core::scoring::electron_density::ElectronDensity Member List

This is the complete list of members for core::scoring::electron_density::ElectronDensity, including all inherited members.

ATOM_MASK	core::scoring::electron_density::ElectronDensity	private
ATOM_MASK_PADDING	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::Real highres_limit, ObjexxFCL::FArray3D< core::Real > &rhoC, ObjexxFCL::FArray3D< core::Real > &mask, core::Real forceB=-1.0, core::Real B_upper_limit=600, core::Real force_mask=-1.0)	core::scoring::electron_density::ElectronDensity
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
CCs	core::scoring::electron_density::ElectronDensity	private
cellAngles	core::scoring::electron_density::ElectronDensity	private
cellDimensions	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
coeffs_density_	core::scoring::electron_density::ElectronDensity	private
compute_symm_rotations(core::pose::Pose const &pose, core::conformation::symmetry::SymmetryInfoCOP symmInfo=nullptr)	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
cosRcellAngles	core::scoring::electron_density::ElectronDensity	private
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, ObjexxFCL::FArray3D< core::Real > &maskC)	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_PointFast(numeric::xyzVector< core::Real > X, numeric::xyzVector< core::Real > &dCCdx)	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
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
effectiveB	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
expandToUnitCell()	core::scoring::electron_density::ElectronDensity	private
f2c	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
force_apix_on_map_load_	core::scoring::electron_density::ElectronDensity	private
get(int i, int j, int k)	core::scoring::electron_density::ElectronDensity	inline
get(numeric::xyzVector< core::Real > X)	core::scoring::electron_density::ElectronDensity
get_c2f() const	core::scoring::electron_density::ElectronDensity	inline
get_cellDimensions() const	core::scoring::electron_density::ElectronDensity	inline
get_data() const	core::scoring::electron_density::ElectronDensity	inline
get_f2c() const	core::scoring::electron_density::ElectronDensity	inline
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
get_voxel_spacing()	core::scoring::electron_density::ElectronDensity	inline
getAtomMask() const	core::scoring::electron_density::ElectronDensity	inline
getCachedScore(core::Size resid)	core::scoring::electron_density::ElectronDensity	inline
getEffectiveBfactor()	core::scoring::electron_density::ElectronDensity	inline
getFdrhoc(OneGaussianScattering S)	core::scoring::electron_density::ElectronDensity	private
getFSC(ObjexxFCL::FArray3D< std::complex< core::Real > > const &Frho1, ObjexxFCL::FArray3D< std::complex< core::Real > > const &Frho2, core::Size nbuckets, core::Real maxreso, core::Real minreso, utility::vector1< core::Real > &FSC, bool S2_bin=false)	core::scoring::electron_density::ElectronDensity
getGrid() const	core::scoring::electron_density::ElectronDensity	inline
getIntensities(ObjexxFCL::FArray3D< std::complex< core::Real > > const &FrhoC, core::Size nbuckets, core::Real maxreso, core::Real minreso, utility::vector1< core::Real > &Imap, 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
getOrigin() const	core::scoring::electron_density::ElectronDensity	inline
getPhaseError(ObjexxFCL::FArray3D< std::complex< core::Real > > const &Frho1, ObjexxFCL::FArray3D< std::complex< core::Real > > const &Frho2, core::Size nbuckets, core::Real maxreso, core::Real minreso, utility::vector1< core::Real > &phaseError, bool S2_bin=false)	core::scoring::electron_density::ElectronDensity
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(ObjexxFCL::FArray3D< core::Real > const &density2, ObjexxFCL::FArray3D< core::Real > const &mask)	core::scoring::electron_density::ElectronDensity
getRSCC(ObjexxFCL::FArray3D< core::Real > &rhoC)	core::scoring::electron_density::ElectronDensity	inline
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
getWindow()	core::scoring::electron_density::ElectronDensity	inline
grad(numeric::xyzVector< core::Real > X)	core::scoring::electron_density::ElectronDensity
grid_	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
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
mapSphericalSamples(ObjexxFCL::FArray3D< core::Real > &mapShellR, core::Size nRsteps, core::Real delR, core::Size B, numeric::xyzVector< core::Real > center, core::Real laplacian_offset)	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
matchAtomFast(int resid, Size atomid, core::conformation::Residue const &rsd, core::pose::Pose const &pose, core::conformation::symmetry::SymmetryInfoCOP symmInfo=nullptr, bool ignoreBs=false)	core::scoring::electron_density::ElectronDensity
matchCentroidPose(core::pose::Pose const &pose, core::conformation::symmetry::SymmetryInfoCOP symmInfo=nullptr, bool cacheCCs=false)	core::scoring::electron_density::ElectronDensity
matchPointFast(numeric::xyzVector< core::Real > X)	core::scoring::electron_density::ElectronDensity
matchPose(core::pose::Pose const &pose, core::conformation::symmetry::SymmetryInfoCOP symmInfo=nullptr, 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=nullptr, 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=nullptr, core::Real sc_scale=1.0)	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	static
origin_	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
reciprocalSpaceFilter(core::Real maxreso, core::Real minreso, core::Real fadewidth)	core::scoring::electron_density::ElectronDensity
remap_symm_	core::scoring::electron_density::ElectronDensity	private
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
RV	core::scoring::electron_density::ElectronDensity	private
S2(int h, int k, int l)	core::scoring::electron_density::ElectronDensity	inline
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< Q > const &density_in)	core::scoring::electron_density::ElectronDensity	inline
set_nres(int nres)	core::scoring::electron_density::ElectronDensity	inline
set_voxel_spacing(numeric::xyzVector< core::Real > apix)	core::scoring::electron_density::ElectronDensity
set_voxel_spacing(core::Real apix)	core::scoring::electron_density::ElectronDensity	inline
setOrigin(numeric::xyzVector< core::Real > newori)	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_fastscoring_first_time(Real scalefactor)	core::scoring::electron_density::ElectronDensity	private
setWindow(core::Size window_in)	core::scoring::electron_density::ElectronDensity	inline
smooth_intensities(utility::vector1< core::Real > &) const	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
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
writeMRC(std::string mapfilestem)	core::scoring::electron_density::ElectronDensity
~ElectronDensity() override	core::scoring::electron_density::ElectronDensity