Rosetta Core  2014.35
Namespaces | Classes | Typedefs | Functions | Variables
core::scoring::electron_density Namespace Reference

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
 

Typedefs

typedef
utility::pointer::owning_ptr
< ElectronDensity
ElectronDensityOP
 
typedef
utility::pointer::owning_ptr
< ElectronDensity const > 
ElectronDensityCOP
 
typedef
utility::pointer::owning_ptr
< ElectronDensityLoader
ElectronDensityLoaderOP
 
typedef
utility::pointer::owning_ptr
< ElectronDensityLoader const > 
ElectronDensityLoaderCOP
 
typedef
utility::pointer::owning_ptr
< ElectronDensityOptions
ElectronDensityOptionsOP
 
typedef
utility::pointer::owning_ptr
< ElectronDensityOptions const > 
ElectronDensityOptionsCOP
 
typedef utility::vector1
< poseCoord
poseCoords
 

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)
 
ElectronDensitygetDensityMap (std::string filename="", bool force_reload=false)
 The EDM instance. More...
 
ElectronDensitygetDensityMap_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::Realinterp_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< doubleconvolute_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 Documentation

Function Documentation

void core::scoring::electron_density::add_dens_scores_from_cmdline_to_scorefxn ( core::scoring::ScoreFunction scorefxn)
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 
)
ObjexxFCL::FArray3D< double > core::scoring::electron_density::convolute_maps ( ObjexxFCL::FArray3D< double > const &  mapA,
ObjexxFCL::FArray3D< double > const &  mapB 
)
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 ( 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 
)
numeric::xyzVector< core::Real > core::scoring::electron_density::interp_dspline ( ObjexxFCL::FArray3D< double > &  coeffs,
numeric::xyzVector< core::Real > const &  idxX 
)
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().

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 
)
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().

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
float core::scoring::electron_density::pos_mod ( float  x,
float  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
bool core::scoring::electron_density::pose_has_nonzero_Bs ( core::pose::Pose const &  pose)
bool core::scoring::electron_density::pose_has_nonzero_Bs ( poseCoords const &  pose)
template<class S , class T >
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(), and numeric::fourier::ifft3().

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 core::chemical::element::N, and spline_coeffs().

void core::scoring::electron_density::spline_coeffs ( ObjexxFCL::FArray4D< double > &  data,
ObjexxFCL::FArray4D< double > &  coeffs 
)
void core::scoring::electron_density::spline_coeffs ( ObjexxFCL::FArray4D< float > &  data,
ObjexxFCL::FArray4D< double > &  coeffs 
)
core::Real core::scoring::electron_density::SQ ( core::Real  N)
inline
float core::scoring::electron_density::square ( float  x)
inline
double core::scoring::electron_density::square ( double  x)
inline
static void core::scoring::electron_density::swap4_aligned ( void *  v,
long  ndata 
)
static
basic::Tracer core::scoring::electron_density::TR ( "core.scoring.electron_density.ElectronDensity"  )

Variable Documentation

const int core::scoring::electron_density::CCP4HDSIZE = 1024
const core::Real core::scoring::electron_density::MAX_FLT = 1e37
basic::Tracer core::scoring::electron_density::TR("core.scoring.electron_density.ElecDensEnergy")
static
basic::Tracer core::scoring::electron_density::TR("core.scoring.electron_density.ElectronDensity") ( "core.scoring.methods.ElecDensEnergy"  )
static

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_PointFast(), 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::matchPointFast(), 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().

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