the map normalisation between on and off.
[in] | normalise | The requested value for the map normalisation (on = true, off = false). |
Definition at line 389 of file ProSHADE.cpp.
void ProSHADE_settings::setOutputFilename | ( | std::string | oFileName | ) |
Sets the requested output file name in the appropriate variable.
This function sets the filename to which the output structure(s) should be saved. This variable is used by multiple tasks and therefore cannot be more specifically described here.
[in] | oFileName | The requested value for the output file name variable. |
Definition at line 636 of file ProSHADE.cpp.
void ProSHADE_settings::setOverlayJsonFile | ( | std::string | filename | ) |
Sets the filename to which the overlay operations are to be save into.
[in] | filename | The filename to which the overlay operations are to be saved to. |
Definition at line 1120 of file ProSHADE.cpp.
void ProSHADE_settings::setOverlaySaveFile | ( | std::string | filename | ) |
Sets the filename to which the overlay structure is to be save into.
[in] | filename | The filename to which the overlay structure is to be saved to. |
Definition at line 1106 of file ProSHADE.cpp.
void ProSHADE_settings::setPDBBFactor | ( | proshade_double | newBF | ) |
Sets the requested B-factor value for PDB files in the appropriate variable.
This function sets the B-factor value for PDB files in the appropriate variable.
[in] | newBF | The requested value for the B-factor value for PDB files for smooth and processible maps. |
Definition at line 373 of file ProSHADE.cpp.
void ProSHADE_settings::setPeakNaiveNoIQR | ( | proshade_double | noIQRs | ) |
Sets the number of IQRs from the median for threshold height a peak needs to be considered a peak.
This function sets the number of IQRs from the median that determine the threshold used to determine if a 'naive' peak is a peak, or just a random local maxim in the background. The set from which median and IQR is computed is the non-peak values.
[in] | noIQRs | The requested number of IQRs from the median. |
Definition at line 867 of file ProSHADE.cpp.
void ProSHADE_settings::setPeakNeighboursNumber | ( | proshade_unsign | pkS | ) |
Sets the number of neighbour values that have to be smaller for an index to be considered a peak.
This function sets the number of neighbouring points (in all three dimensions and both positive and negative direction) that have to have lower value than the currently considered index in order for this index to be considered as a peak.
[in] | pkS | The requested value for the number of neighbours being lower for a peak. |
Definition at line 849 of file ProSHADE.cpp.
void ProSHADE_settings::setPhaseUsage | ( | bool | phaseUsage | ) |
Sets whether the phase information will be used.
This function sets the boolean variable deciding whether the phase information should be used. If not, Patterson maps will be used instead of density maps and the 3D data will be converted to them. Also, only even bands of the spherical harmonics decomposition will be computed as the odd bands must be 0.
[in] | phaseUsage | The requested value for the phase usage switch. |
Definition at line 885 of file ProSHADE.cpp.
void ProSHADE_settings::setProgressiveSphereMapping | ( | bool | progSphMap | ) |
Sets the requested sphere mapping value settings approach in the appropriate variable.
This function sets the progressive sphere mapping approach between on and off.
[in] | com | The requested value for the progressive sphere mapping (on = true, off = false). |
Definition at line 716 of file ProSHADE.cpp.
void ProSHADE_settings::setRecommendedFold | ( | proshade_unsign | val | ) |
Sets the ProSHADE detected symmetry fold.
When symmetry detection is done, the resulting recommended symmetry fold (valid only for C and D symmetry types) will be saved in the settings object by this function.
[in] | val | The recommended symmetry fold for the structure. |
Definition at line 1028 of file ProSHADE.cpp.
void ProSHADE_settings::setRecommendedSymmetry | ( | std::string | val | ) |
Sets the ProSHADE detected symmetry type.
When symmetry detection is done, the resulting recommended symmetry type will be saved in the settings object by this function.
[in] | val | The recommended symmetry type for the structure. |
Definition at line 1009 of file ProSHADE.cpp.
void ProSHADE_settings::setRequestedFold | ( | proshade_unsign | val | ) |
Sets the user requested symmetry fold.
When symmetry detection is started, this symmetry fold will be exclusively sought.
[in] | val | The requested symmetry fold for the structure. |
Definition at line 1060 of file ProSHADE.cpp.
void ProSHADE_settings::setRequestedSymmetry | ( | std::string | val | ) |
Sets the user requested symmetry type.
When symmetry detection is started, this symmetry type will be exclusively sought.
[in] | val | The requested symmetry type for the structure. |
Definition at line 1044 of file ProSHADE.cpp.
void ProSHADE_settings::setResolution | ( | proshade_single | resolution | ) |
Sets the requested resolution in the appropriate variable.
This function sets the resolution in the appropriate variable.
[in] | resolution | The requested value for the resolution to which the computations are to be done. |
Definition at line 357 of file ProSHADE.cpp.
void ProSHADE_settings::setRotationFunctionComputation | ( | bool | rotfVal | ) |
Sets whether the rotation function distance descriptor should be computed.
This function sets the boolean variable deciding whether the inverse SO(3) transform and the rotation function descriptor should be computed or not.
[in] | rotfVal | The requested value for the rotation function descriptor computation switch. |
Definition at line 832 of file ProSHADE.cpp.
void ProSHADE_settings::setSameBoundaries | ( | bool | sameB | ) |
Sets whether same boundaries should be used in the appropriate variable.
This function sets the switch as to whether the same boundaries as for the first map should be forced upon the rest if the input maps.
[in] | sameB | The requested value for the same boundaries as first structure switch variable. |
Definition at line 619 of file ProSHADE.cpp.
void ProSHADE_settings::setSphereDistances | ( | proshade_single | sphDist | ) |
Sets the requested distance between spheres in the appropriate variable.
This function sets the distance between any two consecutive spheres in the sphere mapping of a map in the appropriate variable.
[in] | sphDist | The requested value for distance between spheres (0 = AUTOMATIC DETERMINATION). |
Definition at line 748 of file ProSHADE.cpp.
void ProSHADE_settings::setSymmetryRotFunPeaks | ( | bool | rotFunPeaks | ) |
Sets the symmetry detection algorithm type.
[in] | rotFunPeaks | Should the original peak detection in rotation function space be used (FALSE), or should the new angle-axis space search be used (DEFAULT - TRUE)? |
Definition at line 1134 of file ProSHADE.cpp.
void ProSHADE_settings::setTaylorSeriesCap | ( | proshade_unsign | tayCap | ) |
Sets the requested Taylor series cap for the Gauss-Legendre integration in the appropriate variable.
This function sets the Taylor series maximum limit for the Gauss-Legendre integration between the spheres order value in the appropriate variable.
[in] | tayCap | The requested value for the Taylor series cap. (0 = AUTOMATIC DETERMINATION). |
Definition at line 781 of file ProSHADE.cpp.
void ProSHADE_settings::setTraceSigmaComputation | ( | bool | trSigVal | ) |
Sets whether the trace sigma distance descriptor should be computed.
This function sets the boolean variable deciding whether the E matrices and the trace sigma descriptor should be computed or not.
[in] | trSigVal | The requested value for the trace sigma descriptor computation switch. |
Definition at line 815 of file ProSHADE.cpp.
void ProSHADE_settings::setTypicalNoiseSize | ( | proshade_single | typNoi | ) |
Sets the requested "fake" half-map kernel in the appropriate variable.
This function sets the kernel for creating the "fake" half-map. What is meant here is that a new map is created as the average of neighbours from the original map - this is useful in masking. This value then sets how many neighbours.
[in] | typNoi | The requested value for the typical noise size in Angstrom. |
Definition at line 505 of file ProSHADE.cpp.
void ProSHADE_settings::setVerbosity | ( | proshade_signed | verbosity | ) |
Sets the requested verbosity in the appropriate variable.
This function sets the varbosity of the ProSHADE run in the appropriate variable.
[in] | verbose | The requested value for verbosity. -1 means no output, while 4 means loud output |
Definition at line 421 of file ProSHADE.cpp.