ProSHADE  0.7.6.2 (DEC 2021)
Protein Shape Detection
ProSHADE_data.hpp
Go to the documentation of this file.
1 
24 //==================================================== ProSHADE
25 #include "ProSHADE_peakSearch.hpp"
26 
27 //==================================================== Overinclusion protection
28 #ifndef PROSHADE_DATA
29 #define PROSHADE_DATA
30 
31 //==================================================== ProSHADE_internal_data Namespace
40 namespace ProSHADE_internal_data
41 {
49  {
50  public:
51  //============================================ Variables regarding input file
52  std::string fileName;
53  ProSHADE_internal_io::InputType fileType;
54 
55  //============================================ Variables regarding map
56  proshade_double* internalMap;
57 
58  //============================================ Variables regarding map information
59  proshade_single xDimSize;
60  proshade_single yDimSize;
61  proshade_single zDimSize;
62  proshade_single aAngle;
63  proshade_single bAngle;
64  proshade_single cAngle;
65  proshade_unsign xDimIndices;
66  proshade_unsign yDimIndices;
67  proshade_unsign zDimIndices;
68  proshade_unsign xGridIndices;
69  proshade_unsign yGridIndices;
70  proshade_unsign zGridIndices;
71  proshade_unsign xAxisOrder;
72  proshade_unsign yAxisOrder;
73  proshade_unsign zAxisOrder;
74  proshade_signed xAxisOrigin;
75  proshade_signed yAxisOrigin;
76  proshade_signed zAxisOrigin;
77  proshade_double xCom;
78  proshade_double yCom;
79  proshade_double zCom;
80 
81  //============================================ Variables regarding original input values (i.e. these do not change with ProSHADE manipulations)
82  proshade_single xDimSizeOriginal;
83  proshade_single yDimSizeOriginal;
84  proshade_single zDimSizeOriginal;
85  proshade_unsign xDimIndicesOriginal;
86  proshade_unsign yDimIndicesOriginal;
87  proshade_unsign zDimIndicesOriginal;
88  proshade_signed xAxisOriginOriginal;
89  proshade_signed yAxisOriginOriginal;
90  proshade_signed zAxisOriginOriginal;
91  proshade_double originalMapXCom;
92  proshade_double originalMapYCom;
93  proshade_double originalMapZCom;
94  proshade_double mapMovFromsChangeX;
95  proshade_double mapMovFromsChangeY;
96  proshade_double mapMovFromsChangeZ;
97  proshade_double mapCOMProcessChangeX;
98  proshade_double mapCOMProcessChangeY;
99  proshade_double mapCOMProcessChangeZ;
100 
101  //============================================ Variables regarding rotation and translation of original input files
102  proshade_double originalPdbRotCenX;
103  proshade_double originalPdbRotCenY;
104  proshade_double originalPdbRotCenZ;
105  proshade_double originalPdbTransX;
106  proshade_double originalPdbTransY;
107  proshade_double originalPdbTransZ;
108 
109  //============================================ Variables regarding iterator positions
110  proshade_signed xFrom;
111  proshade_signed yFrom;
112  proshade_signed zFrom;
113  proshade_signed xTo;
114  proshade_signed yTo;
115  proshade_signed zTo ;
116 
117  //============================================ Variables regarding SH mapping spheres
118  std::vector<proshade_single> spherePos;
119  proshade_unsign noSpheres;
121  proshade_complex** sphericalHarmonics;
122  proshade_complex** rotSphericalHarmonics;
123  proshade_unsign maxShellBand;
124 
125  //============================================ Variables regarding shape distance computations
126  proshade_double*** rrpMatrices;
127  proshade_complex*** eMatrices;
128  proshade_double integrationWeight;
129  proshade_complex* so3Coeffs;
130  proshade_complex* so3CoeffsInverse;
131  proshade_complex*** wignerMatrices;
132  proshade_unsign maxCompBand;
133  proshade_complex* translationMap;
134 
135  //============================================ Variables regarding symmetry detection
136  std::vector<ProSHADE_internal_spheres::ProSHADE_rotFun_sphere*> sphereMappedRotFun;
137 
138  //============================================ Control variables
139  bool isEmpty;
140  proshade_unsign inputOrder;
141 
142  protected:
143  void figureIndexStartStop ( void );
144  void setPDBMapValues ( void );
145  void readInMAP ( ProSHADE_settings* settings, proshade_double* maskArr = nullptr, proshade_unsign maskXDim = 0, proshade_unsign maskYDim = 0,
146  proshade_unsign maskZDim = 0, proshade_double* weightsArr = nullptr, proshade_unsign weigXDim = 0, proshade_unsign weigYDim = 0,
147  proshade_unsign weigZDim = 0 );
148  void readInPDB ( ProSHADE_settings* settings );
149  void readInGemmi ( gemmi::Structure gemmiStruct, ProSHADE_settings* settings );
150  void allocateRRPMemory ( );
151 
152  public:
153  //============================================ Constructors / Destructors
154  ProSHADE_data ( );
155  ProSHADE_data ( std::string strName, double *mapVals, int len, proshade_single xDmSz, proshade_single yDmSz,
156  proshade_single zDmSz, proshade_unsign xDmInd, proshade_unsign yDmInd, proshade_unsign zDmInd, proshade_signed xFr,
157  proshade_signed yFr, proshade_signed zFr, proshade_signed xT, proshade_signed yT, proshade_signed zT,
158  proshade_unsign inputO );
159  ~ProSHADE_data ( void );
160 
161  //============================================ Data I/O functions
162  void readInStructure ( std::string fName, proshade_unsign inputO, ProSHADE_settings* settings, proshade_double* maskArr = nullptr, proshade_unsign maskXDim = 0,
163  proshade_unsign maskYDim = 0, proshade_unsign maskZDim = 0, proshade_double* weightsArr = nullptr, proshade_unsign weigXDim = 0,
164  proshade_unsign weigYDim = 0, proshade_unsign weigZDim = 0 );
165  void readInStructure ( gemmi::Structure gemmiStruct, proshade_unsign inputO, ProSHADE_settings* settings );
166  void writeMap ( std::string fName, std::string title = "Created by ProSHADE and written by GEMMI", int mode = 2 );
167  void writePdb ( std::string fName, proshade_double euA = 0.0, proshade_double euB = 0.0, proshade_double euG = 0.0,
168  proshade_double trsX = 0.0, proshade_double trsY = 0.0, proshade_double trsZ = 0.0, proshade_double rotX = 0.0,
169  proshade_double rotY = 0.0, proshade_double rotZ = 0.0, bool firstModel = true );
170  void writeGemmi ( std::string fName, gemmi::Structure gemmiStruct, proshade_double euA = 0.0, proshade_double euB = 0.0, proshade_double euG = 0.0,
171  proshade_double trsX = 0.0, proshade_double trsY = 0.0, proshade_double trsZ = 0.0, proshade_double rotX = 0.0,
172  proshade_double rotY = 0.0, proshade_double rotZ = 0.0, bool firstModel = true );
173  void writeMask ( std::string fName, proshade_double* mask );
174 
175  //============================================ Data processing functions
176  void invertMirrorMap ( ProSHADE_settings* settings );
177  void normaliseMap ( ProSHADE_settings* settings );
178  void maskMap ( ProSHADE_settings* settings );
179  void getReBoxBoundaries ( ProSHADE_settings* settings, proshade_signed*& ret );
180  void createNewMapFromBounds ( ProSHADE_settings* settings, ProSHADE_data*& newStr, proshade_signed* newBounds );
181  void reSampleMap ( ProSHADE_settings* settings );
182  void centreMapOnCOM ( ProSHADE_settings* settings );
183  void addExtraSpace ( ProSHADE_settings* settings );
184  void removePhaseInormation ( ProSHADE_settings* settings );
185  void shiftToBoxCentre ( ProSHADE_settings* settings );
186  void shiftToRotationCentre ( ProSHADE_settings* settings );
187  void processInternalMap ( ProSHADE_settings* settings );
188 
189  //============================================ Data sphere mapping functions
190  void getSpherePositions ( ProSHADE_settings* settings );
191  void mapToSpheres ( ProSHADE_settings* settings );
192  void computeSphericalHarmonics ( ProSHADE_settings* settings );
193 
194  //============================================ Distances pre-computation functions
195  bool shellBandExists ( proshade_unsign shell, proshade_unsign bandVal );
196  void computeRRPMatrices ( ProSHADE_settings* settings );
197  void allocateEMatrices ( proshade_unsign band );
198  void allocateSO3CoeffsSpace ( proshade_unsign band );
200 
201  //============================================ Symmetry detection functions
202  void computeRotationFunction ( ProSHADE_settings* settings );
203  void convertRotationFunction ( ProSHADE_settings* settings );
204  void getRealEMatrixValuesForLM ( proshade_signed band, proshade_signed order1, double *eMatsLMReal, int len );
205  void getImagEMatrixValuesForLM ( proshade_signed band, proshade_signed order1, double *eMatsLMImag, int len );
206  void getRealSO3Coeffs ( double *so3CoefsReal, int len );
207  void getImagSO3Coeffs ( double *so3CoefsImag, int len );
208  void getRealRotFunction ( double *rotFunReal, int len );
209  void getImagRotFunction ( double *rotFunImag, int len );
210  void getRealTranslationFunction ( double *trsFunReal, int len );
211  void getImagTranslationFunction ( double *trsFunImag, int len );
212  void getRotMatrixFromRotFunInds ( proshade_signed aI, proshade_signed bI, proshade_signed gI, double *rotMat, int len );
213  int so3CoeffsArrayIndex ( proshade_signed order1, proshade_signed order2, proshade_signed band );
214  std::vector< proshade_double* > getDihedralSymmetriesList ( ProSHADE_settings* settings, std::vector< proshade_double* >* CSymList );
215  std::vector< proshade_double* > getTetrahedralSymmetriesList ( ProSHADE_settings* settings, std::vector< proshade_double* >* CSymList );
216  std::vector< proshade_double* > getOctahedralSymmetriesList ( ProSHADE_settings* settings, std::vector< proshade_double* >* CSymList );
217  std::vector< proshade_double* > getIcosahedralSymmetriesList ( ProSHADE_settings* settings, std::vector< proshade_double* >* CSymList );
218  std::vector < std::vector< proshade_double* > > getPredictedIcosahedralSymmetriesList ( ProSHADE_settings* settings, std::vector< proshade_double* >* CSymList );
219  std::vector< proshade_double* > getPredictedOctahedralSymmetriesList ( ProSHADE_settings* settings, std::vector< proshade_double* >* CSymList );
220  std::vector< proshade_double* > getPredictedTetrahedralSymmetriesList ( ProSHADE_settings* settings, std::vector< proshade_double* >* CSymList );
221  void detectSymmetryFromAngleAxisSpace ( ProSHADE_settings* settings, std::vector< proshade_double* >* axes, std::vector < std::vector< proshade_double > >* allCs );
222  std::vector< proshade_double* > getCyclicSymmetriesListFromAngleAxis ( ProSHADE_settings* settings );
223  std::vector< proshade_double* > findRequestedCSymmetryFromAngleAxis ( ProSHADE_settings* settings, proshade_unsign fold, proshade_double* peakThres );
224  void saveDetectedSymmetries ( ProSHADE_settings* settings, std::vector< proshade_double* >* CSyms, std::vector < std::vector< proshade_double > >* allCs );
225  std::string getRecommendedSymmetryType ( ProSHADE_settings* settings );
226  proshade_unsign getRecommendedSymmetryFold ( ProSHADE_settings* settings );
227  proshade_unsign getNoRecommendedSymmetryAxes ( ProSHADE_settings* settings );
228  std::vector< std::string > getSymmetryAxis ( ProSHADE_settings* settings, proshade_unsign axisNo );
229  void prepareFSCFourierMemory ( fftw_complex*& mapData, fftw_complex*& origCoeffs, fftw_complex*& fCoeffs, proshade_signed*& binIndexing,
230  proshade_signed* noBins, proshade_double**& bindata, proshade_signed*& binCounts, fftw_plan* planForwardFourier, proshade_double*& fscByBin );
231  proshade_double computeFSC ( ProSHADE_settings* settings, std::vector< proshade_double* >* CSym, size_t symIndex, fftw_complex* mapData,
232  fftw_complex* fCoeffs, fftw_complex* origCoeffs, fftw_plan* planForwardFourier, proshade_signed noBins,
233  proshade_signed *binIndexing, proshade_double**& bindata, proshade_signed*& binCounts, proshade_double*& fscByBin );
234  proshade_double computeFSC ( ProSHADE_settings* settings, proshade_double* sym, fftw_complex* mapData, fftw_complex* fCoeffs, fftw_complex* origCoeffs,
235  fftw_plan* planForwardFourier, proshade_signed noBins, proshade_signed *binIndexing, proshade_double**& bindata,
236  proshade_signed*& binCounts, proshade_double*& fscByBin );
237  void saveRecommendedSymmetry ( ProSHADE_settings* settings, std::vector< proshade_double* >* CSym, std::vector< proshade_double* >* DSym,
238  std::vector< proshade_double* >* TSym, std::vector< proshade_double* >* OSym,
239  std::vector< proshade_double* >* ISym, std::vector< proshade_double* >* axes, fftw_complex* mapData,
240  fftw_complex* origCoeffs, fftw_complex* fCoeffs, fftw_plan* planForwardFourier, proshade_signed noBins, proshade_signed* binIndexing,
241  proshade_double** bindata, proshade_signed* binCounts, proshade_double*& fscByBin );
242  void saveRequestedSymmetryC ( ProSHADE_settings* settings, std::vector< proshade_double* >* CSym, std::vector< proshade_double* >* axes );
243  void saveRequestedSymmetryD ( ProSHADE_settings* settings, std::vector< proshade_double* >* DSym, std::vector< proshade_double* >* axes, fftw_complex* mapData,
244  fftw_complex* origCoeffs, fftw_complex* fCoeffs, fftw_plan* planForwardFourier, proshade_signed noBins, proshade_signed* binIndexing,
245  proshade_double** bindata, proshade_signed* binCounts, proshade_double*& fscByBin );
246  std::vector<std::vector< proshade_double > > getAllGroupElements ( ProSHADE_settings* settings, std::vector< proshade_unsign > axesList, std::string groupType = "", proshade_double matrixTolerance = 0.05 );
247  std::vector<std::vector< proshade_double > > getAllGroupElements ( std::vector < std::vector< proshade_double > >* allCs, std::vector< proshade_unsign > axesList, std::string groupType = "", proshade_double matrixTolerance = 0.05 );
248  void reportSymmetryResults ( ProSHADE_settings* settings );
249 
250  //============================================ Map overlay functions
252  std::vector< proshade_double > getBestRotationMapPeaksEulerAngles ( ProSHADE_settings* settings );
253  std::vector< proshade_double > getBestTranslationMapPeaksAngstrom ( ProSHADE_internal_data::ProSHADE_data* staticStructure );
254  void zeroPaddToDims ( proshade_unsign xDim, proshade_unsign yDim, proshade_unsign zDim );
255  void rotateMapReciprocalSpace ( ProSHADE_settings* settings, proshade_double eulerAlpha, proshade_double eulerBeta, proshade_double eulerGamma );
256  std::vector< proshade_double > rotateMapRealSpace ( proshade_double axX, proshade_double axY, proshade_double axZ, proshade_double axAng, proshade_double*& map );
257  std::vector< proshade_double > rotateMapRealSpaceInPlace ( proshade_double eulA, proshade_double eulB, proshade_double eulG );
258  void translateMap ( proshade_double trsX, proshade_double trsY, proshade_double trsZ );
259  void allocateRotatedSHMemory ( void );
260  void computeRotatedSH ( void );
261  void invertSHCoefficients ( void );
262  void interpolateMapFromSpheres ( proshade_double*& densityMapRotated );
264  void findMapCOM ( void );
265  void writeOutOverlayFiles ( ProSHADE_settings* settings, proshade_double eulA, proshade_double eulB, proshade_double eulG, std::vector< proshade_double >* rotCentre,
266  std::vector< proshade_double >* ultimateTranslation );
267  void reportOverlayResults ( ProSHADE_settings* settings, std::vector < proshade_double >* rotationCentre, std::vector < proshade_double >* eulerAngles,
268  std::vector < proshade_double >* finalTranslation );
269 
270  //============================================ Python access functions
271  void deepCopyMap ( proshade_double*& saveTo, proshade_signed verbose );
272 
273  //============================================ Accessor functions
274  proshade_double getMapValue ( proshade_unsign pos );
275  proshade_unsign getMaxSpheres ( void );
276  proshade_unsign getMaxBand ( void );
277  proshade_double* getRealSphHarmValue ( proshade_unsign band, proshade_unsign order, proshade_unsign shell );
278  proshade_double* getImagSphHarmValue ( proshade_unsign band, proshade_unsign order, proshade_unsign shell );
279  proshade_double getRRPValue ( proshade_unsign band, proshade_unsign sh1, proshade_unsign sh2 );
280  proshade_double getAnySphereRadius ( proshade_unsign shell );
281  proshade_double getIntegrationWeight ( void );
282  proshade_unsign getShellBandwidth ( proshade_unsign shell );
283  proshade_single getSpherePosValue ( proshade_unsign shell );
284  proshade_complex** getEMatrixByBand ( proshade_unsign band );
285  void getEMatrixValue ( proshade_unsign band, proshade_unsign order1, proshade_unsign order2, proshade_double* valueReal, proshade_double* valueImag );
286  proshade_complex* getInvSO3Coeffs ( void );
287  proshade_complex* getSO3Coeffs ( void );
288  proshade_unsign getComparisonBand ( void );
289  void getWignerMatrixValue ( proshade_unsign band, proshade_unsign order1, proshade_unsign order2, proshade_double* valueReal, proshade_double* valueImag );
290  proshade_single getXDimSize ( void );
291  proshade_single getYDimSize ( void );
292  proshade_single getZDimSize ( void );
293  proshade_unsign getXDim ( void );
294  proshade_unsign getYDim ( void );
295  proshade_unsign getZDim ( void );
296  proshade_signed* getXFromPtr ( void );
297  proshade_signed* getYFromPtr ( void );
298  proshade_signed* getZFromPtr ( void );
299  proshade_signed* getXToPtr ( void );
300  proshade_signed* getYToPtr ( void );
301  proshade_signed* getZToPtr ( void );
302  proshade_signed* getXAxisOrigin ( void );
303  proshade_signed* getYAxisOrigin ( void );
304  proshade_signed* getZAxisOrigin ( void );
305  proshade_double*& getInternalMap ( void );
306  proshade_complex* getTranslationFnPointer ( void );
307  std::vector< proshade_double > getMapCOMProcessChange ( void );
308 
309  //============================================ Mutator functions
310  void setIntegrationWeight ( proshade_double intW );
311  void setIntegrationWeightCumul ( proshade_double intW );
312  void setEMatrixValue ( proshade_unsign band, proshade_unsign order1, proshade_unsign order2, proshade_complex val );
313  void normaliseEMatrixValue ( proshade_unsign band, proshade_unsign order1, proshade_unsign order2, proshade_double normF );
314  void setSO3CoeffValue ( proshade_unsign position, proshade_complex val );
315  void setWignerMatrixValue ( proshade_complex val, proshade_unsign band, proshade_unsign order1, proshade_unsign order2 );
316  };
317 
318  //================================================ Support functions
319  std::vector<std::vector< proshade_double > > computeGroupElementsForGroup ( proshade_double xAx, proshade_double yAx, proshade_double zAx, proshade_signed fold );
320 
321  std::vector<std::vector< proshade_double > > joinElementsFromDifferentGroups ( std::vector<std::vector< proshade_double > >* first,
322  std::vector<std::vector< proshade_double > >* second,
323  proshade_double matrixTolerance,
324  bool combine );
325 }
326 
327 #endif
ProSHADE_internal_data::ProSHADE_data::originalMapYCom
proshade_double originalMapYCom
The COM of the first map to be loaded/computed without any furhter changes being reflacted along the ...
Definition: ProSHADE_data.hpp:92
ProSHADE_internal_data::ProSHADE_data::computeSphericalHarmonics
void computeSphericalHarmonics(ProSHADE_settings *settings)
This function computes the spherical harmonics decomposition for the whole structure.
Definition: ProSHADE_data.cpp:1847
ProSHADE_internal_data::ProSHADE_data::mapMovFromsChangeX
proshade_double mapMovFromsChangeX
When the map is translated, the xFrom and xTo values are changed. This variable holds how much they h...
Definition: ProSHADE_data.hpp:94
ProSHADE_internal_data::ProSHADE_data::getEMatrixByBand
proshade_complex ** getEMatrixByBand(proshade_unsign band)
This function allows access to E matrix for a particular band.
Definition: ProSHADE_data.cpp:3817
ProSHADE_internal_data::ProSHADE_data::allocateRotatedSHMemory
void allocateRotatedSHMemory(void)
This function allocates the memory required for storing the rotated Spherical Harmonics coefficients.
Definition: ProSHADE_overlay.cpp:892
ProSHADE_internal_data::ProSHADE_data::getOverlayRotationFunction
void getOverlayRotationFunction(ProSHADE_settings *settings, ProSHADE_internal_data::ProSHADE_data *obj2)
This function computes the overlay rotation function (i.e. the correlation function in SO(3) space).
Definition: ProSHADE_overlay.cpp:35
ProSHADE_internal_data::ProSHADE_data::fileName
std::string fileName
This is the original file from which the data were obtained.
Definition: ProSHADE_data.hpp:52
ProSHADE_internal_data::ProSHADE_data::zFrom
proshade_signed zFrom
This is the starting index along the z axis.
Definition: ProSHADE_data.hpp:112
ProSHADE_internal_data::ProSHADE_data::xDimIndices
proshade_unsign xDimIndices
This is the size of the map cell x dimension in indices.
Definition: ProSHADE_data.hpp:65
ProSHADE_internal_data::ProSHADE_data::getZDimSize
proshade_single getZDimSize(void)
This function allows access to the map size in angstroms along the Z axis.
Definition: ProSHADE_data.cpp:3919
ProSHADE_internal_data::ProSHADE_data::getBestTranslationMapPeaksAngstrom
std::vector< proshade_double > getBestTranslationMapPeaksAngstrom(ProSHADE_internal_data::ProSHADE_data *staticStructure)
This function gets the optimal translation vector and returns it as a standard library vector....
Definition: ProSHADE_overlay.cpp:250
ProSHADE_internal_data::ProSHADE_data::readInMAP
void readInMAP(ProSHADE_settings *settings, proshade_double *maskArr=nullptr, proshade_unsign maskXDim=0, proshade_unsign maskYDim=0, proshade_unsign maskZDim=0, proshade_double *weightsArr=nullptr, proshade_unsign weigXDim=0, proshade_unsign weigYDim=0, proshade_unsign weigZDim=0)
Function for reading map data using gemmi library.
Definition: ProSHADE_data.cpp:619
ProSHADE_internal_data::ProSHADE_data::zDimSizeOriginal
proshade_single zDimSizeOriginal
This is the size of the map cell z dimension in Angstroms.
Definition: ProSHADE_data.hpp:84
ProSHADE_internal_data::ProSHADE_data::createNewMapFromBounds
void createNewMapFromBounds(ProSHADE_settings *settings, ProSHADE_data *&newStr, proshade_signed *newBounds)
This function creates a new structure from the calling structure and new bounds values.
Definition: ProSHADE_data.cpp:1374
ProSHADE_internal_data::ProSHADE_data::xGridIndices
proshade_unsign xGridIndices
As far as I know, this is identical to the xDimIndices.
Definition: ProSHADE_data.hpp:68
ProSHADE_internal_data::ProSHADE_data::computeRotationFunction
void computeRotationFunction(ProSHADE_settings *settings)
This function computes the self-rotation function for this structure.
Definition: ProSHADE_symmetry.cpp:41
ProSHADE_internal_data::ProSHADE_data::translationMap
proshade_complex * translationMap
This is where the translation map will be held, if at all used.
Definition: ProSHADE_data.hpp:133
ProSHADE_internal_data::joinElementsFromDifferentGroups
std::vector< std::vector< proshade_double > > joinElementsFromDifferentGroups(std::vector< std::vector< proshade_double > > *first, std::vector< std::vector< proshade_double > > *second, proshade_double matrixTolerance, bool combine)
This function joins two group element lists using only unique elements.
Definition: ProSHADE_data.cpp:3092
ProSHADE_internal_data::ProSHADE_data::xAxisOrder
proshade_unsign xAxisOrder
This is the order of the x axis.
Definition: ProSHADE_data.hpp:71
ProSHADE_internal_data::ProSHADE_data::rotSphericalHarmonics
proshade_complex ** rotSphericalHarmonics
A set of rotated spherical harmonics values arrays for each sphere, used only if map rotation is requ...
Definition: ProSHADE_data.hpp:122
ProSHADE_internal_data::ProSHADE_data::getReBoxBoundaries
void getReBoxBoundaries(ProSHADE_settings *settings, proshade_signed *&ret)
This function finds the boundaries enclosing positive map values and adds some extra space.
Definition: ProSHADE_data.cpp:1316
ProSHADE_internal_data::ProSHADE_data::getComparisonBand
proshade_unsign getComparisonBand(void)
This function allows access to the maximum band for the comparison.
Definition: ProSHADE_data.cpp:3869
ProSHADE_internal_data::ProSHADE_data::getRecommendedSymmetryFold
proshade_unsign getRecommendedSymmetryFold(ProSHADE_settings *settings)
This function simply returns the detected recommended symmetry fold.
Definition: ProSHADE_data.cpp:4395
ProSHADE_internal_data::ProSHADE_data::sphericalHarmonics
proshade_complex ** sphericalHarmonics
A set of spherical harmonics values arrays for each sphere.
Definition: ProSHADE_data.hpp:121
ProSHADE_internal_data::ProSHADE_data::setIntegrationWeight
void setIntegrationWeight(proshade_double intW)
This function allows setting the integration weight for the object.
Definition: ProSHADE_data.cpp:4087
ProSHADE_internal_data::ProSHADE_data::interpolateMapFromSpheres
void interpolateMapFromSpheres(proshade_double *&densityMapRotated)
This function interpolates the density map from the sphere mapped data.
Definition: ProSHADE_overlay.cpp:1114
ProSHADE_internal_data::ProSHADE_data::cAngle
proshade_single cAngle
This is the angle c of the map cell in degrees.
Definition: ProSHADE_data.hpp:64
ProSHADE_internal_data::ProSHADE_data::so3CoeffsInverse
proshade_complex * so3CoeffsInverse
The inverse coefficients obtained by inverse SO(3) Fourier Transform (SOFT) - i.e....
Definition: ProSHADE_data.hpp:130
ProSHADE_internal_data::ProSHADE_data::getXAxisOrigin
proshade_signed * getXAxisOrigin(void)
This function allows access to the map X axis origin value.
Definition: ProSHADE_data.cpp:4019
ProSHADE_internal_data::ProSHADE_data::normaliseEMatrixValue
void normaliseEMatrixValue(proshade_unsign band, proshade_unsign order1, proshade_unsign order2, proshade_double normF)
This function allows normalising the E matrix value.
Definition: ProSHADE_data.cpp:4136
ProSHADE_internal_data::ProSHADE_data::yCom
proshade_double yCom
The COM of the map after processing along the Y-axis.
Definition: ProSHADE_data.hpp:78
ProSHADE_internal_data::ProSHADE_data::getImagTranslationFunction
void getImagTranslationFunction(double *trsFunImag, int len)
This function fills the input array with the imaginary translation function values.
Definition: ProSHADE_data.cpp:4331
ProSHADE_internal_data::ProSHADE_data::setWignerMatrixValue
void setWignerMatrixValue(proshade_complex val, proshade_unsign band, proshade_unsign order1, proshade_unsign order2)
This function allows setting the Wigner D matrix value by its band, order1 and order2 co-ordinate.
Definition: ProSHADE_data.cpp:4170
ProSHADE_internal_data::ProSHADE_data::saveDetectedSymmetries
void saveDetectedSymmetries(ProSHADE_settings *settings, std::vector< proshade_double * > *CSyms, std::vector< std::vector< proshade_double > > *allCs)
This function takes the results of point group searches and saves then into the output variables.
Definition: ProSHADE_data.cpp:2276
ProSHADE_internal_data::ProSHADE_data::allocateRRPMemory
void allocateRRPMemory()
This function allocates the required memory for the RRP matrices.
Definition: ProSHADE_distances.cpp:31
ProSHADE_internal_data::ProSHADE_data::getEMatrixValue
void getEMatrixValue(proshade_unsign band, proshade_unsign order1, proshade_unsign order2, proshade_double *valueReal, proshade_double *valueImag)
This function allows access to E matrix by knowing the band, order1 and order2 indices.
Definition: ProSHADE_data.cpp:3832
ProSHADE_internal_data::ProSHADE_data::getXDimSize
proshade_single getXDimSize(void)
This function allows access to the map size in angstroms along the X axis.
Definition: ProSHADE_data.cpp:3899
ProSHADE_internal_data::ProSHADE_data::getInternalMap
proshade_double *& getInternalMap(void)
This function allows access to the first map array value address.
Definition: ProSHADE_data.cpp:4049
ProSHADE_internal_data::ProSHADE_data::allocateWignerMatricesSpace
void allocateWignerMatricesSpace()
This function allocates the memory for the Wigner matrices for the calling object.
Definition: ProSHADE_wignerMatrices.cpp:27
ProSHADE_internal_data::ProSHADE_data
This class contains all inputed and derived data for a single structure.
Definition: ProSHADE_data.hpp:49
ProSHADE_internal_data::ProSHADE_data::noSpheres
proshade_unsign noSpheres
The number of spheres with map projected onto them.
Definition: ProSHADE_data.hpp:119
ProSHADE_internal_data::ProSHADE_data::getYDimSize
proshade_single getYDimSize(void)
This function allows access to the map size in angstroms along the Y axis.
Definition: ProSHADE_data.cpp:3909
ProSHADE_internal_data::ProSHADE_data::inputOrder
proshade_unsign inputOrder
This value is the input order - it is useful to know for writing out files, so that they would not ov...
Definition: ProSHADE_data.hpp:140
ProSHADE_internal_data::ProSHADE_data::zDimSize
proshade_single zDimSize
This is the size of the map cell z dimension in Angstroms.
Definition: ProSHADE_data.hpp:61
ProSHADE_internal_data::ProSHADE_data::so3Coeffs
proshade_complex * so3Coeffs
The coefficients obtained by SO(3) Fourier Transform (SOFT), in this case derived from the E matrices...
Definition: ProSHADE_data.hpp:129
ProSHADE_internal_data::ProSHADE_data::getMaxSpheres
proshade_unsign getMaxSpheres(void)
This function returns the number of spheres which contain the whole object.
Definition: ProSHADE_data.cpp:3590
ProSHADE_internal_data::ProSHADE_data::setSO3CoeffValue
void setSO3CoeffValue(proshade_unsign position, proshade_complex val)
This function allows setting the SOFT coefficient values using array position and value.
Definition: ProSHADE_data.cpp:4152
ProSHADE_internal_data::ProSHADE_data::mapCOMProcessChangeX
proshade_double mapCOMProcessChangeX
The change in X axis between the creation of the structure (originalMapXCom) and just before rotation...
Definition: ProSHADE_data.hpp:97
ProSHADE_internal_data::ProSHADE_data::originalMapXCom
proshade_double originalMapXCom
The COM of the first map to be loaded/computed without any furhter changes being reflacted along the ...
Definition: ProSHADE_data.hpp:91
ProSHADE_internal_data::ProSHADE_data::getRotMatrixFromRotFunInds
void getRotMatrixFromRotFunInds(proshade_signed aI, proshade_signed bI, proshade_signed gI, double *rotMat, int len)
This function takes rotation function indices, converts them to Euler angles and these to rotation ma...
Definition: ProSHADE_data.cpp:4352
ProSHADE_internal_data::ProSHADE_data::getBestRotationMapPeaksEulerAngles
std::vector< proshade_double > getBestRotationMapPeaksEulerAngles(ProSHADE_settings *settings)
This function returns a vector of three floats, the three Euler angles of the best peak in the rotati...
Definition: ProSHADE_overlay.cpp:1300
ProSHADE_internal_data::ProSHADE_data::computeRRPMatrices
void computeRRPMatrices(ProSHADE_settings *settings)
This function pre-computes the RRP matrices for a data object.
Definition: ProSHADE_distances.cpp:59
ProSHADE_internal_data::ProSHADE_data::xDimIndicesOriginal
proshade_unsign xDimIndicesOriginal
This is the size of the map cell x dimension in indices.
Definition: ProSHADE_data.hpp:85
ProSHADE_internal_data::ProSHADE_data::getAnySphereRadius
proshade_double getAnySphereRadius(proshade_unsign shell)
This function allows access to the radius of any particular sphere.
Definition: ProSHADE_data.cpp:3770
ProSHADE_internal_data::ProSHADE_data::getSO3Coeffs
proshade_complex * getSO3Coeffs(void)
This function allows access to the SO(3) coefficients array.
Definition: ProSHADE_data.cpp:3858
ProSHADE_internal_data::ProSHADE_data::maxShellBand
proshade_unsign maxShellBand
The maximum band for any shell of the object.
Definition: ProSHADE_data.hpp:123
ProSHADE_internal_data::ProSHADE_data::originalPdbRotCenY
proshade_double originalPdbRotCenY
The centre of rotation as it relates to the original PDB positions (and not the ProSHADE internal map...
Definition: ProSHADE_data.hpp:103
ProSHADE_internal_data::ProSHADE_data::getSpherePositions
void getSpherePositions(ProSHADE_settings *settings)
This function determines the sphere positions (radii) for sphere mapping.
Definition: ProSHADE_data.cpp:1746
ProSHADE_internal_data::ProSHADE_data::invertMirrorMap
void invertMirrorMap(ProSHADE_settings *settings)
Function for inverting the map to its mirror image.
Definition: ProSHADE_data.cpp:1175
ProSHADE_internal_data::ProSHADE_data::getDihedralSymmetriesList
std::vector< proshade_double * > getDihedralSymmetriesList(ProSHADE_settings *settings, std::vector< proshade_double * > *CSymList)
This function obtains a list of all D symmetries from already computed C symmetries list.
Definition: ProSHADE_symmetry.cpp:302
ProSHADE_internal_data::ProSHADE_data::getMapCOMProcessChange
std::vector< proshade_double > getMapCOMProcessChange(void)
This function allows access to the translation caused by structure processing.
Definition: ProSHADE_data.cpp:4069
ProSHADE_internal_data::ProSHADE_data::saveRequestedSymmetryD
void saveRequestedSymmetryD(ProSHADE_settings *settings, std::vector< proshade_double * > *DSym, std::vector< proshade_double * > *axes, fftw_complex *mapData, fftw_complex *origCoeffs, fftw_complex *fCoeffs, fftw_plan *planForwardFourier, proshade_signed noBins, proshade_signed *binIndexing, proshade_double **bindata, proshade_signed *binCounts, proshade_double *&fscByBin)
This function takes the D symmetries and searched for the requested symmetry.
Definition: ProSHADE_data.cpp:2876
ProSHADE_internal_data::ProSHADE_data::mapCOMProcessChangeZ
proshade_double mapCOMProcessChangeZ
The change in Z axis between the creation of the structure (originalMapZCom) and just before rotation...
Definition: ProSHADE_data.hpp:99
ProSHADE_internal_data::ProSHADE_data::xDimSizeOriginal
proshade_single xDimSizeOriginal
This is the size of the map cell x dimension in Angstroms.
Definition: ProSHADE_data.hpp:82
ProSHADE_internal_data::ProSHADE_data::getIntegrationWeight
proshade_double getIntegrationWeight(void)
This function allows access to the integration weight for the object.
Definition: ProSHADE_data.cpp:3781
ProSHADE_internal_data::ProSHADE_data::setIntegrationWeightCumul
void setIntegrationWeightCumul(proshade_double intW)
This function allows setting the cumulative integration weight for the object.
Definition: ProSHADE_data.cpp:4101
ProSHADE_internal_data::ProSHADE_data::zAxisOriginOriginal
proshade_signed zAxisOriginOriginal
This is the origin position along the z axis.
Definition: ProSHADE_data.hpp:90
ProSHADE_internal_spheres::ProSHADE_sphere
This class contains all inputed and derived data for a single sphere.
Definition: ProSHADE_spheres.hpp:49
ProSHADE_internal_data::ProSHADE_data::getSymmetryAxis
std::vector< std::string > getSymmetryAxis(ProSHADE_settings *settings, proshade_unsign axisNo)
This function returns a single symmetry axis as a vector of strings from the recommended symmetry axe...
Definition: ProSHADE_data.cpp:4419
ProSHADE_internal_data::ProSHADE_data::eMatrices
proshade_complex *** eMatrices
The trace sigma and full rotation function c*conj(c) integral tables.
Definition: ProSHADE_data.hpp:127
ProSHADE_internal_data::ProSHADE_data::centreMapOnCOM
void centreMapOnCOM(ProSHADE_settings *settings)
This function shits the map so that its COM is in the centre of the map.
Definition: ProSHADE_data.cpp:1520
ProSHADE_internal_data::ProSHADE_data::getXFromPtr
proshade_signed * getXFromPtr(void)
This function allows access to the map start along the X axis.
Definition: ProSHADE_data.cpp:3959
ProSHADE_internal_data::ProSHADE_data::yDimIndices
proshade_unsign yDimIndices
This is the size of the map cell y dimension in indices.
Definition: ProSHADE_data.hpp:66
ProSHADE_internal_data::ProSHADE_data::xAxisOriginOriginal
proshade_signed xAxisOriginOriginal
This is the origin position along the x axis.
Definition: ProSHADE_data.hpp:88
ProSHADE_internal_data::ProSHADE_data::deepCopyMap
void deepCopyMap(proshade_double *&saveTo, proshade_signed verbose)
This function copies the internal map into the supplied pointer, which it also allocates.
Definition: ProSHADE_data.cpp:3447
ProSHADE_internal_data::ProSHADE_data::getWignerMatrixValue
void getWignerMatrixValue(proshade_unsign band, proshade_unsign order1, proshade_unsign order2, proshade_double *valueReal, proshade_double *valueImag)
This function allows access to the Wigner D matrix by knowing the band, order1 and order2 indices.
Definition: ProSHADE_data.cpp:3884
ProSHADE_internal_data::ProSHADE_data::getShellBandwidth
proshade_unsign getShellBandwidth(proshade_unsign shell)
This function allows access to the bandwidth of a particular shell.
Definition: ProSHADE_data.cpp:3793
ProSHADE_internal_data::ProSHADE_data::yGridIndices
proshade_unsign yGridIndices
As far as I know, this is identical to the yDimIndices.
Definition: ProSHADE_data.hpp:69
ProSHADE_internal_data::ProSHADE_data::zAxisOrigin
proshade_signed zAxisOrigin
This is the origin position along the z axis.
Definition: ProSHADE_data.hpp:76
ProSHADE_internal_data::ProSHADE_data::getNoRecommendedSymmetryAxes
proshade_unsign getNoRecommendedSymmetryAxes(ProSHADE_settings *settings)
This function returns the number of detected recommended symmetry axes.
Definition: ProSHADE_data.cpp:4407
ProSHADE_internal_data::ProSHADE_data::shiftToRotationCentre
void shiftToRotationCentre(ProSHADE_settings *settings)
Function for shifting map so that its rotation centre is at the centre of the box.
Definition: ProSHADE_data.cpp:1140
ProSHADE_internal_data::ProSHADE_data::setPDBMapValues
void setPDBMapValues(void)
Function for determining iterator start and stop positions.
Definition: ProSHADE_data.cpp:824
ProSHADE_internal_data::ProSHADE_data::findMapCOM
void findMapCOM(void)
This function finds the centre of mass of the internal map representation.
Definition: ProSHADE_data.cpp:3535
ProSHADE_internal_data::ProSHADE_data::getRealRotFunction
void getRealRotFunction(double *rotFunReal, int len)
This function fills the input array with the real rotation function values.
Definition: ProSHADE_data.cpp:4277
ProSHADE_internal_data::ProSHADE_data::yDimIndicesOriginal
proshade_unsign yDimIndicesOriginal
This is the size of the map cell y dimension in indices.
Definition: ProSHADE_data.hpp:86
ProSHADE_internal_data::ProSHADE_data::getXDim
proshade_unsign getXDim(void)
This function allows access to the map size in indices along the X axis.
Definition: ProSHADE_data.cpp:3929
ProSHADE_internal_data::ProSHADE_data::originalPdbTransX
proshade_double originalPdbTransX
The optimal translation vector as it relates to the original PDB positions (and not the ProSHADE inte...
Definition: ProSHADE_data.hpp:105
ProSHADE_internal_data::ProSHADE_data::rotateMapReciprocalSpace
void rotateMapReciprocalSpace(ProSHADE_settings *settings, proshade_double eulerAlpha, proshade_double eulerBeta, proshade_double eulerGamma)
This function rotates a map based on the given Euler angles.
Definition: ProSHADE_overlay.cpp:571
ProSHADE_internal_data::ProSHADE_data::zTo
proshade_signed zTo
This is the final index along the z axis.
Definition: ProSHADE_data.hpp:115
ProSHADE_internal_data::ProSHADE_data::computeFSC
proshade_double computeFSC(ProSHADE_settings *settings, std::vector< proshade_double * > *CSym, size_t symIndex, fftw_complex *mapData, fftw_complex *fCoeffs, fftw_complex *origCoeffs, fftw_plan *planForwardFourier, proshade_signed noBins, proshade_signed *binIndexing, proshade_double **&bindata, proshade_signed *&binCounts, proshade_double *&fscByBin)
This function computes FSC for any given axis in the supplied CSym symmetry axes vector.
Definition: ProSHADE_data.cpp:2391
ProSHADE_internal_data::ProSHADE_data::readInStructure
void readInStructure(std::string fName, proshade_unsign inputO, ProSHADE_settings *settings, proshade_double *maskArr=nullptr, proshade_unsign maskXDim=0, proshade_unsign maskYDim=0, proshade_unsign maskZDim=0, proshade_double *weightsArr=nullptr, proshade_unsign weigXDim=0, proshade_unsign weigYDim=0, proshade_unsign weigZDim=0)
This function initialises the basic ProSHADE_data variables and reads in a single structure.
Definition: ProSHADE_data.cpp:509
ProSHADE_internal_data::ProSHADE_data::xTo
proshade_signed xTo
This is the final index along the x axis.
Definition: ProSHADE_data.hpp:113
ProSHADE_internal_data::ProSHADE_data::writeMask
void writeMask(std::string fName, proshade_double *mask)
Function for writing out a mask in MRC MAP format.
Definition: ProSHADE_data.cpp:1038
ProSHADE_internal_data::ProSHADE_data::integrationWeight
proshade_double integrationWeight
The Pearson's c.c. type weighting for the integration.
Definition: ProSHADE_data.hpp:128
ProSHADE_internal_data::ProSHADE_data::saveRequestedSymmetryC
void saveRequestedSymmetryC(ProSHADE_settings *settings, std::vector< proshade_double * > *CSym, std::vector< proshade_double * > *axes)
This function takes the C symmetries and searched for the requested symmetry.
Definition: ProSHADE_data.cpp:2824
ProSHADE_internal_data::ProSHADE_data::mapToSpheres
void mapToSpheres(ProSHADE_settings *settings)
This function converts the internal map onto a set of concentric spheres.
Definition: ProSHADE_data.cpp:1803
ProSHADE_internal_data::ProSHADE_data::xAxisOrigin
proshade_signed xAxisOrigin
This is the origin position along the x axis.
Definition: ProSHADE_data.hpp:74
ProSHADE_internal_data::ProSHADE_data::originalPdbTransY
proshade_double originalPdbTransY
The optimal translation vector as it relates to the original PDB positions (and not the ProSHADE inte...
Definition: ProSHADE_data.hpp:106
ProSHADE_internal_data::ProSHADE_data::rrpMatrices
proshade_double *** rrpMatrices
The energy levels descriptor shell correlation tables.
Definition: ProSHADE_data.hpp:126
ProSHADE_internal_data::ProSHADE_data::yTo
proshade_signed yTo
This is the final index along the y axis.
Definition: ProSHADE_data.hpp:114
ProSHADE_internal_data::ProSHADE_data::xDimSize
proshade_single xDimSize
This is the size of the map cell x dimension in Angstroms.
Definition: ProSHADE_data.hpp:59
ProSHADE_internal_data::ProSHADE_data::computeRotatedSH
void computeRotatedSH(void)
This function multiplies the objects spherical harmonics with the Wigner D matrices,...
Definition: ProSHADE_overlay.cpp:920
ProSHADE_internal_data::ProSHADE_data::mapMovFromsChangeY
proshade_double mapMovFromsChangeY
When the map is translated, the yFrom and yTo values are changed. This variable holds how much they h...
Definition: ProSHADE_data.hpp:95
ProSHADE_internal_data::ProSHADE_data::yAxisOrigin
proshade_signed yAxisOrigin
This is the origin position along the y axis.
Definition: ProSHADE_data.hpp:75
ProSHADE_internal_data::ProSHADE_data::saveRecommendedSymmetry
void saveRecommendedSymmetry(ProSHADE_settings *settings, std::vector< proshade_double * > *CSym, std::vector< proshade_double * > *DSym, std::vector< proshade_double * > *TSym, std::vector< proshade_double * > *OSym, std::vector< proshade_double * > *ISym, std::vector< proshade_double * > *axes, fftw_complex *mapData, fftw_complex *origCoeffs, fftw_complex *fCoeffs, fftw_plan *planForwardFourier, proshade_signed noBins, proshade_signed *binIndexing, proshade_double **bindata, proshade_signed *binCounts, proshade_double *&fscByBin)
This function takes all the detected symmetry results and decides on which are to be recommended for ...
Definition: ProSHADE_data.cpp:2558
ProSHADE_internal_data::ProSHADE_data::computeTranslationMap
void computeTranslationMap(ProSHADE_internal_data::ProSHADE_data *obj1)
This function does the computation of the translation map and saves results internally.
Definition: ProSHADE_overlay.cpp:324
ProSHADE_internal_data::ProSHADE_data::yAxisOrder
proshade_unsign yAxisOrder
This is the order of the y axis.
Definition: ProSHADE_data.hpp:72
ProSHADE_internal_data::ProSHADE_data::getRealSphHarmValue
proshade_double * getRealSphHarmValue(proshade_unsign band, proshade_unsign order, proshade_unsign shell)
This function allows access to the private internal real spherical harmonics values.
Definition: ProSHADE_data.cpp:3744
ProSHADE_internal_data::ProSHADE_data::internalMap
proshade_double * internalMap
The internal map data representation, which may be amended as the run progresses.
Definition: ProSHADE_data.hpp:56
ProSHADE_internal_data::ProSHADE_data::writePdb
void writePdb(std::string fName, proshade_double euA=0.0, proshade_double euB=0.0, proshade_double euG=0.0, proshade_double trsX=0.0, proshade_double trsY=0.0, proshade_double trsZ=0.0, proshade_double rotX=0.0, proshade_double rotY=0.0, proshade_double rotZ=0.0, bool firstModel=true)
This function writes out the co-ordinates file with ProSHADE type rotation and translation applied.
Definition: ProSHADE_data.cpp:959
ProSHADE_internal_data::ProSHADE_data::zDimIndicesOriginal
proshade_unsign zDimIndicesOriginal
This is the size of the map cell z dimension in indices.
Definition: ProSHADE_data.hpp:87
ProSHADE_internal_data::ProSHADE_data::reportOverlayResults
void reportOverlayResults(ProSHADE_settings *settings, std::vector< proshade_double > *rotationCentre, std::vector< proshade_double > *eulerAngles, std::vector< proshade_double > *finalTranslation)
This function reports the results of the overlay mode.
Definition: ProSHADE_data.cpp:4512
ProSHADE_internal_data::ProSHADE_data::xFrom
proshade_signed xFrom
This is the starting index along the x axis.
Definition: ProSHADE_data.hpp:110
ProSHADE_internal_data::ProSHADE_data::writeMap
void writeMap(std::string fName, std::string title="Created by ProSHADE and written by GEMMI", int mode=2)
Function for writing out the internal structure representation in MRC MAP format.
Definition: ProSHADE_data.cpp:892
ProSHADE_internal_data::ProSHADE_data::shellBandExists
bool shellBandExists(proshade_unsign shell, proshade_unsign bandVal)
This function checks if particular shell has a particular band.
Definition: ProSHADE_data.cpp:3637
ProSHADE_internal_data::ProSHADE_data::getMaxBand
proshade_unsign getMaxBand(void)
This function returns the maximum band value for the object.
Definition: ProSHADE_data.cpp:3611
ProSHADE_internal_data::ProSHADE_data::shiftToBoxCentre
void shiftToBoxCentre(ProSHADE_settings *settings)
Function for shifting map so that its centre of box is at required position.
Definition: ProSHADE_data.cpp:1075
ProSHADE_internal_data::ProSHADE_data::translateMap
void translateMap(proshade_double trsX, proshade_double trsY, proshade_double trsZ)
This function simply translates the map by a given number of Angstroms along the three axes.
Definition: ProSHADE_overlay.cpp:868
ProSHADE_internal_data::ProSHADE_data::invertSHCoefficients
void invertSHCoefficients(void)
This function computes the shell mapped data from inverting the Spherical Harmonics coefficients.
Definition: ProSHADE_overlay.cpp:1021
ProSHADE_internal_data::ProSHADE_data::writeGemmi
void writeGemmi(std::string fName, gemmi::Structure gemmiStruct, proshade_double euA=0.0, proshade_double euB=0.0, proshade_double euG=0.0, proshade_double trsX=0.0, proshade_double trsY=0.0, proshade_double trsZ=0.0, proshade_double rotX=0.0, proshade_double rotY=0.0, proshade_double rotZ=0.0, bool firstModel=true)
This function writes out the gemmi::Structure object with ProSHADE type rotation and translation appl...
Definition: ProSHADE_data.cpp:996
ProSHADE_internal_data::ProSHADE_data::getYDim
proshade_unsign getYDim(void)
This function allows access to the map size in indices along the Y axis.
Definition: ProSHADE_data.cpp:3939
ProSHADE_internal_data::ProSHADE_data::maxCompBand
proshade_unsign maxCompBand
The largest comparison band - this variable tells how large arrays will be allocated for the comparis...
Definition: ProSHADE_data.hpp:132
ProSHADE_internal_data::ProSHADE_data::getImagEMatrixValuesForLM
void getImagEMatrixValuesForLM(proshade_signed band, proshade_signed order1, double *eMatsLMImag, int len)
This function fills the input array with the imaginary E matrix values for particular band and order1...
Definition: ProSHADE_data.cpp:4208
ProSHADE_internal_data::ProSHADE_data::maskMap
void maskMap(ProSHADE_settings *settings)
Function for computing the map mask using blurring and X IQRs from median.
Definition: ProSHADE_data.cpp:1276
ProSHADE_internal_data::ProSHADE_data::~ProSHADE_data
~ProSHADE_data(void)
Destructor for the ProSHADE_data class.
Definition: ProSHADE_data.cpp:349
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_internal_data::ProSHADE_data::xCom
proshade_double xCom
The COM of the map after processing along the X-axis.
Definition: ProSHADE_data.hpp:77
ProSHADE_internal_data::ProSHADE_data::getRealTranslationFunction
void getRealTranslationFunction(double *trsFunReal, int len)
This function fills the input array with the real translation function values.
Definition: ProSHADE_data.cpp:4313
ProSHADE_internal_data::ProSHADE_data::readInGemmi
void readInGemmi(gemmi::Structure gemmiStruct, ProSHADE_settings *settings)
Function for reading co-ordinate data from Gemmi object.
Definition: ProSHADE_data.cpp:735
ProSHADE_internal_data::ProSHADE_data::getImagSphHarmValue
proshade_double * getImagSphHarmValue(proshade_unsign band, proshade_unsign order, proshade_unsign shell)
This function allows access to the private internal imaginary spherical harmonics values.
Definition: ProSHADE_data.cpp:3757
ProSHADE_internal_data::ProSHADE_data::originalPdbTransZ
proshade_double originalPdbTransZ
The optimal translation vector as it relates to the original PDB positions (and not the ProSHADE inte...
Definition: ProSHADE_data.hpp:107
ProSHADE_internal_data::ProSHADE_data::writeOutOverlayFiles
void writeOutOverlayFiles(ProSHADE_settings *settings, proshade_double eulA, proshade_double eulB, proshade_double eulG, std::vector< proshade_double > *rotCentre, std::vector< proshade_double > *ultimateTranslation)
This function writes out the rotated map, co-ordinates and transformation JSON file.
Definition: ProSHADE_data.cpp:4478
ProSHADE_internal_data::ProSHADE_data::getPredictedTetrahedralSymmetriesList
std::vector< proshade_double * > getPredictedTetrahedralSymmetriesList(ProSHADE_settings *settings, std::vector< proshade_double * > *CSymList)
This function predicts a list of all T symmetry axes from the already computed C symmetries list.
Definition: ProSHADE_symmetry.cpp:3505
ProSHADE_internal_data::ProSHADE_data::getImagRotFunction
void getImagRotFunction(double *rotFunImag, int len)
This function fills the input array with the imaginary rotation function values.
Definition: ProSHADE_data.cpp:4295
ProSHADE_internal_data::ProSHADE_data::processInternalMap
void processInternalMap(ProSHADE_settings *settings)
This function simply clusters several other functions which should be called together.
Definition: ProSHADE_data.cpp:1695
ProSHADE_internal_data::ProSHADE_data::getTranslationFnPointer
proshade_complex * getTranslationFnPointer(void)
This function allows access to the translation function through a pointer.
Definition: ProSHADE_data.cpp:4059
ProSHADE_internal_data::ProSHADE_data::zCom
proshade_double zCom
The COM of the map after processing along the Z-axis.
Definition: ProSHADE_data.hpp:79
ProSHADE_internal_data::ProSHADE_data::rotateMapRealSpaceInPlace
std::vector< proshade_double > rotateMapRealSpaceInPlace(proshade_double eulA, proshade_double eulB, proshade_double eulG)
This function rotates a map based on the given Euler angles in place.
Definition: ProSHADE_overlay.cpp:805
ProSHADE_internal_data::ProSHADE_data::spherePos
std::vector< proshade_single > spherePos
Vector of sphere radii from the centre of the map.
Definition: ProSHADE_data.hpp:118
ProSHADE_internal_data::ProSHADE_data::getZDim
proshade_unsign getZDim(void)
This function allows access to the map size in indices along the Z axis.
Definition: ProSHADE_data.cpp:3949
ProSHADE_internal_data::ProSHADE_data::getSpherePosValue
proshade_single getSpherePosValue(proshade_unsign shell)
This function allows access to sphere positions.
Definition: ProSHADE_data.cpp:3805
ProSHADE_internal_data::ProSHADE_data::convertRotationFunction
void convertRotationFunction(ProSHADE_settings *settings)
This function converts the self-rotation function of this structure to angle-axis representation.
Definition: ProSHADE_symmetry.cpp:121
ProSHADE_internal_data::ProSHADE_data::getRRPValue
proshade_double getRRPValue(proshade_unsign band, proshade_unsign sh1, proshade_unsign sh2)
This function allows access to the priva internal RRP matrices.
Definition: ProSHADE_data.cpp:3621
ProSHADE_internal_data::ProSHADE_data::mapMovFromsChangeZ
proshade_double mapMovFromsChangeZ
When the map is translated, the zFrom and zTo values are changed. This variable holds how much they h...
Definition: ProSHADE_data.hpp:96
ProSHADE_internal_data::ProSHADE_data::allocateEMatrices
void allocateEMatrices(proshade_unsign band)
This function allocates the required memory for the E matrices.
Definition: ProSHADE_distances.cpp:275
ProSHADE_internal_data::ProSHADE_data::getMapValue
proshade_double getMapValue(proshade_unsign pos)
This function returns the internal map representation value of a particular array position.
Definition: ProSHADE_data.cpp:3601
ProSHADE_internal_data::ProSHADE_data::getImagSO3Coeffs
void getImagSO3Coeffs(double *so3CoefsImag, int len)
This function fills the input array with the imaginary SO(3) coefficient values.
Definition: ProSHADE_data.cpp:4244
ProSHADE_internal_data::ProSHADE_data::getYToPtr
proshade_signed * getYToPtr(void)
This function allows access to the map last position along the Y axis.
Definition: ProSHADE_data.cpp:3999
ProSHADE_internal_data::ProSHADE_data::wignerMatrices
proshade_complex *** wignerMatrices
These matrices are computed for a particular rotation to be done in spherical harmonics.
Definition: ProSHADE_data.hpp:131
ProSHADE_internal_data::ProSHADE_data::fileType
ProSHADE_internal_io::InputType fileType
This is the type of the input file.
Definition: ProSHADE_data.hpp:53
ProSHADE_internal_data::ProSHADE_data::rotateMapRealSpace
std::vector< proshade_double > rotateMapRealSpace(proshade_double axX, proshade_double axY, proshade_double axZ, proshade_double axAng, proshade_double *&map)
This function rotates a map based on the given angle-axis rotation.
Definition: ProSHADE_overlay.cpp:632
ProSHADE_internal_data::ProSHADE_data::getZAxisOrigin
proshade_signed * getZAxisOrigin(void)
This function allows access to the map Z axis origin value.
Definition: ProSHADE_data.cpp:4039
ProSHADE_internal_data::ProSHADE_data::yDimSizeOriginal
proshade_single yDimSizeOriginal
This is the size of the map cell y dimension in Angstroms.
Definition: ProSHADE_data.hpp:83
ProSHADE_internal_data::ProSHADE_data::zAxisOrder
proshade_unsign zAxisOrder
This is the order of the z axis.
Definition: ProSHADE_data.hpp:73
ProSHADE_internal_data::ProSHADE_data::reSampleMap
void reSampleMap(ProSHADE_settings *settings)
This function changes the internal map sampling to conform to particular resolution value.
Definition: ProSHADE_data.cpp:1440
ProSHADE_internal_data::ProSHADE_data::getXToPtr
proshade_signed * getXToPtr(void)
This function allows access to the map last position along the X axis.
Definition: ProSHADE_data.cpp:3989
ProSHADE_internal_data::ProSHADE_data::getYFromPtr
proshade_signed * getYFromPtr(void)
This function allows access to the map start along the Y axis.
Definition: ProSHADE_data.cpp:3969
ProSHADE_internal_data::ProSHADE_data::mapCOMProcessChangeY
proshade_double mapCOMProcessChangeY
The change in Y axis between the creation of the structure (originalMapYCom) and just before rotation...
Definition: ProSHADE_data.hpp:98
ProSHADE_internal_data::ProSHADE_data::bAngle
proshade_single bAngle
This is the angle b of the map cell in degrees.
Definition: ProSHADE_data.hpp:63
ProSHADE_internal_data::ProSHADE_data::yAxisOriginOriginal
proshade_signed yAxisOriginOriginal
This is the origin position along the y axis.
Definition: ProSHADE_data.hpp:89
ProSHADE_internal_data::ProSHADE_data::aAngle
proshade_single aAngle
This is the angle a of the map cell in degrees.
Definition: ProSHADE_data.hpp:62
ProSHADE_internal_data
This namespace contains the structure and functions required for data reading and storing their deriv...
ProSHADE_internal_data::ProSHADE_data::reportSymmetryResults
void reportSymmetryResults(ProSHADE_settings *settings)
This function takes prints the report for symmetry detection.
Definition: ProSHADE_data.cpp:3479
ProSHADE_internal_data::ProSHADE_data::figureIndexStartStop
void figureIndexStartStop(void)
Function for determining iterator start and stop positions.
Definition: ProSHADE_data.cpp:870
ProSHADE_internal_data::ProSHADE_data::isEmpty
bool isEmpty
This variable stated whether the class contains any information.
Definition: ProSHADE_data.hpp:139
ProSHADE_internal_data::ProSHADE_data::getPredictedOctahedralSymmetriesList
std::vector< proshade_double * > getPredictedOctahedralSymmetriesList(ProSHADE_settings *settings, std::vector< proshade_double * > *CSymList)
This function predicts a list of all O symmetry axes from the already computed C symmetries list.
Definition: ProSHADE_symmetry.cpp:1927
ProSHADE_internal_data::ProSHADE_data::getInvSO3Coeffs
proshade_complex * getInvSO3Coeffs(void)
This function allows access to the inverse SO(3) coefficients array.
Definition: ProSHADE_data.cpp:3847
ProSHADE_peakSearch.hpp
This header file declares functions required for 3D map peak searching.
ProSHADE_internal_data::ProSHADE_data::yFrom
proshade_signed yFrom
This is the starting index along the y axis.
Definition: ProSHADE_data.hpp:111
ProSHADE_internal_data::ProSHADE_data::getIcosahedralSymmetriesList
std::vector< proshade_double * > getIcosahedralSymmetriesList(ProSHADE_settings *settings, std::vector< proshade_double * > *CSymList)
This function obtains a list of all I symmetry axes from the already computed C symmetries list.
Definition: ProSHADE_symmetry.cpp:1808
ProSHADE_internal_data::ProSHADE_data::getPredictedIcosahedralSymmetriesList
std::vector< std::vector< proshade_double * > > getPredictedIcosahedralSymmetriesList(ProSHADE_settings *settings, std::vector< proshade_double * > *CSymList)
This function predicts a list of all I symmetry axes from the already computed C symmetries list.
Definition: ProSHADE_symmetry.cpp:1880
ProSHADE_internal_data::ProSHADE_data::getYAxisOrigin
proshade_signed * getYAxisOrigin(void)
This function allows access to the map Y axis origin value.
Definition: ProSHADE_data.cpp:4029
ProSHADE_internal_data::ProSHADE_data::getCyclicSymmetriesListFromAngleAxis
std::vector< proshade_double * > getCyclicSymmetriesListFromAngleAxis(ProSHADE_settings *settings)
This function obtains a list of all C symmetries from the angle-axis space mapped rotation function v...
Definition: ProSHADE_symmetry.cpp:2770
ProSHADE_internal_data::ProSHADE_data::getTetrahedralSymmetriesList
std::vector< proshade_double * > getTetrahedralSymmetriesList(ProSHADE_settings *settings, std::vector< proshade_double * > *CSymList)
This function obtains a list of all T symmetry axes from the already computed C symmetries list.
Definition: ProSHADE_symmetry.cpp:422
ProSHADE_internal_data::ProSHADE_data::originalPdbRotCenZ
proshade_double originalPdbRotCenZ
The centre of rotation as it relates to the original PDB positions (and not the ProSHADE internal map...
Definition: ProSHADE_data.hpp:104
ProSHADE_internal_data::ProSHADE_data::ProSHADE_data
ProSHADE_data()
Constructor for getting empty ProSHADE_data class.
Definition: ProSHADE_data.cpp:93
ProSHADE_internal_data::ProSHADE_data::zDimIndices
proshade_unsign zDimIndices
This is the size of the map cell z dimension in indices.
Definition: ProSHADE_data.hpp:67
ProSHADE_internal_data::computeGroupElementsForGroup
std::vector< std::vector< proshade_double > > computeGroupElementsForGroup(proshade_double xAx, proshade_double yAx, proshade_double zAx, proshade_signed fold)
This function computes the group elements as rotation matrices (except for the identity element) for ...
Definition: ProSHADE_data.cpp:2939
ProSHADE_internal_data::ProSHADE_data::getRecommendedSymmetryType
std::string getRecommendedSymmetryType(ProSHADE_settings *settings)
This function simply returns the detected recommended symmetry type.
Definition: ProSHADE_data.cpp:4384
ProSHADE_internal_data::ProSHADE_data::zGridIndices
proshade_unsign zGridIndices
As far as I know, this is identical to the zDimIndices.
Definition: ProSHADE_data.hpp:70
ProSHADE_internal_data::ProSHADE_data::setEMatrixValue
void setEMatrixValue(proshade_unsign band, proshade_unsign order1, proshade_unsign order2, proshade_complex val)
This function allows setting the E matrix value.
Definition: ProSHADE_data.cpp:4118
ProSHADE_internal_data::ProSHADE_data::spheres
ProSHADE_internal_spheres::ProSHADE_sphere ** spheres
The set of concentric spheres to which the intermal density map has been projected.
Definition: ProSHADE_data.hpp:120
ProSHADE_internal_data::ProSHADE_data::normaliseMap
void normaliseMap(ProSHADE_settings *settings)
Function for normalising the map values to mean 0 and sd 1..
Definition: ProSHADE_data.cpp:1229
ProSHADE_internal_data::ProSHADE_data::findRequestedCSymmetryFromAngleAxis
std::vector< proshade_double * > findRequestedCSymmetryFromAngleAxis(ProSHADE_settings *settings, proshade_unsign fold, proshade_double *peakThres)
This function searches the angle-axis representation of the rotation function for a cyclic point grou...
Definition: ProSHADE_symmetry.cpp:2909
ProSHADE_internal_data::ProSHADE_data::detectSymmetryFromAngleAxisSpace
void detectSymmetryFromAngleAxisSpace(ProSHADE_settings *settings, std::vector< proshade_double * > *axes, std::vector< std::vector< proshade_double > > *allCs)
This function runs the symmetry detection algorithms on this structure using the angle-axis space and...
Definition: ProSHADE_data.cpp:1907
ProSHADE_internal_data::ProSHADE_data::allocateSO3CoeffsSpace
void allocateSO3CoeffsSpace(proshade_unsign band)
This function allocates the memory for the SO(3) coefficients and the inverse for that calling object...
Definition: ProSHADE_distances.cpp:675
ProSHADE_internal_data::ProSHADE_data::originalPdbRotCenX
proshade_double originalPdbRotCenX
The centre of rotation as it relates to the original PDB positions (and not the ProSHADE internal map...
Definition: ProSHADE_data.hpp:102
ProSHADE_internal_data::ProSHADE_data::originalMapZCom
proshade_double originalMapZCom
The COM of the first map to be loaded/computed without any furhter changes being reflacted along the ...
Definition: ProSHADE_data.hpp:93
ProSHADE_internal_data::ProSHADE_data::getOctahedralSymmetriesList
std::vector< proshade_double * > getOctahedralSymmetriesList(ProSHADE_settings *settings, std::vector< proshade_double * > *CSymList)
This function obtains a list of all O symmetry axes from the already computed C symmetries list.
Definition: ProSHADE_symmetry.cpp:1204
ProSHADE_internal_data::ProSHADE_data::getRealSO3Coeffs
void getRealSO3Coeffs(double *so3CoefsReal, int len)
This function fills the input array with the real SO(3) coefficient values.
Definition: ProSHADE_data.cpp:4226
ProSHADE_internal_data::ProSHADE_data::yDimSize
proshade_single yDimSize
This is the size of the map cell y dimension in Angstroms.
Definition: ProSHADE_data.hpp:60
ProSHADE_internal_data::ProSHADE_data::removePhaseInormation
void removePhaseInormation(ProSHADE_settings *settings)
This function removes phase from the map, effectively converting it to Patterson map.
Definition: ProSHADE_data.cpp:3657
ProSHADE_internal_data::ProSHADE_data::zeroPaddToDims
void zeroPaddToDims(proshade_unsign xDim, proshade_unsign yDim, proshade_unsign zDim)
This function changes the size of a structure to fit the supplied new limits.
Definition: ProSHADE_overlay.cpp:433
ProSHADE_internal_data::ProSHADE_data::getAllGroupElements
std::vector< std::vector< proshade_double > > getAllGroupElements(ProSHADE_settings *settings, std::vector< proshade_unsign > axesList, std::string groupType="", proshade_double matrixTolerance=0.05)
This function returns the group elements as rotation matrices of any defined point group.
Definition: ProSHADE_data.cpp:3151
ProSHADE_internal_data::ProSHADE_data::addExtraSpace
void addExtraSpace(ProSHADE_settings *settings)
This function increases the size of the map so that it can add empty space around it.
Definition: ProSHADE_data.cpp:1585
ProSHADE_internal_data::ProSHADE_data::getRealEMatrixValuesForLM
void getRealEMatrixValuesForLM(proshade_signed band, proshade_signed order1, double *eMatsLMReal, int len)
This function fills the input array with the real E matrix values for particular band and order1 (l a...
Definition: ProSHADE_data.cpp:4188
ProSHADE_internal_data::ProSHADE_data::readInPDB
void readInPDB(ProSHADE_settings *settings)
Function for reading pdb data.
Definition: ProSHADE_data.cpp:700
ProSHADE_internal_data::ProSHADE_data::prepareFSCFourierMemory
void prepareFSCFourierMemory(fftw_complex *&mapData, fftw_complex *&origCoeffs, fftw_complex *&fCoeffs, proshade_signed *&binIndexing, proshade_signed *noBins, proshade_double **&bindata, proshade_signed *&binCounts, fftw_plan *planForwardFourier, proshade_double *&fscByBin)
This function allocates the memory and makes all preparations required for FSC computation.
Definition: ProSHADE_data.cpp:2320
ProSHADE_internal_data::ProSHADE_data::getZFromPtr
proshade_signed * getZFromPtr(void)
This function allows access to the map start along the Z axis.
Definition: ProSHADE_data.cpp:3979
ProSHADE_internal_data::ProSHADE_data::getZToPtr
proshade_signed * getZToPtr(void)
This function allows access to the map last position along the Z axis.
Definition: ProSHADE_data.cpp:4009
ProSHADE_internal_data::ProSHADE_data::so3CoeffsArrayIndex
int so3CoeffsArrayIndex(proshade_signed order1, proshade_signed order2, proshade_signed band)
This function gets the SO(3) coefficients array index for a particular so(3) band,...
Definition: ProSHADE_data.cpp:4266