Rosetta 3.4
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core::scoring::electron_density Namespace Reference

Namespaces

namespace  SplineInterp

Classes

class  ElecDensAllAtomCenEnergy
class  ElecDensAllAtomCenEnergyCreator
class  ElecDensCenEnergy
class  ElecDensCenEnergyCreator
class  ElecDensEnergy
class  ElecDensEnergyCreator
class  ElectronDensity
class  FastDensEnergy
class  FastDensEnergyCreator
class  PattersonCorrEnergy
class  PattersonCorrEnergyCreator
class  KromerMann
class  OneGaussianScattering

Functions

static basic::Tracer TR ("core.scoring.methods.ElecDensEnergy")
core::Real SQ (core::Real N)
static basic::Tracer TR ("core.scoring.electron_density.ElecDensEnergy")
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)
ElectronDensitygetDensityMap ()
 The EDM instance.
float pos_mod (float x, float y)
int pos_mod (int x, int y)
double pos_mod (double x, double y)
static basic::Tracer TR ("core.scoring.electron_density.FastDensEnergy")
static basic::Tracer TR ("core.scoring.electron_density.PattersonCorrEnergy")
void add_dens_scores_from_cmdline_to_scorefxn (core::scoring::ScoreFunction &scorefxn)
 read density weights from the cmd line into the scorefunction
core::Real interp_spline (ObjexxFCL::FArray3D< double > &coeffs, numeric::xyzVector< core::Real > const &idxX)
 spline interpolation with periodic boundaries
void spline_coeffs (ObjexxFCL::FArray3D< double > &data, ObjexxFCL::FArray3D< double > &coeffs)
 precompute spline coefficients (float array => double coeffs)
void spline_coeffs (ObjexxFCL::FArray3D< float > &data, ObjexxFCL::FArray3D< double > &coeffs)
 precompute spline coefficients (double array => 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
template<class S , class T >
void resample (ObjexxFCL::FArray3D< S > const &density, ObjexxFCL::FArray3D< T > &newDensity, numeric::xyzVector< core::Size > newDims)
 templated helper function to FFT resample a map
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

const int CCP4HDSIZE = 1024
const core::Real MAX_FLT = 1e37

Function Documentation

void core::scoring::electron_density::add_dens_scores_from_cmdline_to_scorefxn ( core::scoring::ScoreFunction scorefxn)
float core::scoring::electron_density::d2r ( float  d) [inline]
double core::scoring::electron_density::d2r ( double  d) [inline]
bool core::scoring::electron_density::factorsLTE19 ( int  X)

Referenced by findSampling().

bool core::scoring::electron_density::factorsLTE5 ( int  X)

Referenced by findSampling5().

int core::scoring::electron_density::findSampling ( double  MINSMP,
int  NMUL 
)
int core::scoring::electron_density::findSampling5 ( double  MINSMP,
int  NMUL 
)
OneGaussianScattering core::scoring::electron_density::get_A ( std::string  elt)
KromerMann core::scoring::electron_density::get_km ( std::string  elt)

References TR().

ElectronDensity & core::scoring::electron_density::getDensityMap ( )

The EDM instance.

References core::scoring::electron_density::ElectronDensity::isMapLoaded(), core::scoring::electron_density::ElectronDensity::readMRCandResize(), and TR().

Referenced by protocols::electron_density::SetupForDensityScoringMover::apply(), 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(), protocols::electron_density::dockPoseIntoMap(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::ElecDensAllAtomCenEnergy(), core::scoring::electron_density::ElecDensCenEnergy::ElecDensCenEnergy(), core::scoring::electron_density::ElecDensEnergy::ElecDensEnergy(), core::scoring::electron_density::PattersonCorrEnergy::eval_atom_derivative(), core::scoring::electron_density::FastDensEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensCenEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::eval_atom_derivative(), protocols::electron_density::fast2DRotAlignPose(), core::scoring::electron_density::FastDensEnergy::FastDensEnergy(), protocols::electron_density::fastTransAlignPose(), protocols::electron_density::findLoopFromDensity(), protocols::electron_density::findLoopFromPatterson(), core::scoring::electron_density::PattersonCorrEnergy::PattersonCorrEnergy(), core::scoring::electron_density::PattersonCorrEnergy::residue_pair_energy(), core::scoring::electron_density::FastDensEnergy::residue_pair_energy(), core::scoring::electron_density::ElecDensEnergy::residue_pair_energy(), core::scoring::electron_density::PattersonCorrEnergy::setup_for_derivatives(), core::scoring::electron_density::FastDensEnergy::setup_for_derivatives(), core::scoring::electron_density::ElecDensEnergy::setup_for_derivatives(), core::scoring::electron_density::ElecDensCenEnergy::setup_for_derivatives(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::setup_for_derivatives(), core::scoring::electron_density::PattersonCorrEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensCenEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::setup_for_scoring(), and core::scoring::electron_density::PattersonCorrEnergy::update_residue_for_packing().

template<class S >
core::Real core::scoring::electron_density::interp_linear ( ObjexxFCL::FArray3D< S > const &  data,
numeric::xyzVector< core::Real > const &  idxX 
)
core::Real core::scoring::electron_density::interp_spline ( ObjexxFCL::FArray3D< double > &  coeffs,
numeric::xyzVector< core::Real > const &  idxX 
)
bool core::scoring::electron_density::is_missing_density ( numeric::xyzVector< core::Real > const &  X) [inline]
int core::scoring::electron_density::min_mod ( int  x,
int  y 
) [inline]
float core::scoring::electron_density::min_mod ( float  x,
float  y 
) [inline]
double core::scoring::electron_density::min_mod ( double  x,
double  y 
) [inline]
int core::scoring::electron_density::pos_mod ( int  x,
int  y 
) [inline]
double core::scoring::electron_density::pos_mod ( double  x,
double  y 
) [inline]
float core::scoring::electron_density::pos_mod ( float  x,
float  y 
) [inline]
template<class S , class T >
void core::scoring::electron_density::resample ( ObjexxFCL::FArray3D< S > const &  density,
ObjexxFCL::FArray3D< T > &  newDensity,
numeric::xyzVector< core::Size newDims 
)

templated helper function to FFT resample a map

Referenced by core::scoring::electron_density::ElectronDensity::resize().

void core::scoring::electron_density::spline_coeffs ( ObjexxFCL::FArray3D< double > &  data,
ObjexxFCL::FArray3D< double > &  coeffs 
)
void core::scoring::electron_density::spline_coeffs ( ObjexxFCL::FArray3D< float > &  data,
ObjexxFCL::FArray3D< double > &  coeffs 
)

precompute spline coefficients (double array => double coeffs)

References protocols::forge::build::SegmentInsertConnectionScheme::N, and spline_coeffs().

core::Real core::scoring::electron_density::SQ ( core::Real  N) [inline]
double core::scoring::electron_density::square ( double  x) [inline]
float core::scoring::electron_density::square ( float  x) [inline]
static void core::scoring::electron_density::swap4_aligned ( void *  v,
long  ndata 
) [static]
static basic::Tracer core::scoring::electron_density::TR ( "core.scoring.methods.ElecDensEnergy"  ) [static]

Referenced by core::scoring::electron_density::ElectronDensity::compute_symm_rotations(), 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::ElecDensCenEnergy::ElecDensCenEnergy(), core::scoring::electron_density::ElecDensEnergy::ElecDensEnergy(), core::scoring::electron_density::ElectronDensity::ElectronDensity(), get_A(), get_km(), getDensityMap(), 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::PattersonCorrEnergy::residue_pair_energy(), core::scoring::electron_density::ElectronDensity::resize(), core::scoring::electron_density::ElectronDensity::rotAlign2DPose(), core::scoring::electron_density::ElecDensEnergy::setup_for_derivatives(), core::scoring::electron_density::PattersonCorrEnergy::setup_for_scoring(), core::scoring::electron_density::FastDensEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensCenEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::setup_for_scoring(), core::scoring::electron_density::ElectronDensity::showCachedScores(), and core::scoring::electron_density::ElectronDensity::writeMRC().

static basic::Tracer core::scoring::electron_density::TR ( "core.scoring.electron_density.ElecDensEnergy"  ) [static]
static basic::Tracer core::scoring::electron_density::TR ( "core.scoring.electron_density.FastDensEnergy"  ) [static]
basic::Tracer core::scoring::electron_density::TR ( "core.scoring.electron_density.ElectronDensity"  )
static basic::Tracer core::scoring::electron_density::TR ( "core.scoring.electron_density.PattersonCorrEnergy"  ) [static]

Variable Documentation

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