ProSHADE  0.6.5 (NOV 2018)
Protein Shape Descriptors and Symmetry Detection
ProSHADE_internal.h
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1 
19 //============================================ ProSHADE
20 #include "ProSHADE_version.h"
21 #include "ProSHADE_rvapi.h"
22 
23 //============================================ Include once
24 #ifndef __PROSHADE_INTERNAL_LIBRARY__
25 #define __PROSHADE_INTERNAL_LIBRARY__
26 
33 namespace ProSHADE_internal
34 {
35  //======================================== Forward declaration
36  unsigned int checkFileType ( std::string fileName );
37 
38  //======================================== Forward declaration
39  class ProSHADE_comparePairwise;
40 
48  class ProSHADE_symmetry
49  {
50  //==================================== Friends
51  friend class ProSHADE_comparePairwise;
52 
53  private:
54  //==================================== Settings regarding resolutions
55  double mapResolution;
56  std::vector<unsigned int> bandwidth;
57  std::vector<unsigned int> glIntegOrder;
58  std::vector<unsigned int> theta;
59  std::vector<unsigned int> phi;
60 
61  //==================================== Settings regarding B factors
62  double bFactorValue;
63  double bFactorChange;
64 
65  //==================================== Setting regarding maps and removing noise
66  double noIQRsFromMap;
67 
68  //==================================== Settings regarding concentric shells
69  double shellSpacing;
70  unsigned int manualShells;
71 
72  //==================================== Settings regarding map with phases
73  bool useCOM;
74  bool firstLineCOM;
75 
76  //==================================== Settings regarding space around the structure in lattice
77  double extraSpace;
78 
79  //==================================== Settings regarding weighting the distances
80  double alpha;
81  double mPower;
82 
83  //==================================== Settings regarding bands to ignore
84  std::vector<int> ignoreLs;
85 
86  //==================================== Settings regarding the structures to use
87  std::vector <std::string> structFiles;
88 
89  //==================================== Variables holding the results
90  std::vector< std::array<double,8> > rfPeaks;
91  std::vector< std::vector<std::array<double,5> > > tetrSymm;
92  double tetrSymmPeakAvg;
93  std::vector< std::array<double,5> > tetrElems;
94  std::vector< std::vector<std::array<double,5> > > octaSymm;
95  double octaSymmPeakAvg;
96  std::vector< std::array<double,5> > octaElems;
97  std::vector< std::vector<std::array<double,5> > > icosSymm;
98  double icosSymmPeakAvg;
99  std::vector< std::array<double,5> > icosElems;
100 
101  //==================================== Settings regarding peak finding
102  double peakHeightNoIQRs;
103  double peakDistanceForReal;
104  int peakSurroundingPoints;
105 
106  //==================================== Settings regarding axis and angle error tolerance
107  double aaErrorTolerance;
108  double symGapTolerance;
109 
110  //==================================== Are full results needed?
111  bool printFull;
112 
113  public:
114  //==================================== Public variables holding the results
115  std::vector< std::array<double,5> > cnSymm;
116  std::vector< std::array<double,5> > cnSymmClear;
117  std::vector< std::vector<std::array<double,6> > > dnSymm;
118  std::vector< std::vector<std::array<double,6> > > dnSymmClear;
119  std::vector< std::array<double,5> > tetrAxes;
120  std::vector< std::array<double,5> > octaAxes;
121  std::vector< std::array<double,5> > icosAxes;
122  bool inputStructureDataType;
123 
124  //==================================== Public functions
125  ProSHADE_symmetry ( ProSHADE::ProSHADE_settings* settings );
126  ProSHADE_symmetry ( );
127  void printResultsClear ( int verbose );
128  void printResultsClearHTML ( ProSHADE::ProSHADE_settings* settings );
129  void printResultsRequest ( std::string symmetryType,
130  unsigned int symmetryFold,
131  int verbose );
132  void printResultsRequestHTML ( std::string symmetryType,
133  unsigned int symmetryFold,
134  ProSHADE::ProSHADE_settings* settings );
135  std::vector< std::array<double,8> > getRotFnPeaks ( );
136  std::vector< std::array<double,5> > getCSymmetries ( );
137  std::vector< std::vector<std::array<double,6> > > getDSymmetries ( );
138  std::vector< std::array<double,5> > generateTetrAxes ( ProSHADE_comparePairwise* cmpObj,
139  ProSHADE::ProSHADE_settings* settings,
140  std::vector< std::array<double,5> > tetrSymm,
141  std::vector< std::array<double,5> > allCs,
142  double axisErrorTolerance = 0.1,
143  int verbose = 0 );
144  std::vector< std::array<double,5> > generateTetrElements ( std::vector< std::array<double,5> > symmAxes,
145  ProSHADE::ProSHADE_settings* settings,
146  int verbose = 0 );
147  std::vector< std::array<double,5> > generateOctaAxes ( ProSHADE_comparePairwise* cmpObj,
148  ProSHADE::ProSHADE_settings* settings,
149  std::vector< std::array<double,5> > octaSymm,
150  std::vector< std::array<double,5> > allCs,
151  double axisErrorTolerance = 0.1,
152  int verbose = 0 );
153  std::vector< std::array<double,5> > generateOctaElements ( std::vector< std::array<double,5> > symmAxes,
154  ProSHADE::ProSHADE_settings* settings,
155  int verbose = 0 );
156  std::vector< std::array<double,5> > generateIcosAxes ( ProSHADE_comparePairwise* cmpObj,
157  ProSHADE::ProSHADE_settings* settings,
158  std::vector< std::array<double,5> > icosSymm,
159  std::vector< std::array<double,5> > allCs,
160  double axisErrorTolerance = 0.1,
161  int verbose = 0 );
162  std::vector< std::array<double,5> > generateIcosElements ( std::vector< std::array<double,5> > symmAxes,
163  ProSHADE::ProSHADE_settings* settings,
164  int verbose = 0 );
165  };
166 
174  class ProSHADE_data
175  {
176  //==================================== Friends
177  friend class ProSHADE_comparePairwise;
178  friend class ProSHADE_compareOneAgainstAll;
179  friend class ProSHADE_symmetry;
180  friend class ProSHADE_distances;
181  friend class ProSHADE_mapFeatures;
182 
183  private:
184  //==================================== Variables regarding the reading in of the data
185  std::string _inputFileName;
186  bool _fromPDB;
187 
188  //==================================== Variables regarding the shells
189  double _shellSpacing;
190  double _maxExtraCellularSpace;
191  double _xRange;
192  double _yRange;
193  double _zRange;
194  double _xSamplingRate;
195  double _ySamplingRate;
196  double _zSamplingRate;
197  float _xFrom;
198  float _yFrom;
199  float _zFrom;
200  float _xTo;
201  float _yTo;
202  float _zTo;
203  std::vector<double> _shellPlacement;
204 
205  //==================================== Variables regarding the density map
206  double _mapResolution;
207  unsigned int _maxMapU;
208  unsigned int _maxMapV;
209  unsigned int _maxMapW;
210  float *_densityMapMap;
211  bool _densityMapComputed;
212  double _mapMean;
213  double _mapSdev;
214 
215  //==================================== Variables regarding the phase removal from map
216  double _fourierCoeffPower;
217  double _bFactorChange;
218  double *_densityMapCor;
219  double _maxMapRange;
220  std::array<double,3> *_densityMapCorCoords;
221  bool _phaseRemoved;
222  bool _usePhase;
223  bool _keepOrRemove;
224 
225  //==================================== Variables regarding the sphere mapping of phaseless data
226  double _thetaAngle;
227  double _phiAngle;
228  unsigned int _noShellsWithData;
229  double **_shellMappedData;
230  int _xCorrection;
231  int _yCorrection;
232  int _zCorrection;
233  double _xCorrErr;
234  double _yCorrErr;
235  double _zCorrErr;
236  bool _sphereMapped;
237  bool _firstLineCOM;
238 
239  //==================================== Variables regarding the spherical harmonics decomposition
240  unsigned int _bandwidthLimit;
241  unsigned int _oneDimmension;
242  double **_realSHCoeffs;
243  double **_imagSHCoeffs;
244  double *_sphericalHarmonicsWeights;
245  double **_semiNaiveTable;
246  double *_semiNaiveTableSpace;
247  fftw_complex *_shWorkspace;
248  bool _sphericalCoefficientsComputed;
249  bool _wasBandwithGiven;
250  bool _wasThetaGiven;
251  bool _wasPhiGiven;
252  bool _wasGlInterGiven;
253 
254  //==================================== Variables regarding spherical harmonics inverse
255  double **_invRealData;
256  double **_invImagData;
257 
258  //==================================== Variables regarding the energy levels descriptor pre-calculation
259  double ***_rrpMatrices;
260  bool _rrpMatricesPrecomputed;
261 
262  public:
263  //==================================== Public functions
264  ProSHADE_data ( );
265  ProSHADE_data ( ProSHADE_data *copyFrom );
266  ProSHADE_data ( std::ifstream* dbFile, std::string fName, double volThreMin, double volThreMax, int verbose, ProSHADE::ProSHADE_settings* settings, bool saveWithAndWithout = false );
267  ~ProSHADE_data ( );
268 
269  void getDensityMapFromPDB ( std::string fileName, double *shellDistance, double resolution,
270  unsigned int *bandwidth, unsigned int *theta,
271  unsigned int *phi, unsigned int *glIntegOrder,
272  double *extraSpace, bool mapResDefault, ProSHADE::ProSHADE_settings* settings,
273  double Bfactor = 80.0, bool hpFirstLineCom = false, bool overlayDefaults = false );
274  void getDensityMapFromMAP ( std::string fileName, double *shellDistance, double resolution,
275  unsigned int *bandwidth, unsigned int *theta,
276  unsigned int *phi, unsigned int *glIntegOrder,
277  double *extraSpace, bool mapResDefault, bool rotDefaults, ProSHADE::ProSHADE_settings* settings,
278  bool overlayDefaults = false );
279  void maskMap ( int hlpU, int hlpV, int hlpW, double blurBy = 250.0, double maxMapIQR = 3.0, double extraMaskSpace = 3.0 );
280  void normaliseMap ( ProSHADE::ProSHADE_settings* settings );
281  std::array<double,4> getCOMandDist ( ProSHADE::ProSHADE_settings* settings );
282  bool removeIslands ( int hlpU, int hlpV, int hlpW, int verbose = 0, bool runAll = false );
283  void translateMap ( double xShift, double yShift, double zShift );
284  void shiftMap ( double xShift, double yShift, double zShift );
285  void matchMap ( ProSHADE_data *matchTo );
286  std::array<double,6> getDensityMapFromMAPRebox ( std::string fileName, double maxMapIQR, double extraCS, int verbose,
287  bool useCubicMaps, double maskBlurFactor, bool maskBlurFactorGiven,
288  ProSHADE::ProSHADE_settings* settings );
289  void getDensityMapFromMAPFeatures ( std::string fileName, double *minDensPreNorm, double *maxDensPreNorm,
290  double *minDensPostNorm, double *maxDensPostNorm, double *postNormMean,
291  double *postNormSdev, double *maskVolume, double* totalVolume, double *maskMean,
292  double *maskSdev, double *maskMin, double *maskMax, double *maskDensityRMS,
293  double *allDensityRMS, std::array<double,3> *origRanges, std::array<double,3> *origDims,
294  double maxMapIQR, double extraCS, int verbose, bool useCubicMaps, double maskBlurFactor, bool maskBlurFactorGiven,
295  bool reboxAtAll, ProSHADE::ProSHADE_settings* settings );
296  void removePhaseFromMap ( double alpha, double bFac, ProSHADE::ProSHADE_settings* settings );
297  void removePhaseFromMapOverlay ( double alpha, double bFac, ProSHADE::ProSHADE_settings* settings );
298  void keepPhaseInMap ( double alpha, double bFac,
299  unsigned int *bandwidth, unsigned int *theta,
300  unsigned int *phi, unsigned int *glIntegOrder, ProSHADE::ProSHADE_settings* settings,
301  bool useCom = true,
302  double maxMapIQR = 10.0, int verbose = 0,
303  bool clearMapData = true, bool rotDefaults = false, bool overlapDefaults = false,
304  double blurFactor = 500.0, bool maskBlurFactorGiven = false );
305  void mapPhaselessToSphere ( ProSHADE::ProSHADE_settings* settings, double theta, double phi, double shellSz, unsigned int manualShells = 0, bool keepInMemory = false, bool rotDefaults = false );
306  void getSphericalHarmonicsCoeffs ( unsigned int bandwidth, ProSHADE::ProSHADE_settings* settings );
307  void precomputeRotInvDescriptor ( ProSHADE::ProSHADE_settings* settings );
308  std::vector<ProSHADE_data*> fragmentMap ( ProSHADE::ProSHADE_settings* settings, bool userCOM );
309  std::vector< std::vector<int> > findMapIslands ( int hlpU, int hlpV, int hlpW, double *map, double threshold = 0.0 );
310  void writeMap ( std::string fileName,
311  double *map,
312  std::string axOrder = "xyz",
313  float xFrom = std::numeric_limits<float>::infinity(),
314  float yFrom = std::numeric_limits<float>::infinity(),
315  float zFrom = std::numeric_limits<float>::infinity(),
316  float xTo = std::numeric_limits<float>::infinity(),
317  float yTo = std::numeric_limits<float>::infinity(),
318  float zTo = std::numeric_limits<float>::infinity(),
319  float xRange = std::numeric_limits<float>::infinity(),
320  float yRange = std::numeric_limits<float>::infinity(),
321  float zRange = std::numeric_limits<float>::infinity() );
322  void writeMap ( std::string fileName,
323  float *map,
324  std::string axOrder = "xyz",
325  float xFrom = std::numeric_limits<float>::infinity(),
326  float yFrom = std::numeric_limits<float>::infinity(),
327  float zFrom = std::numeric_limits<float>::infinity(),
328  float xTo = std::numeric_limits<float>::infinity(),
329  float yTo = std::numeric_limits<float>::infinity(),
330  float zTo = std::numeric_limits<float>::infinity(),
331  float xRange = std::numeric_limits<float>::infinity(),
332  float yRange = std::numeric_limits<float>::infinity(),
333  float zRange = std::numeric_limits<float>::infinity() );
334  void writePDB ( std::string templateName, std::string outputName,
335  double rotEulA = 0.0,
336  double rotEulB = 0.0,
337  double rotEulG = 0.0,
338  double trsX = 0.0,
339  double trsY = 0.0,
340  double trsZ = 0.0 );
341  void deleteModel ( std::string modelPath );
342 
343  //==================================== Accessor functions
344  inline double getMapXRange ( void ) { return ( this->_xRange ); };
345  inline double getMapYRange ( void ) { return ( this->_yRange ); };
346  inline double getMapZRange ( void ) { return ( this->_zRange ); };
347  inline double* getMap ( void ) { return ( this->_densityMapCor ); };
348 
349  };
350 
358  class ProSHADE_comparePairwise
359  {
360  private:
361  //==================================== Variables regarding sanity check
362  unsigned int _bandwidthLimit;
363  double _shellSpacing;
364  double _thetaAngle;
365  double _phiAngle;
366  double _matrixPowerWeight;
367  unsigned int _minShellsToUse;
368  std::vector<int> _lsToIgnore;
369  bool _bothRRPsPreComputed;
370  bool _keepOrRemove;
371 
372  //==================================== Variables regarding RotInv distance
373  double ***_obj1RRPs;
374  double ***_obj2RRPs;
375  double _distanceRotInv;
376  bool _rotInvComputed;
377 
378  //==================================== Variables regarding TrSigma distance pre-calculation
379  unsigned int _noShellsObj1;
380  unsigned int _noShellsObj2;
381  unsigned int _maxShellsToUse;
382  double **_obj1RealCoeffs;
383  double **_obj1ImagCoeffs;
384  double **_obj2RealCoeffs;
385  double **_obj2ImagCoeffs;
386  std::vector<double> _trSigmaWeights;
387  std::array<double,2> ***_trSigmaEMatrix;
388  bool _trSigmaPreComputed;
389 
390  //==================================== Variables regarding TrSigma distance computation
391  double _distanceTrSigma;
392  bool _trSigmaComputed;
393 
394  //==================================== Variables regarding the SO3 Transform
395  fftw_complex *_so3Coeffs;
396  fftw_complex *_so3InvCoeffs;
397  fftw_complex *_so3Workspace1;
398  fftw_complex *_so3Workspace2;
399  double *_so3Workspace3;
400  bool _so3InvMapComputed;
401 
402  //==================================== Variables regarding the Euler angles
403  std::array<double,3> _eulerAngles;
404  bool _eulerAnglesFound;
405 
406  //==================================== Variables regarding symmetry detection
407  double _peakHeightThr;
408  bool _CSymmsFound;
409  bool _DSymmsFound;
410 
411  //==================================== Variables regarding the Wigner d matrices computation
412  std::vector< std::vector< std::vector< std::array<double,2> > > > _wignerMatrices;
413  bool _wignerMatricesComputed;
414 
415  //==================================== Variables regarding Gauss-Legendre integration
416  unsigned int _glIntegrationOrder;
417  std::vector<double> _glAbscissas;
418  std::vector<double> _glWeights;
419 
420  //==================================== Variables regarding the coefficient rotation
421  bool _structureCoeffsRotated;
422 
423  //==================================== Internal functions
424  double gl20IntRR ( std::vector<double>* vals );
425  std::array<double,2> gl20IntCR ( std::vector< std::array<double,2> >* vals );
426  std::vector<double> getSingularValues ( unsigned int band, unsigned int dim, ProSHADE::ProSHADE_settings* settings );
427  std::vector< std::vector< std::vector<double> > > getSingularValuesUandVMatrix ( std::vector< std::vector<double> > mat, unsigned int dim, ProSHADE::ProSHADE_settings* settings );
428  double maxPeakHeightFromAngleAxis ( double X, double Y, double Z, double Angle, ProSHADE::ProSHADE_settings* settings );
429 
430  public:
431  //==================================== Public functions
432  ProSHADE_comparePairwise ( ProSHADE_data *cmpObj1, ProSHADE_data *cmpObj2, double mPower, std::vector<int> ignoreL, unsigned int order, ProSHADE::ProSHADE_settings* settings );
433  ~ProSHADE_comparePairwise ( );
434 
435  void precomputeTrSigmaDescriptor ( );
436  void getSO3InverseMap ( ProSHADE::ProSHADE_settings* settings );
437  std::array<double,3> getEulerAngles ( ProSHADE::ProSHADE_settings* settings, double* correlation = nullptr );
438  void setEulerAngles ( double alpha, double beta, double gamma );
439  std::vector< std::array<double,8> > getSO3Peaks ( ProSHADE::ProSHADE_settings* settings, double noIQRs = 1.5, bool freeMem = true, int peakSize = 1, double realDist = 0.4, int verbose = 1 );
440  bool checkPeakExistence ( double alpha, double beta, double gamma, ProSHADE::ProSHADE_settings* settings, double passThreshold = 0.3 );
441  std::vector< std::array<double,5> > findCnSymmetry ( std::vector< std::array<double,8> > peaks,
442  ProSHADE::ProSHADE_settings* settings,
443  double axisErrorTolerance = 0.0,
444  bool freeMem = true,
445  double percAllowedToMiss = 0.33,
446  int verbose = 1 );
447  std::vector< std::array<double,5> > findCnSymmetryClear ( std::vector< std::array<double,5> > CnSymm, ProSHADE::ProSHADE_settings* settings, double maxGap = 0.2, bool *pf = nullptr );
448  std::vector< std::vector< std::array<double,6> > > findDnSymmetry ( std::vector< std::array<double,5> > CnSymm, double axisErrorTolerance = 0.1 );
449  std::vector< std::vector< std::array<double,6> > > findDnSymmetryClear ( std::vector< std::vector< std::array<double,6> > > DnSymm, ProSHADE::ProSHADE_settings* settings, double maxGap = 0.2, bool *pf = nullptr );
450  std::vector< std::vector< std::array<double,5> > > findTetrSymmetry ( std::vector< std::array<double,5> > CnSymm, double *tetrSymmPeakAvg, double axisErrorTolerance = 0.1 );
451  std::vector< std::vector< std::array<double,5> > > findOctaSymmetry ( std::vector< std::array<double,5> > CnSymm, double *octaSymmPeakAvg, double axisErrorTolerance = 0.1 );
452  std::vector< std::vector< std::array<double,5> > > findIcosSymmetry ( std::vector< std::array<double,5> > CnSymm, double *icosSymmPeakAvg, double axisErrorTolerance = 0.1 );
453  void generateWignerMatrices ( ProSHADE::ProSHADE_settings* settings );
454  double getRotCoeffDistance ( ProSHADE::ProSHADE_settings* settings );
455  double maxAvgPeakForSymmetry ( double X, double Y, double Z, double Angle, ProSHADE::ProSHADE_settings* settings );
456  void freeInvMap ( );
457  double getPeakThreshold ( );
458  void rotateStructure ( ProSHADE_data *cmpObj1, ProSHADE::ProSHADE_settings* settings,
459  std::string saveName, int verbose = 0, std::string axOrd = "xyz",
460  bool internalUse = false );
461  std::array<double,4> getTranslationFunctionMap ( ProSHADE_data *obj1, ProSHADE_data *obj2, double *ob2XMov = nullptr,
462  double *ob2YMov = nullptr, double *ob2ZMov = nullptr );
463  };
464 
472  class ProSHADE_compareOneAgainstAll
473  {
474  //==================================== Friends
475  friend class ProSHADE_distances;
476 
477  private:
478  //==================================== Just save the input data and make the internal functions do the checks themselves
479  ProSHADE_data *one;
480  ProSHADE_data *two;
481  std::vector<ProSHADE_data*> *all;
482 
483  //==================================== These needs to be the same
484  std::vector<int> _lsToIgnore;
485  double _matrixPowerWeight;
486 
487  //==================================== Simple checks
488  bool _energyLevelsComputed;
489  bool _trSigmaPreComputed;
490  bool _trSigmaComputed;
491  bool _keepOrRemove;
492  bool _so3InvMapComputed;
493  bool _eulerAnglesFound;
494  bool _wignerMatricesComputed;
495  bool _fullDistComputed;
496 
497  //==================================== Result holders
498  std::vector<double> _distancesEnergyLevels;
499  std::vector<double> _distancesTraceSigma;
500  std::vector<double> _distancesFullRotation;
501 
502  //==================================== Internal value holders
503  std::vector< std::vector< std::vector< std::vector< std::array<double,2> > > > > _EMatrices;
504  std::vector<fftw_complex*> _so3InverseCoeffs;
505  std::vector< std::array<double,3> > _eulerAngles;
506  std::vector< std::vector< std::vector< std::vector< std::array<double,2> > > > > _wignerMatrices;
507  std::vector<unsigned int> _enLevelsDoNotFollow;
508  std::vector<unsigned int> _trSigmaDoNotFollow;
509 
510  //==================================== Internal functions
511  double glIntRR ( std::vector<double>* vals, double shellSep, std::vector<double>* glAbscissas, std::vector<double>* glWeights );
512  std::array<double,2> glIntCR ( std::vector< std::array<double,2> >* vals, double shellSep, std::vector<double> *glAbscissas, std::vector<double> *glWeights );
513  std::vector<double> getSingularValues ( unsigned int strNo, unsigned int band, unsigned int dim, ProSHADE::ProSHADE_settings* settings );
514 
515  public:
516  //==================================== Public functions
517  ProSHADE_compareOneAgainstAll ( ProSHADE_data *oneStr, std::vector<ProSHADE_data*> *allStrs,
518  std::vector<int> ignoreL, double matrixPowerWeight, int verbose );
519  ProSHADE_compareOneAgainstAll ( ProSHADE_data *oneStr, ProSHADE_data *twoStr, std::vector<ProSHADE_data*> *allStrs,
520  std::vector<int> ignoreL, double matrixPowerWeight, int verbose );
521  ~ProSHADE_compareOneAgainstAll ( );
522 
523  std::vector<double> getEnergyLevelsDistance ( int verbose, ProSHADE::ProSHADE_settings* settings );
524  void precomputeTrSigmaDescriptor ( double shellSpacing, std::vector<unsigned int>* glIntegOrderVec, ProSHADE::ProSHADE_settings* settings );
525  std::vector<double> getTrSigmaDistance ( int verbose, ProSHADE::ProSHADE_settings* settings );
526  void getSO3InverseMap ( ProSHADE::ProSHADE_settings* settings );
527  std::vector< std::array<double,3> > getEulerAngles ( ProSHADE::ProSHADE_settings* settings );
528  void generateWignerMatrices ( ProSHADE::ProSHADE_settings* settings );
529  std::vector<double> getRotCoeffDistance ( int verbose, ProSHADE::ProSHADE_settings* settings );
530  void alignDensities ( ProSHADE::ProSHADE_settings* settings );
531  };
532 
540  class ProSHADE_distances
541  {
542  private:
543  //==================================== Settings regarding resolutions
544  double mapResolution;
545  unsigned int bandwidth;
546  unsigned int glIntegOrder;
547  unsigned int theta;
548  unsigned int phi;
549  std::vector<unsigned int> bandwidthVec;
550  std::vector<unsigned int> glIntegOrderVec;
551  std::vector<unsigned int> thetaVec;
552  std::vector<unsigned int> phiVec;
553 
554  //==================================== Settings regarding B factors
555  double bFactorValue;
556  double bFactorChange;
557 
558  //==================================== Setting regarding maps and removing noise
559  double noIQRsFromMap;
560 
561  //==================================== Settings regarding concentric shells
562  double shellSpacing;
563  unsigned int manualShells;
564 
565  //==================================== Settings regarding map with phases
566  bool useCOM;
567  bool firstLineCOM;
568 
569  //==================================== Settings regarding space around the structure in lattice
570  double extraSpace;
571  std::vector<double> extraSpaceVec;
572 
573  //==================================== Settings regarding weighting the distances
574  double alpha;
575  double mPower;
576 
577  //==================================== Settings regarding bands to ignore
578  std::vector<int> ignoreLs;
579 
580  //==================================== Settings regarding the structures to use
581  std::vector <std::string> structFiles;
582 
583  //==================================== Settings regarding which distances to compute
584  bool energyLevelDist;
585  bool traceSigmaDist;
586  bool fullRotFnDist;
587 
588  //==================================== Settings regarding dealing with phases
589  bool usePhase;
590  bool saveWithAndWithout;
591 
592  //==================================== Distances holder variables
593  std::vector<double> energyLevelsDistances;
594  std::vector<double> traceSigmaDistances;
595  std::vector<double> fullRotationDistances;
596  std::vector< std::vector<double> > fragEnergyLevelsDistances;
597  std::vector< std::vector<double> > fragTraceSigmaDistances;
598  std::vector< std::vector<double> > fragfullRotationDistances;
599 
600  //==================================== Settings regarding thresholds for hierarchical distance computation
601  double enLevelsThreshold;
602  double trSigmaThreshold;
603 
604  //==================================== Pointer to the comparison object
605  ProSHADE_compareOneAgainstAll *cmpObj;
606 
607  public:
608  //==================================== Public functions
609  ProSHADE_distances ( ProSHADE::ProSHADE_settings* settings );
610  ~ProSHADE_distances ( );
611  void saveDatabase ( ProSHADE::ProSHADE_settings* settings );
612  void compareAgainstDatabase ( ProSHADE::ProSHADE_settings* settings,
613  std::vector<std::string>* matchedStrNames );
614  void compareFragAgainstDatabase ( ProSHADE::ProSHADE_settings* settings,
615  std::vector<std::string>* matchedStrNames );
616  std::vector<double> getEnergyLevelsDistances ( );
617  std::vector<double> getTraceSigmaDistances ( );
618  std::vector<double> getFullRotationDistances ( );
619  std::vector< std::vector<double> > getFragEnergyLevelsDistances( );
620  std::vector< std::vector<double> > getFragTraceSigmaDistances ( );
621  std::vector< std::vector<double> > getFragFullRotationDistances( );
622  };
623 
631  class ProSHADE_mapFeatures
632  {
633  private:
634  //==================================== Private variables
635  ProSHADE_internal::ProSHADE_data* one;
636  double fragBoxSize;
637  std::string mapFragName;
638  double mapFragBoxFraction;
639  double maxMapU;
640  double maxMapV;
641  double maxMapW;
642  double xRange;
643  double yRange;
644  double zRange;
645 
646  double minDensPreNorm;
647  double maxDensPreNorm;
648  double minDensPostNorm;
649  double maxDensPostNorm;
650  double postNormMean;
651  double postNormSdev;
652  double maskVolume;
653  double totalVolume;
654  double maskMean;
655  double maskSdev;
656  double maskMax;
657  double maskMin;
658  double maskDensityRMS;
659  double allDensityRMS;
660  std::array<double,3> origRanges;
661  std::array<double,3> origDims;
662  std::vector<std::string> fragFiles;
663  bool fragFilesExist;
664 
665  public:
666  //==================================== Public functions
667  ProSHADE_mapFeatures ( ProSHADE::ProSHADE_settings *settings );
668  ~ProSHADE_mapFeatures ( );
669 
670  void printInfo ( int verbose );
671  void fragmentMap ( std::string axOrder, int verbose, ProSHADE::ProSHADE_settings* settings );
672  std::vector<std::string> getFragmentsList ( void );
673  void dealWithHalfMaps ( ProSHADE::ProSHADE_settings* settings, double *xTranslate, double *yTranslate, double *zTranslate );
674  };
675 
676 }
677 
678 
679 //============================================ Include once
680 #endif
ProSHADE_internal::ProSHADE_data
This class deals with reading in the data and computing structure specific information including the ...
Definition: ProSHADE_internal.h:174
ProSHADE_internal::ProSHADE_mapFeatures
This class is responsible for reading in map and computing all its features and other possible map ma...
Definition: ProSHADE_internal.h:631
ProSHADE_internal::ProSHADE_symmetry::dnSymmClear
std::vector< std::vector< std::array< double, 6 > > > dnSymmClear
This variable holds the gap corrected Dihedral symmetry results.
Definition: ProSHADE_internal.h:118
ProSHADE_internal::checkFileType
unsigned int checkFileType(std::string fileName)
This function checks the input file for being either PDB or MAP formatted.
Definition: ProSHADE_internal.cpp:70
ProSHADE_internal::ProSHADE_symmetry::cnSymm
std::vector< std::array< double, 5 > > cnSymm
This variable holds the complete Cyclic symmetry results.
Definition: ProSHADE_internal.h:115
ProSHADE_internal::ProSHADE_symmetry::printResultsClear
void printResultsClear(int verbose)
This function prints the cleared results to the screen.
Definition: ProSHADE_internal.cpp:5564
ProSHADE_internal::ProSHADE_symmetry::generateTetrElements
std::vector< std::array< double, 5 > > generateTetrElements(std::vector< std::array< double, 5 > > symmAxes, ProSHADE::ProSHADE_settings *settings, int verbose=0)
This function generates the 12 unique tetrahedral symmetry group elements from the already detected a...
Definition: ProSHADE_SO3transform.cpp:3243
ProSHADE_internal::ProSHADE_symmetry::generateTetrAxes
std::vector< std::array< double, 5 > > generateTetrAxes(ProSHADE_comparePairwise *cmpObj, ProSHADE::ProSHADE_settings *settings, std::vector< std::array< double, 5 > > tetrSymm, std::vector< std::array< double, 5 > > allCs, double axisErrorTolerance=0.1, int verbose=0)
This function generates all the tetrahedral symmetry axes from a pair detected by findTetrSymmetry fu...
Definition: ProSHADE_SO3transform.cpp:2879
ProSHADE_internal
This namespace contains all the internal objects and their forward declarations.
ProSHADE_internal::ProSHADE_symmetry::icosAxes
std::vector< std::array< double, 5 > > icosAxes
This variable holds the 31 unique axes of the octahedral symmetry, if they are found.
Definition: ProSHADE_internal.h:121
ProSHADE_internal::ProSHADE_symmetry::generateOctaElements
std::vector< std::array< double, 5 > > generateOctaElements(std::vector< std::array< double, 5 > > symmAxes, ProSHADE::ProSHADE_settings *settings, int verbose=0)
This function generates the 24 octahedral symmetry group elements from the axes generated by generate...
Definition: ProSHADE_SO3transform.cpp:3921
ProSHADE_internal::ProSHADE_symmetry::generateOctaAxes
std::vector< std::array< double, 5 > > generateOctaAxes(ProSHADE_comparePairwise *cmpObj, ProSHADE::ProSHADE_settings *settings, std::vector< std::array< double, 5 > > octaSymm, std::vector< std::array< double, 5 > > allCs, double axisErrorTolerance=0.1, int verbose=0)
This function generates all the ctahedral symmetry elements from a pair detected by findOctaSymmetry ...
Definition: ProSHADE_SO3transform.cpp:3339
ProSHADE_internal::ProSHADE_comparePairwise
This is the executive class responsible for comparing strictly two structures.
Definition: ProSHADE_internal.h:358
ProSHADE_internal::ProSHADE_symmetry::generateIcosAxes
std::vector< std::array< double, 5 > > generateIcosAxes(ProSHADE_comparePairwise *cmpObj, ProSHADE::ProSHADE_settings *settings, std::vector< std::array< double, 5 > > icosSymm, std::vector< std::array< double, 5 > > allCs, double axisErrorTolerance=0.1, int verbose=0)
This function generates all the icosahedral symmetry elements from a pair detected by findIcosSymmetr...
Definition: ProSHADE_SO3transform.cpp:4047
ProSHADE_internal::ProSHADE_symmetry::cnSymmClear
std::vector< std::array< double, 5 > > cnSymmClear
This variable holds the gap corrected Cyclic symmetry results.
Definition: ProSHADE_internal.h:116
ProSHADE_internal::ProSHADE_symmetry::generateIcosElements
std::vector< std::array< double, 5 > > generateIcosElements(std::vector< std::array< double, 5 > > symmAxes, ProSHADE::ProSHADE_settings *settings, int verbose=0)
This function generates the 60 icosahedral symmetry group elements from the axes generated by generat...
Definition: ProSHADE_SO3transform.cpp:4626
ProSHADE_internal::ProSHADE_symmetry::printResultsClearHTML
void printResultsClearHTML(ProSHADE::ProSHADE_settings *settings)
This function prints the cleared results to the HTML file.
Definition: ProSHADE_internal.cpp:5830
ProSHADE_internal::ProSHADE_symmetry::inputStructureDataType
bool inputStructureDataType
This variable tells whether input data type is PDB or not.
Definition: ProSHADE_internal.h:122
ProSHADE_internal::ProSHADE_symmetry::getCSymmetries
std::vector< std::array< double, 5 > > getCSymmetries()
This function gives the user programmatical access to the detected C-symmetries.
Definition: ProSHADE_internal.cpp:7241
ProSHADE_internal::ProSHADE_symmetry::getRotFnPeaks
std::vector< std::array< double, 8 > > getRotFnPeaks()
This function gives the user programmatical access to the symmetry peaks of the symmetry detection pr...
Definition: ProSHADE_internal.cpp:7218
ProSHADE_internal::ProSHADE_symmetry::printResultsRequestHTML
void printResultsRequestHTML(std::string symmetryType, unsigned int symmetryFold, ProSHADE::ProSHADE_settings *settings)
This function prints the cleared results to the HTML report file.
Definition: ProSHADE_internal.cpp:3661
ProSHADE_internal::ProSHADE_symmetry
This is the class which computes the symmetry in a single structure.
Definition: ProSHADE_internal.h:48
ProSHADE_internal::ProSHADE_symmetry::ProSHADE_symmetry
ProSHADE_symmetry()
Contructor for the ProSHADE_symmetry class.
Definition: ProSHADE_internal.cpp:1133
ProSHADE_internal::ProSHADE_compareOneAgainstAll
This is the executive class responsible for comparing two or more structures.
Definition: ProSHADE_internal.h:472
ProSHADE_internal::ProSHADE_symmetry::tetrAxes
std::vector< std::array< double, 5 > > tetrAxes
This variable holds the 7 unique axes of the tetrahedral symmetry, if they are found.
Definition: ProSHADE_internal.h:119
ProSHADE_internal::ProSHADE_distances
This is the executive class for computing distances between two or more structures.
Definition: ProSHADE_internal.h:540
ProSHADE::ProSHADE_settings
This class stores all the settings and is passed to the executive classes instead of multitude of par...
Definition: ProSHADE.h:74
ProSHADE_internal::ProSHADE_symmetry::octaAxes
std::vector< std::array< double, 5 > > octaAxes
This variable holds the 13 unique axes of the octahedral symmetry, if they are found.
Definition: ProSHADE_internal.h:120
ProSHADE_internal::ProSHADE_symmetry::getDSymmetries
std::vector< std::vector< std::array< double, 6 > > > getDSymmetries()
This function gives the user programmatical access to the detected D-symmetries.
Definition: ProSHADE_internal.cpp:7266
ProSHADE_internal::ProSHADE_symmetry::printResultsRequest
void printResultsRequest(std::string symmetryType, unsigned int symmetryFold, int verbose)
This function prints the cleared results to the screen.
Definition: ProSHADE_internal.cpp:3257
ProSHADE_internal::ProSHADE_symmetry::dnSymm
std::vector< std::vector< std::array< double, 6 > > > dnSymm
This variable holds the complete Dihedral symmetry results.
Definition: ProSHADE_internal.h:117