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Rosetta Core
2014.16.56682
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Namespaces | |
| SplineInterp | |
Classes | |
| class | ElecDensAllAtomCenEnergy |
| class | ElecDensAllAtomCenEnergyCreator |
| class | ElecDensCenEnergy |
| class | ElecDensCenEnergyCreator |
| class | ElecDensEnergy |
| class | ElecDensEnergyCreator |
| class | ElectronDensity |
| class | ElectronDensityLoader |
| class | ElectronDensityLoaderCreator |
| creator for the ElectronDensityLoader class More... | |
| class | ElectronDensityOptions |
| class | ElectronDensityOptionsCreator |
| creator for the ElectronDensityOptions class More... | |
| class | FastDensEnergy |
| class | FastDensEnergyCreator |
| class | KromerMann |
| class | OneGaussianScattering |
| class | PattersonCorrEnergy |
| class | PattersonCorrEnergyCreator |
| struct | poseCoord |
Functions | |
| core::Real | SQ (core::Real N) |
| basic::Tracer | TR ("core.scoring.electron_density.ElectronDensity") |
| float | d2r (float d) |
| double | d2r (double d) |
| float | square (float x) |
| double | square (double x) |
| int | min_mod (int x, int y) |
| float | min_mod (float x, float y) |
| double | min_mod (double x, double y) |
| bool | is_missing_density (numeric::xyzVector< core::Real > const &X) |
| static void | swap4_aligned (void *v, long ndata) |
| ElectronDensity & | getDensityMap (std::string filename="", bool force_reload=false) |
| The EDM instance. More... | |
| ElectronDensity & | getDensityMap_legacy (std::string filename="", bool force_reload=false) |
| The EDM instance. More... | |
| float | pos_mod (float x, float y) |
| int | pos_mod (int x, int y) |
| double | pos_mod (double x, double y) |
| void | add_dens_scores_from_cmdline_to_scorefxn (core::scoring::ScoreFunction &scorefxn) |
| read density weights from the cmd line into the scorefunction More... | |
| bool | pose_has_nonzero_Bs (core::pose::Pose const &pose) |
| helper function quickly guesses if a pose has non-zero B factors More... | |
| bool | pose_has_nonzero_Bs (poseCoords const &pose) |
| core::Real | interp_spline (ObjexxFCL::FArray3D< double > &coeffs, numeric::xyzVector< core::Real > const &idxX) |
| spline interpolation with periodic boundaries More... | |
| numeric::xyzVector< core::Real > | interp_dspline (ObjexxFCL::FArray3D< double > &coeffs, numeric::xyzVector< core::Real > const &idxX) |
| spline interpolation with periodic boundaries More... | |
| void | spline_coeffs (ObjexxFCL::FArray3D< double > &data, ObjexxFCL::FArray3D< double > &coeffs) |
| precompute spline coefficients (float array => double coeffs) More... | |
| void | spline_coeffs (ObjexxFCL::FArray3D< float > &data, ObjexxFCL::FArray3D< double > &coeffs) |
| precompute spline coefficients (double array => double coeffs) More... | |
| void | conj_map_times (ObjexxFCL::FArray3D< std::complex< double > > &map_product, ObjexxFCL::FArray3D< std::complex< double > > const &mapA, ObjexxFCL::FArray3D< std::complex< double > > const &mapB) |
| ObjexxFCL::FArray3D< double > | convolute_maps (ObjexxFCL::FArray3D< double > const &mapA, ObjexxFCL::FArray3D< double > const &mapB) |
| core::Real | interp_spline (ObjexxFCL::FArray4D< double > &coeffs, core::Real slab, numeric::xyzVector< core::Real > const &idxX) |
| 4D interpolants More... | |
| void | interp_dspline (ObjexxFCL::FArray4D< double > &coeffs, numeric::xyzVector< core::Real > const &idxX, core::Real slab, numeric::xyzVector< core::Real > &gradX, core::Real &gradSlab) |
| spline interpolation with periodic boundaries More... | |
| void | spline_coeffs (ObjexxFCL::FArray4D< double > &data, ObjexxFCL::FArray4D< double > &coeffs) |
| void | spline_coeffs (ObjexxFCL::FArray4D< float > &data, ObjexxFCL::FArray4D< double > &coeffs) |
| template<class S > | |
| core::Real | interp_linear (ObjexxFCL::FArray3D< S > const &data, numeric::xyzVector< core::Real > const &idxX) |
| trilinear interpolation with periodic boundaries More... | |
| template<class S , class T > | |
| void | resample (ObjexxFCL::FArray3D< S > const &density, ObjexxFCL::FArray3D< T > &newDensity, numeric::xyzVector< int > newDims) |
| templated helper function to FFT resample a map More... | |
| OneGaussianScattering | get_A (std::string elt) |
| KromerMann | get_km (std::string elt) |
| bool | factorsLTE5 (int X) |
| bool | factorsLTE19 (int X) |
| int | findSampling5 (double MINSMP, int NMUL) |
| int | findSampling (double MINSMP, int NMUL) |
Variables | |
| static basic::Tracer | TR ("core.scoring.methods.ElecDensEnergy") |
| static basic::Tracer | TR ("core.scoring.electron_density.ElecDensEnergy") |
| static basic::Tracer | TR ("core.scoring.electron_density.ElecDensEnergy") |
| const int | CCP4HDSIZE = 1024 |
| const core::Real | MAX_FLT = 1e37 |
| static basic::Tracer | TR ("core.scoring.electron_density.FastDensEnergy") |
| static basic::Tracer | TR ("core.scoring.electron_density.PattersonCorrEnergy") |
| typedef utility::pointer::owning_ptr< ElectronDensity const > core::scoring::electron_density::ElectronDensityCOP |
| typedef utility::pointer::owning_ptr< ElectronDensityLoader const > core::scoring::electron_density::ElectronDensityLoaderCOP |
| typedef utility::pointer::owning_ptr< ElectronDensityLoader > core::scoring::electron_density::ElectronDensityLoaderOP |
| typedef utility::pointer::owning_ptr< ElectronDensity > core::scoring::electron_density::ElectronDensityOP |
| typedef utility::pointer::owning_ptr< ElectronDensityOptions const > core::scoring::electron_density::ElectronDensityOptionsCOP |
| typedef utility::pointer::owning_ptr< ElectronDensityOptions > core::scoring::electron_density::ElectronDensityOptionsOP |
| void core::scoring::electron_density::add_dens_scores_from_cmdline_to_scorefxn | ( | core::scoring::ScoreFunction & | scorefxn | ) |
read density weights from the cmd line into the scorefunction
update scorefxn with density scores from commandline
References core::scoring::elec_dens_fast, core::scoring::elec_dens_whole_structure_allatom, core::scoring::elec_dens_whole_structure_ca, core::scoring::elec_dens_window, option, core::scoring::patterson_cc, core::scoring::ScoreFunction::set_weight(), and user.
| void core::scoring::electron_density::conj_map_times | ( | ObjexxFCL::FArray3D< std::complex< double > > & | map_product, |
| ObjexxFCL::FArray3D< std::complex< double > > const & | mapA, | ||
| ObjexxFCL::FArray3D< std::complex< double > > const & | mapB | ||
| ) |
Referenced by convolute_maps(), and core::scoring::electron_density::ElectronDensity::match_fragment().
| ObjexxFCL::FArray3D< double > core::scoring::electron_density::convolute_maps | ( | ObjexxFCL::FArray3D< double > const & | mapA, |
| ObjexxFCL::FArray3D< double > const & | mapB | ||
| ) |
References conj_map_times(), numeric::fourier::fft3(), and numeric::fourier::ifft3().
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Referenced by findSampling().
Referenced by findSampling5().
References factorsLTE19().
Referenced by core::scoring::electron_density::ElectronDensity::resize().
| OneGaussianScattering core::scoring::electron_density::get_A | ( | std::string | elt | ) |
References basic::options::OptionKeys::edensity::centroid_density_mass, basic::options::OptionKeys::edensity::cryoem_scatterers, basic::options::option, and TR.
Referenced by core::scoring::electron_density::ElectronDensity::calcRhoC(), core::scoring::electron_density::ElectronDensity::compute_rho(), core::scoring::electron_density::ElectronDensity::dCCdB_fastRes(), core::scoring::electron_density::ElectronDensity::dCCdBs(), core::scoring::electron_density::ElectronDensity::dCCdx_fastRes(), core::scoring::electron_density::ElectronDensity::ElectronDensity(), core::scoring::electron_density::ElectronDensity::matchPose(), core::scoring::electron_density::ElectronDensity::matchPoseToPatterson(), core::scoring::electron_density::ElectronDensity::matchRes(), core::scoring::electron_density::ElectronDensity::matchResFast(), core::scoring::electron_density::ElectronDensity::rematchResToPatterson(), core::scoring::electron_density::ElectronDensity::rescale_fastscoring_temp_bins(), core::scoring::electron_density::ElectronDensity::rotAlign2DPose(), core::scoring::electron_density::ElectronDensity::setup_fastscoring_first_time(), core::scoring::electron_density::ElectronDensity::setup_patterson_first_time(), and core::scoring::electron_density::ElectronDensity::updateCachedDensity().
| KromerMann core::scoring::electron_density::get_km | ( | std::string | elt | ) |
References TR.
| ElectronDensity & core::scoring::electron_density::getDensityMap | ( | std::string | filename, |
| bool | force_reload | ||
| ) |
The EDM instance.
References getDensityMap_legacy().
Referenced by core::scoring::electron_density::ElectronDensity::dCCdx_aacen(), core::scoring::electron_density::ElectronDensity::dCCdx_cen(), core::scoring::electron_density::ElectronDensity::dCCdx_fastRes(), core::scoring::electron_density::ElectronDensity::dCCdx_pat(), core::scoring::electron_density::ElectronDensity::dCCdx_res(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::eval_atom_derivative(), core::scoring::electron_density::PattersonCorrEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensCenEnergy::eval_atom_derivative(), core::scoring::electron_density::FastDensEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensEnergy::eval_atom_derivative(), core::scoring::electron_density::PattersonCorrEnergy::PattersonCorrEnergy(), core::scoring::electron_density::FastDensEnergy::residue_pair_energy(), core::scoring::electron_density::ElecDensEnergy::residue_pair_energy(), core::scoring::electron_density::PattersonCorrEnergy::residue_pair_energy(), core::scoring::electron_density::PattersonCorrEnergy::setup_for_derivatives(), core::scoring::electron_density::ElecDensEnergy::setup_for_derivatives(), core::scoring::electron_density::FastDensEnergy::setup_for_derivatives(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::setup_for_derivatives(), core::scoring::electron_density::ElecDensCenEnergy::setup_for_derivatives(), core::scoring::electron_density::PattersonCorrEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensEnergy::setup_for_scoring(), core::scoring::electron_density::FastDensEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensCenEnergy::setup_for_scoring(), and core::scoring::electron_density::PattersonCorrEnergy::update_residue_for_packing().
| ElectronDensity & core::scoring::electron_density::getDensityMap_legacy | ( | std::string | filename, |
| bool | force_reload | ||
| ) |
The EDM instance.
References exit, basic::options::OptionKeys::edensity::grid_spacing, core::scoring::electron_density::ElectronDensity::isMapLoaded(), basic::options::OptionKeys::edensity::mapfile, mapfile, basic::options::OptionKeys::edensity::mapreso, mapreso, basic::options::option, core::scoring::electron_density::ElectronDensity::readMRCandResize(), TR, and user.
Referenced by getDensityMap().
| numeric::xyzVector< core::Real > core::scoring::electron_density::interp_dspline | ( | ObjexxFCL::FArray3D< double > & | coeffs, |
| numeric::xyzVector< core::Real > const & | idxX | ||
| ) |
spline interpolation with periodic boundaries
References core::scoring::electron_density::SplineInterp::grad3().
Referenced by core::scoring::electron_density::ElectronDensity::dCCdB_fastRes(), and core::scoring::electron_density::ElectronDensity::dCCdx_fastRes().
| void core::scoring::electron_density::interp_dspline | ( | ObjexxFCL::FArray4D< double > & | coeffs, |
| numeric::xyzVector< core::Real > const & | idxX, | ||
| core::Real | slab, | ||
| numeric::xyzVector< core::Real > & | gradX, | ||
| core::Real & | gradSlab | ||
| ) |
spline interpolation with periodic boundaries
References core::scoring::electron_density::SplineInterp::grad4().
| core::Real core::scoring::electron_density::interp_linear | ( | ObjexxFCL::FArray3D< S > const & | data, |
| numeric::xyzVector< core::Real > const & | idxX | ||
| ) |
trilinear interpolation with periodic boundaries
References grid.
Referenced by core::scoring::PoissonBoltzmannPotential::get_potential(), core::scoring::electron_density::ElectronDensity::matchPoseToPatterson(), and core::scoring::electron_density::ElectronDensity::rotAlign2DPose().
| core::Real core::scoring::electron_density::interp_spline | ( | ObjexxFCL::FArray3D< double > & | coeffs, |
| numeric::xyzVector< core::Real > const & | idxX | ||
| ) |
spline interpolation with periodic boundaries
References core::scoring::electron_density::SplineInterp::interp3().
Referenced by core::scoring::electron_density::ElectronDensity::dens_grad(), core::scoring::electron_density::ElectronDensity::matchPoseToPatterson(), core::scoring::electron_density::ElectronDensity::matchResFast(), and core::scoring::electron_density::ElectronDensity::rescale_fastscoring_temp_bins().
| core::Real core::scoring::electron_density::interp_spline | ( | ObjexxFCL::FArray4D< double > & | coeffs, |
| core::Real | slab, | ||
| numeric::xyzVector< core::Real > const & | idxX | ||
| ) |
4D interpolants
4d interpolants
spline interpolation with periodic boundaries
References core::scoring::electron_density::SplineInterp::interp4().
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References numeric::xyzVector< class >::length().
Referenced by core::scoring::electron_density::ElectronDensity::compute_rho(), core::scoring::electron_density::ElectronDensity::ElectronDensity(), core::scoring::electron_density::ElectronDensity::matchCentroidPose(), core::scoring::electron_density::ElectronDensity::matchPose(), core::scoring::electron_density::ElectronDensity::matchPoseToPatterson(), core::scoring::electron_density::ElectronDensity::matchRes(), core::scoring::electron_density::ElectronDensity::rematchResToPatterson(), core::scoring::electron_density::ElectronDensity::rotAlign2DPose(), core::scoring::electron_density::ElectronDensity::setup_patterson_first_time(), and core::scoring::electron_density::ElectronDensity::updateCachedDensity().
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Referenced by core::scoring::electron_density::ElectronDensity::calcRhoC(), core::scoring::electron_density::ElectronDensity::compute_rho(), core::scoring::electron_density::ElectronDensity::dCCdB_fastRes(), core::scoring::electron_density::ElectronDensity::dCCdBs(), core::scoring::electron_density::ElectronDensity::dCCdx_fastRes(), core::scoring::electron_density::ElectronDensity::ElectronDensity(), core::scoring::electron_density::ElectronDensity::expandToUnitCell(), core::scoring::electron_density::ElectronDensity::getIntensitiesMasked(), core::scoring::electron_density::ElectronDensity::getModelMapError(), core::scoring::electron_density::ElectronDensity::maskDensityMap(), core::scoring::electron_density::ElectronDensity::matchCentroidPose(), core::scoring::electron_density::ElectronDensity::matchPose(), core::scoring::electron_density::ElectronDensity::matchPoseToPatterson(), core::scoring::electron_density::ElectronDensity::matchResFast(), core::scoring::electron_density::ElectronDensity::rescale_fastscoring_temp_bins(), core::scoring::electron_density::ElectronDensity::rotAlign2DPose(), and core::scoring::electron_density::ElectronDensity::setup_patterson_first_time().
| bool core::scoring::electron_density::pose_has_nonzero_Bs | ( | core::pose::Pose const & | pose | ) |
helper function quickly guesses if a pose has non-zero B factors
References core::chemical::aa_vrt, core::pose::Pose::pdb_info(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().
Referenced by core::scoring::electron_density::ElectronDensity::calcRhoC(), and core::scoring::electron_density::FastDensEnergy::setup_for_scoring().
| bool core::scoring::electron_density::pose_has_nonzero_Bs | ( | poseCoords const & | pose | ) |
| void core::scoring::electron_density::resample | ( | ObjexxFCL::FArray3D< S > const & | density, |
| ObjexxFCL::FArray3D< T > & | newDensity, | ||
| numeric::xyzVector< int > | newDims | ||
| ) |
templated helper function to FFT resample a map
References numeric::fourier::fft3(), numeric::fourier::ifft3(), and j.
Referenced by core::scoring::electron_density::ElectronDensity::resize().
| void core::scoring::electron_density::spline_coeffs | ( | ObjexxFCL::FArray3D< double > & | data, |
| ObjexxFCL::FArray3D< double > & | coeffs | ||
| ) |
precompute spline coefficients (float array => double coeffs)
References core::scoring::electron_density::SplineInterp::compute_coefficients3().
Referenced by core::scoring::electron_density::ElectronDensity::computeGradients(), core::scoring::electron_density::ElectronDensity::matchPoseToPatterson(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::precompute_unweighted_score(), core::scoring::electron_density::ElectronDensity::setup_fastscoring_first_time(), and spline_coeffs().
| void core::scoring::electron_density::spline_coeffs | ( | ObjexxFCL::FArray3D< float > & | data, |
| ObjexxFCL::FArray3D< double > & | coeffs | ||
| ) |
precompute spline coefficients (double array => double coeffs)
References spline_coeffs().
| void core::scoring::electron_density::spline_coeffs | ( | ObjexxFCL::FArray4D< float > & | data, |
| ObjexxFCL::FArray4D< double > & | coeffs | ||
| ) |
References spline_coeffs().
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Referenced by core::scoring::electron_density::ElectronDensity::computeCrystParams(), core::scoring::electron_density::ElectronDensity::matchCentroidPose(), core::scoring::electron_density::ElectronDensity::matchPoseToPatterson(), core::scoring::electron_density::ElectronDensity::rematchResToPatterson(), core::scoring::electron_density::ElectronDensity::rotAlign2DPose(), and core::scoring::electron_density::ElectronDensity::updateCachedDensity().
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| basic::Tracer core::scoring::electron_density::TR | ( | "core.scoring.electron_density.ElectronDensity" | ) |
| const int core::scoring::electron_density::CCP4HDSIZE = 1024 |
| const core::Real core::scoring::electron_density::MAX_FLT = 1e37 |
Referenced by core::scoring::electron_density::ElectronDensity::matchRes().
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Referenced by core::scoring::electron_density::ElectronDensity::calcRhoC(), core::scoring::electron_density::ElectronDensity::compute_rho(), core::scoring::electron_density::ElectronDensity::compute_symm_rotations(), core::scoring::electron_density::ElectronDensity::computeCrystParams(), core::scoring::electron_density::ElectronDensity::computeGradients(), core::scoring::electron_density::ElectronDensity::dCCdB_fastRes(), core::scoring::electron_density::ElectronDensity::dCCdx_aacen(), core::scoring::electron_density::ElectronDensity::dCCdx_cen(), core::scoring::electron_density::ElectronDensity::dCCdx_fastRes(), core::scoring::electron_density::ElectronDensity::dCCdx_pat(), core::scoring::electron_density::ElectronDensity::dCCdx_res(), core::scoring::electron_density::ElectronDensity::ElectronDensity(), get_A(), get_km(), getDensityMap_legacy(), core::scoring::electron_density::ElectronDensity::getIntensities(), core::scoring::electron_density::ElectronDensity::getIntensitiesMasked(), core::scoring::electron_density::ElectronDensity::getMapMapError(), core::scoring::electron_density::ElectronDensity::getModelMapError(), core::scoring::electron_density::ElectronDensity::getResolutionBins(), core::scoring::electron_density::ElectronDensity::initializeSymmOps(), core::scoring::electron_density::ElectronDensity::matchCentroidPose(), core::scoring::electron_density::ElectronDensity::matchPose(), core::scoring::electron_density::ElectronDensity::matchPoseToPatterson(), core::scoring::electron_density::ElectronDensity::matchRes(), core::scoring::electron_density::ElectronDensity::matchResFast(), core::scoring::electron_density::ElectronDensity::readMRCandResize(), core::scoring::electron_density::ElectronDensity::rescale_fastscoring_temp_bins(), core::scoring::electron_density::PattersonCorrEnergy::residue_pair_energy(), core::scoring::electron_density::ElectronDensity::resize(), core::scoring::electron_density::ElectronDensity::rotAlign2DPose(), core::scoring::electron_density::ElectronDensity::scaleIntensities(), core::scoring::electron_density::ElectronDensity::setup_fastscoring_first_time(), core::scoring::electron_density::ElecDensEnergy::setup_for_derivatives(), core::scoring::electron_density::PattersonCorrEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensEnergy::setup_for_scoring(), core::scoring::electron_density::FastDensEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensCenEnergy::setup_for_scoring(), core::scoring::electron_density::ElectronDensity::setup_patterson_first_time(), core::scoring::electron_density::ElectronDensity::showCachedScores(), and core::scoring::electron_density::ElectronDensity::writeMRC().
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1.8.7