| ATOM_MASK | core::scoring::electron_density::ElectronDensity | private |
| ATOM_MASK_PADDING | core::scoring::electron_density::ElectronDensity | private |
| bucket_counts | core::scoring::electron_density::ElectronDensity | private |
| bucket_id | core::scoring::electron_density::ElectronDensity | private |
| c2f | core::scoring::electron_density::ElectronDensity | private |
| CA_MASK | core::scoring::electron_density::ElectronDensity | private |
| calcRhoC(poseCoords const &pose) | core::scoring::electron_density::ElectronDensity | |
| cart2frac(numeric::xyzVector< core::Real > const &cartX, numeric::xyzVector< core::Real > &fracX) const | core::scoring::electron_density::ElectronDensity | inline |
| cart2idx(numeric::xyzVector< core::Real > const &cartX, numeric::xyzVector< core::Real > &idxX) const | core::scoring::electron_density::ElectronDensity | inline |
| CC_aacen | core::scoring::electron_density::ElectronDensity | private |
| CC_cen | core::scoring::electron_density::ElectronDensity | private |
| CC_pat | core::scoring::electron_density::ElectronDensity | private |
| CCs | core::scoring::electron_density::ElectronDensity | private |
| cellAngles | core::scoring::electron_density::ElectronDensity | private |
| cellDimensions | core::scoring::electron_density::ElectronDensity | private |
| centerOfMass | core::scoring::electron_density::ElectronDensity | private |
| clear_dCCdx_res_cache(core::pose::Pose const &pose) | core::scoring::electron_density::ElectronDensity | |
| clearMask() | core::scoring::electron_density::ElectronDensity | inline |
| coeff_grad_x | core::scoring::electron_density::ElectronDensity | mutableprivate |
| coeff_grad_y | core::scoring::electron_density::ElectronDensity | mutableprivate |
| coeff_grad_z | core::scoring::electron_density::ElectronDensity | mutableprivate |
| compute_rho(core::pose::Pose const &pose, utility::vector1< core::id::AtomID > const &atom_ids, ObjexxFCL::FArray3D< double > &rho_calc, ObjexxFCL::FArray3D< double > &inv_rho_mask) | core::scoring::electron_density::ElectronDensity | |
| compute_symm_rotations(core::pose::Pose const &pose, core::conformation::symmetry::SymmetryInfoCOP symmInfo=NULL) | core::scoring::electron_density::ElectronDensity | |
| computeCrystParams() | core::scoring::electron_density::ElectronDensity | private |
| computeGradients() | core::scoring::electron_density::ElectronDensity | private |
| computeStats() | core::scoring::electron_density::ElectronDensity | private |
| cosRcellAngles | core::scoring::electron_density::ElectronDensity | private |
| d_max | core::scoring::electron_density::ElectronDensity | private |
| d_min | core::scoring::electron_density::ElectronDensity | private |
| data() const | core::scoring::electron_density::ElectronDensity | inline |
| dCCdB_fastRes(int atmid, int resid, core::conformation::Residue const &rsd, core::pose::Pose const &pose) | core::scoring::electron_density::ElectronDensity | |
| dCCdBs(core::pose::Pose const &pose, utility::vector1< core::Real > &dE_dvars) | core::scoring::electron_density::ElectronDensity | |
| dCCdx_aacen(int atmid, int resid, numeric::xyzVector< core::Real > const &X, core::pose::Pose const &pose, numeric::xyzVector< core::Real > &gradX) | core::scoring::electron_density::ElectronDensity | |
| dCCdx_cen(int resid, numeric::xyzVector< core::Real > const &X, core::pose::Pose const &pose, numeric::xyzVector< core::Real > &gradX) | core::scoring::electron_density::ElectronDensity | |
| dCCdx_fastRes(int atmid, int resid, numeric::xyzVector< core::Real > const &X, core::conformation::Residue const &rsd, core::pose::Pose const &pose, numeric::xyzVector< core::Real > &gradX) | core::scoring::electron_density::ElectronDensity | |
| dCCdx_pat(int atmid, int resid, numeric::xyzVector< core::Real > const &X, core::pose::Pose const &pose, numeric::xyzVector< core::Real > &gradX) | core::scoring::electron_density::ElectronDensity | |
| dCCdx_res(int atmid, int resid, numeric::xyzVector< core::Real > const &X, core::conformation::Residue const &rsd, core::pose::Pose const &pose, numeric::xyzVector< core::Real > &gradX) | core::scoring::electron_density::ElectronDensity | |
| dCCdxs_aacen | core::scoring::electron_density::ElectronDensity | private |
| dCCdxs_cen | core::scoring::electron_density::ElectronDensity | private |
| dCCdxs_pat | core::scoring::electron_density::ElectronDensity | private |
| dCCdxs_res | core::scoring::electron_density::ElectronDensity | private |
| delt_cart(numeric::xyzVector< core::Real > const &cartX1, numeric::xyzVector< core::Real > const &cartX2) | core::scoring::electron_density::ElectronDensity | |
| dens_grad(numeric::xyzVector< core::Real > const &idxX) const | core::scoring::electron_density::ElectronDensity | |
| dens_max | core::scoring::electron_density::ElectronDensity | private |
| dens_mean | core::scoring::electron_density::ElectronDensity | private |
| dens_min | core::scoring::electron_density::ElectronDensity | private |
| dens_stdev | core::scoring::electron_density::ElectronDensity | private |
| density | core::scoring::electron_density::ElectronDensity | private |
| density_change_trigger() | core::scoring::electron_density::ElectronDensity | private |
| DensScoreInMinimizer | core::scoring::electron_density::ElectronDensity | private |
| effectiveB | core::scoring::electron_density::ElectronDensity | private |
| efforigin | core::scoring::electron_density::ElectronDensity | private |
| ElectronDensity() | core::scoring::electron_density::ElectronDensity | |
| ElectronDensity(utility::vector1< core::pose::PoseOP > poses, core::Real reso, core::Real apix) | core::scoring::electron_density::ElectronDensity | |
| ElectronDensity(ObjexxFCL::FArray3D< T > const &map, core::Real apix=1.0, numeric::xyzVector< core::Real > new_origin=numeric::xyzVector< core::Real >(0, 0, 0), bool fftshift=false) | core::scoring::electron_density::ElectronDensity | inline |
| ExactDerivatives | core::scoring::electron_density::ElectronDensity | private |
| expandToUnitCell() | core::scoring::electron_density::ElectronDensity | private |
| F2 | core::scoring::electron_density::ElectronDensity | private |
| f2c | core::scoring::electron_density::ElectronDensity | private |
| F_s2 | core::scoring::electron_density::ElectronDensity | private |
| fastdens_score | core::scoring::electron_density::ElectronDensity | private |
| fastgrid | core::scoring::electron_density::ElectronDensity | private |
| fastorigin | core::scoring::electron_density::ElectronDensity | private |
| Fdensity | core::scoring::electron_density::ElectronDensity | private |
| Fdrhoc_dx | core::scoring::electron_density::ElectronDensity | private |
| Fdrhoc_dy | core::scoring::electron_density::ElectronDensity | private |
| Fdrhoc_dz | core::scoring::electron_density::ElectronDensity | private |
| force_apix_ | core::scoring::electron_density::ElectronDensity | private |
| frac2cart(numeric::xyzVector< core::Real > const &fracX, numeric::xyzVector< core::Real > &cartX) const | core::scoring::electron_density::ElectronDensity | inline |
| Frho_calc | core::scoring::electron_density::ElectronDensity | private |
| Frho_solv | core::scoring::electron_density::ElectronDensity | private |
| get_cart_unitCell(numeric::xyzVector< core::Real > const &cartX) | core::scoring::electron_density::ElectronDensity | |
| get_nearest_UC(numeric::xyzVector< core::Real > const &cartX_in, numeric::xyzVector< core::Real > const &cartX_ref) | core::scoring::electron_density::ElectronDensity | |
| get_R(int subunit, numeric::xyzMatrix< core::Real > &R) | core::scoring::electron_density::ElectronDensity | inline |
| get_symmMap(int vrtid, utility::vector1< int > &X_map, numeric::xyzMatrix< core::Real > &R) | core::scoring::electron_density::ElectronDensity | inline |
| getAtomMask() const | core::scoring::electron_density::ElectronDensity | inline |
| getCachedScore(core::Size resid) | core::scoring::electron_density::ElectronDensity | inline |
| getCoM() const | core::scoring::electron_density::ElectronDensity | inline |
| getEffOrigin() const | core::scoring::electron_density::ElectronDensity | inline |
| getFdrhoc(OneGaussianScattering S) | core::scoring::electron_density::ElectronDensity | private |
| getFSC(poseCoords const &pose, core::Size nbuckets, core::Real maxreso, core::Real minreso, utility::vector1< core::Real > &FSC, bool masked=false, bool S2_bin=false, core::Real mask_radius=0) | core::scoring::electron_density::ElectronDensity | inline |
| getIntensities(core::Size nbuckets, core::Real maxreso, core::Real minreso, bool S2_bin=false) | core::scoring::electron_density::ElectronDensity | |
| getIntensities(poseCoords const &pose, core::Size nbuckets, core::Real maxreso, core::Real minreso, utility::vector1< core::Real > &Imodel, bool S2_bin=false) | core::scoring::electron_density::ElectronDensity | |
| getIntensitiesMasked(poseCoords const &pose, core::Size nbuckets, core::Real maxreso, core::Real minreso, bool S2_bin=false) | core::scoring::electron_density::ElectronDensity | |
| getMapMapError(ObjexxFCL::FArray3D< float > const &map2, core::Size nbuckets, core::Real maxreso, core::Real minreso, utility::vector1< core::Real > &FSC, utility::vector1< core::Real > &phaseError, utility::vector1< core::Real > &complexPlaneError, bool S2_bin=false) | core::scoring::electron_density::ElectronDensity | |
| getMax() const | core::scoring::electron_density::ElectronDensity | inline |
| getMean() const | core::scoring::electron_density::ElectronDensity | inline |
| getMin() const | core::scoring::electron_density::ElectronDensity | inline |
| getModelMapError(poseCoords const &pose, core::Size nbuckets, core::Real maxreso, core::Real minreso, utility::vector1< core::Real > const &mapmapPhaseError, utility::vector1< core::Real > const &mapmapComplexPlaneError, utility::vector1< core::Real > &FSC, utility::vector1< core::Real > &phaseError, core::Real &phaseErrorSum, core::Real &complexPlaneErrorK, core::Real &complexPlaneErrorProb, bool masked=false, bool S2_bin=false, core::Real mask_radius=0) | core::scoring::electron_density::ElectronDensity | |
| getNumDerivH() const | core::scoring::electron_density::ElectronDensity | inline |
| getOrigin() const | core::scoring::electron_density::ElectronDensity | inline |
| getResolution() const | core::scoring::electron_density::ElectronDensity | inline |
| getResolutionBins(core::Size nbuckets, core::Real maxreso, core::Real minreso, utility::vector1< core::Real > &, utility::vector1< core::Size > &, bool S2_bin=false) | core::scoring::electron_density::ElectronDensity | |
| getRSCC(poseCoords const &pose) | core::scoring::electron_density::ElectronDensity | |
| getRSCC(ObjexxFCL::FArray3D< float > const &map2) | core::scoring::electron_density::ElectronDensity | |
| getScoreWindowContext() const | core::scoring::electron_density::ElectronDensity | inline |
| getSCscaling() | core::scoring::electron_density::ElectronDensity | inline |
| getStdev() const | core::scoring::electron_density::ElectronDensity | inline |
| getsymmOps() const | core::scoring::electron_density::ElectronDensity | inline |
| getTransform() | core::scoring::electron_density::ElectronDensity | inline |
| getUseDensityInMinimizer() const | core::scoring::electron_density::ElectronDensity | inline |
| getUseExactDerivatives() const | core::scoring::electron_density::ElectronDensity | inline |
| getWindow() | core::scoring::electron_density::ElectronDensity | inline |
| grid | core::scoring::electron_density::ElectronDensity | private |
| hires_cut | core::scoring::electron_density::ElectronDensity | private |
| idx2cart(numeric::xyzVector< Q > const &idxX, numeric::xyzVector< core::Real > &cartX) const | core::scoring::electron_density::ElectronDensity | inline |
| idxoffset2cart(numeric::xyzVector< Q > const &idxX, numeric::xyzVector< core::Real > &cartX) const | core::scoring::electron_density::ElectronDensity | inline |
| init() | core::scoring::electron_density::ElectronDensity | |
| initializeSymmOps(utility::vector1< std::string > const &symList) | core::scoring::electron_density::ElectronDensity | private |
| inv_rho_mask | core::scoring::electron_density::ElectronDensity | private |
| isLoaded | core::scoring::electron_density::ElectronDensity | private |
| isMapLoaded() const | core::scoring::electron_density::ElectronDensity | inline |
| kmax_ | core::scoring::electron_density::ElectronDensity | private |
| kmin_ | core::scoring::electron_density::ElectronDensity | private |
| kstep_ | core::scoring::electron_density::ElectronDensity | private |
| legacy_ | core::scoring::electron_density::ElectronDensity | private |
| lowres_cut | core::scoring::electron_density::ElectronDensity | private |
| maskDensityMap(poseCoords const &pose, core::Real radius) | core::scoring::electron_density::ElectronDensity | |
| maskResidues(int scoring_mask) | core::scoring::electron_density::ElectronDensity | inline |
| maskResidues(utility::vector1< int > const &scoring_mask) | core::scoring::electron_density::ElectronDensity | inline |
| match_fragment(ObjexxFCL::FArray3D< double > const &rho_calc, ObjexxFCL::FArray3D< double > const &mask, ObjexxFCL::FArray3D< double > const &rho_obs, core::Real radius=6.0) | core::scoring::electron_density::ElectronDensity | |
| matchCentroidPose(core::pose::Pose const &pose, core::conformation::symmetry::SymmetryInfoCOP symmInfo=NULL, bool cacheCCs=false) | core::scoring::electron_density::ElectronDensity | |
| matchPose(core::pose::Pose const &pose, core::conformation::symmetry::SymmetryInfoCOP symmInfo=NULL, bool cacheCCs=false) | core::scoring::electron_density::ElectronDensity | |
| matchPoseToPatterson(core::pose::Pose const &pose, bool cacheCCs=false) | core::scoring::electron_density::ElectronDensity | |
| matchRes(int resid, core::conformation::Residue const &rsd, core::pose::Pose const &pose, core::conformation::symmetry::SymmetryInfoCOP symmInfo=NULL, bool cacheCCs=false) | core::scoring::electron_density::ElectronDensity | |
| matchResFast(int resid, core::conformation::Residue const &rsd, core::pose::Pose const &pose, core::conformation::symmetry::SymmetryInfoCOP symmInfo=NULL, bool ignoreBs=false) | core::scoring::electron_density::ElectronDensity | |
| maxNominalRes() | core::scoring::electron_density::ElectronDensity | |
| minimumB | core::scoring::electron_density::ElectronDensity | private |
| MINMULT | core::scoring::electron_density::ElectronDensity | private |
| nkbins_ | core::scoring::electron_density::ElectronDensity | private |
| NUM_DERIV_H | core::scoring::electron_density::ElectronDensity | private |
| NUM_DERIV_H_CEN | core::scoring::electron_density::ElectronDensity | private |
| origin | core::scoring::electron_density::ElectronDensity | private |
| p_CoM | core::scoring::electron_density::ElectronDensity | private |
| p_extent | core::scoring::electron_density::ElectronDensity | private |
| p_grid | core::scoring::electron_density::ElectronDensity | private |
| p_o | core::scoring::electron_density::ElectronDensity | private |
| p_origin | core::scoring::electron_density::ElectronDensity | private |
| p_sumC | core::scoring::electron_density::ElectronDensity | private |
| p_sumC2 | core::scoring::electron_density::ElectronDensity | private |
| p_sumCO | core::scoring::electron_density::ElectronDensity | private |
| p_sumO | core::scoring::electron_density::ElectronDensity | private |
| p_sumO2 | core::scoring::electron_density::ElectronDensity | private |
| p_vol | core::scoring::electron_density::ElectronDensity | private |
| PattersonB | core::scoring::electron_density::ElectronDensity | private |
| PattersonEpsilon | core::scoring::electron_density::ElectronDensity | private |
| PattersonMaxR | core::scoring::electron_density::ElectronDensity | private |
| PattersonMinR | core::scoring::electron_density::ElectronDensity | private |
| Pcalc | core::scoring::electron_density::ElectronDensity | private |
| po_bar | core::scoring::electron_density::ElectronDensity | private |
| RcellDimensions | core::scoring::electron_density::ElectronDensity | private |
| readMRCandResize(std::string mapfile, core::Real reso=5.0, core::Real gridSpacing=0.0) | core::scoring::electron_density::ElectronDensity | |
| readMRCandResize(std::istream &mapin, std::string mapfile, core::Real reso=5.0, core::Real gridSpacing=0.0) | core::scoring::electron_density::ElectronDensity | |
| remap_symm_ | core::scoring::electron_density::ElectronDensity | private |
| rematchResToPatterson(core::conformation::Residue const &rsd) const | core::scoring::electron_density::ElectronDensity | |
| rescale_fastscoring_temp_bins(core::pose::Pose const &pose, bool init=false) | core::scoring::electron_density::ElectronDensity | |
| resize(core::Real approxGridSpacing) | core::scoring::electron_density::ElectronDensity | |
| reso | core::scoring::electron_density::ElectronDensity | private |
| rho_calc | core::scoring::electron_density::ElectronDensity | private |
| rho_calc_as | core::scoring::electron_density::ElectronDensity | private |
| rho_calc_atms | core::scoring::electron_density::ElectronDensity | private |
| rho_calc_sum | core::scoring::electron_density::ElectronDensity | private |
| rho_solv | core::scoring::electron_density::ElectronDensity | private |
| rotAlign2DPose(core::pose::Pose const &pose, std::string axis) | core::scoring::electron_density::ElectronDensity | |
| RV | core::scoring::electron_density::ElectronDensity | private |
| S2(int h, int k, int l) | core::scoring::electron_density::ElectronDensity | inlineprivate |
| SC_scaling_ | core::scoring::electron_density::ElectronDensity | private |
| scaleIntensities(utility::vector1< core::Real > I_tgt, core::Real maxreso, core::Real minreso, bool S2_bin=false) | core::scoring::electron_density::ElectronDensity | |
| score_window_context_ | core::scoring::electron_density::ElectronDensity | private |
| scoring_mask_ | core::scoring::electron_density::ElectronDensity | private |
| set_data(ObjexxFCL::FArray3D< double > const &density_in) | core::scoring::electron_density::ElectronDensity | inline |
| set_nres(int nres) | core::scoring::electron_density::ElectronDensity | inline |
| setScoreWindowContext(bool newVal) | core::scoring::electron_density::ElectronDensity | inline |
| setSCscaling(core::Real SC_scalingin) | core::scoring::electron_density::ElectronDensity | inline |
| setup_fastscoring_first_time(core::pose::Pose const &pose) | core::scoring::electron_density::ElectronDensity | private |
| setup_patterson_first_time(core::pose::Pose const &pose) | core::scoring::electron_density::ElectronDensity | private |
| setUseDensityInMinimizer(bool newVal) | core::scoring::electron_density::ElectronDensity | inline |
| setUseExactDerivatives(bool newVal) | core::scoring::electron_density::ElectronDensity | inline |
| setWindow(core::Size window_in) | core::scoring::electron_density::ElectronDensity | inline |
| showCachedScores(utility::vector1< int > const &reses) | core::scoring::electron_density::ElectronDensity | |
| smooth_intensities(utility::vector1< core::Real > &) const | core::scoring::electron_density::ElectronDensity | private |
| suggestRadius() | core::scoring::electron_density::ElectronDensity | private |
| symm_ptrs | core::scoring::electron_density::ElectronDensity | private |
| symmap | core::scoring::electron_density::ElectronDensity | private |
| symmOps | core::scoring::electron_density::ElectronDensity | private |
| symmRotOps | core::scoring::electron_density::ElectronDensity | private |
| updateCachedDensity(core::conformation::Residue const &rsd) | core::scoring::electron_density::ElectronDensity | |
| use_altorigin | core::scoring::electron_density::ElectronDensity | private |
| V | core::scoring::electron_density::ElectronDensity | private |
| voxel_volume() | core::scoring::electron_density::ElectronDensity | inlineprivate |
| WINDOW_ | core::scoring::electron_density::ElectronDensity | private |
| writeMAT(std::string mapfilestem) | core::scoring::electron_density::ElectronDensity | |
| writeMRC(std::string mapfilestem, bool writeRhoCalc=false, bool writeRhoMask=false) | core::scoring::electron_density::ElectronDensity | |
| ~ElectronDensity() | core::scoring::electron_density::ElectronDensity | virtual |
1.8.7