ProSHADE  0.7.6.2 (DEC 2021)
Protein Shape Detection
ProSHADE_settings.hpp
Go to the documentation of this file.
1 
22 //==================================================== ProSHADE
23 #include "ProSHADE_maths.hpp"
24 
25 //==================================================== Overinclusion protection
26 #ifndef PROSHADE_SETTINGS
27 #define PROSHADE_SETTINGS
28 
37 {
38 public:
39  //================================================ Settings regarding the task at hand
40  ProSHADE_Task task;
41 
42  //================================================ Settings regarding the input files
43  std::vector < std::string > inputFiles;
44  bool forceP1;
45  bool removeWaters;
48 
49  //================================================ Settings regarding the resolution of calculations
50  proshade_single requestedResolution;
53 
54  //================================================ Settings regarding the PDB B-factor change
55  proshade_double pdbBFactorNewVal;
56 
57  //================================================ Settings regarding the bandwidth of calculations
58  proshade_unsign maxBandwidth;
59  proshade_double rotationUncertainty;
60 
61  //================================================ Settings regarding the phase
62  bool usePhase;
63 
64  //================================================ Settings regarding the spheres
65  proshade_single maxSphereDists;
66 
67  //================================================ Settings regarding the Gauss-Legendre integration
68  proshade_unsign integOrder;
69  proshade_unsign taylorSeriesCap;
70 
71  //================================================ Settings regarding map normalisation
72  bool normaliseMap;
73 
74  //================================================ Settings regarding map inversion
75  bool invertMap;
76 
77  //================================================ Settings regarding map masking
78  proshade_single blurFactor;
79  proshade_single maskingThresholdIQRs;
80  bool maskMap;
82  proshade_single halfMapKernel;
83  proshade_single correlationKernel;
84  bool saveMask;
85  std::string maskFileName;
86  std::string appliedMaskFileName;
87 
88  //================================================ Settings regarding map weighting
89  std::string fourierWeightsFileName;
90 
91  //================================================ Settings regarding re-boxing
92  bool reBoxMap;
93  proshade_single boundsExtraSpace;
94  proshade_signed boundsSimilarityThreshold;
96  proshade_signed* forceBounds;
97 
98  //================================================ Settings regarding COM
99  bool moveToCOM;
100  std::vector< proshade_double > boxCentre;
101 
102  //================================================ Settings regarding extra cell space
103  proshade_single addExtraSpace;
104  proshade_single coOrdsExtraSpace;
105 
106  //================================================ Settings regarding shell settings
108 
109  //================================================ Settings regarding output file name
110  std::string outName;
111 
112  //================================================ Settings regarding distances computation
114  proshade_double enLevMatrixPowerWeight;
117 
118  //================================================ Settings regarding peak searching
119  proshade_unsign peakNeighbours;
120  proshade_double noIQRsFromMedianNaivePeak;
121 
122  //================================================ Settings regarding 1D grouping
123  proshade_double smoothingFactor;
124 
125  //================================================ Settings regarding the symmetry detection
127  proshade_double symMissPeakThres;
128  proshade_double axisErrTolerance;
129  bool axisErrToleranceDefault;
130  proshade_double minSymPeak;
132  proshade_unsign recommendedSymmetryFold;
133  std::string requestedSymmetryType;
134  proshade_unsign requestedSymmetryFold;
136  proshade_unsign maxSymmetryFold;
137  proshade_double fscThreshold;
138  proshade_double peakThresholdMin;
139  bool fastISearch;
140 
141  //================================================ Settings regarding centre of map
142  std::vector < proshade_double > centrePosition;
143 
144  //================================================ Settings regarding the structure overlay
145  std::string overlayStructureName;
146  std::string rotTrsJSONFile;
147 
148  //================================================ Settings regarding verbosity of the program
149  proshade_signed verbose;
150  proshade_signed messageShift;
151 
152 public:
153  //================================================ Symmetry results holding values. This is required for Python being able to access the results without having the ProSHADE_run object.
154  std::vector < proshade_double* > detectedSymmetry;
155  std::vector < std::vector< proshade_double > > allDetectedCAxes;
156  std::vector < std::vector< proshade_unsign > > allDetectedDAxes;
157  std::vector < proshade_unsign > allDetectedTAxes;
158  std::vector < proshade_unsign > allDetectedOAxes;
159  std::vector < proshade_unsign > allDetectedIAxes;
160 
161 public: // maybe make this protected?
162  //================================================ Variable modifying functions
163  void determineBandwidthFromAngle ( proshade_double uncertainty );
164  void determineBandwidth ( proshade_unsign circumference );
165  void determineSphereDistances ( proshade_single maxMapRange );
166  void determineIntegrationOrder ( proshade_single maxMapRange );
167  void determineAllSHValues ( proshade_unsign xDim, proshade_unsign yDim, proshade_single xDimAngs,
168  proshade_single yDimAngs, proshade_single zDimAngs );
169  void setVariablesLeftOnAuto ( void );
170 
171 public:
172  //================================================ Constructors / Destructors
173 #if defined ( _WIN64 ) || defined ( _WIN32 )
174  __declspec(dllexport) ProSHADE_settings ( );
175  __declspec(dllexport) ProSHADE_settings ( ProSHADE_settings* settings );
176  __declspec(dllexport) ProSHADE_settings ( ProSHADE_Task task );
177  __declspec(dllexport) ~ProSHADE_settings ( );
178 #else
179  ProSHADE_settings ( void );
180  ProSHADE_settings ( ProSHADE_settings* settings );
181  ProSHADE_settings ( ProSHADE_Task task );
182  ~ProSHADE_settings ( void );
183 #endif
184 
185  //================================================ Variable setting functions
186 #if defined ( _WIN64 ) || defined ( _WIN32 )
187  void __declspec(dllexport) addStructure ( std::string structure );
188  void __declspec(dllexport) setResolution ( proshade_single resolution );
189  void __declspec(dllexport) setPDBBFactor ( proshade_double newBF );
190  void __declspec(dllexport) setNormalisation ( bool normalise );
191  void __declspec(dllexport) setMapInversion ( bool mInv );
192  void __declspec(dllexport) setVerbosity ( proshade_signed verbosity );
193  void __declspec(dllexport) setMaskBlurFactor ( proshade_single blurFac );
194  void __declspec(dllexport) setMaskIQR ( proshade_single noIQRs );
195  void __declspec(dllexport) setMasking ( bool mask );
196  void __declspec(dllexport) setCorrelationMasking ( bool corMask );
197  void __declspec(dllexport) setTypicalNoiseSize ( proshade_single typNoi );
198  void __declspec(dllexport) setMinimumMaskSize ( proshade_single minMS );
199  void __declspec(dllexport) setMaskSaving ( bool savMsk );
200  void __declspec(dllexport) setMaskFilename ( std::string mskFln );
201  void __declspec(dllexport) setAppliedMaskFilename ( std::string mskFln );
202  void __declspec(dllexport) setFourierWeightsFilename ( std::string fWgFln );
203  void __declspec(dllexport) setMapReboxing ( bool reBx );
204  void __declspec(dllexport) setBoundsSpace ( proshade_single boundsExSp );
205  void __declspec(dllexport) setBoundsThreshold ( proshade_signed boundsThres );
206  void __declspec(dllexport) setSameBoundaries ( bool sameB );
207  void __declspec(dllexport) setOutputFilename ( std::string oFileName );
208  void __declspec(dllexport) setMapResolutionChange ( bool mrChange );
209  void __declspec(dllexport) setMapResolutionChangeTriLinear ( bool mrChange );
210  void __declspec(dllexport) setMapCentering ( bool com );
211  void __declspec(dllexport) setExtraSpace ( proshade_single exSpace );
212  void __declspec(dllexport) setCoordExtraSpace ( proshade_single exSpace );
213  void __declspec(dllexport) setBoxCentering ( proshade_double xPos, proshade_double yPos, proshade_double zPos );
214  void __declspec(dllexport) setBandwidth ( proshade_unsign band );
215  void __declspec(dllexport) setSphereDistances ( proshade_single sphDist );
216  void __declspec(dllexport) setIntegrationOrder ( proshade_unsign intOrd );
217  void __declspec(dllexport) setTaylorSeriesCap ( proshade_unsign tayCap );
218  void __declspec(dllexport) setProgressiveSphereMapping ( bool progSphMap );
219  void __declspec(dllexport) setEnergyLevelsComputation ( bool enLevDesc );
220  void __declspec(dllexport) setTraceSigmaComputation ( bool trSigVal );
221  void __declspec(dllexport) setRotationFunctionComputation ( bool rotfVal );
222  void __declspec(dllexport) setPeakNeighboursNumber ( proshade_unsign pkS );
223  void __declspec(dllexport) setPeakNaiveNoIQR ( proshade_double noIQRs );
224  void __declspec(dllexport) setPhaseUsage ( bool phaseUsage );
225  void __declspec(dllexport) setEnLevShellWeight ( proshade_double mPower );
226  void __declspec(dllexport) setGroupingSmoothingFactor ( proshade_double smFact );
227  void __declspec(dllexport) setSymmetryCentreSearch ( bool sCen );
228  void __declspec(dllexport) setMissingPeakThreshold ( proshade_double mpThres );
229  void __declspec(dllexport) setAxisComparisonThreshold ( proshade_double axThres );
230  void __declspec(dllexport) setAxisComparisonThresholdBehaviour ( bool behav );
231  void __declspec(dllexport) setMinimumPeakForAxis ( proshade_double minSP );
232  void __declspec(dllexport) setRecommendedSymmetry ( std::string val );
233  void __declspec(dllexport) setRecommendedFold ( proshade_unsign val );
234  void __declspec(dllexport) setRequestedSymmetry ( std::string val );
235  void __declspec(dllexport) setRequestedFold ( proshade_unsign val );
236  void __declspec(dllexport) setDetectedSymmetry ( proshade_double* sym );
237  void __declspec(dllexport) setOverlaySaveFile ( std::string filename );
238  void __declspec(dllexport) setOverlayJsonFile ( std::string filename );
239  void __declspec(dllexport) setBicubicInterpolationSearch ( bool bicubPeaks );
240  void __declspec(dllexport) setMaxSymmetryFold ( proshade_unsign maxFold );
241  void __declspec(dllexport) setFSCThreshold ( proshade_double fscThr );
242  void __declspec(dllexport) setPeakThreshold ( proshade_double peakThr );
243  void __declspec(dllexport) setNegativeDensity ( bool nDens );
244 #else
245  void addStructure ( std::string structure );
246  void setResolution ( proshade_single resolution );
247  void setPDBBFactor ( proshade_double newBF );
248  void setNormalisation ( bool normalise );
249  void setMapInversion ( bool mInv );
250  void setVerbosity ( proshade_signed verbosity );
251  void setMaskBlurFactor ( proshade_single blurFac );
252  void setMaskIQR ( proshade_single noIQRs );
253  void setMasking ( bool mask );
254  void setCorrelationMasking ( bool corMask );
255  void setTypicalNoiseSize ( proshade_single typNoi );
256  void setMinimumMaskSize ( proshade_single minMS );
257  void setMaskSaving ( bool savMsk );
258  void setMaskFilename ( std::string mskFln );
259  void setAppliedMaskFilename ( std::string mskFln );
260  void setFourierWeightsFilename ( std::string fWgFln );
261  void setMapReboxing ( bool reBx );
262  void setBoundsSpace ( proshade_single boundsExSp );
263  void setBoundsThreshold ( proshade_signed boundsThres );
264  void setSameBoundaries ( bool sameB );
265  void setOutputFilename ( std::string oFileName );
266  void setMapResolutionChange ( bool mrChange );
267  void setMapResolutionChangeTriLinear ( bool mrChange );
268  void setMapCentering ( bool com );
269  void setExtraSpace ( proshade_single exSpace );
270  void setCoordExtraSpace ( proshade_single exSpace );
271  void setBoxCentering ( proshade_double xPos, proshade_double yPos, proshade_double zPos );
272  void setBandwidth ( proshade_unsign band );
273  void setSphereDistances ( proshade_single sphDist );
274  void setIntegrationOrder ( proshade_unsign intOrd );
275  void setTaylorSeriesCap ( proshade_unsign tayCap );
276  void setProgressiveSphereMapping ( bool progSphMap );
277  void setEnergyLevelsComputation ( bool enLevDesc );
278  void setTraceSigmaComputation ( bool trSigVal );
279  void setRotationFunctionComputation ( bool rotfVal );
280  void setPeakNeighboursNumber ( proshade_unsign pkS );
281  void setPeakNaiveNoIQR ( proshade_double noIQRs );
282  void setPhaseUsage ( bool phaseUsage );
283  void setEnLevShellWeight ( proshade_double mPower );
284  void setGroupingSmoothingFactor ( proshade_double smFact );
285  void setMissingPeakThreshold ( proshade_double mpThres );
286  void setSymmetryCentreSearch ( bool sCen );
287  void setAxisComparisonThreshold ( proshade_double axThres );
288  void setAxisComparisonThresholdBehaviour ( bool behav );
289  void setMinimumPeakForAxis ( proshade_double minSP );
290  void setRecommendedSymmetry ( std::string val );
291  void setRecommendedFold ( proshade_unsign val );
292  void setRequestedSymmetry ( std::string val );
293  void setRequestedFold ( proshade_unsign val );
294  void setDetectedSymmetry ( proshade_double* sym );
295  void setOverlaySaveFile ( std::string filename );
296  void setOverlayJsonFile ( std::string filename );
297  void setBicubicInterpolationSearch ( bool bicubPeaks );
298  void setMaxSymmetryFold ( proshade_unsign maxFold );
299  void setFSCThreshold ( proshade_double fscThr );
300  void setPeakThreshold ( proshade_double peakThr );
301  void setNegativeDensity ( bool nDens );
302 #endif
303 
304  //================================================ Command line options parsing
305 #if defined ( _WIN64 ) || defined ( _WIN32 )
306  void __declspec(dllexport) getCommandLineParams ( int argc, char** argv );
307 #else
308  void getCommandLineParams ( int argc, char** argv );
309 #endif
310 
311  //================================================ Debugging
312 #if defined ( _WIN64 ) || defined ( _WIN32 )
313  void __declspec(dllexport) printSettings ( void );
314 #else
315  void printSettings ( void );
316 #endif
317 };
318 
319 #endif
ProSHADE_settings::noIQRsFromMedianNaivePeak
proshade_double noIQRsFromMedianNaivePeak
When doing peak searching, how many IQRs from the median the threshold for peak height should be (in ...
Definition: ProSHADE_settings.hpp:120
ProSHADE_settings::setOverlayJsonFile
void setOverlayJsonFile(std::string filename)
Sets the filename to which the overlay operations are to be save into.
Definition: ProSHADE.cpp:1605
ProSHADE_settings::setBoxCentering
void setBoxCentering(proshade_double xPos, proshade_double yPos, proshade_double zPos)
Sets the requested centre of box to be at the real space co-ordinates supplied.
Definition: ProSHADE.cpp:1018
ProSHADE_settings::maxBandwidth
proshade_unsign maxBandwidth
The bandwidth of spherical harmonics decomposition for the largest sphere.
Definition: ProSHADE_settings.hpp:58
ProSHADE_settings::integOrder
proshade_unsign integOrder
The order required for full Gauss-Legendre integration between the spheres.
Definition: ProSHADE_settings.hpp:68
ProSHADE_settings::recommendedSymmetryType
std::string recommendedSymmetryType
The symmetry type that ProSHADE finds the best fitting for the structure. Possible values are "" for ...
Definition: ProSHADE_settings.hpp:131
ProSHADE_settings::rotTrsJSONFile
std::string rotTrsJSONFile
The filename to which the rotation and translation operations are to be saved into.
Definition: ProSHADE_settings.hpp:146
ProSHADE_settings::setEnLevShellWeight
void setEnLevShellWeight(proshade_double mPower)
Sets the weight of shell position for the energy levels computation.
Definition: ProSHADE.cpp:1318
ProSHADE_settings::computeTraceSigmaDesc
bool computeTraceSigmaDesc
If true, the trace sigma descriptor will be computed, otherwise all its computations will be omitted.
Definition: ProSHADE_settings.hpp:115
ProSHADE_settings::findSymCentre
bool findSymCentre
Should phase-less map be used to determine centre of symmetry?
Definition: ProSHADE_settings.hpp:126
ProSHADE_settings::setTraceSigmaComputation
void setTraceSigmaComputation(bool trSigVal)
Sets whether the trace sigma distance descriptor should be computed.
Definition: ProSHADE.cpp:1210
ProSHADE_settings::computeRotationFuncDesc
bool computeRotationFuncDesc
If true, the rotation function descriptor will be computed, otherwise all its computations will be om...
Definition: ProSHADE_settings.hpp:116
ProSHADE_settings::setSameBoundaries
void setSameBoundaries(bool sameB)
Sets whether same boundaries should be used in the appropriate variable.
Definition: ProSHADE.cpp:915
ProSHADE_settings::maxSymmetryFold
proshade_unsign maxSymmetryFold
The highest symmetry fold to search for.
Definition: ProSHADE_settings.hpp:136
ProSHADE_settings::taylorSeriesCap
proshade_unsign taylorSeriesCap
The max limit on the Taylor series expansion done for the abscissas of the Gauss-Legendre integration...
Definition: ProSHADE_settings.hpp:69
ProSHADE_settings::setMinimumMaskSize
void setMinimumMaskSize(proshade_single minMS)
Sets the requested minimum mask size.
Definition: ProSHADE.cpp:753
ProSHADE_settings::determineAllSHValues
void determineAllSHValues(proshade_unsign xDim, proshade_unsign yDim, proshade_single xDimAngs, proshade_single yDimAngs, proshade_single zDimAngs)
This function determines all the required values for spherical harmonics computation.
Definition: ProSHADE.cpp:1853
ProSHADE_settings::setAppliedMaskFilename
void setAppliedMaskFilename(std::string mskFln)
Sets the filename of the mask data that should be applied to the input map.
Definition: ProSHADE.cpp:813
ProSHADE_settings::boundsExtraSpace
proshade_single boundsExtraSpace
The number of extra angstroms to be added to all re-boxing bounds just for safety.
Definition: ProSHADE_settings.hpp:93
ProSHADE_settings::setBicubicInterpolationSearch
void setBicubicInterpolationSearch(bool bicubPeaks)
Sets the bicubic interpolation on peaks.
Definition: ProSHADE.cpp:1623
ProSHADE_settings::setPeakNaiveNoIQR
void setPeakNaiveNoIQR(proshade_double noIQRs)
Sets the number of IQRs from the median for threshold height a peak needs to be considered a peak.
Definition: ProSHADE.cpp:1274
ProSHADE_settings::outName
std::string outName
The file name where the output structure(s) should be saved.
Definition: ProSHADE_settings.hpp:110
ProSHADE_settings::setMapInversion
void setMapInversion(bool mInv)
Sets the requested map inversion value in the appropriate variable.
Definition: ProSHADE.cpp:609
ProSHADE_settings::setMapResolutionChange
void setMapResolutionChange(bool mrChange)
Sets the requested map resolution change decision in the appropriate variable.
Definition: ProSHADE.cpp:956
ProSHADE_settings::setPeakNeighboursNumber
void setPeakNeighboursNumber(proshade_unsign pkS)
Sets the number of neighbour values that have to be smaller for an index to be considered a peak.
Definition: ProSHADE.cpp:1252
ProSHADE_settings::allDetectedDAxes
std::vector< std::vector< proshade_unsign > > allDetectedDAxes
The vector of all detected dihedral symmetry axes indices in allDetectedCAxes.
Definition: ProSHADE_settings.hpp:156
ProSHADE_settings::blurFactor
proshade_single blurFactor
This is the amount by which B-factors should be increased to create the blurred map for masking.
Definition: ProSHADE_settings.hpp:78
ProSHADE_settings::maskMap
bool maskMap
Should the map be masked from noise?
Definition: ProSHADE_settings.hpp:80
ProSHADE_settings::requestedSymmetryFold
proshade_unsign requestedSymmetryFold
The fold of the requested symmetry (only applicable to C and D symmetry types).
Definition: ProSHADE_settings.hpp:134
ProSHADE_settings::requestedSymmetryType
std::string requestedSymmetryType
The symmetry type requested by the user. Allowed values are C, D, T, O and I.
Definition: ProSHADE_settings.hpp:133
ProSHADE_settings::setSphereDistances
void setSphereDistances(proshade_single sphDist)
Sets the requested distance between spheres in the appropriate variable.
Definition: ProSHADE.cpp:1107
ProSHADE_settings::setVerbosity
void setVerbosity(proshade_signed verbosity)
Sets the requested verbosity in the appropriate variable.
Definition: ProSHADE.cpp:629
ProSHADE_settings::removeNegativeDensity
bool removeNegativeDensity
Should the negative density be removed from input files?
Definition: ProSHADE_settings.hpp:47
ProSHADE_settings::setMinimumPeakForAxis
void setMinimumPeakForAxis(proshade_double minSP)
Sets the minimum peak height for symmetry axis to be considered.
Definition: ProSHADE.cpp:1447
ProSHADE_maths.hpp
This header file declares all the functions required for computing various information from the ProSH...
ProSHADE_settings::saveMask
bool saveMask
Should the mask be saved?
Definition: ProSHADE_settings.hpp:84
ProSHADE_settings::requestedResolution
proshade_single requestedResolution
The resolution to which the calculations are to be done.
Definition: ProSHADE_settings.hpp:50
ProSHADE_settings::minSymPeak
proshade_double minSymPeak
Minimum average peak for symmetry axis to be considered as "real".
Definition: ProSHADE_settings.hpp:130
ProSHADE_settings::setAxisComparisonThresholdBehaviour
void setAxisComparisonThresholdBehaviour(bool behav)
Sets the automatic symmetry axis tolerance decreasing.
Definition: ProSHADE.cpp:1426
ProSHADE_settings::setDetectedSymmetry
void setDetectedSymmetry(proshade_double *sym)
Sets the final detected symmetry axes information.
Definition: ProSHADE.cpp:1553
ProSHADE_settings::progressiveSphereMapping
bool progressiveSphereMapping
If true, each shell will have its own angular resolution dependent on the actual number of map points...
Definition: ProSHADE_settings.hpp:107
ProSHADE_settings::maxSphereDists
proshade_single maxSphereDists
The distance between spheres in spherical mapping for the largest sphere.
Definition: ProSHADE_settings.hpp:65
ProSHADE_settings::symMissPeakThres
proshade_double symMissPeakThres
Percentage of peaks that could be missing that would warrant starting the missing peaks search proced...
Definition: ProSHADE_settings.hpp:127
ProSHADE_settings::setPDBBFactor
void setPDBBFactor(proshade_double newBF)
Sets the requested B-factor value for PDB files in the appropriate variable.
Definition: ProSHADE.cpp:569
ProSHADE_settings::addStructure
void addStructure(std::string structure)
Adds a structure file name to the appropriate variable.
Definition: ProSHADE.cpp:529
ProSHADE_settings::determineIntegrationOrder
void determineIntegrationOrder(proshade_single maxMapRange)
This function determines the integration order for the between spheres integration.
Definition: ProSHADE.cpp:1809
ProSHADE_settings::setMaskIQR
void setMaskIQR(proshade_single noIQRs)
Sets the requested number of IQRs for masking threshold in the appropriate variable.
Definition: ProSHADE.cpp:670
ProSHADE_settings::setMissingPeakThreshold
void setMissingPeakThreshold(proshade_double mpThres)
Sets the threshold for starting the missing peaks procedure.
Definition: ProSHADE.cpp:1361
ProSHADE_settings::maskingThresholdIQRs
proshade_single maskingThresholdIQRs
Number of inter-quartile ranges from the median to be used for thresholding the blurred map for maski...
Definition: ProSHADE_settings.hpp:79
ProSHADE_settings::useCorrelationMasking
bool useCorrelationMasking
Should the blurring masking (false) or the correlation masking (true) be used?
Definition: ProSHADE_settings.hpp:81
ProSHADE_settings::usePhase
bool usePhase
If true, the full data will be used, if false, Patterson maps will be used instead and phased data wi...
Definition: ProSHADE_settings.hpp:62
ProSHADE_settings::setSymmetryCentreSearch
void setSymmetryCentreSearch(bool sCen)
Sets the symmetry centre search on or off.
Definition: ProSHADE.cpp:1382
ProSHADE_settings::setMapCentering
void setMapCentering(bool com)
Sets the requested map centering decision value in the appropriate variable.
Definition: ProSHADE.cpp:996
ProSHADE_settings::setMaskBlurFactor
void setMaskBlurFactor(proshade_single blurFac)
Sets the requested map blurring factor in the appropriate variable.
Definition: ProSHADE.cpp:649
ProSHADE_settings::allDetectedTAxes
std::vector< proshade_unsign > allDetectedTAxes
The vector of all detected tetrahedral symmetry axes indices in allDetectedCAxes.
Definition: ProSHADE_settings.hpp:157
ProSHADE_settings::setPeakThreshold
void setPeakThreshold(proshade_double peakThr)
Sets the minimum peak height threshold for axis to be considered possible.
Definition: ProSHADE.cpp:1677
ProSHADE_settings::setPhaseUsage
void setPhaseUsage(bool phaseUsage)
Sets whether the phase information will be used.
Definition: ProSHADE.cpp:1296
ProSHADE_settings::maskFileName
std::string maskFileName
The filename to which mask should be saved.
Definition: ProSHADE_settings.hpp:85
ProSHADE_settings::allDetectedOAxes
std::vector< proshade_unsign > allDetectedOAxes
The vector of all detected octahedral symmetry axes indices in allDetectedCAxes.
Definition: ProSHADE_settings.hpp:158
ProSHADE_settings::verbose
proshade_signed verbose
Should the software report on the progress, or just be quiet? Value between -1 (nothing) and 4 (loud)
Definition: ProSHADE_settings.hpp:149
ProSHADE_settings::setFSCThreshold
void setFSCThreshold(proshade_double fscThr)
Sets the minimum FSC threshold for axis to be considered detected.
Definition: ProSHADE.cpp:1659
ProSHADE_settings::setBandwidth
void setBandwidth(proshade_unsign band)
Sets the requested spherical harmonics bandwidth in the appropriate variable.
Definition: ProSHADE.cpp:1087
ProSHADE_settings::messageShift
proshade_signed messageShift
This value allows shifting the messages to create more readable log for sub-processes.
Definition: ProSHADE_settings.hpp:150
ProSHADE_settings::setBoundsSpace
void setBoundsSpace(proshade_single boundsExSp)
Sets the requested number of angstroms for extra space in re-boxing in the appropriate variable.
Definition: ProSHADE.cpp:874
ProSHADE_settings::changeMapResolutionTriLinear
bool changeMapResolutionTriLinear
Should maps be re-sampled to obtain the required resolution?
Definition: ProSHADE_settings.hpp:52
ProSHADE_settings::setOutputFilename
void setOutputFilename(std::string oFileName)
Sets the requested output file name in the appropriate variable.
Definition: ProSHADE.cpp:936
ProSHADE_settings::useBiCubicInterpolationOnPeaks
bool useBiCubicInterpolationOnPeaks
This variable switch decides whether best symmetry is detected from peak indices, or whether bicubic ...
Definition: ProSHADE_settings.hpp:135
ProSHADE_settings::setAxisComparisonThreshold
void setAxisComparisonThreshold(proshade_double axThres)
Sets the threshold for matching symmetry axes.
Definition: ProSHADE.cpp:1403
ProSHADE_settings::peakThresholdMin
proshade_double peakThresholdMin
The threshold for peak height above which axes are considered possible.
Definition: ProSHADE_settings.hpp:138
ProSHADE_settings::forceP1
bool forceP1
Should the P1 spacegroup be forced on the input PDB files?
Definition: ProSHADE_settings.hpp:44
ProSHADE_settings::setTypicalNoiseSize
void setTypicalNoiseSize(proshade_single typNoi)
Sets the requested "fake" half-map kernel in the appropriate variable.
Definition: ProSHADE.cpp:733
ProSHADE_settings::task
ProSHADE_Task task
This custom type variable determines which task to perfom (i.e. symmetry detection,...
Definition: ProSHADE_settings.hpp:40
ProSHADE_settings::setMaskFilename
void setMaskFilename(std::string mskFln)
Sets where the mask should be saved.
Definition: ProSHADE.cpp:793
ProSHADE_settings::setCoordExtraSpace
void setCoordExtraSpace(proshade_single exSpace)
Sets the requested co-ordinates extra space value in the appropriate variable.
Definition: ProSHADE.cpp:1067
ProSHADE_settings::reBoxMap
bool reBoxMap
This switch decides whether re-boxing is needed.
Definition: ProSHADE_settings.hpp:92
ProSHADE_settings::appliedMaskFileName
std::string appliedMaskFileName
The filename from which mask data will be read from.
Definition: ProSHADE_settings.hpp:86
ProSHADE_settings::coOrdsExtraSpace
proshade_single coOrdsExtraSpace
This number of Angstroms will be added before and any co-ordinates to make sure there is no atom dire...
Definition: ProSHADE_settings.hpp:104
ProSHADE_settings::normaliseMap
bool normaliseMap
Should the map be normalised to mean 0 sd 1?
Definition: ProSHADE_settings.hpp:72
ProSHADE_settings::addExtraSpace
proshade_single addExtraSpace
If this value is non-zero, this many angstroms of empty space will be added to the internal map.
Definition: ProSHADE_settings.hpp:103
ProSHADE_settings::setRequestedFold
void setRequestedFold(proshade_unsign val)
Sets the user requested symmetry fold.
Definition: ProSHADE.cpp:1532
ProSHADE_settings
This class stores all the settings and is passed to the executive classes instead of a multitude of p...
Definition: ProSHADE_settings.hpp:37
ProSHADE_settings::fscThreshold
proshade_double fscThreshold
The threshold for FSC value under which the axis is considered to be likely noise.
Definition: ProSHADE_settings.hpp:137
ProSHADE_settings::determineBandwidthFromAngle
void determineBandwidthFromAngle(proshade_double uncertainty)
This function determines the bandwidth for the spherical harmonics computation from the allowed rotat...
Definition: ProSHADE.cpp:1746
ProSHADE_settings::getCommandLineParams
void getCommandLineParams(int argc, char **argv)
This function parses the command line arguments into the settings object.
Definition: ProSHADE.cpp:2135
ProSHADE_settings::setMapReboxing
void setMapReboxing(bool reBx)
Sets whether re-boxing needs to be done in the appropriate variable.
Definition: ProSHADE.cpp:853
ProSHADE_settings::setRecommendedSymmetry
void setRecommendedSymmetry(std::string val)
Sets the ProSHADE detected symmetry type.
Definition: ProSHADE.cpp:1469
ProSHADE_settings::setMaxSymmetryFold
void setMaxSymmetryFold(proshade_unsign maxFold)
Sets the maximum symmetry fold (well, the maximum prime symmetry fold).
Definition: ProSHADE.cpp:1641
ProSHADE_settings::correlationKernel
proshade_single correlationKernel
This value in Angstrom will be used as the kernel for the map-FHM correlation computation.
Definition: ProSHADE_settings.hpp:83
ProSHADE_settings::setNegativeDensity
void setNegativeDensity(bool nDens)
Sets the internal variable deciding whether input files negative density should be removed.
Definition: ProSHADE.cpp:1695
ProSHADE_settings::invertMap
bool invertMap
Should the map be inverted? Only use this if you think you have the wrong hand in your map.
Definition: ProSHADE_settings.hpp:75
ProSHADE_settings::setTaylorSeriesCap
void setTaylorSeriesCap(proshade_unsign tayCap)
Sets the requested Taylor series cap for the Gauss-Legendre integration in the appropriate variable.
Definition: ProSHADE.cpp:1148
ProSHADE_settings::centrePosition
std::vector< proshade_double > centrePosition
The position of the centre of the map in "real space" co-ordinates.
Definition: ProSHADE_settings.hpp:142
ProSHADE_settings::boundsSimilarityThreshold
proshade_signed boundsSimilarityThreshold
Number of indices which can be added just to make sure same size in indices is achieved.
Definition: ProSHADE_settings.hpp:94
ProSHADE_settings::setCorrelationMasking
void setCorrelationMasking(bool corMask)
Sets the requested map masking type in the appropriate variable.
Definition: ProSHADE.cpp:711
ProSHADE_settings::setProgressiveSphereMapping
void setProgressiveSphereMapping(bool progSphMap)
Sets the requested sphere mapping value settings approach in the appropriate variable.
Definition: ProSHADE.cpp:1168
ProSHADE_settings::changeMapResolution
bool changeMapResolution
Should maps be re-sampled to obtain the required resolution?
Definition: ProSHADE_settings.hpp:51
ProSHADE_settings::setIntegrationOrder
void setIntegrationOrder(proshade_unsign intOrd)
Sets the requested order for the Gauss-Legendre integration in the appropriate variable.
Definition: ProSHADE.cpp:1127
ProSHADE_settings::setRotationFunctionComputation
void setRotationFunctionComputation(bool rotfVal)
Sets whether the rotation function distance descriptor should be computed.
Definition: ProSHADE.cpp:1231
ProSHADE_settings::rotationUncertainty
proshade_double rotationUncertainty
Alternative to bandwidth - the angle in degrees to which the rotation function accuracy should be com...
Definition: ProSHADE_settings.hpp:59
ProSHADE_settings::~ProSHADE_settings
~ProSHADE_settings(void)
Destructor for the ProSHADE_settings class.
Definition: ProSHADE.cpp:488
ProSHADE_settings::setOverlaySaveFile
void setOverlaySaveFile(std::string filename)
Sets the filename to which the overlay structure is to be save into.
Definition: ProSHADE.cpp:1587
ProSHADE_settings::overlayStructureName
std::string overlayStructureName
The filename to which the rotated and translated moving structure is to be saved.
Definition: ProSHADE_settings.hpp:145
ProSHADE_settings::determineBandwidth
void determineBandwidth(proshade_unsign circumference)
This function determines the bandwidth for the spherical harmonics computation.
Definition: ProSHADE.cpp:1714
ProSHADE_settings::moveToCOM
bool moveToCOM
Logical value stating whether the structure should be moved to have its Centre Of Mass (COM) in the m...
Definition: ProSHADE_settings.hpp:99
ProSHADE_settings::peakNeighbours
proshade_unsign peakNeighbours
Number of points in any direction that have to be lower than the considered index in order to conside...
Definition: ProSHADE_settings.hpp:119
ProSHADE_settings::smoothingFactor
proshade_double smoothingFactor
This factor decides how small the group sizes should be - larger factor means more smaller groups.
Definition: ProSHADE_settings.hpp:123
ProSHADE_settings::setFourierWeightsFilename
void setFourierWeightsFilename(std::string fWgFln)
Sets the filename of the mask data that should be applied to the input map.
Definition: ProSHADE.cpp:833
ProSHADE_settings::halfMapKernel
proshade_single halfMapKernel
This value in Angstrom will be used as the kernel for the "fake half-map" computation.
Definition: ProSHADE_settings.hpp:82
ProSHADE_settings::boxCentre
std::vector< proshade_double > boxCentre
If box centre is to be in any other location, this variable will hold the real space location that sh...
Definition: ProSHADE_settings.hpp:100
ProSHADE_settings::determineSphereDistances
void determineSphereDistances(proshade_single maxMapRange)
This function determines the sphere distances for sphere mapping.
Definition: ProSHADE.cpp:1777
ProSHADE_settings::setGroupingSmoothingFactor
void setGroupingSmoothingFactor(proshade_double smFact)
Sets the grouping smoothing factor into the proper variable.
Definition: ProSHADE.cpp:1340
ProSHADE_settings::setRequestedSymmetry
void setRequestedSymmetry(std::string val)
Sets the user requested symmetry type.
Definition: ProSHADE.cpp:1512
ProSHADE_settings::setExtraSpace
void setExtraSpace(proshade_single exSpace)
Sets the requested map extra space value in the appropriate variable.
Definition: ProSHADE.cpp:1047
ProSHADE_settings::allDetectedIAxes
std::vector< proshade_unsign > allDetectedIAxes
The vector of all detected icosahedral symmetry axes indices in allDetectedCAxes.
Definition: ProSHADE_settings.hpp:159
ProSHADE_settings::forceBounds
proshade_signed * forceBounds
These will be the boundaries to be forced upon the map.
Definition: ProSHADE_settings.hpp:96
ProSHADE_settings::fourierWeightsFileName
std::string fourierWeightsFileName
The filename from which Fourier weights data will be read from.
Definition: ProSHADE_settings.hpp:89
ProSHADE_settings::detectedSymmetry
std::vector< proshade_double * > detectedSymmetry
The vector of detected symmetry axes.
Definition: ProSHADE_settings.hpp:154
ProSHADE_settings::recommendedSymmetryFold
proshade_unsign recommendedSymmetryFold
The fold of the recommended symmetry C or D type, 0 otherwise.
Definition: ProSHADE_settings.hpp:132
ProSHADE_settings::inputFiles
std::vector< std::string > inputFiles
This vector contains the filenames of all input structure files.
Definition: ProSHADE_settings.hpp:43
ProSHADE_settings::setMapResolutionChangeTriLinear
void setMapResolutionChangeTriLinear(bool mrChange)
Sets the requested map resolution change decision using tri-linear interpolation in the appropriate v...
Definition: ProSHADE.cpp:976
ProSHADE_settings::setMaskSaving
void setMaskSaving(bool savMsk)
Sets whether the mask should be saved.
Definition: ProSHADE.cpp:773
ProSHADE_settings::ProSHADE_settings
ProSHADE_settings(void)
Contructor for the ProSHADE_settings class.
Definition: ProSHADE.cpp:37
ProSHADE_settings::firstModelOnly
bool firstModelOnly
Shoud only the first PDB model be used, or should all models be used?
Definition: ProSHADE_settings.hpp:46
ProSHADE_settings::setBoundsThreshold
void setBoundsThreshold(proshade_signed boundsThres)
Sets the threshold for number of indices difference acceptable to make index sizes same in the approp...
Definition: ProSHADE.cpp:894
ProSHADE_settings::axisErrTolerance
proshade_double axisErrTolerance
Allowed error on vector axis in in dot product ( acos ( 1 - axErr ) is the allowed difference in radi...
Definition: ProSHADE_settings.hpp:128
ProSHADE_settings::useSameBounds
bool useSameBounds
Switch to say that the same boundaries as used for the first should be used for all input maps.
Definition: ProSHADE_settings.hpp:95
ProSHADE_settings::setMasking
void setMasking(bool mask)
Sets the requested map masking decision value in the appropriate variable.
Definition: ProSHADE.cpp:690
ProSHADE_settings::pdbBFactorNewVal
proshade_double pdbBFactorNewVal
Change all PDB B-factors to this value (for smooth maps).
Definition: ProSHADE_settings.hpp:55
ProSHADE_settings::setRecommendedFold
void setRecommendedFold(proshade_unsign val)
Sets the ProSHADE detected symmetry fold.
Definition: ProSHADE.cpp:1492
ProSHADE_settings::setVariablesLeftOnAuto
void setVariablesLeftOnAuto(void)
Function to determine general values that the user left on auto-determination.
Definition: ProSHADE.cpp:503
ProSHADE_settings::removeWaters
bool removeWaters
Should all waters be removed from input PDB files?
Definition: ProSHADE_settings.hpp:45
ProSHADE_settings::setResolution
void setResolution(proshade_single resolution)
Sets the requested resolution in the appropriate variable.
Definition: ProSHADE.cpp:549
ProSHADE_settings::allDetectedCAxes
std::vector< std::vector< proshade_double > > allDetectedCAxes
The vector of all detected cyclic symmetry axes.
Definition: ProSHADE_settings.hpp:155
ProSHADE_settings::printSettings
void printSettings(void)
This function prints the current values in the settings object.
Definition: ProSHADE.cpp:2723
ProSHADE_settings::fastISearch
bool fastISearch
Should FSC be computed for all possible I matches, or just for the best one according to FR?
Definition: ProSHADE_settings.hpp:139
ProSHADE_settings::enLevMatrixPowerWeight
proshade_double enLevMatrixPowerWeight
If RRP matrices shell position is to be weighted by putting the position as an exponent,...
Definition: ProSHADE_settings.hpp:114
ProSHADE_settings::setNormalisation
void setNormalisation(bool normalise)
Sets the requested map normalisation value in the appropriate variable.
Definition: ProSHADE.cpp:589
ProSHADE_settings::setEnergyLevelsComputation
void setEnergyLevelsComputation(bool enLevDesc)
Sets whether the energy level distance descriptor should be computed.
Definition: ProSHADE.cpp:1189
ProSHADE_settings::computeEnergyLevelsDesc
bool computeEnergyLevelsDesc
If true, the energy levels descriptor will be computed, otherwise all its computations will be omitte...
Definition: ProSHADE_settings.hpp:113