#include <ElectronDensity.hh>

Inheritance diagram for core::scoring::electron_density::ElectronDensity:

Collaboration diagram for core::scoring::electron_density::ElectronDensity:

Public Member Functions
virtual	~ElectronDensity ()
	Automatically generated virtual destructor for class deriving directly from ReferenceCount. More...

	ElectronDensity ()
	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 ()

bool	readMRCandResize (std::string mapfile, core::Real reso=5.0, core::Real gridSpacing=0.0)
	Load an MRC (="new-CCP4") density map. More...

bool	readMRCandResize (std::istream &mapin, std::string mapfile, core::Real reso=5.0, core::Real gridSpacing=0.0)
	Load an MRC (="new-CCP4") density map. More...

bool	writeMRC (std::string mapfilestem)
	(debugging) Write MRC mapfile More...

bool	writeMAT (std::string mapfilestem)
	(debugging) Write MATLAB v5 mapfile More...

numeric::xyzMatrix< core::Real >	rotAlign2DPose (core::pose::Pose const &pose, std::string axis)
	Align a pose about a 2D rotation axis. More...

core::Real	matchCentroidPose (core::pose::Pose const &pose, core::conformation::symmetry::SymmetryInfoCOP symmInfo=NULL, 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=NULL, bool cacheCCs=false)
	Quickly matches a centroid pose into a low-resolution density map by placing a single Gaussian at each atom. More...

core::Real	matchPoseToPatterson (core::pose::Pose const &pose, bool cacheCCs=false)
	Match a pose to a patterson map. More...

core::Real	rematchResToPatterson (core::conformation::Residue const &rsd) const
	Rematch the pose to a patterson map, using previous rho_calc with only rsd changed. More...

void	updateCachedDensity (core::conformation::Residue const &rsd)
	Update cached rho_calc by changing residue 'rsd'. More...

core::Real	matchRes (int resid, core::conformation::Residue const &rsd, core::pose::Pose const &pose, core::conformation::symmetry::SymmetryInfoCOP symmInfo=NULL, 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=NULL)
	Match a residue's conformation to the density map. Same as matchRes, but using a fast approximation to the match function. More...

void	compute_symm_rotations (core::pose::Pose const &pose, core::conformation::symmetry::SymmetryInfoCOP symmInfo=NULL)
	Computes the symmatric rotation matrices. 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...

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	dCCdx_pat (int atmid, int resid, numeric::xyzVector< core::Real > const &X, core::pose::Pose const &pose, numeric::xyzVector< core::Real > &gradX)
	Return the gradient of patterson-CC w.r.t. atom X's movement. 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::Real >	getTransform ()
	Get the transformation from indices to Cartesian coords using 'real' origin. More...

void	set_nres (int nres)
	set # of residues More...

void	showCachedScores (utility::vector1< int > const &reses)
	Print cached CCs. More...

core::Real	getCachedScore (core::Size resid)

void	setUseDensityInMinimizer (bool newVal)

bool	getUseDensityInMinimizer () const

void	setUseExactDerivatives (bool newVal)

bool	getUseExactDerivatives () const

void	setWindow (core::Size window_in)

core::Size	getWindow ()

void	setScoreWindowContext (bool newVal)

bool	getScoreWindowContext () const

bool	isMapLoaded () const

core::Real	getNumDerivH () const

core::Real	getMean () const

core::Real	getMin () const

core::Real	getMax () const

core::Real	getStdev () const

core::Real	getResolution () const

numeric::xyzVector< core::Real >	getCoM () const

numeric::xyzVector< core::Real >	getOrigin () const

numeric::xyzVector< core::Real >	getEffOrigin () const

utility::vector1 < core::kinematics::RT >	getsymmOps () const

void	maskResidues (int scoring_mask)

void	maskResidues (utility::vector1< int > const &scoring_mask)

void	clearMask ()

ObjexxFCL::FArray3D< float > const &	data () const

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

void	cart2frac (numeric::xyzVector< core::Real > const &cartX, numeric::xyzVector< core::Real > &fracX) const

void	frac2cart (numeric::xyzVector< core::Real > const &fracX, numeric::xyzVector< core::Real > &cartX) const

numeric::xyzVector< core::Real >	delt_cart (numeric::xyzVector< core::Real > const &cartX1, numeric::xyzVector< core::Real > const &cartX2)

numeric::xyzVector< core::Real >	get_cart_unitCell (numeric::xyzVector< core::Real > const &cartX)

numeric::xyzVector< core::Real >	get_nearest_UC (numeric::xyzVector< core::Real > const &cartX_in, numeric::xyzVector< core::Real > const &cartX_ref)

numeric::xyzVector< core::Real >	dens_grad (numeric::xyzVector< core::Real > const &idxX) const

void	resize (core::Real approxGridSpacing)
	resize the map via FFT More...

void	get_symmMap (int vrtid, utility::vector1< int > &X_map, numeric::xyzMatrix< core::Real > &R)

void	get_R (int subunit, numeric::xyzMatrix< core::Real > &R)

Private Member Functions
void	computeGradients ()

void	computeStats ()

int	suggestRadius ()

void	initializeSymmOps (utility::vector1< std::string > const &symList)

void	computeCrystParams ()

void	expandToUnitCell ()

void	setup_patterson_first_time (core::pose::Pose const &pose)
	Precomputes a bunch of stuff for patterson map scoring. More...

void	setup_fastscoring_first_time (core::pose::Pose const &pose)
	setup oversampled maps for fast density scoring More...

utility::vector1 < ObjexxFCL::FArray3D < std::complex< double > > * >	getFdrhoc (OneGaussianScattering S)

double	S2 (int h, int k, int l)

Private Attributes
bool	isLoaded

ObjexxFCL::FArray3D< float >	density

ObjexxFCL::FArray3D < std::complex< double > >	Fdensity

std::map< core::Size, bool >	scoring_mask_

core::Real	reso

core::Real	ATOM_MASK

core::Real	CA_MASK

core::Real	force_apix_

core::Size	WINDOW_

bool	score_window_context_

bool	remap_symm_

bool	DensScoreInMinimizer

bool	ExactDerivatives

core::Real	NUM_DERIV_H

core::Real	NUM_DERIV_H_CEN

core::Real	PattersonB

core::Real	PattersonMinR

core::Real	PattersonMaxR

ObjexxFCL::FArray3D< float >	PattersonEpsilon

ObjexxFCL::FArray3D< double >	p_o

double	po_bar

ObjexxFCL::FArray3D< double >	fastdens_score

ObjexxFCL::FArray3D< double >	fastdens_dscoredx

ObjexxFCL::FArray3D< double >	fastdens_dscoredy

ObjexxFCL::FArray3D< double >	fastdens_dscoredz

numeric::xyzVector< int >	fastgrid

numeric::xyzVector< core::Real >	fastorigin

ObjexxFCL::FArray3D< double >	rho_calc
	TONS OF CACHED STUFF. More...

core::Real	rho_calc_sum

ObjexxFCL::FArray3D < std::complex< double > >	Frho_calc

utility::vector1< core::Size >	bucket_counts

ObjexxFCL::FArray3D< core::Size >	bucket_id

core::Real	lowres_cut

core::Real	hires_cut

ObjexxFCL::FArray3D< double >	F_s2

ObjexxFCL::FArray3D< double >	Pcalc

utility::vector1< core::Real >	F2

utility::vector1 < ObjexxFCL::FArray3D < core::Size > >	symm_ptrs

std::map< int, ObjexxFCL::FArray3D < std::complex< double > > >	Fdrhoc_dx

std::map< int, ObjexxFCL::FArray3D < std::complex< double > > >	Fdrhoc_dy

std::map< int, ObjexxFCL::FArray3D < std::complex< double > > >	Fdrhoc_dz

utility::vector1 < utility::vector1 < numeric::xyzVector < core::Real > > >	rho_calc_atms

utility::vector1 < utility::vector1 < OneGaussianScattering > >	rho_calc_as

core::Real	p_sumC

core::Real	p_sumC2

core::Real	p_sumO

core::Real	p_sumO2

core::Real	p_sumCO

core::Real	p_vol

numeric::xyzVector< core::Real >	d_min

numeric::xyzVector< core::Real >	d_max

numeric::xyzVector< core::Real >	p_extent

numeric::xyzVector< core::Real >	p_origin

numeric::xyzVector< core::Size >	p_grid

numeric::xyzVector< core::Real >	p_CoM

core::Real	max_del_grid

numeric::xyzVector< int >	grid

numeric::xyzVector< core::Real >	origin

numeric::xyzVector< core::Real >	efforigin

utility::vector1< core::Real >	CCs

core::Real	CC_cen

core::Real	CC_aacen

core::Real	CC_pat

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< double >	coeff_grad_x
	VISUALIZATION-SPECIFIC. More...

ObjexxFCL::FArray3D< double >	coeff_grad_y

ObjexxFCL::FArray3D< double >	coeff_grad_z

numeric::xyzMatrix< core::Real >	f2c
	CRYSTAL INFO. More...

numeric::xyzMatrix< core::Real >	c2f

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::Size >	MINMULT

numeric::xyzVector< core::Real >	centerOfMass

core::Real	dens_mean

core::Real	dens_min

core::Real	dens_max

core::Real	dens_stdev

Detailed Description

Definition at line 49 of file ElectronDensity.hh.

Constructor & Destructor Documentation

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

virtual

Automatically generated virtual destructor for class deriving directly from ReferenceCount.

Auto-generated virtual destructor

Definition at line 79 of file ElectronDensity.cc.

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

constructor

null constructor

Definition at line 202 of file ElectronDensity.cc.

References core::init().

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

calulated density from a vector of poses

Definition at line 208 of file ElectronDensity.cc.

References core::chemical::aa_vrt, protocols::forge::build::SegmentInsertConnectionScheme::C, core::scoring::electron_density::OneGaussianScattering::C(), core::scoring::electron_density::findSampling5(), core::scoring::electron_density::get_A(), core::scoring::electron_density::is_missing_density(), core::scoring::electron_density::OneGaussianScattering::k(), core::conformation::Residue::nheavyatoms(), core::scoring::electron_density::pos_mod(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::scoring::electron_density::TR().

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)

Definition at line 61 of file ElectronDensity.hh.

References cellAngles, cellDimensions, density, efforigin, grid, init(), isLoaded, origin, and core::scoring::electron_density::pos_mod().

Member Function Documentation

void core::scoring::electron_density::ElectronDensity::cart2frac	(	numeric::xyzVector< core::Real > const &	cartX,
		numeric::xyzVector< core::Real > &	fracX
	)		const

inline

Definition at line 327 of file ElectronDensity.hh.

References c2f.

void core::scoring::electron_density::ElectronDensity::cart2idx	(	numeric::xyzVector< core::Real > const &	cartX,
		numeric::xyzVector< core::Real > &	idxX
	)		const

inline

Definition at line 301 of file ElectronDensity.hh.

References c2f, efforigin, and grid.

void core::scoring::electron_density::ElectronDensity::clear_dCCdx_res_cache ( core::pose::Pose const & pose)

Resets the counters used for derivative computation in sliding-window/fast scoring.

Definition at line 2523 of file ElectronDensity.cc.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::sequence::end, core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

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

void core::scoring::electron_density::ElectronDensity::clearMask ( )

inline

Definition at line 287 of file ElectronDensity.hh.

References scoring_mask_.

Referenced by protocols::electron_density::SetupForDensityScoringMover::apply(), and protocols::electron_density::findLoopFromPatterson().

void core::scoring::electron_density::ElectronDensity::compute_symm_rotations	(	core::pose::Pose const &	pose,
		core::conformation::symmetry::SymmetryInfoCOP	symmInfo = `NULL`
	)

Computes the symmatric rotation matrices.

Computes the symmatric rotation matrices. Stores mapping in 'symmap'.

Definition at line 2392 of file ElectronDensity.cc.

References core::conformation::Residue::atom(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::get_outgoing_edges(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), core::scoring::electron_density::TR(), and core::conformation::Atom::xyz().

Referenced by core::scoring::electron_density::ElecDensEnergy::setup_for_derivatives(), and core::scoring::electron_density::FastDensEnergy::setup_for_derivatives().

void core::scoring::electron_density::ElectronDensity::computeCrystParams ( )

private

Definition at line 4092 of file ElectronDensity.cc.

References core::id::D, core::scoring::electron_density::d2r(), core::scoring::sa, core::scoring::electron_density::square(), and core::scoring::electron_density::TR().

void core::scoring::electron_density::ElectronDensity::computeGradients ( )

private

Definition at line 4001 of file ElectronDensity.cc.

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

void core::scoring::electron_density::ElectronDensity::computeStats ( )

private

Definition at line 4046 of file ElectronDensity.cc.

References protocols::forge::build::SegmentInsertConnectionScheme::N, core::scoring::electron_density::TR(), and trans().

ObjexxFCL::FArray3D< float > const& core::scoring::electron_density::ElectronDensity::data ( ) const

inline

Definition at line 295 of file ElectronDensity.hh.

References density.

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.

Definition at line 3167 of file ElectronDensity.cc.

References core::scoring::electron_density::getDensityMap(), matchPose(), core::pose::Pose::set_xyz(), core::io::serialization::size(), and 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.

Definition at line 3100 of file ElectronDensity.cc.

References core::scoring::electron_density::getDensityMap(), matchPose(), core::pose::Pose::set_xyz(), and 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
	)

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.

Definition at line 2957 of file ElectronDensity.cc.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::conformation::Residue::atom(), core::scoring::electron_density::getDensityMap(), core::scoring::electron_density::interp_spline(), matchRes(), matchResFast(), core::pose::Pose::residue(), core::scoring::electron_density::TR(), core::scoring::rna::X, and core::conformation::Atom::xyz().

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

void 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
	)

Return the gradient of patterson-CC w.r.t. atom X's movement.

Definition at line 3236 of file ElectronDensity.cc.

References core::scoring::electron_density::getDensityMap(), matchPoseToPatterson(), core::pose::Pose::set_xyz(), core::io::serialization::size(), and core::scoring::electron_density::TR().

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

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.

Definition at line 3023 of file ElectronDensity.cc.

References core::conformation::Residue::atom(), core::scoring::electron_density::getDensityMap(), matchRes(), core::io::serialization::size(), core::scoring::electron_density::TR(), and core::conformation::Atom::xyz().

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

numeric::xyzVector< core::Real > core::scoring::electron_density::ElectronDensity::delt_cart	(	numeric::xyzVector< core::Real > const &	cartX1,
		numeric::xyzVector< core::Real > const &	cartX2
	)

Definition at line 1176 of file ElectronDensity.cc.

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

Definition at line 392 of file ElectronDensity.cc.

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

Referenced by protocols::viewer::triangleIterator::evalGradient().

void core::scoring::electron_density::ElectronDensity::expandToUnitCell ( )

private

Definition at line 3721 of file ElectronDensity.cc.

References core::pack::interaction_graph::debug, core::scoring::electron_density::pos_mod(), and writeMRC().

void core::scoring::electron_density::ElectronDensity::frac2cart	(	numeric::xyzVector< core::Real > const &	fracX,
		numeric::xyzVector< core::Real > &	cartX
	)		const

inline

Definition at line 330 of file ElectronDensity.hh.

References f2c.

numeric::xyzVector< core::Real > core::scoring::electron_density::ElectronDensity::get_cart_unitCell ( numeric::xyzVector< core::Real > const & cartX)

Definition at line 1235 of file ElectronDensity.cc.

numeric::xyzVector< core::Real > core::scoring::electron_density::ElectronDensity::get_nearest_UC	(	numeric::xyzVector< core::Real > const &	cartX_in,
		numeric::xyzVector< core::Real > const &	cartX_ref
	)

Definition at line 1201 of file ElectronDensity.cc.

References core::kinematics::tree::distance_squared().

void core::scoring::electron_density::ElectronDensity::get_R	(	int	subunit,
		numeric::xyzMatrix< core::Real > &	R
	)

inline

Definition at line 352 of file ElectronDensity.hh.

References symmap.

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

void core::scoring::electron_density::ElectronDensity::get_symmMap	(	int	vrtid,
		utility::vector1< int > &	X_map,
		numeric::xyzMatrix< core::Real > &	R
	)

inline

Definition at line 345 of file ElectronDensity.hh.

References symmap.

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

core::Real core::scoring::electron_density::ElectronDensity::getCachedScore ( core::Size resid)

inline

Definition at line 247 of file ElectronDensity.hh.

References CCs.

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

numeric::xyzVector<core::Real> core::scoring::electron_density::ElectronDensity::getCoM ( ) const

inline

Definition at line 275 of file ElectronDensity.hh.

References centerOfMass.

Referenced by protocols::electron_density::fastTransAlignPose().

numeric::xyzVector<core::Real> core::scoring::electron_density::ElectronDensity::getEffOrigin ( ) const

inline

Definition at line 277 of file ElectronDensity.hh.

References efforigin.

utility::vector1< ObjexxFCL::FArray3D< std::complex< double > > * > core::scoring::electron_density::ElectronDensity::getFdrhoc ( OneGaussianScattering S)

private

get Fdrho_d(xyz) compute if not already computed returns pointers to FArray

Definition at line 1251 of file ElectronDensity.cc.

References core::scoring::electron_density::OneGaussianScattering::a(), protocols::forge::build::SegmentInsertConnectionScheme::C, core::scoring::electron_density::OneGaussianScattering::C(), and core::scoring::electron_density::OneGaussianScattering::k().

core::Real core::scoring::electron_density::ElectronDensity::getMax ( ) const

inline

Definition at line 272 of file ElectronDensity.hh.

References dens_max.

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

inline

Definition at line 270 of file ElectronDensity.hh.

References dens_mean.

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

inline

Definition at line 271 of file ElectronDensity.hh.

References dens_min.

core::Real core::scoring::electron_density::ElectronDensity::getNumDerivH ( ) const

inline

Definition at line 269 of file ElectronDensity.hh.

References NUM_DERIV_H.

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

inline

Definition at line 276 of file ElectronDensity.hh.

References origin.

core::Real core::scoring::electron_density::ElectronDensity::getResolution ( ) const

inline

Definition at line 274 of file ElectronDensity.hh.

References reso.

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

inline

Definition at line 264 of file ElectronDensity.hh.

References score_window_context_.

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

inline

Definition at line 273 of file ElectronDensity.hh.

References dens_stdev.

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

inline

Definition at line 278 of file ElectronDensity.hh.

References symmOps.

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

inline

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

Definition at line 227 of file ElectronDensity.hh.

References grid, idx2cart(), and origin.

bool core::scoring::electron_density::ElectronDensity::getUseDensityInMinimizer ( ) const

inline

Definition at line 255 of file ElectronDensity.hh.

References DensScoreInMinimizer.

Referenced by protocols::electron_density::dockPoseIntoMap().

bool core::scoring::electron_density::ElectronDensity::getUseExactDerivatives ( ) const

inline

Definition at line 258 of file ElectronDensity.hh.

References ExactDerivatives.

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

inline

Definition at line 261 of file ElectronDensity.hh.

References WINDOW_.

template<class Q >

void core::scoring::electron_density::ElectronDensity::idx2cart	(	numeric::xyzVector< Q > const &	idxX,
		numeric::xyzVector< core::Real > &	cartX
	)		const

inline

Definition at line 309 of file ElectronDensity.hh.

References efforigin, f2c, and grid.

Referenced by protocols::electron_density::fastTransAlignPose(), and getTransform().

template<class Q >

void core::scoring::electron_density::ElectronDensity::idxoffset2cart	(	numeric::xyzVector< Q > const &	idxX,
		numeric::xyzVector< core::Real > &	cartX
	)		const

inline

Definition at line 317 of file ElectronDensity.hh.

References f2c, and grid.

void core::scoring::electron_density::ElectronDensity::init ( void )

Definition at line 349 of file ElectronDensity.cc.

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

Definition at line 3623 of file ElectronDensity.cc.

References rot(), core::scoring::electron_density::TR(), and trans().

bool core::scoring::electron_density::ElectronDensity::isMapLoaded ( ) const

inline

Definition at line 268 of file ElectronDensity.hh.

References isLoaded.

Referenced by core::scoring::electron_density::ElecDensAllAtomCenEnergy::ElecDensAllAtomCenEnergy(), core::scoring::electron_density::ElecDensCenEnergy::ElecDensCenEnergy(), core::scoring::electron_density::ElecDensEnergy::ElecDensEnergy(), core::scoring::electron_density::FastDensEnergy::FastDensEnergy(), core::scoring::electron_density::getDensityMap_legacy(), and core::scoring::electron_density::PattersonCorrEnergy::PattersonCorrEnergy().

void core::scoring::electron_density::ElectronDensity::maskResidues ( int scoring_mask)

inline

Definition at line 280 of file ElectronDensity.hh.

References scoring_mask_.

Referenced by protocols::electron_density::SetupForDensityScoringMover::apply(), and protocols::electron_density::findLoopFromPatterson().

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

inline

Definition at line 283 of file ElectronDensity.hh.

References scoring_mask_.

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

Quickly matches a centroid pose into a low-resolution density map by placing a single Gaussian at each CA.

Definition at line 680 of file ElectronDensity.cc.

References protocols::forge::build::SegmentInsertConnectionScheme::C, core::scoring::electron_density::is_missing_density(), core::chemical::ResidueType::is_protein(), core::scoring::electron_density::pos_mod(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::scoring::electron_density::square(), core::pose::Pose::total_residue(), core::scoring::electron_density::TR(), and core::conformation::Atom::xyz().

Referenced by core::scoring::electron_density::ElecDensCenEnergy::setup_for_derivatives(), and core::scoring::electron_density::ElecDensCenEnergy::setup_for_scoring().

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

Quickly matches a centroid pose into a low-resolution density map by placing a single Gaussian at each atom.

Match a residue to the density map, returning correlation coefficient between map and pose

Definition at line 915 of file ElectronDensity.cc.

References core::chemical::aa_vrt, protocols::forge::build::SegmentInsertConnectionScheme::C, core::scoring::electron_density::OneGaussianScattering::C(), core::scoring::electron_density::get_A(), core::scoring::electron_density::is_missing_density(), core::scoring::electron_density::OneGaussianScattering::k(), core::conformation::Residue::nheavyatoms(), core::scoring::electron_density::pos_mod(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::scoring::electron_density::TR().

Referenced by dCCdx_aacen(), dCCdx_cen(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::setup_for_derivatives(), and core::scoring::electron_density::ElecDensAllAtomCenEnergy::setup_for_scoring().

core::Real core::scoring::electron_density::ElectronDensity::matchPoseToPatterson	(	core::pose::Pose const &	pose,
		bool	cacheCCs = `false`
	)

Match a pose to a patterson map.

Match pose to patterson map.

Definition at line 1727 of file ElectronDensity.cc.

Referenced by dCCdx_pat(), protocols::electron_density::findLoopFromPatterson(), core::scoring::electron_density::PattersonCorrEnergy::setup_for_derivatives(), and core::scoring::electron_density::PattersonCorrEnergy::setup_for_scoring().

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 = `NULL`,
		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

Definition at line 2537 of file ElectronDensity.cc.

References core::conformation::Residue::atom(), core::conformation::Residue::atom_type_index(), core::conformation::Residue::atom_type_set(), protocols::forge::build::SegmentInsertConnectionScheme::C, core::scoring::electron_density::OneGaussianScattering::C(), core::graph::Node::const_edge_list_end(), 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::graph::Edge::get_first_node_ind(), core::graph::Edge::get_node(), core::graph::Edge::get_second_node_ind(), core::kinematics::FoldTree::is_cutpoint(), core::scoring::electron_density::is_missing_density(), core::scoring::electron_density::OneGaussianScattering::k(), core::scoring::electron_density::MAX_FLT, core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), core::scoring::electron_density::TR(), writeMRC(), and core::conformation::Atom::xyz().

Referenced by protocols::hybridization::CartesianSampler::compute_fragment_bias(), dCCdx_fastRes(), dCCdx_res(), 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 = `NULL`
	)

Match a residue's conformation to the density map. Same as matchRes, but using a fast approximation to the match function.

Match a residue to the density map. Use the fast version of the scoring function.

Definition at line 2918 of file ElectronDensity.cc.

References core::conformation::Residue::atom(), core::scoring::electron_density::interp_spline(), core::conformation::Residue::nheavyatoms(), core::scoring::electron_density::TR(), and core::conformation::Atom::xyz().

Referenced by dCCdx_fastRes(), and core::scoring::electron_density::FastDensEnergy::residue_pair_energy().

bool core::scoring::electron_density::ElectronDensity::readMRCandResize	(	std::string	mapfile,
		core::Real	reso = `5.0`,
		core::Real	gridSpacing = `0.0`
	)

Load an MRC (="new-CCP4") density map.

Definition at line 3306 of file ElectronDensity.cc.

Referenced by core::scoring::electron_density::getDensityMap_legacy().

bool core::scoring::electron_density::ElectronDensity::readMRCandResize	(	std::istream &	mapin,
		std::string	mapfile,
		core::Real	reso = `5.0`,
		core::Real	gridSpacing = `0.0`
	)

Load an MRC (="new-CCP4") density map.

Definition at line 3322 of file ElectronDensity.cc.

References core::scoring::electron_density::CCP4HDSIZE, core::sequence::end, core::scoring::electron_density::get_A(), core::scoring::electron_density::OneGaussianScattering::k(), core::id::swap(), core::scoring::electron_density::swap4_aligned(), and core::scoring::electron_density::TR().

core::Real core::scoring::electron_density::ElectronDensity::rematchResToPatterson ( core::conformation::Residue const & rsd) const

Rematch the pose to a patterson map, using previous rho_calc with only rsd changed.

Rematch the pose to a patterson map, using previous rho_calc with only rsd changed do not change rho_calc or update cache DOES NOT WORK WITH MASK!

Definition at line 2121 of file ElectronDensity.cc.

References core::conformation::Residue::atom(), core::conformation::Residue::atom_type_index(), core::conformation::Residue::atom_type_set(), protocols::forge::build::SegmentInsertConnectionScheme::C, core::scoring::electron_density::OneGaussianScattering::C(), core::scoring::electron_density::get_A(), core::scoring::electron_density::is_missing_density(), core::scoring::electron_density::OneGaussianScattering::k(), core::conformation::Residue::nheavyatoms(), core::conformation::Residue::seqpos(), and core::scoring::electron_density::square().

Referenced by core::scoring::electron_density::PattersonCorrEnergy::residue_pair_energy().

void core::scoring::electron_density::ElectronDensity::resize ( core::Real approxGridSpacing)

resize the map via FFT

Definition at line 3956 of file ElectronDensity.cc.

References core::scoring::electron_density::findSampling(), core::scoring::electron_density::resample(), and core::scoring::electron_density::TR().

numeric::xyzMatrix< core::Real > core::scoring::electron_density::ElectronDensity::rotAlign2DPose	(	core::pose::Pose const &	pose,
		std::string	axis
	)

Align a pose about a 2D rotation axis.

Match a residue to the density map, returning correlation coefficient between map and pose

Definition at line 405 of file ElectronDensity.cc.

Referenced by protocols::electron_density::fast2DRotAlignPose().

double core::scoring::electron_density::ElectronDensity::S2	(	int	h,
		int	k,
		int	l
	)

inlineprivate

Definition at line 384 of file ElectronDensity.hh.

References cosRcellAngles, and RcellDimensions.

void core::scoring::electron_density::ElectronDensity::set_nres ( int nres)

inline

set # of residues

Definition at line 234 of file ElectronDensity.hh.

References CCs, dCCdxs_aacen, dCCdxs_cen, dCCdxs_pat, dCCdxs_res, and symmap.

Referenced by protocols::electron_density::findLoopFromDensity(), core::scoring::electron_density::PattersonCorrEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::setup_for_scoring(), and core::scoring::electron_density::ElecDensCenEnergy::setup_for_scoring().

void core::scoring::electron_density::ElectronDensity::setScoreWindowContext ( bool newVal)

inline

Definition at line 263 of file ElectronDensity.hh.

References score_window_context_.

Referenced by protocols::hybridization::CartesianSampler::compute_fragment_bias().

void core::scoring::electron_density::ElectronDensity::setup_fastscoring_first_time ( core::pose::Pose const & pose)

private

setup oversampled maps for fast density scoring

Definition at line 1314 of file ElectronDensity.cc.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::pack::interaction_graph::debug, core::scoring::electron_density::findSampling(), core::scoring::electron_density::get_A(), core::scoring::electron_density::OneGaussianScattering::k(), core::conformation::Residue::nheavyatoms(), core::scoring::electron_density::resample(), core::pose::Pose::residue(), core::scoring::electron_density::spline_coeffs(), core::pose::Pose::total_residue(), core::scoring::electron_density::TR(), and writeMRC().

void core::scoring::electron_density::ElectronDensity::setup_patterson_first_time ( core::pose::Pose const & pose)

private

Precomputes a bunch of stuff for patterson map scoring.

Definition at line 1444 of file ElectronDensity.cc.

References core::chemical::aa_vrt, core::pack::interaction_graph::debug, core::scoring::electron_density::findSampling5(), core::scoring::electron_density::get_A(), core::scoring::electron_density::is_missing_density(), protocols::features::L, core::conformation::Residue::nheavyatoms(), core::scoring::electron_density::pos_mod(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), core::scoring::electron_density::TR(), and writeMRC().

void core::scoring::electron_density::ElectronDensity::setUseDensityInMinimizer ( bool newVal)

inline

Definition at line 254 of file ElectronDensity.hh.

References DensScoreInMinimizer.

Referenced by protocols::electron_density::dockPoseIntoMap().

void core::scoring::electron_density::ElectronDensity::setUseExactDerivatives ( bool newVal)

inline

Definition at line 257 of file ElectronDensity.hh.

References ExactDerivatives.

void core::scoring::electron_density::ElectronDensity::setWindow ( core::Size window_in)

inline

Definition at line 260 of file ElectronDensity.hh.

References WINDOW_.

Referenced by protocols::hybridization::CartesianSampler::compute_fragment_bias().

void core::scoring::electron_density::ElectronDensity::showCachedScores ( utility::vector1< int > const & reses)

Print cached CCs.

Definition at line 3778 of file ElectronDensity.cc.

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

int core::scoring::electron_density::ElectronDensity::suggestRadius ( )

private

void core::scoring::electron_density::ElectronDensity::updateCachedDensity ( core::conformation::Residue const & rsd)

Update cached rho_calc by changing residue 'rsd'.

Definition at line 2291 of file ElectronDensity.cc.

References core::conformation::Residue::atom(), core::conformation::Residue::atom_type_index(), core::conformation::Residue::atom_type_set(), protocols::forge::build::SegmentInsertConnectionScheme::C, core::scoring::electron_density::OneGaussianScattering::C(), core::scoring::electron_density::get_A(), core::scoring::electron_density::is_missing_density(), core::scoring::electron_density::OneGaussianScattering::k(), core::conformation::Residue::nheavyatoms(), core::conformation::Residue::seqpos(), and core::scoring::electron_density::square().

Referenced by core::scoring::electron_density::PattersonCorrEnergy::update_residue_for_packing().

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

(debugging) Write MATLAB v5 mapfile

Definition at line 3786 of file ElectronDensity.cc.

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

(debugging) Write MRC mapfile

Definition at line 3862 of file ElectronDensity.cc.

References core::scoring::electron_density::CCP4HDSIZE, and core::scoring::electron_density::TR().

Referenced by expandToUnitCell(), matchPoseToPatterson(), matchRes(), rotAlign2DPose(), setup_fastscoring_first_time(), and setup_patterson_first_time().

Member Data Documentation

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

private

Definition at line 408 of file ElectronDensity.hh.

utility::vector1<core::Size> core::scoring::electron_density::ElectronDensity::bucket_counts

private

Definition at line 433 of file ElectronDensity.hh.

ObjexxFCL::FArray3D< core::Size > core::scoring::electron_density::ElectronDensity::bucket_id

private

Definition at line 434 of file ElectronDensity.hh.

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

private

Definition at line 496 of file ElectronDensity.hh.

Referenced by cart2frac(), and cart2idx().

core::Real core::scoring::electron_density::ElectronDensity::CA_MASK

private

Definition at line 408 of file ElectronDensity.hh.

core::Real core::scoring::electron_density::ElectronDensity::CC_aacen

private

Definition at line 470 of file ElectronDensity.hh.

core::Real core::scoring::electron_density::ElectronDensity::CC_cen

private

Definition at line 470 of file ElectronDensity.hh.

core::Real core::scoring::electron_density::ElectronDensity::CC_pat

private

Definition at line 470 of file ElectronDensity.hh.

utility::vector1<core::Real> core::scoring::electron_density::ElectronDensity::CCs

private

Definition at line 469 of file ElectronDensity.hh.

Referenced by getCachedScore(), and set_nres().

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

private

Definition at line 499 of file ElectronDensity.hh.

Referenced by ElectronDensity().

numeric::xyzVector<float> core::scoring::electron_density::ElectronDensity::cellDimensions

private

Definition at line 499 of file ElectronDensity.hh.

Referenced by ElectronDensity().

numeric::xyzVector<core::Real> core::scoring::electron_density::ElectronDensity::centerOfMass

private

Definition at line 513 of file ElectronDensity.hh.

Referenced by getCoM().

ObjexxFCL::FArray3D< double > core::scoring::electron_density::ElectronDensity::coeff_grad_x

mutableprivate

VISUALIZATION-SPECIFIC.

Definition at line 489 of file ElectronDensity.hh.

ObjexxFCL::FArray3D< double > core::scoring::electron_density::ElectronDensity::coeff_grad_y

mutableprivate

Definition at line 489 of file ElectronDensity.hh.

ObjexxFCL::FArray3D< double > core::scoring::electron_density::ElectronDensity::coeff_grad_z

mutableprivate

Definition at line 489 of file ElectronDensity.hh.

numeric::xyzVector<float> core::scoring::electron_density::ElectronDensity::cosRcellAngles

private

Definition at line 500 of file ElectronDensity.hh.

Referenced by S2().

numeric::xyzVector< core::Real > core::scoring::electron_density::ElectronDensity::d_max

private

Definition at line 458 of file ElectronDensity.hh.

numeric::xyzVector< core::Real > core::scoring::electron_density::ElectronDensity::d_min

private

Definition at line 458 of file ElectronDensity.hh.

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

private

Definition at line 472 of file ElectronDensity.hh.

Referenced by set_nres().

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

private

Definition at line 471 of file ElectronDensity.hh.

Referenced by set_nres().

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

private

Definition at line 474 of file ElectronDensity.hh.

Referenced by set_nres().

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

private

Definition at line 473 of file ElectronDensity.hh.

Referenced by set_nres().

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

private

Definition at line 514 of file ElectronDensity.hh.

Referenced by getMax().

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

private

Definition at line 514 of file ElectronDensity.hh.

Referenced by getMean().

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

private

Definition at line 514 of file ElectronDensity.hh.

Referenced by getMin().

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

private

Definition at line 514 of file ElectronDensity.hh.

Referenced by getStdev().

ObjexxFCL::FArray3D< float > core::scoring::electron_density::ElectronDensity::density

private

Definition at line 401 of file ElectronDensity.hh.

Referenced by data(), and ElectronDensity().

bool core::scoring::electron_density::ElectronDensity::DensScoreInMinimizer

private

Definition at line 412 of file ElectronDensity.hh.

Referenced by getUseDensityInMinimizer(), and setUseDensityInMinimizer().

numeric::xyzVector< core::Real > core::scoring::electron_density::ElectronDensity::efforigin

private

Definition at line 466 of file ElectronDensity.hh.

Referenced by cart2idx(), ElectronDensity(), getEffOrigin(), and idx2cart().

bool core::scoring::electron_density::ElectronDensity::ExactDerivatives

private

Definition at line 412 of file ElectronDensity.hh.

Referenced by getUseExactDerivatives(), and setUseExactDerivatives().

utility::vector1<core::Real> core::scoring::electron_density::ElectronDensity::F2

private

Definition at line 438 of file ElectronDensity.hh.

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

private

CRYSTAL INFO.

Definition at line 496 of file ElectronDensity.hh.

Referenced by frac2cart(), idx2cart(), and idxoffset2cart().

ObjexxFCL::FArray3D< double > core::scoring::electron_density::ElectronDensity::F_s2

private

Definition at line 436 of file ElectronDensity.hh.

ObjexxFCL::FArray3D< double > core::scoring::electron_density::ElectronDensity::fastdens_dscoredx

private

Definition at line 422 of file ElectronDensity.hh.

ObjexxFCL::FArray3D< double > core::scoring::electron_density::ElectronDensity::fastdens_dscoredy

private

Definition at line 422 of file ElectronDensity.hh.

ObjexxFCL::FArray3D< double > core::scoring::electron_density::ElectronDensity::fastdens_dscoredz

private

Definition at line 422 of file ElectronDensity.hh.

ObjexxFCL::FArray3D< double > core::scoring::electron_density::ElectronDensity::fastdens_score

private

Definition at line 421 of file ElectronDensity.hh.

numeric::xyzVector< int > core::scoring::electron_density::ElectronDensity::fastgrid

private

Definition at line 423 of file ElectronDensity.hh.

numeric::xyzVector< core::Real > core::scoring::electron_density::ElectronDensity::fastorigin

private

Definition at line 424 of file ElectronDensity.hh.

ObjexxFCL::FArray3D< std::complex<double> > core::scoring::electron_density::ElectronDensity::Fdensity

private

Definition at line 404 of file ElectronDensity.hh.

std::map< int , ObjexxFCL::FArray3D< std::complex<double> > > core::scoring::electron_density::ElectronDensity::Fdrhoc_dx

private

Definition at line 446 of file ElectronDensity.hh.

std::map< int , ObjexxFCL::FArray3D< std::complex<double> > > core::scoring::electron_density::ElectronDensity::Fdrhoc_dy

private

Definition at line 447 of file ElectronDensity.hh.

std::map< int , ObjexxFCL::FArray3D< std::complex<double> > > core::scoring::electron_density::ElectronDensity::Fdrhoc_dz

private

Definition at line 448 of file ElectronDensity.hh.

core::Real core::scoring::electron_density::ElectronDensity::force_apix_

private

Definition at line 408 of file ElectronDensity.hh.

ObjexxFCL::FArray3D< std::complex<double> > core::scoring::electron_density::ElectronDensity::Frho_calc

private

Definition at line 432 of file ElectronDensity.hh.

numeric::xyzVector< int > core::scoring::electron_density::ElectronDensity::grid

private

Definition at line 465 of file ElectronDensity.hh.

Referenced by cart2idx(), ElectronDensity(), getTransform(), idx2cart(), and idxoffset2cart().

core::Real core::scoring::electron_density::ElectronDensity::hires_cut

private

Definition at line 435 of file ElectronDensity.hh.

bool core::scoring::electron_density::ElectronDensity::isLoaded

private

Definition at line 398 of file ElectronDensity.hh.

Referenced by ElectronDensity(), and isMapLoaded().

core::Real core::scoring::electron_density::ElectronDensity::lowres_cut

private

Definition at line 435 of file ElectronDensity.hh.

core::Real core::scoring::electron_density::ElectronDensity::max_del_grid

private

Definition at line 464 of file ElectronDensity.hh.

numeric::xyzVector<core::Size> core::scoring::electron_density::ElectronDensity::MINMULT

private

Definition at line 510 of file ElectronDensity.hh.

core::Real core::scoring::electron_density::ElectronDensity::NUM_DERIV_H

private

Definition at line 413 of file ElectronDensity.hh.

Referenced by getNumDerivH().

core::Real core::scoring::electron_density::ElectronDensity::NUM_DERIV_H_CEN

private

Definition at line 413 of file ElectronDensity.hh.

numeric::xyzVector< core::Real > core::scoring::electron_density::ElectronDensity::origin

private

Definition at line 466 of file ElectronDensity.hh.

Referenced by ElectronDensity(), getOrigin(), and getTransform().

numeric::xyzVector< core::Real > core::scoring::electron_density::ElectronDensity::p_CoM

private

Definition at line 461 of file ElectronDensity.hh.

numeric::xyzVector< core::Real > core::scoring::electron_density::ElectronDensity::p_extent

private

Definition at line 459 of file ElectronDensity.hh.

numeric::xyzVector< core::Size > core::scoring::electron_density::ElectronDensity::p_grid

private

Definition at line 460 of file ElectronDensity.hh.

ObjexxFCL::FArray3D< double > core::scoring::electron_density::ElectronDensity::p_o

private

Definition at line 417 of file ElectronDensity.hh.

numeric::xyzVector< core::Real > core::scoring::electron_density::ElectronDensity::p_origin

private

Definition at line 459 of file ElectronDensity.hh.

core::Real core::scoring::electron_density::ElectronDensity::p_sumC

private

Definition at line 455 of file ElectronDensity.hh.

core::Real core::scoring::electron_density::ElectronDensity::p_sumC2

private

Definition at line 455 of file ElectronDensity.hh.

core::Real core::scoring::electron_density::ElectronDensity::p_sumCO

private

Definition at line 455 of file ElectronDensity.hh.

core::Real core::scoring::electron_density::ElectronDensity::p_sumO

private

Definition at line 455 of file ElectronDensity.hh.

core::Real core::scoring::electron_density::ElectronDensity::p_sumO2

private

Definition at line 455 of file ElectronDensity.hh.

core::Real core::scoring::electron_density::ElectronDensity::p_vol

private

Definition at line 455 of file ElectronDensity.hh.

core::Real core::scoring::electron_density::ElectronDensity::PattersonB

private

Definition at line 413 of file ElectronDensity.hh.

ObjexxFCL::FArray3D< float > core::scoring::electron_density::ElectronDensity::PattersonEpsilon

private

Definition at line 414 of file ElectronDensity.hh.

core::Real core::scoring::electron_density::ElectronDensity::PattersonMaxR

private

Definition at line 413 of file ElectronDensity.hh.

core::Real core::scoring::electron_density::ElectronDensity::PattersonMinR

private

Definition at line 413 of file ElectronDensity.hh.

ObjexxFCL::FArray3D< double > core::scoring::electron_density::ElectronDensity::Pcalc

private

Definition at line 437 of file ElectronDensity.hh.

double core::scoring::electron_density::ElectronDensity::po_bar

private

Definition at line 418 of file ElectronDensity.hh.

numeric::xyzVector<float> core::scoring::electron_density::ElectronDensity::RcellDimensions

private

Definition at line 500 of file ElectronDensity.hh.

Referenced by S2().

bool core::scoring::electron_density::ElectronDensity::remap_symm_

private

Definition at line 410 of file ElectronDensity.hh.

core::Real core::scoring::electron_density::ElectronDensity::reso

private

Definition at line 408 of file ElectronDensity.hh.

Referenced by getResolution().

ObjexxFCL::FArray3D< double > core::scoring::electron_density::ElectronDensity::rho_calc

private

TONS OF CACHED STUFF.

Definition at line 430 of file ElectronDensity.hh.

utility::vector1< utility::vector1< OneGaussianScattering > > core::scoring::electron_density::ElectronDensity::rho_calc_as

private

Definition at line 452 of file ElectronDensity.hh.

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

private

Definition at line 451 of file ElectronDensity.hh.

core::Real core::scoring::electron_density::ElectronDensity::rho_calc_sum

private

Definition at line 431 of file ElectronDensity.hh.

core::Real core::scoring::electron_density::ElectronDensity::RV

private

Definition at line 501 of file ElectronDensity.hh.

bool core::scoring::electron_density::ElectronDensity::score_window_context_

private

Definition at line 410 of file ElectronDensity.hh.

Referenced by getScoreWindowContext(), and setScoreWindowContext().

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

private

Definition at line 407 of file ElectronDensity.hh.

Referenced by clearMask(), and maskResidues().

utility::vector1< ObjexxFCL::FArray3D< core::Size > > core::scoring::electron_density::ElectronDensity::symm_ptrs

private

Definition at line 441 of file ElectronDensity.hh.

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)

Definition at line 481 of file ElectronDensity.hh.

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

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

private

Definition at line 506 of file ElectronDensity.hh.

Referenced by getsymmOps().

utility::vector1< numeric::xyzMatrix<core::Real> > core::scoring::electron_density::ElectronDensity::symmRotOps

private

Definition at line 507 of file ElectronDensity.hh.

core::Real core::scoring::electron_density::ElectronDensity::V

private

Definition at line 501 of file ElectronDensity.hh.

core::Size core::scoring::electron_density::ElectronDensity::WINDOW_

private

Definition at line 409 of file ElectronDensity.hh.

Referenced by getWindow(), and setWindow().

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

src/core/scoring/electron_density/ElectronDensity.hh
src/core/scoring/electron_density/ElectronDensity.cc

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

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