#include <ElectronDensity.hh>

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 (used for debugging only!) More...

void	init ()
	Initialize map from cmd line options. More...

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, bool writeRhoCalc=false, bool writeRhoMask=false)
	(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)
	Match a pose into a medium-resolution density map by placing a single Gaussian at each atom. More...

void	maskDensityMap (poseCoords const &pose, core::Real radius)
	mask the density map (like chimera 'zone' but sigmoidal mask) More...

void	getResolutionBins (core::Size nbuckets, core::Real maxreso, core::Real minreso, utility::vector1< core::Real > &, utility::vector1< core::Size > &, bool S2_bin=false)
	get resolution bins (informational) More...

utility::vector1< core::Real >	getIntensities (core::Size nbuckets, core::Real maxreso, core::Real minreso, bool S2_bin=false)
	Compute map intensities. More...

utility::vector1< core::Real >	getIntensitiesMasked (poseCoords const &pose, core::Size nbuckets, core::Real maxreso, core::Real minreso, bool S2_bin=false)
	Compute map intensities, masked by a pose. More...

void	getIntensities (poseCoords const &pose, core::Size nbuckets, core::Real maxreso, core::Real minreso, utility::vector1< core::Real > &Imodel, bool S2_bin=false)
	Compute intensities from a pose. More...

void	getMapMapError (ObjexxFCL::FArray3D< float > const &map2, core::Size nbuckets, core::Real maxreso, core::Real minreso, utility::vector1< core::Real > &FSC, utility::vector1< core::Real > &phaseError, utility::vector1< core::Real > &complexPlaneError, bool S2_bin=false)
	Compute map-map FSC & errors. More...

void	getModelMapError (poseCoords const &pose, core::Size nbuckets, core::Real maxreso, core::Real minreso, utility::vector1< core::Real > const &mapmapPhaseError, utility::vector1< core::Real > const &mapmapComplexPlaneError, utility::vector1< core::Real > &FSC, utility::vector1< core::Real > &phaseError, core::Real &phaseErrorSum, core::Real &complexPlaneErrorK, core::Real &complexPlaneErrorProb, bool masked=false, bool S2_bin=false, core::Real mask_radius=0)
	Compute model-map FSC & errors. More...

void	getFSC (poseCoords const &pose, core::Size nbuckets, core::Real maxreso, core::Real minreso, utility::vector1< core::Real > &FSC, bool masked=false, bool S2_bin=false, core::Real mask_radius=0)
	Compute model-map FSC & errors. More...

core::Real	getRSCC (poseCoords const &pose)
	Compute model-map RSCC. More...

core::Real	getRSCC (ObjexxFCL::FArray3D< float > const &map2)
	Compute map-map RSCC. More...

void	scaleIntensities (utility::vector1< core::Real > I_tgt, core::Real maxreso, core::Real minreso, bool S2_bin=false)
	Compute intensities, update density. More...

void	calcRhoC (poseCoords const &pose)

core::Real	maxNominalRes ()

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, bool ignoreBs=false)
	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...

core::Real	matchPointFast (numeric::xyzVector< core::Real > X)
	access fastdens scoring for a single point More...

void	dCCdx_PointFast (numeric::xyzVector< core::Real > X, numeric::xyzVector< core::Real > &dCCdx)
	access fastdens scoring for a single point More...

void	dCCdx_res (int atmid, int resid, numeric::xyzVector< core::Real > const &X, core::conformation::Residue const &rsd, core::pose::Pose const &pose, numeric::xyzVector< core::Real > &gradX)
	Return the gradient of CC w.r.t. atom X's movement Uses information stored from the previous call to matchRes with this resid. More...

void	dCCdx_fastRes (int atmid, int resid, numeric::xyzVector< core::Real > const &X, core::conformation::Residue const &rsd, core::pose::Pose const &pose, numeric::xyzVector< core::Real > &gradX)
	Return the gradient of "fast CC" w.r.t. atom X's movement Uses information stored from the previous call to matchRes with this resid. More...

Real	dCCdB_fastRes (int atmid, int resid, core::conformation::Residue const &rsd, core::pose::Pose const &pose)
	Gradient of CC w.r.t B factors. More...

void	dCCdBs (core::pose::Pose const &pose, utility::vector1< core::Real > &dE_dvars)
	calculate all gradients of CC w.r.t B factors (slow more precise version) More...

void	rescale_fastscoring_temp_bins (core::pose::Pose const &pose, bool init=false)

void	dCCdx_cen (int resid, numeric::xyzVector< core::Real > const &X, core::pose::Pose const &pose, numeric::xyzVector< core::Real > &gradX)
	Return the gradient of CC w.r.t. res X's CA's movement Centroid-mode analogue of dCCdx. More...

void	dCCdx_aacen (int atmid, int resid, numeric::xyzVector< core::Real > const &X, core::pose::Pose const &pose, numeric::xyzVector< core::Real > &gradX)
	Return the gradient of whole-structure-CC w.r.t. atom X's movement non-sliding-window analogue of dCCdx. More...

void	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...

void	compute_rho (core::pose::Pose const &pose, utility::vector1< core::id::AtomID > const &atom_ids, ObjexxFCL::FArray3D< double > &rho_calc, ObjexxFCL::FArray3D< double > &inv_rho_mask)
	compute rho_c based on a list of atoms More...

numeric::xyzVector< double >	match_fragment (ObjexxFCL::FArray3D< double > const &rho_calc, ObjexxFCL::FArray3D< double > const &mask, ObjexxFCL::FArray3D< double > const &rho_obs, core::Real radius=6.0)

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	setSCscaling (core::Real SC_scalingin)

core::Real	getSCscaling ()

void	setWindow (core::Size window_in)

core::Size	getWindow ()

void	setScoreWindowContext (bool newVal)

bool	getScoreWindowContext () const

bool	isMapLoaded () const

core::Real	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

core::Real	getAtomMask () const

void	maskResidues (int scoring_mask)

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

void	clearMask ()

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

void	set_data (ObjexxFCL::FArray3D< double > const &density_in)

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::xyzMatrix< core::Real >	get_f2c ()

numeric::xyzMatrix< core::Real >	get_c2f ()

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	density_change_trigger ()
	The function is called everytime the density changes. More...

void	smooth_intensities (utility::vector1< core::Real > &) const

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...

void	setup_fastscoring_first_time (Real scalefactor)

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

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

double	voxel_volume ()

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::Real	SC_scaling_

core::Real	ATOM_MASK_PADDING

core::Size	WINDOW_

bool	score_window_context_

bool	remap_symm_

bool	legacy_

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::FArray4D< double >	fastdens_score

core::Size	nkbins_

core::Real	kmin_

core::Real	kmax_

core::Real	kstep_

numeric::xyzVector< int >	fastgrid

numeric::xyzVector< core::Real >	fastorigin

ObjexxFCL::FArray3D< double >	rho_calc
	TONS OF CACHED STUFF <<< this should live in its own class! More...

ObjexxFCL::FArray3D< double >	rho_solv

ObjexxFCL::FArray3D< double >	inv_rho_mask

core::Real	rho_calc_sum

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

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

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	minimumB

core::Real	effectiveB

numeric::xyzVector< int >	grid

numeric::xyzVector< core::Real >	origin

numeric::xyzVector< core::Real >	efforigin

bool	use_altorigin

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

Constructor & Destructor Documentation

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

virtual

Automatically generated virtual destructor for class deriving directly from ReferenceCount.

Auto-generated virtual destructor

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

constructor

null constructor

References core::init::init().

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

calulated density from a vector of poses

References core::chemical::aa_vrt, core::scoring::electron_density::OneGaussianScattering::C(), d_max, d_min, density, core::scoring::electron_density::findSampling5(), core::scoring::electron_density::get_A(), grid, core::scoring::electron_density::is_missing_density(), core::scoring::electron_density::OneGaussianScattering::k(), core::conformation::Residue::nheavyatoms(), nres, 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 (used for debugging only!)

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::calcRhoC ( poseCoords const & pose )

References core::scoring::electron_density::OneGaussianScattering::C(), density, numeric::fourier::fft3(), core::scoring::electron_density::get_A(), grid, core::scoring::electron_density::OneGaussianScattering::k(), core::scoring::electron_density::pos_mod(), core::scoring::electron_density::pose_has_nonzero_Bs(), and core::scoring::electron_density::TR.

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

inline

References c2f.

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

inline

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.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, begin, 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

References scoring_mask_.

void core::scoring::electron_density::ElectronDensity::compute_rho	(	core::pose::Pose const &	pose,
		utility::vector1< core::id::AtomID > const &	atom_ids,
		ObjexxFCL::FArray3D< double > &	rho_calc,
		ObjexxFCL::FArray3D< double > &	inv_rho_mask
	)

compute rho_c based on a list of atoms

References core::conformation::Residue::atom(), core::conformation::Residue::atom_type_index(), core::conformation::Residue::atom_type_set(), core::scoring::electron_density::OneGaussianScattering::C(), core::scoring::electron_density::get_A(), grid, core::scoring::electron_density::is_missing_density(), core::scoring::electron_density::OneGaussianScattering::k(), core::conformation::Residue::last_backbone_atom(), basic::options::option, core::scoring::electron_density::pos_mod(), core::pose::Pose::residue(), basic::options::OptionKeys::edensity::sc_scaling, and core::scoring::electron_density::TR.

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'.

References numeric::alignVectorSets(), core::conformation::Residue::atom(), numeric::xyzMatrix< class >::col_x(), numeric::xyzMatrix< class >::col_y(), numeric::xyzMatrix< class >::col_z(), exit, core::pose::Pose::fold_tree(), utility::pointer::owning_ptr< T >::get(), core::kinematics::FoldTree::get_outgoing_edges(), l, nres, core::pose::Pose::residue(), numeric::xyzMatrix< class >::rows(), 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

References core::id::D, core::scoring::electron_density::d2r(), numeric::xyzMatrix< class >::rows(), core::scoring::sa, core::scoring::electron_density::square(), core::scoring::electron_density::TR, and core::chemical::element::V.

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

private

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

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

private

References density, core::chemical::element::N, and sum().

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

inline

References density.

Real core::scoring::electron_density::ElectronDensity::dCCdB_fastRes	(	int	atmid,
		int	resid,
		core::conformation::Residue const &	rsd,
		core::pose::Pose const &	pose
	)

Gradient of CC w.r.t B factors.

References core::scoring::electron_density::OneGaussianScattering::a(), core::conformation::Residue::aa(), core::chemical::aa_vrt, core::conformation::Residue::atom_type_index(), core::conformation::Residue::atom_type_set(), core::chemical::element::B, core::scoring::electron_density::OneGaussianScattering::dk(), core::scoring::electron_density::get_A(), core::scoring::electron_density::interp_dspline(), core::scoring::electron_density::OneGaussianScattering::k(), core::pose::Pose::pdb_info(), core::scoring::electron_density::pos_mod(), core::pose::Pose::residue(), core::conformation::Residue::seqpos(), core::scoring::electron_density::TR, core::chemical::element::W, and core::conformation::Residue::xyz().

void core::scoring::electron_density::ElectronDensity::dCCdBs	(	core::pose::Pose const &	pose,
		utility::vector1< core::Real > &	dE_dvars
	)

calculate all gradients of CC w.r.t B factors (slow more precise version)

References core::chemical::aa_vrt, core::scoring::electron_density::OneGaussianScattering::C(), core::pose::Pose::conformation(), density, core::scoring::electron_density::OneGaussianScattering::dk(), core::scoring::electron_density::get_A(), grid, core::pose::symmetry::is_symmetric(), core::scoring::electron_density::OneGaussianScattering::k(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::pdb_info(), core::scoring::electron_density::pos_mod(), core::pose::Pose::residue(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), core::pose::Pose::total_residue(), and core::scoring::electron_density::poseCoord::x_.

void core::scoring::electron_density::ElectronDensity::dCCdx_aacen	(	int	atmid,
		int	resid,
		numeric::xyzVector< core::Real > const &	X,
		core::pose::Pose const &	pose,
		numeric::xyzVector< core::Real > &	gradX
	)

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

References exit, 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.

References exit, 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.

References core::scoring::electron_density::OneGaussianScattering::a(), core::conformation::Residue::aa(), core::chemical::aa_vrt, core::conformation::Residue::atom(), core::conformation::Residue::atom_type_index(), core::conformation::Residue::atom_type_set(), core::chemical::element::B, core::scoring::electron_density::get_A(), core::scoring::electron_density::getDensityMap(), core::scoring::electron_density::interp_dspline(), core::scoring::electron_density::OneGaussianScattering::k(), matchRes(), matchResFast(), core::pose::Pose::pdb_info(), core::scoring::electron_density::pos_mod(), core::pose::Pose::residue(), core::conformation::Residue::seqpos(), core::scoring::electron_density::TR, core::chemical::element::W, 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.

References exit, 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_PointFast	(	numeric::xyzVector< core::Real >	X,
		numeric::xyzVector< core::Real > &	dCCdx
	)

access fastdens scoring for a single point

References core::scoring::electron_density::interp_dspline(), core::scoring::electron_density::pos_mod(), and core::scoring::electron_density::TR.

void core::scoring::electron_density::ElectronDensity::dCCdx_res	(	int	atmid,
		int	resid,
		numeric::xyzVector< core::Real > const &	X,
		core::conformation::Residue const &	rsd,
		core::pose::Pose const &	pose,
		numeric::xyzVector< core::Real > &	gradX
	)

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

References core::conformation::Residue::atom(), exit, 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
	)

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

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

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

private

The function is called everytime the density changes.

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

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

private

References basic::options::OptionKeys::edensity::debug, density, grid, basic::options::option, 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

References f2c.

numeric::xyzMatrix<core::Real> core::scoring::electron_density::ElectronDensity::get_c2f ( )

inline

References c2f.

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

numeric::xyzMatrix<core::Real> core::scoring::electron_density::ElectronDensity::get_f2c ( )

inline

References f2c.

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
	)

References distance_squared(), numeric::xyzVector< class >::distance_squared(), and numeric::xyzVector< class >::length_squared().

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

inline

References runtime_assert, and 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

References runtime_assert, and 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::getAtomMask ( ) const

inline

References ATOM_MASK.

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

inline

References CCs, and runtime_assert.

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

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

inline

References centerOfMass.

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

inline

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

References core::scoring::electron_density::OneGaussianScattering::a(), core::scoring::electron_density::OneGaussianScattering::C(), numeric::fourier::fft3(), grid, and core::scoring::electron_density::OneGaussianScattering::k().

void core::scoring::electron_density::ElectronDensity::getFSC	(	poseCoords const &	pose,
		core::Size	nbuckets,
		core::Real	maxreso,
		core::Real	minreso,
		utility::vector1< core::Real > &	FSC,
		bool	masked = `false`,
		bool	S2_bin = `false`,
		core::Real	mask_radius = `0`
	)

inline

Compute model-map FSC & errors.

References getModelMapError().

utility::vector1< core::Real > core::scoring::electron_density::ElectronDensity::getIntensities	(	core::Size	nbuckets,
		core::Real	maxreso,
		core::Real	minreso,
		bool	S2_bin = `false`
	)

Compute map intensities.

Compute intensities from model.

References density, numeric::fourier::fft3(), core::chemical::element::H, core::chemical::element::K, core::scoring::func::L(), and core::scoring::electron_density::TR.

void core::scoring::electron_density::ElectronDensity::getIntensities	(	poseCoords const &	pose,
		core::Size	nbuckets,
		core::Real	maxreso,
		core::Real	minreso,
		utility::vector1< core::Real > &	Imodel,
		bool	S2_bin = `false`
	)

Compute intensities from a pose.

Compute intensities from model.

References density, numeric::fourier::fft3(), core::chemical::element::H, core::chemical::element::K, core::scoring::func::L(), runtime_assert, and core::scoring::electron_density::TR.

utility::vector1< core::Real > core::scoring::electron_density::ElectronDensity::getIntensitiesMasked	(	poseCoords const &	pose,
		core::Size	nbuckets,
		core::Real	maxreso,
		core::Real	minreso,
		bool	S2_bin = `false`
	)

Compute map intensities, masked by a pose.

Compute intensities from model, applying a mask first.

References density, numeric::fourier::fft3(), grid, core::chemical::element::H, core::chemical::element::K, core::scoring::func::L(), core::scoring::electron_density::pos_mod(), radius, and core::scoring::electron_density::TR.

void core::scoring::electron_density::ElectronDensity::getMapMapError	(	ObjexxFCL::FArray3D< float > const &	map2,
		core::Size	nbuckets,
		core::Real	maxreso,
		core::Real	minreso,
		utility::vector1< core::Real > &	FSC,
		utility::vector1< core::Real > &	phaseError,
		utility::vector1< core::Real > &	complexPlaneError,
		bool	S2_bin = `false`
	)

Compute map-map FSC & errors.

References density, numeric::fourier::fft3(), core::chemical::element::H, core::chemical::element::K, core::scoring::func::L(), runtime_assert, and core::scoring::electron_density::TR.

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

inline

References dens_max.

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

inline

References dens_mean.

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

inline

References dens_min.

void core::scoring::electron_density::ElectronDensity::getModelMapError	(	poseCoords const &	pose,
		core::Size	nbuckets,
		core::Real	maxreso,
		core::Real	minreso,
		utility::vector1< core::Real > const &	mapmapPhaseError,
		utility::vector1< core::Real > const &	mapmapComplexPlaneError,
		utility::vector1< core::Real > &	FSC,
		utility::vector1< core::Real > &	phaseError,
		core::Real &	phaseErrorSum,
		core::Real &	complexPlaneErrorK,
		core::Real &	complexPlaneErrorProb,
		bool	masked = `false`,
		bool	S2_bin = `false`,
		core::Real	mask_radius = `0`
	)

Compute model-map FSC & errors.

References density, numeric::statistics::errf(), numeric::statistics::errfc(), numeric::fourier::fft3(), grid, core::chemical::element::H, core::chemical::element::K, core::scoring::func::L(), log(), core::scoring::electron_density::pos_mod(), radius, runtime_assert, and core::scoring::electron_density::TR.

Referenced by getFSC().

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

inline

References NUM_DERIV_H.

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

inline

References origin.

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

inline

References reso.

void core::scoring::electron_density::ElectronDensity::getResolutionBins	(	core::Size	nbuckets,
		core::Real	maxreso,
		core::Real	minreso,
		utility::vector1< core::Real > &	resbins,
		utility::vector1< core::Size > &	counts,
		bool	S2_bin = `false`
	)

get resolution bins (informational)

References density, core::chemical::element::H, core::chemical::element::K, core::scoring::func::L(), and core::scoring::electron_density::TR.

core::Real core::scoring::electron_density::ElectronDensity::getRSCC ( poseCoords const & pose )

Compute model-map RSCC.

References density, and runtime_assert.

core::Real core::scoring::electron_density::ElectronDensity::getRSCC ( ObjexxFCL::FArray3D< float > const & map2 )

Compute map-map RSCC.

References density, and runtime_assert.

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

inline

References score_window_context_.

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

inline

References SC_scaling_.

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

inline

References dens_stdev.

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

inline

References symmOps.

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

inline

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

References grid, idx2cart(), and origin.

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

inline

References DensScoreInMinimizer.

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

inline

References ExactDerivatives.

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

inline

References WINDOW_.

template<class Q >

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

inline

References efforigin, f2c, and grid.

Referenced by getTransform().

template<class Q >

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

inline

References f2c, and grid.

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

Initialize map from cmd line options.

Referenced by ElectronDensity().

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

private

also sets MINMULT(XYZ) eventually replace with cctbx

References utility::string_split(), and core::scoring::electron_density::TR.

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

inline

References isLoaded.

Referenced by core::scoring::electron_density::getDensityMap_legacy(), and core::scoring::electron_density::PattersonCorrEnergy::PattersonCorrEnergy().

void core::scoring::electron_density::ElectronDensity::maskDensityMap	(	poseCoords const &	pose,
		core::Real	radius
	)

mask the density map (like chimera 'zone' but sigmoidal mask)

References basic::options::OptionKeys::edensity::debug, density, grid, basic::options::option, core::scoring::electron_density::pos_mod(), and writeMRC().

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

inline

References scoring_mask_.

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

inline

References scoring_mask_.

numeric::xyzVector< double > core::scoring::electron_density::ElectronDensity::match_fragment	(	ObjexxFCL::FArray3D< double > const &	rho_calc,
		ObjexxFCL::FArray3D< double > const &	mask,
		ObjexxFCL::FArray3D< double > const &	rho_obs,
		core::Real	radius = `6.0`
	)

References core::scoring::electron_density::conj_map_times(), density, numeric::fourier::fft3(), grid, numeric::fourier::ifft3(), and min_score.

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.

References density, utility::pointer::owning_ptr< T >::get(), grid, core::scoring::electron_density::is_missing_density(), core::chemical::ResidueType::is_protein(), nres, 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::matchPointFast ( numeric::xyzVector< core::Real > X )

access fastdens scoring for a single point

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

References core::scoring::electron_density::interp_spline(), core::scoring::electron_density::pos_mod(), and core::scoring::electron_density::TR.

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

Match a pose into a medium-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

References core::chemical::aa_vrt, core::scoring::electron_density::OneGaussianScattering::C(), density, utility::pointer::owning_ptr< T >::get(), core::scoring::electron_density::get_A(), grid, core::scoring::electron_density::is_missing_density(), core::scoring::electron_density::OneGaussianScattering::k(), core::conformation::Residue::nheavyatoms(), nres, basic::options::option, core::scoring::electron_density::pos_mod(), core::pose::Pose::residue(), basic::options::OptionKeys::edensity::sc_scaling, 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.

Referenced by dCCdx_pat(), 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

References core::conformation::Residue::atom(), core::conformation::Residue::atom_type_index(), core::conformation::Residue::atom_type_set(), core::scoring::electron_density::OneGaussianScattering::C(), core::graph::Node::const_edge_list_end(), basic::options::OptionKeys::edensity::debug, density, core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), core::pose::Pose::fold_tree(), utility::pointer::owning_ptr< T >::get(), 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(), grid, core::kinematics::FoldTree::is_cutpoint(), core::scoring::electron_density::is_missing_density(), core::scoring::electron_density::OneGaussianScattering::k(), core::conformation::Residue::last_backbone_atom(), core::scoring::electron_density::MAX_FLT, core::conformation::Residue::nheavyatoms(), nres, basic::options::option, core::pose::Pose::residue(), core::pose::Pose::total_residue(), core::scoring::electron_density::TR, basic::options::OptionKeys::edensity::unmask_bb, writeMRC(), and core::conformation::Atom::xyz().

Referenced by 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`,
		bool	ignoreBs = `false`
	)

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.

References core::scoring::electron_density::OneGaussianScattering::a(), core::conformation::Residue::atom(), core::conformation::Residue::atom_type_index(), core::conformation::Residue::atom_type_set(), core::chemical::element::B, utility::pointer::owning_ptr< T >::get(), core::scoring::electron_density::get_A(), core::scoring::electron_density::interp_spline(), core::scoring::electron_density::OneGaussianScattering::k(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::pdb_info(), core::scoring::electron_density::pos_mod(), score, core::conformation::Residue::seqpos(), core::scoring::electron_density::TR, core::chemical::element::W, and core::conformation::Atom::xyz().

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

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

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

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.

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.

References basic::options::OptionKeys::edensity::atom_mask_min, core::scoring::electron_density::CCP4HDSIZE, density, core::sequence::end, grid, core::scoring::func::L(), mode, basic::options::option, core::id::swap(), core::scoring::electron_density::swap4_aligned(), core::scoring::electron_density::TR, and user.

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!

References core::conformation::Residue::atom(), core::conformation::Residue::atom_type_index(), core::conformation::Residue::atom_type_set(), core::scoring::electron_density::OneGaussianScattering::C(), basic::options::OptionKeys::patterson::dont_use_symm_in_pcalc, numeric::fourier::fft3(), core::scoring::electron_density::get_A(), grid, numeric::fourier::ifft3(), core::scoring::electron_density::is_missing_density(), core::scoring::electron_density::OneGaussianScattering::k(), core::conformation::Residue::nheavyatoms(), basic::options::option, 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::rescale_fastscoring_temp_bins	(	core::pose::Pose const &	pose,
		bool	init = `false`
	)

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

resize the map via FFT

References density, exit, core::scoring::electron_density::findSampling(), grid, 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

References core::chemical::aa_vrt, core::scoring::electron_density::OneGaussianScattering::C(), basic::options::OptionKeys::edensity::debug, density, numeric::fourier::fft(), core::scoring::electron_density::get_A(), grid, numeric::fourier::ifft(), core::scoring::electron_density::interp_linear(), core::scoring::electron_density::is_missing_density(), core::scoring::electron_density::OneGaussianScattering::k(), core::conformation::Residue::nheavyatoms(), nres, nshells, basic::options::option, core::scoring::electron_density::pos_mod(), core::pose::Pose::residue(), rotation, basic::options::OptionKeys::edensity::sc_scaling, core::scoring::electron_density::square(), core::pose::Pose::total_residue(), core::scoring::electron_density::TR, and writeMRC().

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

inlineprivate

References cosRcellAngles, and RcellDimensions.

void core::scoring::electron_density::ElectronDensity::scaleIntensities	(	utility::vector1< core::Real >	I_tgt,
		core::Real	maxreso,
		core::Real	minreso,
		bool	S2_bin = `false`
	)

Compute intensities, update density.

References density, numeric::fourier::fft3(), core::chemical::element::H, numeric::fourier::ifft3(), core::chemical::element::K, core::scoring::func::L(), and core::scoring::electron_density::TR.

void core::scoring::electron_density::ElectronDensity::set_data ( ObjexxFCL::FArray3D< double > const & density_in )

inline

References density.

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

inline

set # of residues

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

Referenced by 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

References score_window_context_.

void core::scoring::electron_density::ElectronDensity::setSCscaling ( core::Real SC_scalingin )

inline

References SC_scaling_.

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

private

setup oversampled maps for fast density scoring

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

void core::scoring::electron_density::ElectronDensity::setup_fastscoring_first_time ( Real scalefactor )

private

References core::scoring::electron_density::OneGaussianScattering::B(), basic::options::OptionKeys::edensity::debug, density, basic::options::OptionKeys::edensity::fastdens_params, fastdens_params, numeric::fourier::fft3(), core::scoring::electron_density::get_A(), grid, numeric::fourier::ifft3(), core::scoring::electron_density::OneGaussianScattering::k(), basic::options::option, runtime_assert, core::chemical::element::S, core::scoring::electron_density::spline_coeffs(), core::scoring::electron_density::TR, user, 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.

References core::chemical::aa_vrt, basic::options::OptionKeys::patterson::Bsol, d_max, d_min, basic::options::OptionKeys::edensity::debug, density, basic::options::OptionKeys::patterson::dont_use_symm_in_pcalc, numeric::fourier::fft3(), core::scoring::electron_density::findSampling5(), basic::options::OptionKeys::patterson::Fsol, core::scoring::electron_density::get_A(), grid, core::chemical::element::H, numeric::fourier::ifft3(), core::scoring::electron_density::is_missing_density(), core::chemical::element::K, core::scoring::func::L(), core::conformation::Residue::nheavyatoms(), basic::options::OptionKeys::patterson::no_ecalc, nres, basic::options::OptionKeys::patterson::nshells, basic::options::option, core::scoring::electron_density::pos_mod(), core::pose::Pose::residue(), basic::options::OptionKeys::patterson::resolution_cutoffs, basic::options::OptionKeys::patterson::rmsd, rmsd, core::pose::Pose::total_residue(), core::scoring::electron_density::TR, user, and writeMRC().

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

inline

References DensScoreInMinimizer.

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

inline

References ExactDerivatives.

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

inline

References WINDOW_.

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

Print cached CCs.

References core::scoring::electron_density::TR.

void core::scoring::electron_density::ElectronDensity::smooth_intensities ( utility::vector1< core::Real > & Is ) const

private

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'.

References core::conformation::Residue::atom(), core::conformation::Residue::atom_type_index(), core::conformation::Residue::atom_type_set(), core::scoring::electron_density::OneGaussianScattering::C(), core::scoring::electron_density::get_A(), grid, 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().

double core::scoring::electron_density::ElectronDensity::voxel_volume ( )

inlineprivate

References grid, and V.

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

(debugging) Write MATLAB v5 mapfile

References density, and out.

bool core::scoring::electron_density::ElectronDensity::writeMRC	(	std::string	mapfilestem,
		bool	writeRhoCalc = `false`,
		bool	writeRhoMask = `false`
	)

(debugging) Write MRC mapfile

References core::scoring::electron_density::CCP4HDSIZE, density, grid, runtime_assert, and core::scoring::electron_density::TR.

Referenced by expandToUnitCell(), maskDensityMap(), 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

Referenced by getAtomMask().

core::Real core::scoring::electron_density::ElectronDensity::ATOM_MASK_PADDING

private

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

private

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

private

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

private

Referenced by cart2frac(), cart2idx(), and get_c2f().

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

private

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

private

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

private

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

private

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

private

Referenced by getCachedScore(), and set_nres().

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

private

Referenced by ElectronDensity().

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

private

Referenced by ElectronDensity().

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

private

Referenced by getCoM().

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

mutableprivate

VISUALIZATION-SPECIFIC.

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

mutableprivate

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

mutableprivate

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

private

Referenced by S2().

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

private

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

private

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

private

Referenced by set_nres().

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

private

Referenced by set_nres().

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

private

Referenced by set_nres().

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

private

Referenced by set_nres().

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

private

Referenced by getMax().

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

private

Referenced by getMean().

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

private

Referenced by getMin().

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

private

Referenced by getStdev().

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

private

Referenced by data(), ElectronDensity(), and set_data().

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

private

Referenced by getUseDensityInMinimizer(), and setUseDensityInMinimizer().

core::Real core::scoring::electron_density::ElectronDensity::effectiveB

private

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

private

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

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

private

Referenced by getUseExactDerivatives(), and setUseExactDerivatives().

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

private

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

private

CRYSTAL INFO.

Referenced by frac2cart(), get_f2c(), idx2cart(), and idxoffset2cart().

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

private

ObjexxFCL::FArray4D< double > core::scoring::electron_density::ElectronDensity::fastdens_score

private

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

private

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

private

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

private

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

private

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

private

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

private

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

private

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

private

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

private

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

private

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

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

private

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

private

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

private

Referenced by ElectronDensity(), and isMapLoaded().

core::Real core::scoring::electron_density::ElectronDensity::kmax_

private

core::Real core::scoring::electron_density::ElectronDensity::kmin_

private

core::Real core::scoring::electron_density::ElectronDensity::kstep_

private

bool core::scoring::electron_density::ElectronDensity::legacy_

private

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

private

core::Real core::scoring::electron_density::ElectronDensity::minimumB

private

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

private

core::Size core::scoring::electron_density::ElectronDensity::nkbins_

private

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

private

Referenced by getNumDerivH().

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

private

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

private

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

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

private

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

private

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

private

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

private

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

private

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

private

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

private

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

private

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

private

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

private

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

private

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

private

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

private

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

private

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

private

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

private

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

private

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

private

Referenced by S2().

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

private

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

private

Referenced by getResolution().

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

private

TONS OF CACHED STUFF <<< this should live in its own class!

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

private

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

private

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

private

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

private

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

private

core::Real core::scoring::electron_density::ElectronDensity::SC_scaling_

private

Referenced by getSCscaling(), and setSCscaling().

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

private

Referenced by getScoreWindowContext(), and setScoreWindowContext().

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

private

Referenced by clearMask(), and maskResidues().

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

private

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

private

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

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

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

private

Referenced by getsymmOps().

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

private

bool core::scoring::electron_density::ElectronDensity::use_altorigin

private

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

private

Referenced by voxel_volume().

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

private

Referenced by getWindow(), and setWindow().

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

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

Public Member Functions

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation