- a -

• alignDensities() : ProSHADE_internal::ProSHADE_compareOneAgainstAll
• appendStructure() : ProSHADE::ProSHADE_settings

- c -

• checkPeakExistence() : ProSHADE_internal::ProSHADE_comparePairwise
• compareAgainstDatabase() : ProSHADE_internal::ProSHADE_distances
• compareFragAgainstDatabase() : ProSHADE_internal::ProSHADE_distances

- d -

• dealWithHalfMaps() : ProSHADE_internal::ProSHADE_mapFeatures

- f -

• findCnSymmetry() : ProSHADE_internal::ProSHADE_comparePairwise
• findCnSymmetryClear() : ProSHADE_internal::ProSHADE_comparePairwise
• findDnSymmetry() : ProSHADE_internal::ProSHADE_comparePairwise
• findDnSymmetryClear() : ProSHADE_internal::ProSHADE_comparePairwise
• findIcosSymmetry() : ProSHADE_internal::ProSHADE_comparePairwise
• findMapIslands() : ProSHADE_internal::ProSHADE_data
• findOctaSymmetry() : ProSHADE_internal::ProSHADE_comparePairwise
• findTetrSymmetry() : ProSHADE_internal::ProSHADE_comparePairwise
• fragmentMap() : ProSHADE_internal::ProSHADE_data , ProSHADE_internal::ProSHADE_mapFeatures
• freeInvMap() : ProSHADE_internal::ProSHADE_comparePairwise

- g -

• generateIcosAxes() : ProSHADE_internal::ProSHADE_symmetry
• generateIcosElements() : ProSHADE_internal::ProSHADE_symmetry
• generateOctaAxes() : ProSHADE_internal::ProSHADE_symmetry
• generateOctaElements() : ProSHADE_internal::ProSHADE_symmetry
• generateTetrAxes() : ProSHADE_internal::ProSHADE_symmetry
• generateTetrElements() : ProSHADE_internal::ProSHADE_symmetry
• generateWignerMatrices() : ProSHADE_internal::ProSHADE_compareOneAgainstAll , ProSHADE_internal::ProSHADE_comparePairwise
• getClearCyclicSymmetries() : ProSHADE::ProSHADE
• getClearDihedralSymmetries() : ProSHADE::ProSHADE
• getCOMandDist() : ProSHADE_internal::ProSHADE_data
• getCommandLineParams() : ProSHADE::ProSHADE_settings
• getCrossCorrDists() : ProSHADE::ProSHADE
• getCSymmetries() : ProSHADE_internal::ProSHADE_symmetry
• getCyclicSymmetries() : ProSHADE::ProSHADE
• getCyclicSymmetriesPy() : ProSHADE::ProSHADE
• getDensityMapFromMAP() : ProSHADE_internal::ProSHADE_data
• getDensityMapFromMAPFeatures() : ProSHADE_internal::ProSHADE_data
• getDensityMapFromMAPRebox() : ProSHADE_internal::ProSHADE_data
• getDensityMapFromPDB() : ProSHADE_internal::ProSHADE_data
• getDihedralSymmetries() : ProSHADE::ProSHADE
• getDihedralSymmetriesPy() : ProSHADE::ProSHADE
• getDSymmetries() : ProSHADE_internal::ProSHADE_symmetry
• getEnergyLevelsDistance() : ProSHADE_internal::ProSHADE_compareOneAgainstAll
• getEnergyLevelsDistances() : ProSHADE_internal::ProSHADE_distances
• getEulerAngles() : ProSHADE_internal::ProSHADE_compareOneAgainstAll , ProSHADE_internal::ProSHADE_comparePairwise
• getFragEnergyLevelsDistances() : ProSHADE_internal::ProSHADE_distances
• getFragFullRotationDistances() : ProSHADE_internal::ProSHADE_distances
• getFragmentsList() : ProSHADE_internal::ProSHADE_mapFeatures
• getFragTraceSigmaDistances() : ProSHADE_internal::ProSHADE_distances
• getFullRotationDistances() : ProSHADE_internal::ProSHADE_distances
• getIcosahedralSymmetries() : ProSHADE::ProSHADE
• getIcosahedralSymmetriesPy() : ProSHADE::ProSHADE
• getMapFragments() : ProSHADE::ProSHADE
• getOctahedralSymmetries() : ProSHADE::ProSHADE
• getOctahedralSymmetriesPy() : ProSHADE::ProSHADE
• getPeakThreshold() : ProSHADE_internal::ProSHADE_comparePairwise
• getProSHADEVersion() : ProSHADE::ProSHADE
• getRecommendedSymmetry() : ProSHADE::ProSHADE
• getRecommendedSymmetryElementsPy() : ProSHADE::ProSHADE
• getRotCoeffDistance() : ProSHADE_internal::ProSHADE_compareOneAgainstAll , ProSHADE_internal::ProSHADE_comparePairwise
• getRotFnPeaks() : ProSHADE_internal::ProSHADE_symmetry
• getRotFunctionDists() : ProSHADE::ProSHADE
• getSO3InverseMap() : ProSHADE_internal::ProSHADE_compareOneAgainstAll , ProSHADE_internal::ProSHADE_comparePairwise
• getSO3Peaks() : ProSHADE_internal::ProSHADE_comparePairwise
• getSpecificSymmetryElements() : ProSHADE::ProSHADE
• getSpecificSymmetryElementsPy() : ProSHADE::ProSHADE
• getSphericalHarmonicsCoeffs() : ProSHADE_internal::ProSHADE_data
• getTetrahedralSymmetries() : ProSHADE::ProSHADE
• getTetrahedralSymmetriesPy() : ProSHADE::ProSHADE
• getTraceSigmaDistances() : ProSHADE_internal::ProSHADE_distances
• getTraceSigmaDists() : ProSHADE::ProSHADE
• getTranslationFunctionMap() : ProSHADE_internal::ProSHADE_comparePairwise
• getTrSigmaDistance() : ProSHADE_internal::ProSHADE_compareOneAgainstAll

- k -

• keepPhaseInMap() : ProSHADE_internal::ProSHADE_data

- m -

• mapPhaselessToSphere() : ProSHADE_internal::ProSHADE_data
• maskMap() : ProSHADE_internal::ProSHADE_data
• matchMap() : ProSHADE_internal::ProSHADE_data
• maxAvgPeakForSymmetry() : ProSHADE_internal::ProSHADE_comparePairwise

- n -

• normaliseMap() : ProSHADE_internal::ProSHADE_data

- p -

• precomputeRotInvDescriptor() : ProSHADE_internal::ProSHADE_data
• precomputeTrSigmaDescriptor() : ProSHADE_internal::ProSHADE_compareOneAgainstAll , ProSHADE_internal::ProSHADE_comparePairwise
• printInfo() : ProSHADE_internal::ProSHADE_mapFeatures
• printResultsClear() : ProSHADE_internal::ProSHADE_symmetry
• printResultsClearHTML() : ProSHADE_internal::ProSHADE_symmetry
• printResultsRequest() : ProSHADE_internal::ProSHADE_symmetry
• printResultsRequestHTML() : ProSHADE_internal::ProSHADE_symmetry
• printSettings() : ProSHADE::ProSHADE_settings
• ProSHADE() : ProSHADE::ProSHADE
• ProSHADE_compareOneAgainstAll() : ProSHADE_internal::ProSHADE_compareOneAgainstAll
• ProSHADE_comparePairwise() : ProSHADE_internal::ProSHADE_comparePairwise
• ProSHADE_data() : ProSHADE_internal::ProSHADE_data
• ProSHADE_distances() : ProSHADE_internal::ProSHADE_distances
• ProSHADE_mapFeatures() : ProSHADE_internal::ProSHADE_mapFeatures
• ProSHADE_settings() : ProSHADE::ProSHADE_settings
• ProSHADE_symmetry() : ProSHADE_internal::ProSHADE_symmetry

- r -

• removeIslands() : ProSHADE_internal::ProSHADE_data
• removePhaseFromMap() : ProSHADE_internal::ProSHADE_data
• removePhaseFromMapOverlay() : ProSHADE_internal::ProSHADE_data
• rotateStructure() : ProSHADE_internal::ProSHADE_comparePairwise

- s -

• saveDatabase() : ProSHADE_internal::ProSHADE_distances
• setEulerAngles() : ProSHADE_internal::ProSHADE_comparePairwise
• shiftMap() : ProSHADE_internal::ProSHADE_data

- t -

• translateMap() : ProSHADE_internal::ProSHADE_data

- ~ -

• ~ProSHADE() : ProSHADE::ProSHADE
• ~ProSHADE_compareOneAgainstAll() : ProSHADE_internal::ProSHADE_compareOneAgainstAll
• ~ProSHADE_comparePairwise() : ProSHADE_internal::ProSHADE_comparePairwise
• ~ProSHADE_data() : ProSHADE_internal::ProSHADE_data
• ~ProSHADE_distances() : ProSHADE_internal::ProSHADE_distances
• ~ProSHADE_mapFeatures() : ProSHADE_internal::ProSHADE_mapFeatures