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
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
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_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
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
DensScoreInMinimizer	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_dscoredx	core::scoring::electron_density::ElectronDensity	private
fastdens_dscoredy	core::scoring::electron_density::ElectronDensity	private
fastdens_dscoredz	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
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
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
getMax() const	core::scoring::electron_density::ElectronDensity	inline
getMean() const	core::scoring::electron_density::ElectronDensity	inline
getMin() const	core::scoring::electron_density::ElectronDensity	inline
getNumDerivH() const	core::scoring::electron_density::ElectronDensity	inline
getOrigin() const	core::scoring::electron_density::ElectronDensity	inline
getResolution() const	core::scoring::electron_density::ElectronDensity	inline
getScoreWindowContext() const	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
isLoaded	core::scoring::electron_density::ElectronDensity	private
isMapLoaded() const	core::scoring::electron_density::ElectronDensity	inline
lowres_cut	core::scoring::electron_density::ElectronDensity	private
maskResidues(int scoring_mask)	core::scoring::electron_density::ElectronDensity	inline
maskResidues(utility::vector1< int > const &scoring_mask)	core::scoring::electron_density::ElectronDensity	inline
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)	core::scoring::electron_density::ElectronDensity
max_del_grid	core::scoring::electron_density::ElectronDensity	private
MINMULT	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
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
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
score_window_context_	core::scoring::electron_density::ElectronDensity	private
scoring_mask_	core::scoring::electron_density::ElectronDensity	private
set_nres(int nres)	core::scoring::electron_density::ElectronDensity	inline
setScoreWindowContext(bool newVal)	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
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
V	core::scoring::electron_density::ElectronDensity	private
WINDOW_	core::scoring::electron_density::ElectronDensity	private
writeMAT(std::string mapfilestem)	core::scoring::electron_density::ElectronDensity
writeMRC(std::string mapfilestem)	core::scoring::electron_density::ElectronDensity
~ElectronDensity()	core::scoring::electron_density::ElectronDensity	virtual