#include <ElectronDensity.hh>

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

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

	ElectronDensity ()
	default 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 ()
	initialize vars from command line options More...

bool	readMRCandResize (std::string const &mapfile, core::Real reso=5.0, core::Real gridSpacing=0.0)
	Load an MRC density map. More...

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

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

void	mapSphericalSamples (ObjexxFCL::FArray3D< core::Real > &mapShellR, core::Size nRsteps, core::Real delR, core::Size B, numeric::xyzVector< core::Real > center, core::Real laplacian_offset)
	resample the map in spherical shells around a pose More...

core::Real	matchCentroidPose (core::pose::Pose const &pose, core::conformation::symmetry::SymmetryInfoCOP symmInfo=nullptr, 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	matchPoseInPocket (core::pose::Pose const &pose, numeric::xyzVector< core::Real > center, core::Real radius, core::conformation::symmetry::SymmetryInfoCOP symmInfo=nullptr, bool cacheCCs=false)

core::Real	matchPose (core::pose::Pose const &pose, core::conformation::symmetry::SymmetryInfoCOP symmInfo=nullptr, bool cacheCCs=false)
	Match a pose into a medium-resolution density map by placing a single Gaussian at each atom. 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 More...

void	getIntensities (ObjexxFCL::FArray3D< std::complex< core::Real > > const &FrhoC, core::Size nbuckets, core::Real maxreso, core::Real minreso, utility::vector1< core::Real > &Imap, bool S2_bin=false)
	Compute map intensities, masked by a pose. Also compute mask intensities. More...

void	getFSC (ObjexxFCL::FArray3D< std::complex< core::Real > > const &Frho1, ObjexxFCL::FArray3D< std::complex< core::Real > > const &Frho2, core::Size nbuckets, core::Real maxreso, core::Real minreso, utility::vector1< core::Real > &FSC, bool S2_bin=false)
	Compute map-map FSC. More...

void	getPhaseError (ObjexxFCL::FArray3D< std::complex< core::Real > > const &Frho1, ObjexxFCL::FArray3D< std::complex< core::Real > > const &Frho2, core::Size nbuckets, core::Real maxreso, core::Real minreso, utility::vector1< core::Real > &phaseError, bool S2_bin=false)
	Compute map-map phase error. More...

void	calcRhoC (poseCoords const &pose, core::Real highres_limit, ObjexxFCL::FArray3D< core::Real > &rhoC, ObjexxFCL::FArray3D< core::Real > &mask, core::Real forceB=-1.0, core::Real B_upper_limit=600, core::Real force_mask=-1.0)
	get Rho Calc More...

core::Real	getRSCC (ObjexxFCL::FArray3D< core::Real > const &density2, ObjexxFCL::FArray3D< core::Real > const &mask)
	Real-space correlation. More...

core::Real	getRSCC (ObjexxFCL::FArray3D< core::Real > &rhoC)
	Real-space correlation. More...

void	scaleIntensities (utility::vector1< core::Real > I_tgt, core::Real maxreso, core::Real minreso, bool S2_bin=false)
	Scale map intensities to a target spectum. More...

void	reciprocalSpaceFilter (core::Real maxreso, core::Real minreso, core::Real fadewidth)
	Filter the map in reciprocal space. More...

core::Real	maxNominalRes ()
	Return the highest possible resolution relection in reciprocal space for the given grid. More...

core::Real	matchRes (int resid, core::conformation::Residue const &rsd, core::pose::Pose const &pose, core::conformation::symmetry::SymmetryInfoCOP symmInfo=nullptr, bool bfactors=false, 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=nullptr, core::Real sc_scale=1.0)
	Match a residue's conformation to the density map. Same as matchRes, but using a fast approximation to the match function. More...

core::Real	matchAtomFast (int resid, Size atomid, core::conformation::Residue const &rsd, core::pose::Pose const &pose, core::conformation::symmetry::SymmetryInfoCOP symmInfo=nullptr, bool ignoreBs=false)
	Matches an individual atom to the density using the fast approximation. More...

void	compute_symm_rotations (core::pose::Pose const &pose, core::conformation::symmetry::SymmetryInfoCOP symmInfo=nullptr)
	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, ObjexxFCL::FArray3D< core::Real > &maskC)
	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	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	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	getResolution () const

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

void	setOrigin (numeric::xyzVector< core::Real > newori)

numeric::xyzVector< int >	getGrid () const

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

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

core::Real	getAtomMask () const

void	setAtomMask (core::Real newVal)

void	maskResidues (int scoring_mask)
	set scoring to use only a subset of residues More...

void	maskResidues (utility::vector1< int > const &scoring_mask)
	set scoring to use only a subset of residues More...

void	clearMask ()
	reset scoring to use all residues More...

ObjexxFCL::FArray3D< float > const &	get_data () const
	access raw density data More...

template<class Q >
void	set_data (ObjexxFCL::FArray3D< Q > const &density_in)
	set raw density data. Assumes new map sampling grid same as current More...

core::Real	get (int i, int j, int k)
	get the density at a grid point More...

core::Real	get (numeric::xyzVector< core::Real > X)
	get the interpolated density at a point in index space More...

numeric::xyzVector< core::Real >	grad (numeric::xyzVector< core::Real > X)
	get the interpolated gradient at a point in index space More...

void	set_voxel_spacing (numeric::xyzVector< core::Real > apix)
	set voxel spacing of the map More...

void	set_voxel_spacing (core::Real apix)
	set voxel spacing of the map More...

numeric::xyzVector< core::Real >	get_voxel_spacing ()
	set voxel spacing of the map More...

core::Real	getCachedScore (core::Size resid)
	get the precomputed CC (THIS SHOULD LIVE IN POSE DATACACHE!) More...

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

numeric::xyzMatrix< core::Real >	get_f2c () const
	get frac<=>cartesian conversion matrices More...

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

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

void	get_symmMap (int vrtid, utility::vector1< int > &X_map, numeric::xyzMatrix< core::Real > &R)
	get symmetrized gradients for -score_symm_complex More...

void	get_R (int subunit, numeric::xyzMatrix< core::Real > &R) const
	gets rotation vactor for subunit 'subunit' in last-scored pose (Rosetta symmetry) More...

core::Real	getEffectiveBfactor () const
	get the "effective B factor": a global b factor based on map resolution More...

core::Real	S2 (int h, int k, int l) const

void	computeStats ()

core::Real	getMean () const

core::Real	getMin () const

core::Real	getMax () const

core::Real	getStdev () const

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

numeric::xyzVector< core::Real >	periodic_mod (numeric::xyzVector< core::Real > const &fracX, numeric::xyzVector< core::Real > const &grid, numeric::xyzVector< core::Real > const &origin) const

double	get_voxel_volume ()

Static Public Attributes
static core::Real	NUM_DERIV_H = 0.01

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

void	computeCrystParams ()

void	expandToUnitCell ()

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< core::Real > > * >	getFdrhoc (OneGaussianScattering S)

core::Real	voxel_volume ()

Private Attributes
bool	isLoaded_

ObjexxFCL::FArray3D< float >	density

ObjexxFCL::FArray3D< core::Real >	coeffs_density_

ObjexxFCL::FArray3D< std::complex< core::Real > >	Fdensity_

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

core::Real	reso_

core::Real	ATOM_MASK

core::Real	CA_MASK

core::Real	force_apix_on_map_load_

core::Real	SC_scaling_

core::Real	ATOM_MASK_PADDING

core::Size	WINDOW_

bool	score_window_context_

bool	remap_symm_

bool	periodicity_

ObjexxFCL::FArray4D< core::Real >	fastdens_score

core::Size	nkbins_

core::Real	kmin_

core::Real	kmax_

core::Real	kstep_

numeric::xyzVector< int >	fastgrid

numeric::xyzVector< core::Real >	fastorigin

core::Real	minimumB

core::Real	effectiveB

numeric::xyzVector< int >	grid_

numeric::xyzVector< core::Real >	origin_

bool	use_altorigin

core::Real	dens_mean

core::Real	dens_min

core::Real	dens_max

core::Real	dens_stdev

utility::vector1< core::Real >	CCs
	CACHED STUFF that is not thread safe and should live in its own class. More...

core::Real	CC_cen

core::Real	CC_aacen

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< core::Real >	coeff_grad_x
	VISUALIZATION-SPECIFIC. More...

ObjexxFCL::FArray3D< core::Real >	coeff_grad_y

ObjexxFCL::FArray3D< core::Real >	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

Constructor & Destructor Documentation

◆ ~ElectronDensity()

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

overridedefault

Automatically generated virtual destructor for class deriving directly from VirtualBase.

Auto-generated virtual destructor

◆ ElectronDensity() [1/3]

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

default constructor

null constructor

References core::init::init().

◆ ElectronDensity() [2/3]

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

"rho_calc" constructor: make a map from a vector of poses

References 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::scoring::electron_density::poseCoord::B_, core::scoring::electron_density::poseCoord::elt_, core::scoring::electron_density::findSampling5(), core::init::init(), protocols::mean_field::max(), protocols::mean_field::min(), core::conformation::Residue::nheavyatoms(), core::scoring::electron_density::pose_has_nonzero_Bs(), core::pose::Pose::residue(), core::pose::Pose::size(), core::scoring::electron_density::TR(), core::scoring::electron_density::poseCoord::x_, core::conformation::Atom::xyz(), and core::conformation::Residue::xyz().

◆ ElectronDensity() [3/3]

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!)

References cellAngles, cellDimensions, density, grid_, init(), isLoaded_, origin_, and core::scoring::electron_density::pos_mod().

Member Function Documentation

◆ calcRhoC()

void core::scoring::electron_density::ElectronDensity::calcRhoC	(	poseCoords const &	pose,
		core::Real	highres_limit,
		ObjexxFCL::FArray3D< core::Real > &	rhoC,
		ObjexxFCL::FArray3D< core::Real > &	mask,
		core::Real	forceB = `-1.0`,
		core::Real	B_upper_limit = `600`,
		core::Real	force_mask = `-1.0`
	)

get Rho Calc

References core::chemical::element::C, core::scoring::electron_density::OneGaussianScattering::C(), core::scoring::electron_density::get_A(), core::chemical::element::H, core::chemical::element::K, core::scoring::electron_density::OneGaussianScattering::k(), protocols::features::L, protocols::mean_field::min(), core::scoring::electron_density::pose_has_nonzero_Bs(), and core::scoring::electron_density::TR().

Referenced by protocols::electron_density::ReportFSC::apply(), protocols::electron_density::ScaleMapIntensities::apply(), protocols::electron_density::BfactorMultifunc::operator()(), protocols::electron_density::remove_occupied_density_from_density(), and protocols::electron_density::VoxelSpacingMultifunc::VoxelSpacingMultifunc().

◆ cart2idx()

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

inline

References c2f, grid_, and origin_.

Referenced by protocols::electron_density::DensitySymmInfo::mask_asu(), matchPoseInPocket(), protocols::electron_density::DockFragmentsIntoDensityMover::predefine_search(), and protocols::electron_density::DockPDBIntoDensityMover::predefine_search().

◆ clear_dCCdx_res_cache()

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, core::sequence::end, core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by core::energy_methods::ElecDensEnergy::setup_for_derivatives().

◆ clearMask()

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

inline

reset scoring to use all residues

References scoring_mask_.

Referenced by protocols::electron_density::SetupForDensityScoringMover::apply().

◆ compute_symm_rotations()

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

Computes the symmatric rotation matrices.

Compute symmetric transformations needed by -score_symm_complex.

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

◆ computeCrystParams()

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

private

References core::id::D, core::scoring::electron_density::d2r(), protocols::mean_field::max(), protocols::mean_field::min(), core::scoring::sa, core::scoring::electron_density::square(), core::scoring::electron_density::TR(), and core::chemical::element::V.

◆ computeGradients()

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

private

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

◆ computeStats()

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

References protocols::mean_field::max(), protocols::mean_field::min(), core::chemical::element::N, and core::simple_metrics::metrics::sum.

◆ dCCdB_fastRes()

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::pose::Pose::residue(), core::conformation::Residue::seqpos(), core::scoring::electron_density::TR(), core::chemical::element::W, protocols::comparative_modeling::features::X, and core::conformation::Residue::xyz().

Referenced by protocols::electron_density::BfactorMultifunc::dfunc().

◆ dCCdBs()

void core::scoring::electron_density::ElectronDensity::dCCdBs	(	core::pose::Pose const &	pose,
		utility::vector1< core::Real > &	dE_dvars,
		ObjexxFCL::FArray3D< core::Real > &	maskC
	)

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

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::conformation::Residue::atom_type(), core::conformation::Residue::atom_type_index(), core::conformation::Residue::atom_type_set(), core::scoring::electron_density::poseCoord::B_, core::chemical::element::C, core::scoring::electron_density::OneGaussianScattering::C(), core::pose::Pose::conformation(), core::scoring::electron_density::OneGaussianScattering::dk(), core::scoring::electron_density::poseCoord::elt_, core::scoring::electron_density::get_A(), core::pose::symmetry::is_symmetric(), core::chemical::AtomType::is_virtual(), core::scoring::electron_density::OneGaussianScattering::k(), protocols::mean_field::min(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::pose::Pose::size(), core::scoring::electron_density::poseCoord::x_, and core::conformation::Residue::xyz().

Referenced by protocols::electron_density::BfactorMultifunc::dfunc().

◆ dCCdx_aacen()

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

Referenced by core::energy_methods::ElecDensAllAtomCenEnergy::eval_atom_derivative().

◆ dCCdx_cen()

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

Referenced by core::energy_methods::ElecDensCenEnergy::eval_atom_derivative().

◆ dCCdx_fastRes()

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_type_index(), core::conformation::Residue::atom_type_set(), core::chemical::element::B, core::scoring::electron_density::get_A(), core::scoring::electron_density::interp_dspline(), core::scoring::electron_density::OneGaussianScattering::k(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::conformation::Residue::seqpos(), core::scoring::electron_density::TR(), core::chemical::element::W, and protocols::comparative_modeling::features::X.

Referenced by core::energy_methods::FastDensEnergy::eval_residue_pair_derivatives().

◆ dCCdx_PointFast()

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::TR(), and protocols::comparative_modeling::features::X.

◆ dCCdx_res()

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::scoring::electron_density::TR().

Referenced by core::energy_methods::ElecDensEnergy::eval_atom_derivative().

◆ dens_grad()

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().

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

◆ density_change_trigger()

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

private

The function is called everytime the density changes.

Referenced by set_data().

◆ expandToUnitCell()

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

private

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

◆ get() [1/2]

core::Real core::scoring::electron_density::ElectronDensity::get	(	int	i,
		int	j,
		int	k
	)

inline

get the density at a grid point

References density.

Referenced by protocols::electron_density::VoxelSpacingMultifunc::dfunc(), and protocols::electron_density::VoxelSpacingMultifunc::operator()().

◆ get() [2/2]

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

get the interpolated density at a point in index space

References core::scoring::electron_density::interp_spline(), core::scoring::electron_density::spline_coeffs(), and protocols::comparative_modeling::features::X.

◆ get_c2f()

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

inline

References c2f.

Referenced by protocols::electron_density::DensitySymmInfo::autocorrelate().

◆ get_cellDimensions()

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

inline

References cellDimensions.

◆ get_data()

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

inline

access raw density data

References density.

Referenced by protocols::electron_density::ScaleMapIntensities::apply(), protocols::electron_density::DensitySymmInfo::autocorrelate(), protocols::electron_density::remove_occupied_density_from_density(), protocols::electron_density::select_density_points(), and protocols::ligand_docking::ga_ligand_dock::LigandAligner::select_points().

◆ get_f2c()

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

inline

get frac<=>cartesian conversion matrices

References f2c.

Referenced by protocols::electron_density::DensitySymmInfo::autocorrelate(), protocols::electron_density::VoxelSpacingMultifunc::foldInChanges(), and protocols::electron_density::DensitySymmInfo::mask_asu().

◆ get_R()

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

inline

gets rotation vactor for subunit 'subunit' in last-scored pose (Rosetta symmetry)

References symmap.

Referenced by core::energy_methods::ElecDensAllAtomCenEnergy::eval_atom_derivative(), core::energy_methods::ElecDensCenEnergy::eval_atom_derivative(), core::energy_methods::ElecDensEnergy::eval_atom_derivative(), and core::energy_methods::FastDensEnergy::eval_residue_pair_derivatives().

◆ get_symmMap()

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

inline

get symmetrized gradients for -score_symm_complex

References symmap.

Referenced by core::energy_methods::ElecDensAllAtomCenEnergy::eval_atom_derivative(), core::energy_methods::ElecDensCenEnergy::eval_atom_derivative(), core::energy_methods::ElecDensEnergy::eval_atom_derivative(), and core::energy_methods::FastDensEnergy::eval_residue_pair_derivatives().

◆ get_voxel_spacing()

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

inline

set voxel spacing of the map

References cellDimensions, and grid_.

Referenced by protocols::electron_density::ReportFSC::apply(), and protocols::electron_density::VoxelSpacingMultifunc::foldInChanges().

◆ get_voxel_volume()

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

inline

References grid_.

Referenced by protocols::ligand_docking::ga_ligand_dock::LigandAligner::select_points().

◆ getAtomMask()

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

inline

References ATOM_MASK.

Referenced by protocols::electron_density::ReportFSC::apply().

◆ getCachedScore()

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

inline

get the precomputed CC (THIS SHOULD LIVE IN POSE DATACACHE!)

References CCs.

Referenced by core::energy_methods::ElecDensEnergy::eval_atom_derivative().

◆ getEffectiveBfactor()

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

inline

get the "effective B factor": a global b factor based on map resolution

References effectiveB.

Referenced by protocols::electron_density::pose_spherical_samples(), protocols::electron_density::remove_occupied_density_from_density(), and core::energy_methods::FastDensEnergy::setup_for_scoring().

◆ getFdrhoc()

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

private

◆ getFSC()

void core::scoring::electron_density::ElectronDensity::getFSC	(	ObjexxFCL::FArray3D< std::complex< core::Real > > const &	Frho1,
		ObjexxFCL::FArray3D< std::complex< core::Real > > const &	Frho2,
		core::Size	nbuckets,
		core::Real	maxreso,
		core::Real	minreso,
		utility::vector1< core::Real > &	FSC,
		bool	S2_bin = `false`
	)

Compute map-map FSC.

Compute model-map FSC & errors.

References core::chemical::element::H, core::chemical::element::K, protocols::features::L, protocols::mean_field::min(), and core::scoring::electron_density::TR().

Referenced by protocols::electron_density::ReportFSC::apply().

◆ getGrid()

numeric::xyzVector<int> core::scoring::electron_density::ElectronDensity::getGrid ( ) const

inline

References grid_.

Referenced by protocols::electron_density::VoxelSpacingMultifunc::foldInChanges().

◆ getIntensities()

void core::scoring::electron_density::ElectronDensity::getIntensities	(	ObjexxFCL::FArray3D< std::complex< core::Real > > const &	FrhoC,
		core::Size	nbuckets,
		core::Real	maxreso,
		core::Real	minreso,
		utility::vector1< core::Real > &	Imap,
		bool	S2_bin = `false`
	)

Compute map intensities, masked by a pose. Also compute mask intensities.

References core::chemical::element::H, core::chemical::element::K, protocols::features::L, protocols::mean_field::min(), and core::scoring::electron_density::TR().

Referenced by protocols::electron_density::ScaleMapIntensities::apply().

◆ getMax()

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

inline

References dens_max.

◆ getMean()

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

inline

References dens_mean.

◆ getMin()

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

inline

References dens_min.

◆ getOrigin()

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

inline

References origin_.

Referenced by protocols::electron_density::ReportFSC::apply(), and protocols::electron_density::VoxelSpacingMultifunc::foldInChanges().

◆ getPhaseError()

void core::scoring::electron_density::ElectronDensity::getPhaseError	(	ObjexxFCL::FArray3D< std::complex< core::Real > > const &	Frho1,
		ObjexxFCL::FArray3D< std::complex< core::Real > > const &	Frho2,
		core::Size	nbuckets,
		core::Real	maxreso,
		core::Real	minreso,
		utility::vector1< core::Real > &	phaseError,
		bool	S2_bin = `false`
	)

Compute map-map phase error.

References core::chemical::element::H, core::chemical::element::K, protocols::features::L, protocols::mean_field::max(), protocols::mean_field::min(), and core::scoring::electron_density::TR().

◆ getResolution()

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

inline

References reso_.

◆ getResolutionBins()

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

References core::chemical::element::H, core::chemical::element::K, protocols::features::L, protocols::mean_field::min(), and core::scoring::electron_density::TR().

Referenced by protocols::electron_density::ReportFSC::apply(), and protocols::electron_density::ScaleMapIntensities::apply().

◆ getRSCC() [1/2]

core::Real core::scoring::electron_density::ElectronDensity::getRSCC ( ObjexxFCL::FArray3D< core::Real > & rhoC )

inline

Real-space correlation.

References getRSCC().

◆ getRSCC() [2/2]

core::Real core::scoring::electron_density::ElectronDensity::getRSCC	(	ObjexxFCL::FArray3D< core::Real > const &	density2,
		ObjexxFCL::FArray3D< core::Real > const &	mask
	)

Real-space correlation.

Referenced by getRSCC(), and protocols::electron_density::BfactorMultifunc::operator()().

◆ getScoreWindowContext()

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

inline

References score_window_context_.

◆ getSCscaling()

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

inline

References SC_scaling_.

◆ getStdev()

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

inline

References dens_stdev.

◆ getsymmOps()

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

inline

References symmOps.

◆ getTransform()

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_.

◆ getWindow()

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

inline

References WINDOW_.

◆ grad()

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

get the interpolated gradient at a point in index space

References core::scoring::electron_density::interp_dspline(), core::scoring::electron_density::spline_coeffs(), and protocols::comparative_modeling::features::X.

Referenced by protocols::electron_density::VoxelSpacingMultifunc::dfunc().

◆ idx2cart()

template<class Q >

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

inline

References f2c, grid_, and origin_.

Referenced by protocols::electron_density::DensitySymmInfo::autocorrelate(), protocols::electron_density::cluster_RBfitResultDB_fast(), protocols::electron_density::density_grid_search(), protocols::electron_density::dump_points_to_search_to_pdb_or_txt(), protocols::ligand_docking::ga_ligand_dock::LigandAligner::erode_points(), protocols::ligand_docking::ga_ligand_dock::LigandAligner::find_biggest_skeleton(), getTransform(), protocols::loop_grower::DensSkeleton::path_length(), protocols::electron_density::select_density_points(), and protocols::ligand_docking::ga_ligand_dock::LigandAligner::select_points().

◆ idxoffset2cart()

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_.

Referenced by protocols::electron_density::DockFragmentsIntoDensityMover::map_from_spectrum(), and protocols::electron_density::map_from_spectrum().

◆ init()

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

initialize vars from command line options

Referenced by ElectronDensity().

◆ initializeSymmOps()

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

private

also sets MINMULT(XYZ) eventually replace with cctbx

References protocols::cryst::denom(), and core::scoring::electron_density::TR().

◆ isMapLoaded()

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

inline

References isLoaded_.

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

◆ mapSphericalSamples()

void core::scoring::electron_density::ElectronDensity::mapSphericalSamples	(	ObjexxFCL::FArray3D< core::Real > &	mapShellR,
		core::Size	nRsteps,
		core::Real	delR,
		core::Size	B,
		numeric::xyzVector< core::Real >	center,
		core::Real	laplacian_offset
	)

resample the map in spherical shells around a pose

References core::chemical::element::B, core::conformation::membrane::center, core::scoring::electron_density::interp_spline(), core::scoring::electron_density::spline_coeffs(), and core::scoring::electron_density::TR().

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

◆ maskResidues() [1/2]

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

inline

set scoring to use only a subset of residues

References scoring_mask_.

Referenced by protocols::electron_density::SetupForDensityScoringMover::apply().

◆ maskResidues() [2/2]

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

inline

set scoring to use only a subset of residues

References scoring_mask_.

◆ matchAtomFast()

core::Real core::scoring::electron_density::ElectronDensity::matchAtomFast	(	int	resid,
		Size	atomid,
		core::conformation::Residue const &	rsd,
		core::pose::Pose const &	pose,
		core::conformation::symmetry::SymmetryInfoCOP	symmInfo = `nullptr`,
		bool	ignoreBs = `false`
	)

Matches an individual atom to the density using the fast approximation.

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, core::scoring::electron_density::get_A(), core::scoring::electron_density::interp_spline(), core::scoring::electron_density::OneGaussianScattering::k(), core::pose::Pose::pdb_info(), protocols::hybridization::score, core::conformation::Residue::seqpos(), core::scoring::electron_density::TR(), core::chemical::element::W, and core::conformation::Atom::xyz().

Referenced by core::energy_methods::FastDensEnergy::atomistic_energy(), and protocols::loop_grower::LoopGrower::modifieddensity().

◆ matchCentroidPose()

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

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

References core::pose::motif::a(), core::conformation::Residue::atom(), core::chemical::element::C, core::chemical::ResidueTypeBase::is_protein(), protocols::mean_field::max(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::size(), core::scoring::electron_density::square(), core::scoring::electron_density::TR(), and core::conformation::Atom::xyz().

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

◆ matchPointFast()

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

access fastdens scoring for a single point

Match an atom to the density map. Use the fast version of the scoring function and default atom type.

References core::scoring::electron_density::interp_spline(), core::scoring::electron_density::TR(), and protocols::comparative_modeling::features::X.

◆ matchPose()

core::Real core::scoring::electron_density::ElectronDensity::matchPose	(	core::pose::Pose const &	pose,
		core::conformation::symmetry::SymmetryInfoCOP	symmInfo = `nullptr`,
		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::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::C, core::scoring::electron_density::OneGaussianScattering::C(), core::scoring::electron_density::get_A(), core::scoring::electron_density::OneGaussianScattering::k(), core::conformation::Residue::last_backbone_atom(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), core::pose::Pose::size(), core::scoring::electron_density::TR(), and core::conformation::Atom::xyz().

Referenced by protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_pose_density_correlation(), core::energy_methods::ElecDensAllAtomCenEnergy::setup_for_derivatives(), and core::energy_methods::ElecDensAllAtomCenEnergy::setup_for_scoring().

◆ matchPoseInPocket()

core::Real core::scoring::electron_density::ElectronDensity::matchPoseInPocket	(	core::pose::Pose const &	pose,
		numeric::xyzVector< core::Real >	center,
		core::Real	radius,
		core::conformation::symmetry::SymmetryInfoCOP	symmInfo = `nullptr`,
		bool	cacheCCs = `false`
	)

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

References 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::C, core::scoring::electron_density::OneGaussianScattering::C(), cart2idx(), core::conformation::membrane::center, core::scoring::electron_density::get_A(), core::scoring::electron_density::getDensityMap(), core::scoring::electron_density::OneGaussianScattering::k(), core::conformation::Residue::last_backbone_atom(), core::conformation::Residue::nheavyatoms(), core::scoring::electron_density::pos_mod(), core::pose::Pose::residue(), core::pose::Pose::size(), core::scoring::electron_density::TR(), and core::conformation::Atom::xyz().

Referenced by protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_pocket_density_correlation().

◆ matchRes()

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 = `nullptr`,
		bool	bfactors = `false`,
		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::chemical::element::C, core::scoring::electron_density::OneGaussianScattering::C(), 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::kinematics::FoldTree::is_cutpoint(), core::conformation::Residue::is_polymer(), core::scoring::electron_density::OneGaussianScattering::k(), core::conformation::Residue::last_backbone_atom(), protocols::mean_field::max(), core::scoring::electron_density::MAX_FLT, protocols::mean_field::min(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::pose::Pose::size(), core::scoring::electron_density::TR(), writeMRC(), and core::conformation::Atom::xyz().

Referenced by protocols::electron_density::DensityZscores::apply(), protocols::task_operations::SelectByDensityFitOperation::apply(), core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric::calculate(), core::scoring::electron_density::calculate_density_nbr(), protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_ligand_density_correlation(), protocols::hybridization::FragmentBiasAssigner::density(), protocols::rotamer_recovery::RRComparerElecDensDiff::measure_rotamer_recovery(), protocols::loop_grower::LoopGrower::modifieddensity(), core::energy_methods::ElecDensEnergy::residue_pair_energy(), and core::energy_methods::ElecDensEnergy::setup_for_derivatives().

◆ matchResFast()

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 = `nullptr`,
		core::Real	sc_scale = `1.0`
	)

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, core::scoring::electron_density::get_A(), core::scoring::electron_density::interp_spline(), core::scoring::electron_density::OneGaussianScattering::k(), core::conformation::Residue::last_backbone_atom(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::pdb_info(), protocols::hybridization::score, core::conformation::Residue::seqpos(), core::scoring::electron_density::TR(), core::chemical::element::W, and core::conformation::Atom::xyz().

Referenced by core::energy_methods::FastDensEnergy::atomistic_energy(), protocols::loop_grower::LoopGrower::check_auto_stop(), protocols::ligand_docking::ga_ligand_dock::GridScorer::density_score(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_1b_energy(), protocols::electron_density::BfactorMultifunc::operator()(), and core::energy_methods::FastDensEnergy::residue_pair_energy().

◆ maxNominalRes()

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

Return the highest possible resolution relection in reciprocal space for the given grid.

References core::chemical::element::S.

◆ periodic_mod()

numeric::xyzVector< core::Real > core::scoring::electron_density::ElectronDensity::periodic_mod	(	numeric::xyzVector< core::Real > const &	fracX,
		numeric::xyzVector< core::Real > const &	grid,
		numeric::xyzVector< core::Real > const &	origin
	)		const

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

◆ readMRCandResize() [1/2]

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 density map.

References core::sequence::end, protocols::mean_field::max(), core::id::swap(), core::scoring::electron_density::swap4_aligned(), and core::scoring::electron_density::TR().

◆ readMRCandResize() [2/2]

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

Load an MRC density map.

Referenced by protocols::loop_grower::DensSkeleton::DensSkeleton(), core::scoring::electron_density::getDensityMap_legacy(), and protocols::loop_grower::DensSkeleton::load_density().

◆ reciprocalSpaceFilter()

void core::scoring::electron_density::ElectronDensity::reciprocalSpaceFilter	(	core::Real	maxreso,
		core::Real	minreso,
		core::Real	fadewidth
	)

Filter the map in reciprocal space.

References core::chemical::element::H, core::chemical::element::K, and protocols::features::L.

Referenced by protocols::electron_density::ScaleMapIntensities::apply().

◆ rescale_fastscoring_temp_bins()

void core::scoring::electron_density::ElectronDensity::rescale_fastscoring_temp_bins	(	core::pose::Pose const &	pose,
		bool	init = `false`
	)

Referenced by protocols::electron_density::BfactorFittingMover::apply().

◆ resize()

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

resize the map via FFT resampling

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

◆ S2()

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

inline

References cosRcellAngles, and RcellDimensions.

◆ scaleIntensities()

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

Scale map intensities to a target spectum.

References core::chemical::element::H, core::chemical::element::K, protocols::features::L, protocols::mean_field::min(), and core::scoring::electron_density::TR().

Referenced by protocols::electron_density::ScaleMapIntensities::apply().

◆ set_data()

template<class Q >

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

inline

set raw density data. Assumes new map sampling grid same as current

References density, and density_change_trigger().

Referenced by protocols::electron_density::ScaleMapIntensities::apply(), protocols::electron_density::DensitySymmInfo::autocorrelate(), protocols::electron_density::remove_occupied_density_from_density(), and protocols::electron_density::select_density_points().

◆ set_nres()

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 protocols::task_operations::SelectByDensityFitOperation::apply(), protocols::electron_density::findLoopFromDensity(), protocols::rotamer_recovery::RRComparerElecDensDiff::measure_rotamer_recovery(), core::energy_methods::ElecDensAllAtomCenEnergy::setup_for_scoring(), core::energy_methods::ElecDensCenEnergy::setup_for_scoring(), and core::energy_methods::ElecDensEnergy::setup_for_scoring().

◆ set_voxel_spacing() [1/2]

void core::scoring::electron_density::ElectronDensity::set_voxel_spacing ( core::Real apix )

inline

set voxel spacing of the map

References set_voxel_spacing().

◆ set_voxel_spacing() [2/2]

void core::scoring::electron_density::ElectronDensity::set_voxel_spacing ( numeric::xyzVector< core::Real > apix )

set voxel spacing of the map

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

Referenced by protocols::electron_density::VoxelSpacingMultifunc::foldInChanges(), and set_voxel_spacing().

◆ setAtomMask()

void core::scoring::electron_density::ElectronDensity::setAtomMask ( core::Real newVal )

inline

References ATOM_MASK.

◆ setOrigin()

void core::scoring::electron_density::ElectronDensity::setOrigin ( numeric::xyzVector< core::Real > newori )

inline

References origin_.

◆ setScoreWindowContext()

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

inline

References score_window_context_.

Referenced by protocols::electron_density::DensityZscores::apply(), protocols::task_operations::SelectByDensityFitOperation::apply(), core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric::calculate(), core::scoring::electron_density::calculate_density_nbr(), protocols::hybridization::FragmentBiasAssigner::density(), and protocols::rotamer_recovery::RRComparerElecDensDiff::measure_rotamer_recovery().

◆ setSCscaling()

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

inline

References SC_scaling_.

Referenced by protocols::cryst::LoadDensityMapMover::apply(), and protocols::loop_grower::LoopGrower::modifieddensity().

◆ setup_fastscoring_first_time() [1/2]

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::pose::Pose::size(), and core::scoring::electron_density::TR().

◆ setup_fastscoring_first_time() [2/2]

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

private

References core::scoring::electron_density::OneGaussianScattering::B(), core::chemical::element::C, core::pack::interaction_graph::debug, core::scoring::electron_density::get_A(), core::scoring::electron_density::OneGaussianScattering::k(), protocols::mean_field::max(), protocols::mean_field::min(), core::chemical::element::S, core::scoring::electron_density::spline_coeffs(), core::scoring::electron_density::TR(), and writeMRC().

◆ setWindow()

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

inline

References WINDOW_.

Referenced by protocols::cryst::LoadDensityMapMover::apply(), protocols::electron_density::DensityZscores::apply(), protocols::task_operations::SelectByDensityFitOperation::apply(), core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric::calculate(), core::scoring::electron_density::calculate_density_nbr(), protocols::hybridization::FragmentBiasAssigner::density(), protocols::hybridization::MRMover::init(), and protocols::rotamer_recovery::RRComparerElecDensDiff::measure_rotamer_recovery().

◆ smooth_intensities()

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

private

◆ voxel_volume()

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

inlineprivate

References grid_.

◆ writeMRC()

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

(debugging) Write MRC mapfile

References core::conformation::membrane::out, and core::scoring::electron_density::TR().

Referenced by protocols::electron_density::ScaleMapIntensities::apply(), protocols::electron_density::VoxelSpacingRefinementMover::apply(), protocols::electron_density::DensitySymmInfo::autocorrelate(), core::energy_methods::FiberDiffractionEnergyDens::calculate_rho_fast2(), protocols::electron_density::density_grid_search(), expandToUnitCell(), protocols::electron_density::DockFragmentsIntoDensityMover::map_from_spectrum(), matchRes(), protocols::electron_density::remove_occupied_density_from_density(), protocols::electron_density::select_density_points(), and setup_fastscoring_first_time().

Member Data Documentation

◆ ATOM_MASK

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

private

Referenced by getAtomMask(), and setAtomMask().

◆ ATOM_MASK_PADDING

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

private

◆ c2f

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

private

Referenced by cart2idx(), and get_c2f().

◆ CA_MASK

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

private

◆ CC_aacen

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

private

◆ CC_cen

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

private

◆ CCs

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

private

CACHED STUFF that is not thread safe and should live in its own class.

Referenced by getCachedScore(), and set_nres().

◆ cellAngles

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

private

Referenced by ElectronDensity().

◆ cellDimensions

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

private

Referenced by ElectronDensity(), get_cellDimensions(), and get_voxel_spacing().

◆ coeff_grad_x

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

mutableprivate

VISUALIZATION-SPECIFIC.

◆ coeff_grad_y

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

private

◆ coeff_grad_z

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

private

◆ coeffs_density_

ObjexxFCL::FArray3D< core::Real > core::scoring::electron_density::ElectronDensity::coeffs_density_

private

◆ cosRcellAngles

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

private

Referenced by S2().

◆ dCCdxs_aacen

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

private

Referenced by set_nres().

◆ dCCdxs_cen

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

private

Referenced by set_nres().

◆ dCCdxs_pat

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

private

Referenced by set_nres().

◆ dCCdxs_res

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

private

Referenced by set_nres().

◆ dens_max

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

private

Referenced by getMax().

◆ dens_mean

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

private

Referenced by getMean().

◆ dens_min

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

private

Referenced by getMin().

◆ dens_stdev

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

private

Referenced by getStdev().

◆ density

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

private

Referenced by ElectronDensity(), get(), get_data(), and set_data().

◆ effectiveB

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

private

Referenced by getEffectiveBfactor().

◆ f2c

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

private

CRYSTAL INFO.

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

◆ fastdens_score

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

private

◆ fastgrid

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

private

◆ fastorigin

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

private

◆ Fdensity_

ObjexxFCL::FArray3D< std::complex< core::Real > > core::scoring::electron_density::ElectronDensity::Fdensity_

private

◆ force_apix_on_map_load_

core::Real core::scoring::electron_density::ElectronDensity::force_apix_on_map_load_

private

◆ grid_

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

private

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

◆ isLoaded_

bool core::scoring::electron_density::ElectronDensity::isLoaded_

private

Referenced by ElectronDensity(), and isMapLoaded().

◆ kmax_

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

private

◆ kmin_

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

private

◆ kstep_

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

private

◆ minimumB

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

private

◆ MINMULT

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

private

◆ nkbins_

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

private

◆ NUM_DERIV_H

core::Real core::scoring::electron_density::ElectronDensity::NUM_DERIV_H = 0.01

static

◆ origin_

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

private

Referenced by cart2idx(), ElectronDensity(), getOrigin(), getTransform(), idx2cart(), and setOrigin().

◆ periodicity_

bool core::scoring::electron_density::ElectronDensity::periodicity_

private

◆ RcellDimensions

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

private

Referenced by S2().

◆ remap_symm_

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

private

◆ reso_

core::Real core::scoring::electron_density::ElectronDensity::reso_

private

Referenced by getResolution().

◆ RV

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

private

◆ SC_scaling_

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

private

Referenced by getSCscaling(), and setSCscaling().

◆ score_window_context_

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

private

Referenced by getScoreWindowContext(), and setScoreWindowContext().

◆ scoring_mask_

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

private

Referenced by clearMask(), and maskResidues().

◆ symmap

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().

◆ symmOps

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

private

Referenced by getsymmOps().

◆ symmRotOps

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

private

◆ use_altorigin

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

private

◆ V

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

private

◆ WINDOW_

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

Static Public Attributes

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

◆ ~ElectronDensity()

◆ ElectronDensity() [1/3]

◆ ElectronDensity() [2/3]

◆ ElectronDensity() [3/3]

Member Function Documentation

◆ calcRhoC()

◆ cart2idx()

◆ clear_dCCdx_res_cache()

◆ clearMask()

◆ compute_symm_rotations()

◆ computeCrystParams()

◆ computeGradients()

◆ computeStats()

◆ dCCdB_fastRes()

◆ dCCdBs()

◆ dCCdx_aacen()

◆ dCCdx_cen()

◆ dCCdx_fastRes()

◆ dCCdx_PointFast()

◆ dCCdx_res()

◆ dens_grad()

◆ density_change_trigger()

◆ expandToUnitCell()

◆ get() [1/2]

◆ get() [2/2]

◆ get_c2f()

◆ get_cellDimensions()

◆ get_data()

◆ get_f2c()

◆ get_R()

◆ get_symmMap()

◆ get_voxel_spacing()

◆ get_voxel_volume()

◆ getAtomMask()

◆ getCachedScore()

◆ getEffectiveBfactor()

◆ getFdrhoc()

◆ getFSC()

◆ getGrid()

◆ getIntensities()

◆ getMax()

◆ getMean()

◆ getMin()

◆ getOrigin()

◆ getPhaseError()

◆ getResolution()

◆ getResolutionBins()

◆ getRSCC() [1/2]

◆ getRSCC() [2/2]

◆ getScoreWindowContext()

◆ getSCscaling()

◆ getStdev()

◆ getsymmOps()

◆ getTransform()

◆ getWindow()

◆ grad()

◆ idx2cart()

◆ idxoffset2cart()

◆ init()

◆ initializeSymmOps()

◆ isMapLoaded()

◆ mapSphericalSamples()

◆ maskResidues() [1/2]

◆ maskResidues() [2/2]

◆ matchAtomFast()

◆ matchCentroidPose()

◆ matchPointFast()

◆ matchPose()

◆ matchPoseInPocket()

◆ matchRes()

◆ matchResFast()

◆ maxNominalRes()

◆ periodic_mod()

◆ readMRCandResize() [1/2]

◆ readMRCandResize() [2/2]