ProSHADE  0.7.6.0 (JUL 2021)
Protein Shape Detection
pyProSHADE.cpp
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1 
22 //==================================================== Include PyBind11 header
23 #include <pybind11/pybind11.h>
24 #include <pybind11/stl.h>
25 #include <pybind11/numpy.h>
26 
27 //==================================================== Add the ProSHADE_settings and ProSHADE_run classes to the PyBind11 module
28 void add_settingsClass ( pybind11::module& pyProSHADE )
29 {
30  //================================================ Export the ProSHADE_settings class
31  pybind11::class_ < ProSHADE_settings > ( pyProSHADE, "ProSHADE_settings" )
32 
33  //============================================ Constructors (destructors do not need wrappers???)
34  .def ( pybind11::init < > ( ) )
35  .def ( pybind11::init < ProSHADE_Task > ( ), pybind11::arg ( "task" ) )
36 
37  //============================================ Member variables
38  .def_readwrite ( "task", &ProSHADE_settings::task )
39 
40  .def_readwrite ( "inputFiles", &ProSHADE_settings::inputFiles )
41  .def_readwrite ( "forceP1", &ProSHADE_settings::forceP1 )
42  .def_readwrite ( "removeNegativeDensity", &ProSHADE_settings::removeNegativeDensity )
43  .def_readwrite ( "removeWaters", &ProSHADE_settings::removeWaters )
44  .def_readwrite ( "firstModelOnly", &ProSHADE_settings::firstModelOnly )
45 
46  .def_readwrite ( "requestedResolution", &ProSHADE_settings::requestedResolution )
47  .def_readwrite ( "changeMapResolution", &ProSHADE_settings::changeMapResolution )
48  .def_readwrite ( "changeMapResolutionTriLinear", &ProSHADE_settings::changeMapResolutionTriLinear )
49 
50  .def_readwrite ( "pdbBFactorNewVal", &ProSHADE_settings::pdbBFactorNewVal )
51 
52  .def_readwrite ( "maxBandwidth", &ProSHADE_settings::maxBandwidth )
53  .def_readwrite ( "rotationUncertainty", &ProSHADE_settings::rotationUncertainty )
54 
55  .def_readwrite ( "usePhase", &ProSHADE_settings::usePhase )
56 
57  .def_readwrite ( "maxSphereDists", &ProSHADE_settings::maxSphereDists )
58 
59  .def_readwrite ( "integOrder", &ProSHADE_settings::integOrder )
60  .def_readwrite ( "taylorSeriesCap", &ProSHADE_settings::taylorSeriesCap )
61 
62  .def_readwrite ( "normaliseMap", &ProSHADE_settings::normaliseMap )
63 
64  .def_readwrite ( "invertMap", &ProSHADE_settings::invertMap )
65 
66  .def_readwrite ( "blurFactor", &ProSHADE_settings::blurFactor )
67  .def_readwrite ( "maskingThresholdIQRs", &ProSHADE_settings::maskingThresholdIQRs )
68  .def_readwrite ( "maskMap", &ProSHADE_settings::maskMap )
69  .def_readwrite ( "useCorrelationMasking", &ProSHADE_settings::useCorrelationMasking )
70  .def_readwrite ( "halfMapKernel", &ProSHADE_settings::halfMapKernel )
71  .def_readwrite ( "correlationKernel", &ProSHADE_settings::correlationKernel )
72  .def_readwrite ( "saveMask", &ProSHADE_settings::saveMask )
73  .def_readwrite ( "maskFileName", &ProSHADE_settings::maskFileName )
74  .def_readwrite ( "appliedMaskFileName", &ProSHADE_settings::appliedMaskFileName )
75 
76  .def_readwrite ( "reBoxMap", &ProSHADE_settings::reBoxMap )
77  .def_readwrite ( "boundsExtraSpace", &ProSHADE_settings::boundsExtraSpace )
78  .def_readwrite ( "boundsSimilarityThreshold", &ProSHADE_settings::boundsSimilarityThreshold )
79  .def_readwrite ( "useSameBounds", &ProSHADE_settings::useSameBounds )
80  .def_readwrite ( "forceBounds", &ProSHADE_settings::forceBounds )
81 
82  .def_readwrite ( "moveToCOM", &ProSHADE_settings::moveToCOM )
83 
84  .def_readwrite ( "addExtraSpace", &ProSHADE_settings::addExtraSpace )
85 
86  .def_readwrite ( "progressiveSphereMapping", &ProSHADE_settings::progressiveSphereMapping )
87 
88  .def_readwrite ( "outName", &ProSHADE_settings::outName )
89 
90  .def_readwrite ( "computeEnergyLevelsDesc", &ProSHADE_settings::computeEnergyLevelsDesc )
91  .def_readwrite ( "enLevMatrixPowerWeight", &ProSHADE_settings::enLevMatrixPowerWeight )
92  .def_readwrite ( "computeTraceSigmaDesc", &ProSHADE_settings::computeTraceSigmaDesc )
93  .def_readwrite ( "computeRotationFuncDesc", &ProSHADE_settings::computeRotationFuncDesc )
94 
95  .def_readwrite ( "peakNeighbours", &ProSHADE_settings::peakNeighbours )
96  .def_readwrite ( "noIQRsFromMedianNaivePeak", &ProSHADE_settings::noIQRsFromMedianNaivePeak )
97 
98  .def_readwrite ( "smoothingFactor", &ProSHADE_settings::smoothingFactor )
99 
100  .def_readwrite ( "symMissPeakThres", &ProSHADE_settings::symMissPeakThres )
101  .def_readwrite ( "axisErrTolerance", &ProSHADE_settings::axisErrTolerance )
102  .def_readwrite ( "axisErrToleranceDefault", &ProSHADE_settings::axisErrToleranceDefault )
103  .def_readwrite ( "minSymPeak", &ProSHADE_settings::minSymPeak )
104  .def_readwrite ( "recommendedSymmetryType", &ProSHADE_settings::recommendedSymmetryType )
105  .def_readwrite ( "recommendedSymmetryFold", &ProSHADE_settings::recommendedSymmetryFold )
106  .def_readwrite ( "requestedSymmetryType", &ProSHADE_settings::requestedSymmetryType )
107  .def_readwrite ( "requestedSymmetryFold", &ProSHADE_settings::requestedSymmetryFold )
108  .def_readwrite ( "usePeakSearchInRotationFunctionSpace", &ProSHADE_settings::usePeakSearchInRotationFunctionSpace)
109  .def_readwrite ( "useBiCubicInterpolationOnPeaks", &ProSHADE_settings::useBiCubicInterpolationOnPeaks )
110  .def_readwrite ( "maxSymmetryFold", &ProSHADE_settings::maxSymmetryFold )
111  .def_readwrite ( "fscThreshold", &ProSHADE_settings::fscThreshold )
112  .def_readwrite ( "peakThresholdMin", &ProSHADE_settings::peakThresholdMin )
113 
114  .def_readwrite ( "overlayStructureName", &ProSHADE_settings::overlayStructureName )
115  .def_readwrite ( "rotTrsJSONFile", &ProSHADE_settings::rotTrsJSONFile )
116 
117  .def_readwrite ( "verbose", &ProSHADE_settings::verbose )
118 
119  //============================================ Mutators
120  .def ( "addStructure", &ProSHADE_settings::addStructure, "Adds a structure file name to the appropriate variable.", pybind11::arg ( "structure" ) )
121  .def ( "setResolution", &ProSHADE_settings::setResolution, "This function sets the resolution in the appropriate variable.", pybind11::arg ( "resolution" ) )
122  .def ( "setPDBBFactor", &ProSHADE_settings::setPDBBFactor, "Sets the requested B-factor value for PDB files in the appropriate variable.", pybind11::arg ( "newBF" ) )
123  .def ( "setNormalisation", &ProSHADE_settings::setNormalisation, "Sets the requested map normalisation value in the appropriate variable.", pybind11::arg ( "normalise" ) )
124  .def ( "setMapInversion", &ProSHADE_settings::setMapInversion, "Sets the requested map inversion value in the appropriate variable.", pybind11::arg ( "mInv" ) )
125  .def ( "setVerbosity", &ProSHADE_settings::setVerbosity, "Sets the requested verbosity in the appropriate variable.", pybind11::arg ( "verbosity" ) )
126  .def ( "setMaskBlurFactor", &ProSHADE_settings::setMaskBlurFactor, "Sets the requested map blurring factor in the appropriate variable.", pybind11::arg ( "blurFac" ) )
127  .def ( "setMaskIQR", &ProSHADE_settings::setMaskIQR, "Sets the requested number of IQRs for masking threshold in the appropriate variable.", pybind11::arg ( "noIQRs" ) )
128  .def ( "setMasking", &ProSHADE_settings::setMasking, "Sets the requested map masking decision value in the appropriate variable.", pybind11::arg ( "mask" ) )
129  .def ( "setCorrelationMasking", &ProSHADE_settings::setCorrelationMasking, "Sets the requested map masking type in the appropriate variable.", pybind11::arg ( "corMask" ) )
130  .def ( "setTypicalNoiseSize", &ProSHADE_settings::setTypicalNoiseSize, "Sets the requested \"fake\" half-map kernel in the appropriate variable.", pybind11::arg ( "typNoi" ) )
131  .def ( "setMinimumMaskSize", &ProSHADE_settings::setMinimumMaskSize, "Sets the requested minimum mask size.", pybind11::arg ( "minMS" ) )
132  .def ( "setMaskSaving", &ProSHADE_settings::setMaskSaving, "Sets whether the mask should be saved.", pybind11::arg ( "savMsk" ) )
133  .def ( "setMaskFilename", &ProSHADE_settings::setMaskFilename, "Sets where the mask should be saved.", pybind11::arg ( "mskFln" ) )
134  .def ( "setAppliedMaskFilename", &ProSHADE_settings::setAppliedMaskFilename, "Sets the filename of the mask data that should be applied to the input map.", pybind11::arg ( "mskFln" ) )
135  .def ( "setMapReboxing", &ProSHADE_settings::setMapReboxing, "Sets whether re-boxing needs to be done in the appropriate variable.", pybind11::arg ( "reBx" ) )
136  .def ( "setBoundsSpace", &ProSHADE_settings::setBoundsSpace, "Sets the requested number of angstroms for extra space in re-boxing in the appropriate variable.", pybind11::arg ( "boundsExSp" ) )
137  .def ( "setBoundsThreshold", &ProSHADE_settings::setBoundsThreshold, "Sets the threshold for number of indices difference acceptable to make index sizes same in the appropriate variable.", pybind11::arg ( "boundsThres" ) )
138  .def ( "setSameBoundaries", &ProSHADE_settings::setSameBoundaries, "Sets whether same boundaries should be used in the appropriate variable.", pybind11::arg ( "sameB" ) )
139  .def ( "setOutputFilename", &ProSHADE_settings::setOutputFilename, "Sets the requested output file name in the appropriate variable.", pybind11::arg ( "oFileName" ) )
140  .def ( "setMapResolutionChange", &ProSHADE_settings::setMapResolutionChange, "Sets the requested map resolution change decision in the appropriate variable.", pybind11::arg ( "mrChange" ) )
141  .def ( "setMapResolutionChangeTriLinear", &ProSHADE_settings::setMapResolutionChangeTriLinear, "Sets the requested map resolution change decision using tri-linear interpolation in the appropriate variable.", pybind11::arg ( "mrChange" ) )
142  .def ( "setMapCentering", &ProSHADE_settings::setMapCentering, "Sets the requested map centering decision value in the appropriate variable.", pybind11::arg ( "com" ) )
143  .def ( "setExtraSpace", &ProSHADE_settings::setExtraSpace, "Sets the requested map extra space value in the appropriate variable.", pybind11::arg ( "exSpace" ) )
144  .def ( "setBandwidth", &ProSHADE_settings::setBandwidth, "Sets the requested spherical harmonics bandwidth in the appropriate variable.", pybind11::arg ( "band" ) )
145  .def ( "setProgressiveSphereMapping", &ProSHADE_settings::setProgressiveSphereMapping, "Sets the requested sphere mapping value settings approach in the appropriate variable.", pybind11::arg ( "progSphMap" ) )
146  .def ( "setSphereDistances", &ProSHADE_settings::setSphereDistances, "Sets the requested distance between spheres in the appropriate variable.", pybind11::arg ( "sphDist" ) )
147  .def ( "setIntegrationOrder", &ProSHADE_settings::setIntegrationOrder, "Sets the requested order for the Gauss-Legendre integration in the appropriate variable.", pybind11::arg ( "intOrd" ) )
148  .def ( "setTaylorSeriesCap", &ProSHADE_settings::setTaylorSeriesCap, "Sets the requested Taylor series cap for the Gauss-Legendre integration in the appropriate variable.", pybind11::arg ( "tayCap" ) )
149  .def ( "setEnergyLevelsComputation", &ProSHADE_settings::setEnergyLevelsComputation, "Sets whether the energy level distance descriptor should be computed.", pybind11::arg ( "enLevDesc" ) )
150  .def ( "setTraceSigmaComputation", &ProSHADE_settings::setTraceSigmaComputation, "Sets whether the trace sigma distance descriptor should be computed.", pybind11::arg ( "trSigVal" ) )
151  .def ( "setRotationFunctionComputation", &ProSHADE_settings::setRotationFunctionComputation, "Sets whether the rotation function distance descriptor should be computed.", pybind11::arg ( "rotfVal" ) )
152  .def ( "setPeakNeighboursNumber", &ProSHADE_settings::setPeakNeighboursNumber, "Sets the number of neighbour values that have to be smaller for an index to be considered a peak.", pybind11::arg ( "pkS" ) )
153  .def ( "setPeakNaiveNoIQR", &ProSHADE_settings::setPeakNaiveNoIQR, "Sets the number of IQRs from the median for threshold height a peak needs to be considered a peak.", pybind11::arg ( "noIQRs" ) )
154  .def ( "setPhaseUsage", &ProSHADE_settings::setPhaseUsage, "Sets whether the phase information will be used.", pybind11::arg ( "phaseUsage" ) )
155  .def ( "setEnLevShellWeight", &ProSHADE_settings::setEnLevShellWeight, "Sets the weight of shell position for the energy levels computation.", pybind11::arg ( "mPower" ) )
156  .def ( "setGroupingSmoothingFactor", &ProSHADE_settings::setGroupingSmoothingFactor, "Sets the grouping smoothing factor into the proper variable.", pybind11::arg ( "smFact" ) )
157  .def ( "setMissingPeakThreshold", &ProSHADE_settings::setMissingPeakThreshold, "Sets the threshold for starting the missing peaks procedure.", pybind11::arg ( "mpThres" ) )
158  .def ( "setAxisComparisonThreshold", &ProSHADE_settings::setAxisComparisonThreshold, "Sets the threshold for matching symmetry axes.", pybind11::arg ( "axThres" ) )
159  .def ( "setAxisComparisonThresholdBehaviour", &ProSHADE_settings::setAxisComparisonThresholdBehaviour, "Sets the automatic symmetry axis tolerance decreasing.", pybind11::arg ( "behav" ) )
160  .def ( "setMinimumPeakForAxis", &ProSHADE_settings::setMinimumPeakForAxis, "Sets the minimum peak height for symmetry axis to be considered.", pybind11::arg ( "minSP" ) )
161  .def ( "setRecommendedSymmetry", &ProSHADE_settings::setRecommendedSymmetry, "Sets the ProSHADE detected symmetry type.", pybind11::arg ( "val" ) )
162  .def ( "setRecommendedFold", &ProSHADE_settings::setRecommendedFold, "Sets the ProSHADE detected symmetry fold.", pybind11::arg ( "val" ) )
163  .def ( "setRequestedSymmetry", &ProSHADE_settings::setRequestedSymmetry, "Sets the user requested symmetry type.", pybind11::arg ( "val" ) )
164  .def ( "setRequestedFold", &ProSHADE_settings::setRequestedFold, "Sets the user requested symmetry fold.", pybind11::arg ( "val" ) )
165  .def ( "setDetectedSymmetry", &ProSHADE_settings::setDetectedSymmetry, "Sets the final detected symmetry axes information.", pybind11::arg ( "sym" ) )
166  .def ( "setOverlaySaveFile", &ProSHADE_settings::setOverlaySaveFile, "Sets the filename to which the overlay structure is to be save into.", pybind11::arg ( "filename" ) )
167  .def ( "setOverlayJsonFile", &ProSHADE_settings::setOverlayJsonFile, "Sets the filename to which the overlay operations are to be save into.", pybind11::arg ( "filename" ) )
168  .def ( "setSymmetryRotFunPeaks", &ProSHADE_settings::setSymmetryRotFunPeaks, "Sets the symmetry detection algorithm type.", pybind11::arg ( "rotFunPeaks" ) )
169  .def ( "setBicubicInterpolationSearch", &ProSHADE_settings::setBicubicInterpolationSearch, "Sets the bicubic interpolation on peaks.", pybind11::arg ( "bicubPeaks" ) )
170  .def ( "setMaxSymmetryFold", &ProSHADE_settings::setMaxSymmetryFold, "Sets the maximum symmetry fold (well, the maximum prime symmetry fold).", pybind11::arg ( "maxFold" ) )
171  .def ( "setFSCThreshold", &ProSHADE_settings::setFSCThreshold, "Sets the minimum FSC threshold for axis to be considered detected.", pybind11::arg ( "fscThr" ) )
172  .def ( "setPeakThreshold", &ProSHADE_settings::setPeakThreshold, "Sets the minimum peak height threshold for axis to be considered possible.", pybind11::arg ( "peakThr" ) )
173  .def ( "setNegativeDensity", &ProSHADE_settings::setNegativeDensity, "Sets the internal variable deciding whether input files negative density should be removed.", pybind11::arg ( "nDens" ) )
174 
175  //============================================ Command line parsing
176  .def ( "getCommandLineParams",
177  [] ( ProSHADE_settings &self, std::vector < std::string > args )
178  {
179  std::vector < char * > cstrs; cstrs.reserve ( args.size() );
180 
181  for ( auto &s : args )
182  cstrs.push_back ( const_cast < char * > ( s.c_str ( ) ) );
183 
184  return self.getCommandLineParams ( static_cast< int > ( cstrs.size ( ) ), cstrs.data ( ) );
185  }, "This function takes a VectorOfStrings and parses it as if it were command line arguments, filling in the calling ProSHADE_settings class with the values." )
186 
187  //============================================ Debugging
188  .def ( "printSettings", &ProSHADE_settings::printSettings, "This function prints the current values in the settings object." )
189 
190  //============================================ Description
191  .def ( "__repr__", [] ( ) { return "<ProSHADE_settings class object> (Settings class is used to set all settings values in a single place)"; } );
192 
193  //================================================ Export the ProSHADE_run class
194  pybind11::class_ < ProSHADE_run > ( pyProSHADE, "ProSHADE_run" )
195 
196  //============================================ Constructors (destructors do not need wrappers???)
197  .def ( pybind11::init < ProSHADE_settings* > ( ) )
198 
199  //============================================ General accessors
200  .def ( "getNoStructures", &ProSHADE_run::getNoStructures, "This function returns the number of structures used." )
201  .def ( "getVerbose", &ProSHADE_run::getVerbose, "This function returns the verbose value." )
202 
203  //============================================ Distances results accessor functions wrapped as lambda functions for numpy return types
204  .def ( "getEnergyLevelsVector",
205  [] ( ProSHADE_run &self ) -> pybind11::array_t < float >
206  {
207  //== Get the values
208  std::vector< proshade_double > vals = self.getEnergyLevelsVector ();
209 
210  //== Allocate memory for the numpy values
211  float* npVals = new float[static_cast<unsigned int> (vals.size())];
212  ProSHADE_internal_misc::checkMemoryAllocation ( npVals, __FILE__, __LINE__, __func__ );
213 
214  //== Copy values
215  for ( proshade_unsign iter = 0; iter < static_cast<proshade_unsign> ( vals.size() ); iter++ ) { npVals[iter] = static_cast< float > ( vals.at(iter) ); }
216 
217  //== Create capsules to make sure memory is released properly from the allocating language (C++ in this case)
218  pybind11::capsule pyCapsuleEnLevs ( npVals, []( void *f ) { float* foo = reinterpret_cast< float* > ( f ); delete foo; } );
219 
220  //== Copy the value
221  pybind11::array_t < float > retArr = pybind11::array_t<float> ( { static_cast<unsigned int> (vals.size()) }, // Shape
222  { sizeof(float) }, // C-stype strides
223  npVals, // Data
224  pyCapsuleEnLevs ); // Capsule (C++ destructor, basically)
225 
226  //== Done
227  return ( retArr );
228  }, "This function returns the energy level distances vector from the first to all other structures." )
229 
230  .def ( "getTraceSigmaVector",
231  [] ( ProSHADE_run &self ) -> pybind11::array_t < float >
232  {
233  //== Get the values
234  std::vector< proshade_double > vals = self.getTraceSigmaVector ();
235 
236  //== Allocate memory for the numpy values
237  float* npVals = new float[static_cast<unsigned int> (vals.size())];
238  ProSHADE_internal_misc::checkMemoryAllocation ( npVals, __FILE__, __LINE__, __func__ );
239 
240  //== Copy values
241  for ( proshade_unsign iter = 0; iter < static_cast<proshade_unsign> ( vals.size() ); iter++ ) { npVals[iter] = static_cast< float > ( vals.at(iter) ); }
242 
243  //== Create capsules to make sure memory is released properly from the allocating language (C++ in this case)
244  pybind11::capsule pyCapsuleTrSigs ( npVals, []( void *f ) { float* foo = reinterpret_cast< float* > ( f ); delete foo; } );
245 
246  //== Copy the value
247  pybind11::array_t < float > retArr = pybind11::array_t<float> ( { static_cast<unsigned int> (vals.size()) }, // Shape
248  { sizeof(float) }, // C-stype strides
249  npVals, // Data
250  pyCapsuleTrSigs ); // Capsule (C++ destructor, basically)
251 
252  //== Done
253  return ( retArr );
254  }, "This function returns the trace sigma distances vector from the first to all other structures." )
255 
256  .def ( "getRotationFunctionVector",
257  [] ( ProSHADE_run &self ) -> pybind11::array_t < float >
258  {
259  //== Get the values
260  std::vector< proshade_double > vals = self.getRotationFunctionVector ();
261 
262  //== Allocate memory for the numpy values
263  float* npVals = new float[static_cast<unsigned int> (vals.size())];
264  ProSHADE_internal_misc::checkMemoryAllocation ( npVals, __FILE__, __LINE__, __func__ );
265 
266  //== Copy values
267  for ( proshade_unsign iter = 0; iter < static_cast<proshade_unsign> ( vals.size() ); iter++ ) { npVals[iter] = static_cast< float > ( vals.at(iter) ); }
268 
269  //== Create capsules to make sure memory is released properly from the allocating language (C++ in this case)
270  pybind11::capsule pyCapsuleRotFun ( npVals, []( void *f ) { float* foo = reinterpret_cast< float* > ( f ); delete foo; } );
271 
272  //== Copy the value
273  pybind11::array_t < float > retArr = pybind11::array_t<float> ( { static_cast<unsigned int> (vals.size()) }, // Shape
274  { sizeof(float) }, // C-stype strides
275  npVals, // Data
276  pyCapsuleRotFun ); // Capsule (C++ destructor, basically)
277 
278  //== Done
279  return ( retArr );
280  }, "This function returns the full rotation function distances vector from the first to all other structures." )
281 
282  //============================================ Symmetry results accessor functions
283  .def ( "getSymmetryType", &ProSHADE_run::getSymmetryType, "This is the main accessor function for the user to get to know what symmetry type ProSHADE has detected and recommends." )
284  .def ( "getSymmetryFold", &ProSHADE_run::getSymmetryFold, "This is the main accessor function for the user to get to know what symmetry fold ProSHADE has detected and recommends." )
285  .def ( "getSymmetryAxis", &ProSHADE_run::getSymmetryAxis, "This function returns a single symmetry axis as a vector of strings from the recommended symmetry axes list.", pybind11::arg ( "axisNo" ) )
286  .def ( "getAllCSyms",
287  [] ( ProSHADE_run &self ) -> pybind11::array_t < float >
288  {
289  //== Get the values
290  std::vector< std::vector< proshade_double > > vals = self.getAllCSyms ();
291 
292  //== Allocate memory for the numpy values
293  float* npVals = new float[static_cast<unsigned int> ( vals.size() * 7 )];
294  ProSHADE_internal_misc::checkMemoryAllocation ( npVals, __FILE__, __LINE__, __func__ );
295 
296  //== Copy values
297  for ( proshade_unsign iter = 0; iter < static_cast<proshade_unsign> ( vals.size() ); iter++ ) { for ( proshade_unsign it = 0; it < 7; it++ ) { npVals[(iter*7)+it] = static_cast< float > ( vals.at(iter).at(it) ); } }
298 
299  //== Create capsules to make sure memory is released properly from the allocating language (C++ in this case)
300  pybind11::capsule pyCapsuleSymList ( npVals, []( void *f ) { float* foo = reinterpret_cast< float* > ( f ); delete foo; } );
301 
302  //== Copy the value
303  pybind11::array_t < float > retArr = pybind11::array_t<float> ( { static_cast<int> ( vals.size() ), static_cast<int> ( 7 ) }, // Shape
304  { 7 * sizeof(float), sizeof(float) }, // C-stype strides
305  npVals, // Data
306  pyCapsuleSymList ); // Capsule
307 
308  //== Done
309  return ( retArr );
310  }, "This function returns a all symmetry axes as a 2D numpy array." )
311  .def ( "getMapCOMProcessChange",
312  [] ( ProSHADE_run &self ) -> pybind11::array_t < float >
313  {
314  //== Get the values
315  std::vector< proshade_double > vals = self.getMapCOMProcessChange ();
316 
317  //== Allocate memory for the numpy values
318  float* npVals = new float[static_cast<unsigned int> ( 3 )];
319  ProSHADE_internal_misc::checkMemoryAllocation ( npVals, __FILE__, __LINE__, __func__ );
320 
321  //== Copy values
322  for ( proshade_unsign iter = 0; iter < 3; iter++ ) { npVals[iter] = static_cast< float > ( vals.at(iter) ); }
323 
324  //== Create capsules to make sure memory is released properly from the allocating language (C++ in this case)
325  pybind11::capsule pyCapsuleSymShift ( npVals, []( void *f ) { float* foo = reinterpret_cast< float* > ( f ); delete foo; } );
326 
327  //== Copy the value
328  pybind11::array_t < float > retArr = pybind11::array_t<float> ( { static_cast<int> ( vals.size() ) }, // Shape
329  { sizeof(float) }, // C-stype strides
330  npVals, // Data
331  pyCapsuleSymShift ); // Capsule
332 
333  //== Done
334  return ( retArr );
335  }, "This function returns the shift in Angstrom applied to the internal map representation in order to align its COM with the centre of box." )
336 
337  //============================================ Reboxing results accessor functions as lambda functions directly returning numpy arrays
338  .def ( "getOriginalBounds",
339  [] ( ProSHADE_run &self, proshade_unsign strNo ) -> pybind11::array_t < float >
340  {
341  //== Get values
342  std::vector< proshade_signed > vals = self.getOriginalBounds ( strNo );
343 
344  //== Allocate memory for the numpy values
345  float* npVals = new float[static_cast<proshade_unsign> ( vals.size() )];
346  ProSHADE_internal_misc::checkMemoryAllocation ( npVals, __FILE__, __LINE__, __func__ );
347 
348  //== Copy values
349  for ( proshade_unsign iter = 0; iter < static_cast<proshade_unsign> ( vals.size() ); iter++ ) { npVals[iter] = vals.at(iter); }
350 
351  //== Create capsules to make sure memory is released properly from the allocating language (C++ in this case)
352  pybind11::capsule pyCapsuleOrigBnds ( npVals, []( void *f ) { float* foo = reinterpret_cast< float* > ( f ); delete foo; } );
353 
354  //== Copy the value
355  pybind11::array_t < float > retArr = pybind11::array_t<float> ( { static_cast<proshade_unsign> ( vals.size() ) }, // Shape
356  { sizeof(float) }, // C-stype strides
357  npVals, // Data
358  pyCapsuleOrigBnds ); // Capsule (C++ destructor, basically)
359 
360  //== Done
361  return ( retArr );
362  }, "This function returns the original structure boundaries as numpy array." )
363 
364  .def ( "getReBoxedBounds",
365  [] ( ProSHADE_run &self, proshade_unsign strNo ) -> pybind11::array_t < float >
366  {
367  //== Get values
368  std::vector< proshade_signed > vals = self.getReBoxedBounds ( strNo );
369 
370  //== Allocate memory for the numpy values
371  float* npVals = new float[static_cast<proshade_unsign> ( vals.size() )];
372  ProSHADE_internal_misc::checkMemoryAllocation ( npVals, __FILE__, __LINE__, __func__ );
373 
374  //== Copy values
375  for ( proshade_unsign iter = 0; iter < static_cast<proshade_unsign> ( vals.size() ); iter++ ) { npVals[iter] = vals.at(iter); }
376 
377  //== Create capsules to make sure memory is released properly from the allocating language (C++ in this case)
378  pybind11::capsule pyCapsuleReBoBnds ( npVals, []( void *f ) { float* foo = reinterpret_cast< float* > ( f ); delete foo; } );
379 
380  //== Copy the value
381  pybind11::array_t < float > retArr = pybind11::array_t<float> ( { static_cast<proshade_unsign> ( vals.size() ) }, // Shape
382  { sizeof(float) }, // C-stype strides
383  npVals, // Data
384  pyCapsuleReBoBnds ); // Capsule (C++ destructor, basically)
385 
386  //== Done
387  return ( retArr );
388  }, "This function returns the re-boxed structure boundaries as numpy array." )
389 
390 
391  .def ( "getReBoxedMap",
392  [] ( ProSHADE_run &self, proshade_unsign strNo ) -> pybind11::array_t < float >
393  {
394  //== Get the values
395  std::vector< proshade_signed > vals = self.getReBoxedBounds ( strNo );
396 
397  //== Determine dimensions
398  proshade_unsign xDim = static_cast< proshade_unsign > ( vals.at(1) ) - static_cast< proshade_unsign > ( vals.at(0) ) + 1;
399  proshade_unsign yDim = static_cast< proshade_unsign > ( vals.at(3) ) - static_cast< proshade_unsign > ( vals.at(2) ) + 1;
400  proshade_unsign zDim = static_cast< proshade_unsign > ( vals.at(5) ) - static_cast< proshade_unsign > ( vals.at(4) ) + 1;
401 
402  //== Allocate memory for the numpy values
403  float* npVals = new float[xDim * yDim * zDim];
404  ProSHADE_internal_misc::checkMemoryAllocation ( npVals, __FILE__, __LINE__, __func__ );
405 
406  //== Copy values
407  for ( proshade_unsign iter = 0; iter < (xDim * yDim * zDim); iter++ ) { npVals[iter] = static_cast< float > ( self.getMapValue ( strNo, iter ) ); }
408 
409  //== Create capsules to make sure memory is released properly from the allocating language (C++ in this case)
410  pybind11::capsule pyCapsuleRebMap ( npVals, []( void *f ) { float* foo = reinterpret_cast< float* > ( f ); delete foo; } );
411 
412  //== Copy the value
413  pybind11::array_t < float > retArr = pybind11::array_t<float> ( { xDim, yDim, zDim }, // Shape
414  { yDim * zDim * sizeof(float), zDim * sizeof(float), sizeof(float) }, // C-stype strides
415  npVals, // Data
416  pyCapsuleRebMap ); // Capsule
417 
418  //== Done
419  return ( retArr );
420  }, "This function returns the re-boxed structure map as a numpy 3D array." )
421 
422  //============================================ Overlay results accessor functions as lambda functions directly returning numpy arrays
423  .def ( "getEulerAngles",
424  [] ( ProSHADE_run &self ) -> pybind11::array_t < float >
425  {
426  //== Get the values
427  std::vector< proshade_double > vals = self.getEulerAngles ( );
428 
429  //== Allocate memory for the numpy values
430  float* npVals = new float[static_cast<proshade_unsign> ( vals.size() )];
431  ProSHADE_internal_misc::checkMemoryAllocation ( npVals, __FILE__, __LINE__, __func__ );
432 
433  //== Copy values
434  for ( proshade_unsign iter = 0; iter < static_cast<proshade_unsign> ( vals.size() ); iter++ ) { npVals[iter] = static_cast< float > ( vals.at(iter) ); }
435 
436  //== Create capsules to make sure memory is released properly from the allocating language (C++ in this case)
437  pybind11::capsule pyCapsuleEulAngs ( npVals, []( void *f ) { float* foo = reinterpret_cast< float* > ( f ); delete foo; } );
438 
439  //== Copy the value
440  pybind11::array_t < float > retArr = pybind11::array_t<float> ( { static_cast<proshade_unsign> ( vals.size() ) }, // Shape
441  { sizeof(float) }, // C-stype strides
442  npVals, // Data
443  pyCapsuleEulAngs ); // Capsule
444 
445  //== Done
446  return ( retArr );
447  }, "This function returns the vector of Euler angles with best overlay correlation." )
448 
449  .def ( "getOptimalRotMat",
450  [] ( ProSHADE_run &self ) -> pybind11::array_t < float >
451  {
452  //== Get the values
453  std::vector< proshade_double > vals = self.getOptimalRotMat ( );
454 
455  //== Allocate memory for the numpy values
456  float* npVals = new float[static_cast<proshade_unsign> ( vals.size() )];
457  ProSHADE_internal_misc::checkMemoryAllocation ( npVals, __FILE__, __LINE__, __func__ );
458 
459  //== Copy values
460  for ( proshade_unsign iter = 0; iter < static_cast<proshade_unsign> ( vals.size() ); iter++ ) { npVals[iter] = static_cast< float > ( vals.at(iter) ); }
461 
462  //== Create capsules to make sure memory is released properly from the allocating language (C++ in this case)
463  pybind11::capsule pyCapsuleRotMat ( npVals, []( void *f ) { float* foo = reinterpret_cast< float* > ( f ); delete foo; } );
464 
465  //== Copy the value
466  pybind11::array_t < float > retArr = pybind11::array_t<float> ( { 3, 3 }, // Shape
467  { 3 * sizeof(float), sizeof(float) }, // C-stype strides
468  npVals, // Data
469  pyCapsuleRotMat ); // Capsule
470 
471  //== Done
472  return ( retArr );
473  }, "This function returns the vector of Euler angles with best overlay correlation." )
474 
475  .def ( "getTranslationToOrigin",
476  [] ( ProSHADE_run &self ) -> pybind11::array_t < float >
477  {
478  //== Get the values
479  std::vector< proshade_double > vals = self.getTranslationToOrigin ( );
480 
481  //== Allocate memory for the numpy values
482  float* npVals = new float[static_cast<proshade_unsign> ( vals.size() )];
483  ProSHADE_internal_misc::checkMemoryAllocation ( npVals, __FILE__, __LINE__, __func__ );
484 
485  //== Copy values
486  for ( proshade_unsign iter = 0; iter < static_cast<proshade_unsign> ( vals.size() ); iter++ ) { npVals[iter] = static_cast< float > ( vals.at(iter) ); }
487 
488  //== Create capsules to make sure memory is released properly from the allocating language (C++ in this case)
489  pybind11::capsule pyCapsuleTTO ( npVals, []( void *f ) { float* foo = reinterpret_cast< float* > ( f ); delete foo; } );
490 
491  //== Copy the value
492  pybind11::array_t < float > retArr = pybind11::array_t<float> ( { static_cast<proshade_unsign> ( vals.size() ) }, // Shape
493  { sizeof(float) }, // C-stype strides
494  npVals, // Data
495  pyCapsuleTTO ); // Capsule
496 
497  //== Done
498  return ( retArr );
499  }, "This function returns the negative values of the position of the rotation centre (the point about which the rotation should be done)." )
500  .def ( "getOriginToOverlayTranslation",
501  [] ( ProSHADE_run &self ) -> pybind11::array_t < float >
502  {
503  //== Get the values
504  std::vector< proshade_double > vals = self.getOriginToOverlayTranslation ( );
505 
506  //== Allocate memory for the numpy values
507  float* npVals = new float[static_cast<proshade_unsign> ( vals.size() )];
508  ProSHADE_internal_misc::checkMemoryAllocation ( npVals, __FILE__, __LINE__, __func__ );
509 
510  //== Copy values
511  for ( proshade_unsign iter = 0; iter < static_cast<proshade_unsign> ( vals.size() ); iter++ ) { npVals[iter] = static_cast< float > ( vals.at(iter) ); }
512 
513  //== Create capsules to make sure memory is released properly from the allocating language (C++ in this case)
514  pybind11::capsule pyCapsuleOTOT ( npVals, []( void *f ) { float* foo = reinterpret_cast< float* > ( f ); delete foo; } );
515 
516  //== Copy the value
517  pybind11::array_t < float > retArr = pybind11::array_t<float> ( { static_cast<proshade_unsign> ( vals.size() ) }, // Shape
518  { sizeof(float) }, // C-stype strides
519  npVals, // Data
520  pyCapsuleOTOT ); // Capsule
521 
522  //== Done
523  return ( retArr );
524  }, "This function returns the translation required to move the structure from origin to optimal overlay." )
525 
526 
527  //============================================ Description
528  .def ( "__repr__", [] ( ) { return "<ProSHADE_run class object> (Run class constructor takes a ProSHADE_settings object and completes a single run according to the settings object information)"; } );
529 }
ProSHADE_settings::noIQRsFromMedianNaivePeak
proshade_double noIQRsFromMedianNaivePeak
When doing peak searching, how many IQRs from the median the threshold for peak height should be (in ...
Definition: ProSHADE_settings.hpp:115
ProSHADE_settings::setOverlayJsonFile
void setOverlayJsonFile(std::string filename)
Sets the filename to which the overlay operations are to be save into.
Definition: ProSHADE.cpp:1346
ProSHADE_settings::maxBandwidth
proshade_unsign maxBandwidth
The bandwidth of spherical harmonics decomposition for the largest sphere.
Definition: ProSHADE_settings.hpp:58
ProSHADE_settings::integOrder
proshade_unsign integOrder
The order required for full Gauss-Legendre integration between the spheres.
Definition: ProSHADE_settings.hpp:68
ProSHADE_settings::recommendedSymmetryType
std::string recommendedSymmetryType
The symmetry type that ProSHADE finds the best fitting for the structure. Possible values are "" for ...
Definition: ProSHADE_settings.hpp:125
ProSHADE_settings::rotTrsJSONFile
std::string rotTrsJSONFile
The filename to which the rotation and translation operations are to be saved into.
Definition: ProSHADE_settings.hpp:137
ProSHADE_settings::setEnLevShellWeight
void setEnLevShellWeight(proshade_double mPower)
Sets the weight of shell position for the energy levels computation.
Definition: ProSHADE.cpp:1080
ProSHADE_settings::computeTraceSigmaDesc
bool computeTraceSigmaDesc
If true, the trace sigma descriptor will be computed, otherwise all its computations will be omitted.
Definition: ProSHADE_settings.hpp:110
ProSHADE_settings::setTraceSigmaComputation
void setTraceSigmaComputation(bool trSigVal)
Sets whether the trace sigma distance descriptor should be computed.
Definition: ProSHADE.cpp:972
ProSHADE_settings::computeRotationFuncDesc
bool computeRotationFuncDesc
If true, the rotation function descriptor will be computed, otherwise all its computations will be om...
Definition: ProSHADE_settings.hpp:111
ProSHADE_settings::setSameBoundaries
void setSameBoundaries(bool sameB)
Sets whether same boundaries should be used in the appropriate variable.
Definition: ProSHADE.cpp:728
ProSHADE_settings::maxSymmetryFold
proshade_unsign maxSymmetryFold
The highest symmetry fold to search for.
Definition: ProSHADE_settings.hpp:131
ProSHADE_settings::taylorSeriesCap
proshade_unsign taylorSeriesCap
The max limit on the Taylor series expansion done for the abscissas of the Gauss-Legendre integration...
Definition: ProSHADE_settings.hpp:69
ProSHADE_settings::setMinimumMaskSize
void setMinimumMaskSize(proshade_single minMS)
Sets the requested minimum mask size.
Definition: ProSHADE.cpp:586
ProSHADE_settings::setAppliedMaskFilename
void setAppliedMaskFilename(std::string mskFln)
Sets the filename of the mask data that should be applied to the input map.
Definition: ProSHADE.cpp:646
ProSHADE_settings::boundsExtraSpace
proshade_single boundsExtraSpace
The number of extra angstroms to be added to all re-boxing bounds just for safety.
Definition: ProSHADE_settings.hpp:90
ProSHADE_settings::setBicubicInterpolationSearch
void setBicubicInterpolationSearch(bool bicubPeaks)
Sets the bicubic interpolation on peaks.
Definition: ProSHADE.cpp:1382
ProSHADE_settings::setPeakNaiveNoIQR
void setPeakNaiveNoIQR(proshade_double noIQRs)
Sets the number of IQRs from the median for threshold height a peak needs to be considered a peak.
Definition: ProSHADE.cpp:1036
ProSHADE_settings::outName
std::string outName
The file name where the output structure(s) should be saved.
Definition: ProSHADE_settings.hpp:105
ProSHADE_settings::setMapInversion
void setMapInversion(bool mInv)
Sets the requested map inversion value in the appropriate variable.
Definition: ProSHADE.cpp:442
ProSHADE_settings::setMapResolutionChange
void setMapResolutionChange(bool mrChange)
Sets the requested map resolution change decision in the appropriate variable.
Definition: ProSHADE.cpp:769
ProSHADE_settings::setPeakNeighboursNumber
void setPeakNeighboursNumber(proshade_unsign pkS)
Sets the number of neighbour values that have to be smaller for an index to be considered a peak.
Definition: ProSHADE.cpp:1014
ProSHADE_settings::blurFactor
proshade_single blurFactor
This is the amount by which B-factors should be increased to create the blurred map for masking.
Definition: ProSHADE_settings.hpp:78
ProSHADE_settings::maskMap
bool maskMap
Should the map be masked from noise?
Definition: ProSHADE_settings.hpp:80
ProSHADE_settings::requestedSymmetryFold
proshade_unsign requestedSymmetryFold
The fold of the requested symmetry (only applicable to C and D symmetry types).
Definition: ProSHADE_settings.hpp:128
ProSHADE_settings::requestedSymmetryType
std::string requestedSymmetryType
The symmetry type requested by the user. Allowed values are C, D, T, O and I.
Definition: ProSHADE_settings.hpp:127
ProSHADE_settings::setSphereDistances
void setSphereDistances(proshade_single sphDist)
Sets the requested distance between spheres in the appropriate variable.
Definition: ProSHADE.cpp:869
ProSHADE_settings::setVerbosity
void setVerbosity(proshade_signed verbosity)
Sets the requested verbosity in the appropriate variable.
Definition: ProSHADE.cpp:462
ProSHADE_settings::removeNegativeDensity
bool removeNegativeDensity
Should the negative density be removed from input files?
Definition: ProSHADE_settings.hpp:47
ProSHADE_settings::setMinimumPeakForAxis
void setMinimumPeakForAxis(proshade_double minSP)
Sets the minimum peak height for symmetry axis to be considered.
Definition: ProSHADE.cpp:1188
ProSHADE_settings::saveMask
bool saveMask
Should the mask be saved?
Definition: ProSHADE_settings.hpp:84
ProSHADE_settings::requestedResolution
proshade_single requestedResolution
The resolution to which the calculations are to be done.
Definition: ProSHADE_settings.hpp:50
ProSHADE_settings::minSymPeak
proshade_double minSymPeak
Minimum average peak for symmetry axis to be considered as "real".
Definition: ProSHADE_settings.hpp:124
ProSHADE_settings::setAxisComparisonThresholdBehaviour
void setAxisComparisonThresholdBehaviour(bool behav)
Sets the automatic symmetry axis tolerance decreasing.
Definition: ProSHADE.cpp:1167
ProSHADE_settings::setDetectedSymmetry
void setDetectedSymmetry(proshade_double *sym)
Sets the final detected symmetry axes information.
Definition: ProSHADE.cpp:1294
ProSHADE_settings::progressiveSphereMapping
bool progressiveSphereMapping
If true, each shell will have its own angular resolution dependent on the actual number of map points...
Definition: ProSHADE_settings.hpp:102
ProSHADE_settings::maxSphereDists
proshade_single maxSphereDists
The distance between spheres in spherical mapping for the largest sphere.
Definition: ProSHADE_settings.hpp:65
ProSHADE_settings::symMissPeakThres
proshade_double symMissPeakThres
Percentage of peaks that could be missing that would warrant starting the missing peaks search proced...
Definition: ProSHADE_settings.hpp:121
ProSHADE_settings::setPDBBFactor
void setPDBBFactor(proshade_double newBF)
Sets the requested B-factor value for PDB files in the appropriate variable.
Definition: ProSHADE.cpp:402
ProSHADE_settings::addStructure
void addStructure(std::string structure)
Adds a structure file name to the appropriate variable.
Definition: ProSHADE.cpp:362
ProSHADE_settings::setMaskIQR
void setMaskIQR(proshade_single noIQRs)
Sets the requested number of IQRs for masking threshold in the appropriate variable.
Definition: ProSHADE.cpp:503
ProSHADE_settings::setMissingPeakThreshold
void setMissingPeakThreshold(proshade_double mpThres)
Sets the threshold for starting the missing peaks procedure.
Definition: ProSHADE.cpp:1123
ProSHADE_run::getVerbose
proshade_signed getVerbose(void)
This function returns the verbose value.
Definition: ProSHADE.cpp:2793
ProSHADE_settings::maskingThresholdIQRs
proshade_single maskingThresholdIQRs
Number of inter-quartile ranges from the median to be used for thresholding the blurred map for maski...
Definition: ProSHADE_settings.hpp:79
ProSHADE_settings::useCorrelationMasking
bool useCorrelationMasking
Should the blurring masking (false) or the correlation masking (true) be used?
Definition: ProSHADE_settings.hpp:81
ProSHADE_settings::usePhase
bool usePhase
If true, the full data will be used, if false, Patterson maps will be used instead and phased data wi...
Definition: ProSHADE_settings.hpp:62
ProSHADE_settings::setMapCentering
void setMapCentering(bool com)
Sets the requested map centering decision value in the appropriate variable.
Definition: ProSHADE.cpp:809
ProSHADE_settings::setMaskBlurFactor
void setMaskBlurFactor(proshade_single blurFac)
Sets the requested map blurring factor in the appropriate variable.
Definition: ProSHADE.cpp:482
ProSHADE_settings::setPeakThreshold
void setPeakThreshold(proshade_double peakThr)
Sets the minimum peak height threshold for axis to be considered possible.
Definition: ProSHADE.cpp:1436
ProSHADE_settings::setPhaseUsage
void setPhaseUsage(bool phaseUsage)
Sets whether the phase information will be used.
Definition: ProSHADE.cpp:1058
ProSHADE_settings::maskFileName
std::string maskFileName
The filename to which mask should be saved.
Definition: ProSHADE_settings.hpp:85
ProSHADE_settings::verbose
proshade_signed verbose
Should the software report on the progress, or just be quiet? Value between -1 (nothing) and 4 (loud)
Definition: ProSHADE_settings.hpp:140
ProSHADE_settings::setFSCThreshold
void setFSCThreshold(proshade_double fscThr)
Sets the minimum FSC threshold for axis to be considered detected.
Definition: ProSHADE.cpp:1418
ProSHADE_settings::setBandwidth
void setBandwidth(proshade_unsign band)
Sets the requested spherical harmonics bandwidth in the appropriate variable.
Definition: ProSHADE.cpp:849
ProSHADE_settings::setBoundsSpace
void setBoundsSpace(proshade_single boundsExSp)
Sets the requested number of angstroms for extra space in re-boxing in the appropriate variable.
Definition: ProSHADE.cpp:687
ProSHADE_settings::changeMapResolutionTriLinear
bool changeMapResolutionTriLinear
Should maps be re-sampled to obtain the required resolution?
Definition: ProSHADE_settings.hpp:52
ProSHADE_settings::setOutputFilename
void setOutputFilename(std::string oFileName)
Sets the requested output file name in the appropriate variable.
Definition: ProSHADE.cpp:749
ProSHADE_settings::useBiCubicInterpolationOnPeaks
bool useBiCubicInterpolationOnPeaks
This variable switch decides whether best symmetry is detected from peak indices, or whether bicubic ...
Definition: ProSHADE_settings.hpp:130
ProSHADE_run::getSymmetryAxis
std::vector< std::string > getSymmetryAxis(proshade_unsign axisNo)
This function returns a single symmetry axis as a vector of strings from the recommended symmetry axe...
Definition: ProSHADE.cpp:2827
ProSHADE_settings::setAxisComparisonThreshold
void setAxisComparisonThreshold(proshade_double axThres)
Sets the threshold for matching symmetry axes.
Definition: ProSHADE.cpp:1144
ProSHADE_settings::peakThresholdMin
proshade_double peakThresholdMin
The threshold for peak height above which axes are considered possible.
Definition: ProSHADE_settings.hpp:133
ProSHADE_settings::forceP1
bool forceP1
Should the P1 spacegroup be forced on the input PDB files?
Definition: ProSHADE_settings.hpp:44
ProSHADE_settings::setTypicalNoiseSize
void setTypicalNoiseSize(proshade_single typNoi)
Sets the requested "fake" half-map kernel in the appropriate variable.
Definition: ProSHADE.cpp:566
ProSHADE_run
This class provides the access point to the library.
Definition: ProSHADE.hpp:39
ProSHADE_settings::task
ProSHADE_Task task
This custom type variable determines which task to perfom (i.e. symmetry detection,...
Definition: ProSHADE_settings.hpp:40
ProSHADE_settings::setMaskFilename
void setMaskFilename(std::string mskFln)
Sets where the mask should be saved.
Definition: ProSHADE.cpp:626
ProSHADE_run::getSymmetryFold
proshade_unsign getSymmetryFold(void)
This is the main accessor function for the user to get to know what symmetry fold ProSHADE has detect...
Definition: ProSHADE.cpp:1811
ProSHADE_settings::reBoxMap
bool reBoxMap
This switch decides whether re-boxing is needed.
Definition: ProSHADE_settings.hpp:89
ProSHADE_settings::setSymmetryRotFunPeaks
void setSymmetryRotFunPeaks(bool rotFunPeaks)
Sets the symmetry detection algorithm type.
Definition: ProSHADE.cpp:1364
ProSHADE_settings::appliedMaskFileName
std::string appliedMaskFileName
The filename from which mask data will be read from.
Definition: ProSHADE_settings.hpp:86
ProSHADE_settings::normaliseMap
bool normaliseMap
Should the map be normalised to mean 0 sd 1?
Definition: ProSHADE_settings.hpp:72
ProSHADE_settings::addExtraSpace
proshade_single addExtraSpace
If this value is non-zero, this many angstroms of empty space will be added to the internal map.
Definition: ProSHADE_settings.hpp:99
ProSHADE_settings::setRequestedFold
void setRequestedFold(proshade_unsign val)
Sets the user requested symmetry fold.
Definition: ProSHADE.cpp:1273
ProSHADE_settings
This class stores all the settings and is passed to the executive classes instead of a multitude of p...
Definition: ProSHADE_settings.hpp:37
ProSHADE_settings::fscThreshold
proshade_double fscThreshold
The threshold for FSC value under which the axis is considered to be likely noise.
Definition: ProSHADE_settings.hpp:132
ProSHADE_run::getSymmetryType
std::string getSymmetryType(void)
This is the main accessor function for the user to get to know what symmetry type ProSHADE has detect...
Definition: ProSHADE.cpp:1796
ProSHADE_settings::setMapReboxing
void setMapReboxing(bool reBx)
Sets whether re-boxing needs to be done in the appropriate variable.
Definition: ProSHADE.cpp:666
ProSHADE_settings::setRecommendedSymmetry
void setRecommendedSymmetry(std::string val)
Sets the ProSHADE detected symmetry type.
Definition: ProSHADE.cpp:1210
ProSHADE_settings::setMaxSymmetryFold
void setMaxSymmetryFold(proshade_unsign maxFold)
Sets the maximum symmetry fold (well, the maximum prime symmetry fold).
Definition: ProSHADE.cpp:1400
ProSHADE_settings::correlationKernel
proshade_single correlationKernel
This value in Angstrom will be used as the kernel for the map-FHM correlation computation.
Definition: ProSHADE_settings.hpp:83
ProSHADE_settings::setNegativeDensity
void setNegativeDensity(bool nDens)
Sets the internal variable deciding whether input files negative density should be removed.
Definition: ProSHADE.cpp:1454
ProSHADE_settings::invertMap
bool invertMap
Should the map be inverted? Only use this if you think you have the wrong hand in your map.
Definition: ProSHADE_settings.hpp:75
ProSHADE_settings::setTaylorSeriesCap
void setTaylorSeriesCap(proshade_unsign tayCap)
Sets the requested Taylor series cap for the Gauss-Legendre integration in the appropriate variable.
Definition: ProSHADE.cpp:910
ProSHADE_settings::boundsSimilarityThreshold
proshade_signed boundsSimilarityThreshold
Number of indices which can be added just to make sure same size in indices is achieved.
Definition: ProSHADE_settings.hpp:91
ProSHADE_settings::setCorrelationMasking
void setCorrelationMasking(bool corMask)
Sets the requested map masking type in the appropriate variable.
Definition: ProSHADE.cpp:544
ProSHADE_settings::setProgressiveSphereMapping
void setProgressiveSphereMapping(bool progSphMap)
Sets the requested sphere mapping value settings approach in the appropriate variable.
Definition: ProSHADE.cpp:930
ProSHADE_settings::changeMapResolution
bool changeMapResolution
Should maps be re-sampled to obtain the required resolution?
Definition: ProSHADE_settings.hpp:51
ProSHADE_settings::setIntegrationOrder
void setIntegrationOrder(proshade_unsign intOrd)
Sets the requested order for the Gauss-Legendre integration in the appropriate variable.
Definition: ProSHADE.cpp:889
ProSHADE_settings::setRotationFunctionComputation
void setRotationFunctionComputation(bool rotfVal)
Sets whether the rotation function distance descriptor should be computed.
Definition: ProSHADE.cpp:993
ProSHADE_settings::rotationUncertainty
proshade_double rotationUncertainty
Alternative to bandwidth - the angle in degrees to which the rotation function accuracy should be com...
Definition: ProSHADE_settings.hpp:59
ProSHADE_settings::setOverlaySaveFile
void setOverlaySaveFile(std::string filename)
Sets the filename to which the overlay structure is to be save into.
Definition: ProSHADE.cpp:1328
ProSHADE_settings::overlayStructureName
std::string overlayStructureName
The filename to which the rotated and translated moving structure is to be saved.
Definition: ProSHADE_settings.hpp:136
ProSHADE_settings::moveToCOM
bool moveToCOM
Logical value stating whether the structure should be moved to have its Centre Of Mass (COM) in the m...
Definition: ProSHADE_settings.hpp:96
ProSHADE_settings::peakNeighbours
proshade_unsign peakNeighbours
Number of points in any direction that have to be lower than the considered index in order to conside...
Definition: ProSHADE_settings.hpp:114
ProSHADE_settings::smoothingFactor
proshade_double smoothingFactor
This factor decides how small the group sizes should be - larger factor means more smaller groups.
Definition: ProSHADE_settings.hpp:118
ProSHADE_settings::halfMapKernel
proshade_single halfMapKernel
This value in Angstrom will be used as the kernel for the "fake half-map" computation.
Definition: ProSHADE_settings.hpp:82
ProSHADE_internal_misc::checkMemoryAllocation
void checkMemoryAllocation(chVar checkVar, std::string fileP, unsigned int lineP, std::string funcP, std::string infoP="This error may occurs when ProSHADE requests memory to be\n : allocated to it and this operation fails. This could\n : happen when not enough memory is available, either due to\n : other processes using a lot of memory, or when the machine\n : does not have sufficient memory available. Re-run to see\n : if this problem persists.")
Checks if memory was allocated properly.
Definition: ProSHADE_misc.hpp:67
ProSHADE_settings::setGroupingSmoothingFactor
void setGroupingSmoothingFactor(proshade_double smFact)
Sets the grouping smoothing factor into the proper variable.
Definition: ProSHADE.cpp:1102
ProSHADE_settings::setRequestedSymmetry
void setRequestedSymmetry(std::string val)
Sets the user requested symmetry type.
Definition: ProSHADE.cpp:1253
ProSHADE_settings::setExtraSpace
void setExtraSpace(proshade_single exSpace)
Sets the requested map extra space value in the appropriate variable.
Definition: ProSHADE.cpp:829
ProSHADE_settings::forceBounds
proshade_signed * forceBounds
These will be the boundaries to be forced upon the map.
Definition: ProSHADE_settings.hpp:93
ProSHADE_settings::recommendedSymmetryFold
proshade_unsign recommendedSymmetryFold
The fold of the recommended symmetry C or D type, 0 otherwise.
Definition: ProSHADE_settings.hpp:126
ProSHADE_settings::inputFiles
std::vector< std::string > inputFiles
This vector contains the filenames of all input structure files.
Definition: ProSHADE_settings.hpp:43
ProSHADE_settings::setMapResolutionChangeTriLinear
void setMapResolutionChangeTriLinear(bool mrChange)
Sets the requested map resolution change decision using tri-linear interpolation in the appropriate v...
Definition: ProSHADE.cpp:789
ProSHADE_settings::setMaskSaving
void setMaskSaving(bool savMsk)
Sets whether the mask should be saved.
Definition: ProSHADE.cpp:606
ProSHADE_settings::firstModelOnly
bool firstModelOnly
Shoud only the first PDB model be used, or should all models be used?
Definition: ProSHADE_settings.hpp:46
ProSHADE_settings::setBoundsThreshold
void setBoundsThreshold(proshade_signed boundsThres)
Sets the threshold for number of indices difference acceptable to make index sizes same in the approp...
Definition: ProSHADE.cpp:707
ProSHADE_settings::axisErrTolerance
proshade_double axisErrTolerance
Allowed error on vector axis in in dot product ( acos ( 1 - axErr ) is the allowed difference in radi...
Definition: ProSHADE_settings.hpp:122
ProSHADE_settings::useSameBounds
bool useSameBounds
Switch to say that the same boundaries as used for the first should be used for all input maps.
Definition: ProSHADE_settings.hpp:92
ProSHADE_settings::setMasking
void setMasking(bool mask)
Sets the requested map masking decision value in the appropriate variable.
Definition: ProSHADE.cpp:523
ProSHADE_settings::pdbBFactorNewVal
proshade_double pdbBFactorNewVal
Change all PDB B-factors to this value (for smooth maps).
Definition: ProSHADE_settings.hpp:55
ProSHADE_settings::setRecommendedFold
void setRecommendedFold(proshade_unsign val)
Sets the ProSHADE detected symmetry fold.
Definition: ProSHADE.cpp:1233
ProSHADE_settings::usePeakSearchInRotationFunctionSpace
bool usePeakSearchInRotationFunctionSpace
This variable switch decides whether symmetry detection will be done using peak search in rotation fu...
Definition: ProSHADE_settings.hpp:129
ProSHADE_settings::removeWaters
bool removeWaters
Should all waters be removed from input PDB files?
Definition: ProSHADE_settings.hpp:45
ProSHADE_settings::setResolution
void setResolution(proshade_single resolution)
Sets the requested resolution in the appropriate variable.
Definition: ProSHADE.cpp:382
ProSHADE_settings::printSettings
void printSettings(void)
This function prints the current values in the settings object.
Definition: ProSHADE.cpp:2466
ProSHADE_run::getNoStructures
proshade_unsign getNoStructures(void)
This function returns the number of structures used.
Definition: ProSHADE.cpp:2783
ProSHADE_settings::enLevMatrixPowerWeight
proshade_double enLevMatrixPowerWeight
If RRP matrices shell position is to be weighted by putting the position as an exponent,...
Definition: ProSHADE_settings.hpp:109
ProSHADE_settings::setNormalisation
void setNormalisation(bool normalise)
Sets the requested map normalisation value in the appropriate variable.
Definition: ProSHADE.cpp:422
ProSHADE_settings::setEnergyLevelsComputation
void setEnergyLevelsComputation(bool enLevDesc)
Sets whether the energy level distance descriptor should be computed.
Definition: ProSHADE.cpp:951
ProSHADE_settings::computeEnergyLevelsDesc
bool computeEnergyLevelsDesc
If true, the energy levels descriptor will be computed, otherwise all its computations will be omitte...
Definition: ProSHADE_settings.hpp:108