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core::scoring::electron_density::ElectronDensity Class Reference

#include <ElectronDensity.hh>

Inheritance diagram for core::scoring::electron_density::ElectronDensity:
Inheritance graph
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Public Member Functions

 ~ElectronDensity () override
 Automatically generated virtual destructor for class deriving directly from VirtualBase. More...
 
 ElectronDensity ()
 default constructor More...
 
 ElectronDensity (utility::vector1< core::pose::PoseOP > poses, core::Real reso, core::Real apix)
 calulated density from a vector of poses More...
 
template<class T >
 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)
 constructor from an FArray3D (debugging only!) More...
 
void init ()
 initialize vars from command line options More...
 
bool readMRCandResize (std::string mapfile, core::Real reso=5.0, core::Real gridSpacing=0.0)
 Load an MRC density map. More...
 
bool readMRCandResize (std::istream &mapin, std::string mapfile, core::Real reso=5.0, core::Real gridSpacing=0.0)
 Load an MRC density map. More...
 
bool writeMRC (std::string mapfilestem)
 (debugging) Write MRC mapfile More...
 
void mapSphericalSamples (ObjexxFCL::FArray3D< core::Real > &mapShellR, core::Size nRsteps, core::Real delR, core::Size B, numeric::xyzVector< core::Real > center, core::Real laplacian_offset)
 resample the map in spherical shells around a pose More...
 
core::Real matchCentroidPose (core::pose::Pose const &pose, core::conformation::symmetry::SymmetryInfoCOP symmInfo=nullptr, bool cacheCCs=false)
 Quickly matches a centroid pose into a low-resolution density map by placing a single Gaussian at each CA. More...
 
core::Real matchPose (core::pose::Pose const &pose, core::conformation::symmetry::SymmetryInfoCOP symmInfo=nullptr, bool cacheCCs=false)
 Match a pose into a medium-resolution density map by placing a single Gaussian at each atom. More...
 
void getResolutionBins (core::Size nbuckets, core::Real maxreso, core::Real minreso, utility::vector1< core::Real > &, utility::vector1< core::Size > &, bool S2_bin=false)
 get resolution bins More...
 
void 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)
 Compute map intensities, masked by a pose. Also compute mask intensities. More...
 
void 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)
 Compute map-map FSC. More...
 
void 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)
 Compute map-map phase error. More...
 
void 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)
 get Rho Calc More...
 
core::Real getRSCC (ObjexxFCL::FArray3D< core::Real > const &density2, ObjexxFCL::FArray3D< core::Real > const &mask)
 Real-space correlation. More...
 
core::Real getRSCC (ObjexxFCL::FArray3D< core::Real > &rhoC)
 Real-space correlation. More...
 
void scaleIntensities (utility::vector1< core::Real > I_tgt, core::Real maxreso, core::Real minreso, bool S2_bin=false)
 Scale map intensities to a target spectum. More...
 
void reciprocalSpaceFilter (core::Real maxreso, core::Real minreso, core::Real fadewidth)
 Filter the map in reciprocal space. More...
 
core::Real maxNominalRes ()
 Return the highest possible resolution relection in reciprocal space for the given grid. More...
 
core::Real matchRes (int resid, core::conformation::Residue const &rsd, core::pose::Pose const &pose, core::conformation::symmetry::SymmetryInfoCOP symmInfo=nullptr, bool cacheCCs=false)
 Match a residue's conformation to the density map. Backbone atoms from adjacent residues are also used for scoring. Returns the correlation coefficient between map and pose Internally stores per-res CCs, per-atom dCC/dxs. More...
 
core::Real 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)
 Match a residue's conformation to the density map. Same as matchRes, but using a fast approximation to the match function. More...
 
core::Real matchAtomFast (int resid, Size atomid, core::conformation::Residue const &rsd, core::pose::Pose const &pose, core::conformation::symmetry::SymmetryInfoCOP symmInfo=nullptr, bool ignoreBs=false)
 Matches an individual atom to the density using the fast approximation. More...
 
void compute_symm_rotations (core::pose::Pose const &pose, core::conformation::symmetry::SymmetryInfoCOP symmInfo=nullptr)
 Computes the symmatric rotation matrices. More...
 
core::Real matchPointFast (numeric::xyzVector< core::Real > X)
 access fastdens scoring for a single point More...
 
void dCCdx_PointFast (numeric::xyzVector< core::Real > X, numeric::xyzVector< core::Real > &dCCdx)
 access fastdens scoring for a single point More...
 
void 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)
 Return the gradient of CC w.r.t. atom X's movement Uses information stored from the previous call to matchRes with this resid. More...
 
void 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)
 Return the gradient of "fast CC" w.r.t. atom X's movement Uses information stored from the previous call to matchRes with this resid. More...
 
Real dCCdB_fastRes (int atmid, int resid, core::conformation::Residue const &rsd, core::pose::Pose const &pose)
 Gradient of CC w.r.t B factors. More...
 
void dCCdBs (core::pose::Pose const &pose, utility::vector1< core::Real > &dE_dvars, ObjexxFCL::FArray3D< core::Real > &maskC)
 calculate all gradients of CC w.r.t B factors (slow more precise version) More...
 
void rescale_fastscoring_temp_bins (core::pose::Pose const &pose, bool init=false)
 
void dCCdx_cen (int resid, numeric::xyzVector< core::Real > const &X, core::pose::Pose const &pose, numeric::xyzVector< core::Real > &gradX)
 Return the gradient of CC w.r.t. res X's CA's movement Centroid-mode analogue of dCCdx. More...
 
void dCCdx_aacen (int atmid, int resid, numeric::xyzVector< core::Real > const &X, core::pose::Pose const &pose, numeric::xyzVector< core::Real > &gradX)
 Return the gradient of whole-structure-CC w.r.t. atom X's movement non-sliding-window analogue of dCCdx. More...
 
void clear_dCCdx_res_cache (core::pose::Pose const &pose)
 Resets the counters used for derivative computation in sliding-window/fast scoring. More...
 
numeric::xyzVector< core::RealgetTransform ()
 Get the transformation from indices to Cartesian coords using 'real' origin. More...
 
void set_nres (int nres)
 set # of residues More...
 
void setSCscaling (core::Real SC_scalingin)
 
core::Real getSCscaling ()
 
void setWindow (core::Size window_in)
 
core::Size getWindow ()
 
void setScoreWindowContext (bool newVal)
 
bool getScoreWindowContext () const
 
bool isMapLoaded () const
 
core::Real getResolution () const
 
numeric::xyzVector< core::RealgetOrigin () const
 
void setOrigin (numeric::xyzVector< core::Real > newori)
 
numeric::xyzVector< int > getGrid () const
 
numeric::xyzVector< core::Realget_cellDimensions () const
 
utility::vector1
< core::kinematics::RT
getsymmOps () const
 
core::Real getAtomMask () const
 
void maskResidues (int scoring_mask)
 set scoring to use only a subset of residues More...
 
void maskResidues (utility::vector1< int > const &scoring_mask)
 set scoring to use only a subset of residues More...
 
void clearMask ()
 reset scoring to use all residues More...
 
ObjexxFCL::FArray3D< float >
const & 
get_data () const
 access raw density data More...
 
template<class Q >
void set_data (ObjexxFCL::FArray3D< Q > const &density_in)
 set raw density data. Assumes new map sampling grid same as current More...
 
core::Real get (int i, int j, int k)
 get the density at a grid point More...
 
core::Real get (numeric::xyzVector< core::Real > X)
 get the interpolated density at a point in index space More...
 
numeric::xyzVector< core::Realgrad (numeric::xyzVector< core::Real > X)
 get the interpolated gradient at a point in index space More...
 
void set_voxel_spacing (numeric::xyzVector< core::Real > apix)
 set voxel spacing of the map More...
 
void set_voxel_spacing (core::Real apix)
 set voxel spacing of the map More...
 
numeric::xyzVector< core::Realget_voxel_spacing ()
 set voxel spacing of the map More...
 
core::Real getCachedScore (core::Size resid)
 get the precomputed CC (THIS SHOULD LIVE IN POSE DATACACHE!) More...
 
void cart2idx (numeric::xyzVector< core::Real > const &cartX, numeric::xyzVector< core::Real > &idxX) const
 
template<class Q >
void idx2cart (numeric::xyzVector< Q > const &idxX, numeric::xyzVector< core::Real > &cartX) const
 
template<class Q >
void idxoffset2cart (numeric::xyzVector< Q > const &idxX, numeric::xyzVector< core::Real > &cartX) const
 
numeric::xyzMatrix< core::Realget_f2c () const
 get frac<=>cartesian conversion matrices More...
 
numeric::xyzMatrix< core::Realget_c2f () const
 
void resize (core::Real approxGridSpacing)
 resize the map via FFT resampling More...
 
void get_symmMap (int vrtid, utility::vector1< int > &X_map, numeric::xyzMatrix< core::Real > &R)
 get symmetrized gradients for -score_symm_complex More...
 
void get_R (int subunit, numeric::xyzMatrix< core::Real > &R)
 gets rotation vactor for subunit 'subunit' in last-scored pose (Rosetta symmetry) More...
 
core::Real getEffectiveBfactor ()
 get the "effective B factor": a global b factor based on map resolution More...
 
core::Real S2 (int h, int k, int l)
 
void computeStats ()
 
core::Real getMean () const
 
core::Real getMin () const
 
core::Real getMax () const
 
core::Real getStdev () const
 
numeric::xyzVector< core::Realdens_grad (numeric::xyzVector< core::Real > const &idxX) const
 

Static Public Attributes

static core::Real NUM_DERIV_H = 0.01
 

Private Member Functions

void density_change_trigger ()
 The function is called everytime the density changes. More...
 
void smooth_intensities (utility::vector1< core::Real > &) const
 
void computeGradients ()
 
void initializeSymmOps (utility::vector1< std::string > const &symList)
 
void computeCrystParams ()
 
void expandToUnitCell ()
 
void setup_fastscoring_first_time (core::pose::Pose const &pose)
 setup oversampled maps for fast density scoring More...
 
void setup_fastscoring_first_time (Real scalefactor)
 
utility::vector1
< ObjexxFCL::FArray3D
< std::complex< core::Real > > * > 
getFdrhoc (OneGaussianScattering S)
 
core::Real voxel_volume ()
 

Private Attributes

bool isLoaded_
 
ObjexxFCL::FArray3D< float > density
 
ObjexxFCL::FArray3D< core::Realcoeffs_density_
 
ObjexxFCL::FArray3D
< std::complex< core::Real > > 
Fdensity_
 
std::map< core::Size, boolscoring_mask_
 
core::Real reso_
 
core::Real ATOM_MASK
 
core::Real CA_MASK
 
core::Real force_apix_on_map_load_
 
core::Real SC_scaling_
 
core::Real ATOM_MASK_PADDING
 
core::Size WINDOW_
 
bool score_window_context_
 
bool remap_symm_
 
ObjexxFCL::FArray4D< core::Realfastdens_score
 
core::Size nkbins_
 
core::Real kmin_
 
core::Real kmax_
 
core::Real kstep_
 
numeric::xyzVector< int > fastgrid
 
numeric::xyzVector< core::Realfastorigin
 
core::Real minimumB
 
core::Real effectiveB
 
numeric::xyzVector< int > grid_
 
numeric::xyzVector< core::Realorigin_
 
bool use_altorigin
 
core::Real dens_mean
 
core::Real dens_min
 
core::Real dens_max
 
core::Real dens_stdev
 
utility::vector1< core::RealCCs
 CACHED STUFF that is not thread safe and should live in its own class. More...
 
core::Real CC_cen
 
core::Real CC_aacen
 
utility::vector1
< numeric::xyzVector
< core::Real > > 
dCCdxs_cen
 
utility::vector1
< utility::vector1
< numeric::xyzVector
< core::Real > > > 
dCCdxs_aacen
 
utility::vector1
< utility::vector1
< numeric::xyzVector
< core::Real > > > 
dCCdxs_res
 
utility::vector1
< utility::vector1
< numeric::xyzVector
< core::Real > > > 
dCCdxs_pat
 
std::map< int, std::pair
< utility::vector1< int >
, numeric::xyzMatrix
< core::Real > > > 
symmap
 SYMMETRY (Rosetta's symmetry, not necessarily crystal symmetry) More...
 
ObjexxFCL::FArray3D< core::Realcoeff_grad_x
 VISUALIZATION-SPECIFIC. More...
 
ObjexxFCL::FArray3D< core::Realcoeff_grad_y
 
ObjexxFCL::FArray3D< core::Realcoeff_grad_z
 
numeric::xyzMatrix< core::Realf2c
 CRYSTAL INFO. More...
 
numeric::xyzMatrix< core::Realc2f
 
numeric::xyzVector< float > cellDimensions
 
numeric::xyzVector< float > cellAngles
 
numeric::xyzVector< float > RcellDimensions
 
numeric::xyzVector< float > cosRcellAngles
 
core::Real V
 
core::Real RV
 
utility::vector1
< core::kinematics::RT
symmOps
 
utility::vector1
< numeric::xyzMatrix
< core::Real > > 
symmRotOps
 
numeric::xyzVector< core::SizeMINMULT
 

Constructor & Destructor Documentation

core::scoring::electron_density::ElectronDensity::~ElectronDensity ( )
overridedefault

Automatically generated virtual destructor for class deriving directly from VirtualBase.

Auto-generated virtual destructor

core::scoring::electron_density::ElectronDensity::ElectronDensity ( )

default constructor

null constructor

References core::init::init().

core::scoring::electron_density::ElectronDensity::ElectronDensity ( utility::vector1< core::pose::PoseOP poses,
core::Real  reso,
core::Real  apix 
)
template<class T >
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 
)
inline

constructor from an FArray3D (debugging only!)

References cellAngles, cellDimensions, density, grid_, init(), isLoaded_, origin_, and core::scoring::electron_density::pos_mod().

Member Function Documentation

void core::scoring::electron_density::ElectronDensity::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 
)
void core::scoring::electron_density::ElectronDensity::cart2idx ( numeric::xyzVector< core::Real > const &  cartX,
numeric::xyzVector< core::Real > &  idxX 
) const
inline
void core::scoring::electron_density::ElectronDensity::clear_dCCdx_res_cache ( core::pose::Pose const &  pose)
void core::scoring::electron_density::ElectronDensity::clearMask ( )
inline

reset scoring to use all residues

References scoring_mask_.

Referenced by protocols::electron_density::SetupForDensityScoringMover::apply().

void core::scoring::electron_density::ElectronDensity::compute_symm_rotations ( core::pose::Pose const &  pose,
core::conformation::symmetry::SymmetryInfoCOP  symmInfo = nullptr 
)
void core::scoring::electron_density::ElectronDensity::computeCrystParams ( )
private
void core::scoring::electron_density::ElectronDensity::computeGradients ( )
private
void core::scoring::electron_density::ElectronDensity::computeStats ( )
Real core::scoring::electron_density::ElectronDensity::dCCdB_fastRes ( int  atmid,
int  resid,
core::conformation::Residue const &  rsd,
core::pose::Pose const &  pose 
)
void core::scoring::electron_density::ElectronDensity::dCCdBs ( core::pose::Pose const &  pose,
utility::vector1< core::Real > &  dE_dvars,
ObjexxFCL::FArray3D< core::Real > &  maskC 
)
void 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 
)

Return the gradient of whole-structure-CC w.r.t. atom X's movement non-sliding-window analogue of dCCdx.

References core::scoring::electron_density::TR().

Referenced by core::scoring::electron_density::ElecDensAllAtomCenEnergy::eval_atom_derivative().

void 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 
)

Return the gradient of CC w.r.t. res X's CA's movement Centroid-mode analogue of dCCdx.

References core::scoring::electron_density::TR().

Referenced by core::scoring::electron_density::ElecDensCenEnergy::eval_atom_derivative().

void 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 
)
void core::scoring::electron_density::ElectronDensity::dCCdx_PointFast ( numeric::xyzVector< core::Real X,
numeric::xyzVector< core::Real > &  dCCdx 
)
void 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 
)

Return the gradient of CC w.r.t. atom X's movement Uses information stored from the previous call to matchRes with this resid.

References core::scoring::electron_density::TR().

Referenced by core::scoring::electron_density::ElecDensEnergy::eval_atom_derivative().

numeric::xyzVector< core::Real > core::scoring::electron_density::ElectronDensity::dens_grad ( numeric::xyzVector< core::Real > const &  idxX) const
void core::scoring::electron_density::ElectronDensity::density_change_trigger ( )
private

The function is called everytime the density changes.

Referenced by set_data().

void core::scoring::electron_density::ElectronDensity::expandToUnitCell ( )
private
core::Real core::scoring::electron_density::ElectronDensity::get ( int  i,
int  j,
int  k 
)
inline
core::Real core::scoring::electron_density::ElectronDensity::get ( numeric::xyzVector< core::Real X)

get the interpolated density at a point in index space

References core::scoring::electron_density::interp_spline(), and core::scoring::electron_density::spline_coeffs().

numeric::xyzMatrix<core::Real> core::scoring::electron_density::ElectronDensity::get_c2f ( ) const
inline
numeric::xyzVector<core::Real> core::scoring::electron_density::ElectronDensity::get_cellDimensions ( ) const
inline

References cellDimensions.

ObjexxFCL::FArray3D< float > const& core::scoring::electron_density::ElectronDensity::get_data ( ) const
inline
numeric::xyzMatrix<core::Real> core::scoring::electron_density::ElectronDensity::get_f2c ( ) const
inline
void core::scoring::electron_density::ElectronDensity::get_R ( int  subunit,
numeric::xyzMatrix< core::Real > &  R 
)
inline
void core::scoring::electron_density::ElectronDensity::get_symmMap ( int  vrtid,
utility::vector1< int > &  X_map,
numeric::xyzMatrix< core::Real > &  R 
)
inline
numeric::xyzVector<core::Real> core::scoring::electron_density::ElectronDensity::get_voxel_spacing ( )
inline
core::Real core::scoring::electron_density::ElectronDensity::getAtomMask ( ) const
inline
core::Real core::scoring::electron_density::ElectronDensity::getCachedScore ( core::Size  resid)
inline

get the precomputed CC (THIS SHOULD LIVE IN POSE DATACACHE!)

References CCs.

Referenced by core::scoring::electron_density::ElecDensEnergy::eval_atom_derivative().

core::Real core::scoring::electron_density::ElectronDensity::getEffectiveBfactor ( )
inline

get the "effective B factor": a global b factor based on map resolution

References effectiveB.

Referenced by core::scoring::electron_density::FastDensEnergy::setup_for_scoring().

utility::vector1< ObjexxFCL::FArray3D< std::complex<core::Real> > * > core::scoring::electron_density::ElectronDensity::getFdrhoc ( OneGaussianScattering  S)
private
void core::scoring::electron_density::ElectronDensity::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 
)
numeric::xyzVector<int> core::scoring::electron_density::ElectronDensity::getGrid ( ) const
inline
void core::scoring::electron_density::ElectronDensity::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::Real core::scoring::electron_density::ElectronDensity::getMax ( ) const
inline

References dens_max.

core::Real core::scoring::electron_density::ElectronDensity::getMean ( ) const
inline

References dens_mean.

core::Real core::scoring::electron_density::ElectronDensity::getMin ( ) const
inline

References dens_min.

numeric::xyzVector<core::Real> core::scoring::electron_density::ElectronDensity::getOrigin ( ) const
inline
void core::scoring::electron_density::ElectronDensity::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::Real core::scoring::electron_density::ElectronDensity::getResolution ( ) const
inline

References reso_.

void core::scoring::electron_density::ElectronDensity::getResolutionBins ( core::Size  nbuckets,
core::Real  maxreso,
core::Real  minreso,
utility::vector1< core::Real > &  resbins,
utility::vector1< core::Size > &  counts,
bool  S2_bin = false 
)
core::Real core::scoring::electron_density::ElectronDensity::getRSCC ( ObjexxFCL::FArray3D< core::Real > const &  density2,
ObjexxFCL::FArray3D< core::Real > const &  mask 
)

Real-space correlation.

Referenced by getRSCC(), and protocols::electron_density::BfactorMultifunc::operator()().

core::Real core::scoring::electron_density::ElectronDensity::getRSCC ( ObjexxFCL::FArray3D< core::Real > &  rhoC)
inline

Real-space correlation.

References getRSCC().

bool core::scoring::electron_density::ElectronDensity::getScoreWindowContext ( ) const
inline

References score_window_context_.

core::Real core::scoring::electron_density::ElectronDensity::getSCscaling ( )
inline

References SC_scaling_.

core::Real core::scoring::electron_density::ElectronDensity::getStdev ( ) const
inline

References dens_stdev.

utility::vector1< core::kinematics::RT > core::scoring::electron_density::ElectronDensity::getsymmOps ( ) const
inline

References symmOps.

numeric::xyzVector<core::Real> core::scoring::electron_density::ElectronDensity::getTransform ( )
inline

Get the transformation from indices to Cartesian coords using 'real' origin.

References grid_, idx2cart(), and origin_.

core::Size core::scoring::electron_density::ElectronDensity::getWindow ( )
inline

References WINDOW_.

numeric::xyzVector< core::Real > core::scoring::electron_density::ElectronDensity::grad ( numeric::xyzVector< core::Real X)
template<class Q >
void core::scoring::electron_density::ElectronDensity::idx2cart ( numeric::xyzVector< Q > const &  idxX,
numeric::xyzVector< core::Real > &  cartX 
) const
inline
template<class Q >
void core::scoring::electron_density::ElectronDensity::idxoffset2cart ( numeric::xyzVector< Q > const &  idxX,
numeric::xyzVector< core::Real > &  cartX 
) const
inline
void core::scoring::electron_density::ElectronDensity::init ( void  )

initialize vars from command line options

Referenced by ElectronDensity().

void core::scoring::electron_density::ElectronDensity::initializeSymmOps ( utility::vector1< std::string > const &  symList)
private

also sets MINMULT(XYZ) eventually replace with cctbx

References protocols::cryst::denom(), and core::scoring::electron_density::TR().

bool core::scoring::electron_density::ElectronDensity::isMapLoaded ( ) const
inline
void core::scoring::electron_density::ElectronDensity::mapSphericalSamples ( ObjexxFCL::FArray3D< core::Real > &  mapShellR,
core::Size  nRsteps,
core::Real  delR,
core::Size  B,
numeric::xyzVector< core::Real center,
core::Real  laplacian_offset 
)
void core::scoring::electron_density::ElectronDensity::maskResidues ( int  scoring_mask)
inline

set scoring to use only a subset of residues

References scoring_mask_.

Referenced by protocols::electron_density::SetupForDensityScoringMover::apply().

void core::scoring::electron_density::ElectronDensity::maskResidues ( utility::vector1< int > const &  scoring_mask)
inline

set scoring to use only a subset of residues

References scoring_mask_.

core::Real core::scoring::electron_density::ElectronDensity::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::Real core::scoring::electron_density::ElectronDensity::matchCentroidPose ( core::pose::Pose const &  pose,
core::conformation::symmetry::SymmetryInfoCOP  symmInfo = nullptr,
bool  cacheCCs = false 
)
core::Real core::scoring::electron_density::ElectronDensity::matchPointFast ( numeric::xyzVector< core::Real X)

access fastdens scoring for a single point

Match an atom to the density map. Use the fast version of the scoring function and default atom type.

References core::scoring::electron_density::interp_spline(), core::scoring::electron_density::pos_mod(), core::scoring::electron_density::TR(), and protocols::comparative_modeling::features::X.

core::Real core::scoring::electron_density::ElectronDensity::matchPose ( core::pose::Pose const &  pose,
core::conformation::symmetry::SymmetryInfoCOP  symmInfo = nullptr,
bool  cacheCCs = false 
)
core::Real 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 
)

Match a residue's conformation to the density map. Backbone atoms from adjacent residues are also used for scoring. Returns the correlation coefficient between map and pose Internally stores per-res CCs, per-atom dCC/dxs.

Match a residue to the density map, returning correlation coefficient between map and residue. Caches information about scoring, to be used in derivative computation

References core::conformation::Residue::atom(), core::conformation::Residue::atom_type_index(), core::conformation::Residue::atom_type_set(), core::chemical::element::C, core::scoring::electron_density::OneGaussianScattering::C(), core::pack::interaction_graph::debug, core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), core::pose::Pose::fold_tree(), core::scoring::electron_density::get_A(), core::kinematics::FoldTree::is_cutpoint(), core::scoring::electron_density::OneGaussianScattering::k(), core::conformation::Residue::last_backbone_atom(), protocols::mean_field::max(), core::scoring::electron_density::MAX_FLT, protocols::mean_field::min(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), core::pose::Pose::size(), core::scoring::electron_density::TR(), writeMRC(), and core::conformation::Atom::xyz().

Referenced by protocols::task_operations::SelectByDensityFitOperation::apply(), core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric::calculate(), core::scoring::electron_density::calculate_density_nbr(), protocols::hybridization::FragmentBiasAssigner::density(), protocols::rotamer_recovery::RRComparerElecDensDiff::measure_rotamer_recovery(), protocols::loop_grower::LoopGrower::modifieddensity(), core::scoring::electron_density::ElecDensEnergy::residue_pair_energy(), and core::scoring::electron_density::ElecDensEnergy::setup_for_derivatives().

core::Real 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::Real core::scoring::electron_density::ElectronDensity::maxNominalRes ( )

Return the highest possible resolution relection in reciprocal space for the given grid.

References core::chemical::element::S.

bool core::scoring::electron_density::ElectronDensity::readMRCandResize ( std::string  mapfile,
core::Real  reso = 5.0,
core::Real  gridSpacing = 0.0 
)
bool core::scoring::electron_density::ElectronDensity::readMRCandResize ( std::istream &  mapin,
std::string  mapfile,
core::Real  reso = 5.0,
core::Real  gridSpacing = 0.0 
)
void core::scoring::electron_density::ElectronDensity::reciprocalSpaceFilter ( core::Real  maxreso,
core::Real  minreso,
core::Real  fadewidth 
)
void core::scoring::electron_density::ElectronDensity::rescale_fastscoring_temp_bins ( core::pose::Pose const &  pose,
bool  init = false 
)
void core::scoring::electron_density::ElectronDensity::resize ( core::Real  approxGridSpacing)
core::Real core::scoring::electron_density::ElectronDensity::S2 ( int  h,
int  k,
int  l 
)
inline

References cosRcellAngles, and RcellDimensions.

void core::scoring::electron_density::ElectronDensity::scaleIntensities ( utility::vector1< core::Real I_tgt,
core::Real  maxreso,
core::Real  minreso,
bool  S2_bin = false 
)
template<class Q >
void core::scoring::electron_density::ElectronDensity::set_data ( ObjexxFCL::FArray3D< Q > const &  density_in)
inline
void core::scoring::electron_density::ElectronDensity::set_nres ( int  nres)
inline
void core::scoring::electron_density::ElectronDensity::set_voxel_spacing ( numeric::xyzVector< core::Real apix)
void core::scoring::electron_density::ElectronDensity::set_voxel_spacing ( core::Real  apix)
inline

set voxel spacing of the map

References set_voxel_spacing().

void core::scoring::electron_density::ElectronDensity::setOrigin ( numeric::xyzVector< core::Real newori)
inline

References origin_.

void core::scoring::electron_density::ElectronDensity::setScoreWindowContext ( bool  newVal)
inline
void core::scoring::electron_density::ElectronDensity::setSCscaling ( core::Real  SC_scalingin)
inline
void core::scoring::electron_density::ElectronDensity::setup_fastscoring_first_time ( core::pose::Pose const &  pose)
private

setup oversampled maps for fast density scoring

References core::pose::Pose::size(), and core::scoring::electron_density::TR().

void core::scoring::electron_density::ElectronDensity::setup_fastscoring_first_time ( Real  scalefactor)
private
void core::scoring::electron_density::ElectronDensity::setWindow ( core::Size  window_in)
inline
void core::scoring::electron_density::ElectronDensity::smooth_intensities ( utility::vector1< core::Real > &  Is) const
private
core::Real core::scoring::electron_density::ElectronDensity::voxel_volume ( )
inlineprivate

References grid_.

bool core::scoring::electron_density::ElectronDensity::writeMRC ( std::string  mapfilestem)

Member Data Documentation

core::Real core::scoring::electron_density::ElectronDensity::ATOM_MASK
private

Referenced by getAtomMask().

core::Real core::scoring::electron_density::ElectronDensity::ATOM_MASK_PADDING
private
numeric::xyzMatrix<core::Real> core::scoring::electron_density::ElectronDensity::c2f
private

Referenced by cart2idx(), and get_c2f().

core::Real core::scoring::electron_density::ElectronDensity::CA_MASK
private
core::Real core::scoring::electron_density::ElectronDensity::CC_aacen
private
core::Real core::scoring::electron_density::ElectronDensity::CC_cen
private
utility::vector1<core::Real> core::scoring::electron_density::ElectronDensity::CCs
private

CACHED STUFF that is not thread safe and should live in its own class.

Referenced by getCachedScore(), and set_nres().

numeric::xyzVector<float> core::scoring::electron_density::ElectronDensity::cellAngles
private

Referenced by ElectronDensity().

numeric::xyzVector<float> core::scoring::electron_density::ElectronDensity::cellDimensions
private
ObjexxFCL::FArray3D< core::Real > core::scoring::electron_density::ElectronDensity::coeff_grad_x
mutableprivate

VISUALIZATION-SPECIFIC.

ObjexxFCL::FArray3D< core::Real > core::scoring::electron_density::ElectronDensity::coeff_grad_y
mutableprivate
ObjexxFCL::FArray3D< core::Real > core::scoring::electron_density::ElectronDensity::coeff_grad_z
mutableprivate
ObjexxFCL::FArray3D< core::Real > core::scoring::electron_density::ElectronDensity::coeffs_density_
private
numeric::xyzVector<float> core::scoring::electron_density::ElectronDensity::cosRcellAngles
private

Referenced by S2().

utility::vector1< utility::vector1< numeric::xyzVector< core::Real > > > core::scoring::electron_density::ElectronDensity::dCCdxs_aacen
private

Referenced by set_nres().

utility::vector1< numeric::xyzVector< core::Real > > core::scoring::electron_density::ElectronDensity::dCCdxs_cen
private

Referenced by set_nres().

utility::vector1< utility::vector1< numeric::xyzVector< core::Real > > > core::scoring::electron_density::ElectronDensity::dCCdxs_pat
private

Referenced by set_nres().

utility::vector1< utility::vector1< numeric::xyzVector< core::Real > > > core::scoring::electron_density::ElectronDensity::dCCdxs_res
private

Referenced by set_nres().

core::Real core::scoring::electron_density::ElectronDensity::dens_max
private

Referenced by getMax().

core::Real core::scoring::electron_density::ElectronDensity::dens_mean
private

Referenced by getMean().

core::Real core::scoring::electron_density::ElectronDensity::dens_min
private

Referenced by getMin().

core::Real core::scoring::electron_density::ElectronDensity::dens_stdev
private

Referenced by getStdev().

ObjexxFCL::FArray3D< float > core::scoring::electron_density::ElectronDensity::density
private
core::Real core::scoring::electron_density::ElectronDensity::effectiveB
private

Referenced by getEffectiveBfactor().

numeric::xyzMatrix<core::Real> core::scoring::electron_density::ElectronDensity::f2c
private

CRYSTAL INFO.

Referenced by get_f2c(), idx2cart(), and idxoffset2cart().

ObjexxFCL::FArray4D< core::Real > core::scoring::electron_density::ElectronDensity::fastdens_score
private
numeric::xyzVector< int > core::scoring::electron_density::ElectronDensity::fastgrid
private
numeric::xyzVector< core::Real > core::scoring::electron_density::ElectronDensity::fastorigin
private
ObjexxFCL::FArray3D< std::complex< core::Real > > core::scoring::electron_density::ElectronDensity::Fdensity_
private
core::Real core::scoring::electron_density::ElectronDensity::force_apix_on_map_load_
private
numeric::xyzVector< int > core::scoring::electron_density::ElectronDensity::grid_
private
bool core::scoring::electron_density::ElectronDensity::isLoaded_
private

Referenced by ElectronDensity(), and isMapLoaded().

core::Real core::scoring::electron_density::ElectronDensity::kmax_
private
core::Real core::scoring::electron_density::ElectronDensity::kmin_
private
core::Real core::scoring::electron_density::ElectronDensity::kstep_
private
core::Real core::scoring::electron_density::ElectronDensity::minimumB
private
numeric::xyzVector<core::Size> core::scoring::electron_density::ElectronDensity::MINMULT
private
core::Size core::scoring::electron_density::ElectronDensity::nkbins_
private
core::Real core::scoring::electron_density::ElectronDensity::NUM_DERIV_H = 0.01
static
numeric::xyzVector< core::Real > core::scoring::electron_density::ElectronDensity::origin_
private
numeric::xyzVector<float> core::scoring::electron_density::ElectronDensity::RcellDimensions
private

Referenced by S2().

bool core::scoring::electron_density::ElectronDensity::remap_symm_
private
core::Real core::scoring::electron_density::ElectronDensity::reso_
private

Referenced by getResolution().

core::Real core::scoring::electron_density::ElectronDensity::RV
private
core::Real core::scoring::electron_density::ElectronDensity::SC_scaling_
private

Referenced by getSCscaling(), and setSCscaling().

bool core::scoring::electron_density::ElectronDensity::score_window_context_
private
std::map< core::Size, bool > core::scoring::electron_density::ElectronDensity::scoring_mask_
private

Referenced by clearMask(), and maskResidues().

std::map< int , std::pair< utility::vector1<int> , numeric::xyzMatrix<core::Real> > > core::scoring::electron_density::ElectronDensity::symmap
private

SYMMETRY (Rosetta's symmetry, not necessarily crystal symmetry)

Referenced by get_R(), get_symmMap(), and set_nres().

utility::vector1< core::kinematics::RT > core::scoring::electron_density::ElectronDensity::symmOps
private

Referenced by getsymmOps().

utility::vector1< numeric::xyzMatrix<core::Real> > core::scoring::electron_density::ElectronDensity::symmRotOps
private
bool core::scoring::electron_density::ElectronDensity::use_altorigin
private
core::Real core::scoring::electron_density::ElectronDensity::V
private
core::Size core::scoring::electron_density::ElectronDensity::WINDOW_
private

Referenced by getWindow(), and setWindow().


The documentation for this class was generated from the following files: