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

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)

ElectronDensity &	getDensityMap (std::string filename="", bool force_reload=false)
	The EDM instance. More...

ElectronDensity &	getDensityMap_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::Real >	interp_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< double >	convolute_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

typedef utility::pointer::owning_ptr< ElectronDensity const > core::scoring::electron_density::ElectronDensityCOP

typedef utility::pointer::owning_ptr< ElectronDensityLoader const > core::scoring::electron_density::ElectronDensityLoaderCOP

typedef utility::pointer::owning_ptr< ElectronDensityLoader > core::scoring::electron_density::ElectronDensityLoaderOP

typedef utility::pointer::owning_ptr< ElectronDensity > core::scoring::electron_density::ElectronDensityOP

typedef utility::pointer::owning_ptr< ElectronDensityOptions const > core::scoring::electron_density::ElectronDensityOptionsCOP

typedef utility::pointer::owning_ptr< ElectronDensityOptions > core::scoring::electron_density::ElectronDensityOptionsOP

typedef utility::vector1< poseCoord > core::scoring::electron_density::poseCoords

Function Documentation

void core::scoring::electron_density::add_dens_scores_from_cmdline_to_scorefxn ( core::scoring::ScoreFunction & scorefxn )

read density weights from the cmd line into the scorefunction

update scorefxn with density scores from commandline

References core::scoring::elec_dens_fast, core::scoring::elec_dens_whole_structure_allatom, core::scoring::elec_dens_whole_structure_ca, core::scoring::elec_dens_window, option, core::scoring::patterson_cc, core::scoring::ScoreFunction::set_weight(), and user.

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
	)

Referenced by convolute_maps(), and core::scoring::electron_density::ElectronDensity::match_fragment().

ObjexxFCL::FArray3D< double > core::scoring::electron_density::convolute_maps	(	ObjexxFCL::FArray3D< double > const &	mapA,
		ObjexxFCL::FArray3D< double > const &	mapB
	)

References conj_map_times(), numeric::fourier::fft3(), and numeric::fourier::ifft3().

float core::scoring::electron_density::d2r ( float d )

inline

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

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
	)

References factorsLTE19(), and core::chemical::element::N.

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

int core::scoring::electron_density::findSampling5	(	double	MINSMP,
		int	NMUL
	)

References factorsLTE5(), and core::chemical::element::N.

Referenced by core::scoring::electron_density::ElectronDensity::ElectronDensity(), and core::scoring::electron_density::ElectronDensity::setup_patterson_first_time().

OneGaussianScattering core::scoring::electron_density::get_A ( std::string elt )

References basic::options::OptionKeys::edensity::centroid_density_mass, basic::options::OptionKeys::edensity::cryoem_scatterers, basic::options::option, and TR.

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().

ElectronDensity & core::scoring::electron_density::getDensityMap_legacy	(	std::string	filename,
		bool	force_reload
	)

The EDM instance.

References exit, basic::options::OptionKeys::edensity::grid_spacing, core::scoring::electron_density::ElectronDensity::isMapLoaded(), basic::options::OptionKeys::edensity::mapfile, mapfile, basic::options::OptionKeys::edensity::mapreso, mapreso, basic::options::option, core::scoring::electron_density::ElectronDensity::readMRCandResize(), TR, and user.

Referenced by getDensityMap().

numeric::xyzVector< core::Real > core::scoring::electron_density::interp_dspline	(	ObjexxFCL::FArray3D< double > &	coeffs,
		numeric::xyzVector< core::Real > const &	idxX
	)

spline interpolation with periodic boundaries

References core::scoring::electron_density::SplineInterp::grad3().

Referenced by core::scoring::electron_density::ElectronDensity::dCCdB_fastRes(), core::scoring::electron_density::ElectronDensity::dCCdx_fastRes(), and core::scoring::electron_density::ElectronDensity::dCCdx_PointFast().

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
	)

trilinear interpolation with periodic boundaries

References grid, and core::chemical::element::S.

Referenced by core::scoring::PoissonBoltzmannPotential::get_potential(), core::scoring::electron_density::ElectronDensity::matchPoseToPatterson(), and core::scoring::electron_density::ElectronDensity::rotAlign2DPose().

core::Real core::scoring::electron_density::interp_spline	(	ObjexxFCL::FArray3D< double > &	coeffs,
		numeric::xyzVector< core::Real > const &	idxX
	)

spline interpolation with periodic boundaries

References core::scoring::electron_density::SplineInterp::interp3().

Referenced by core::scoring::electron_density::ElectronDensity::dens_grad(), core::scoring::electron_density::ElectronDensity::matchPointFast(), core::scoring::electron_density::ElectronDensity::matchPoseToPatterson(), core::scoring::electron_density::ElectronDensity::matchResFast(), and core::scoring::electron_density::ElectronDensity::rescale_fastscoring_temp_bins().

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

References numeric::xyzVector< class >::length().

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 )

helper function quickly guesses if a pose has non-zero B factors

References core::chemical::aa_vrt, core::chemical::element::B, core::pose::Pose::pdb_info(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Referenced by core::scoring::electron_density::ElectronDensity::calcRhoC(), and core::scoring::electron_density::FastDensEnergy::setup_for_scoring().

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
	)

precompute spline coefficients (float array => double coeffs)

References core::scoring::electron_density::SplineInterp::compute_coefficients3().

Referenced by core::scoring::electron_density::ElectronDensity::computeGradients(), core::scoring::electron_density::ElectronDensity::matchPoseToPatterson(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::precompute_unweighted_score(), core::scoring::electron_density::ElectronDensity::setup_fastscoring_first_time(), and spline_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
	)

References core::scoring::electron_density::SplineInterp::compute_coefficients4().

void core::scoring::electron_density::spline_coeffs	(	ObjexxFCL::FArray4D< float > &	data,
		ObjexxFCL::FArray4D< double > &	coeffs
	)

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

core::Real core::scoring::electron_density::SQ ( core::Real N )

inline

References core::chemical::element::N.

Referenced by core::scoring::electron_density::ElecDensAllAtomCenEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensCenEnergy::eval_atom_derivative(), and core::scoring::electron_density::ElecDensEnergy::eval_atom_derivative().

float core::scoring::electron_density::square ( float x )

inline

Referenced by core::scoring::electron_density::ElectronDensity::computeCrystParams(), core::scoring::electron_density::ElectronDensity::matchCentroidPose(), core::scoring::electron_density::ElectronDensity::matchPoseToPatterson(), core::scoring::electron_density::ElectronDensity::rematchResToPatterson(), core::scoring::electron_density::ElectronDensity::rotAlign2DPose(), and core::scoring::electron_density::ElectronDensity::updateCachedDensity().

double core::scoring::electron_density::square ( double x )

inline

static void core::scoring::electron_density::swap4_aligned	(	void *	v,
		long	ndata
	)

static

References core::chemical::element::N.

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

basic::Tracer core::scoring::electron_density::TR ( "core.scoring.electron_density.ElectronDensity" )

Variable Documentation

const int core::scoring::electron_density::CCP4HDSIZE = 1024

Referenced by core::scoring::electron_density::ElectronDensity::readMRCandResize(), and core::scoring::electron_density::ElectronDensity::writeMRC().

const core::Real core::scoring::electron_density::MAX_FLT = 1e37

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

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

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

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

Namespaces

Classes

Typedefs

Functions

Variables

Typedef Documentation

Function Documentation

Variable Documentation