core::scoring::electron_density::ElectronDensity Class Reference

#include <ElectronDensity.hh>

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

List of all members.

Public Member Functions
	ElectronDensity ()
	constructor
	ElectronDensity (utility::vector1< core::pose::PoseOP > poses, core::Real reso, core::Real apix)
	calulated density from a vector of poses
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)
bool	readMRCandResize (std::string mapfile, core::Real reso=5.0, core::Real gridSpacing=0.0)
	Load an MRC (="new-CCP4") density map.
bool	writeMRC (std::string mapfilestem)
	(debugging) Write MRC mapfile
bool	writeMAT (std::string mapfilestem)
	(debugging) Write MATLAB v5 mapfile
numeric::xyzMatrix< core::Real >	rotAlign2DPose (core::pose::Pose const &pose, std::string axis)
	Align a pose about a 2D rotation axis.
core::Real	matchCentroidPose (core::pose::Pose const &pose, const core::conformation::symmetry::SymmetryInfo *symmInfo=NULL, bool cacheCCs=false)
	Quickly matches a centroid pose into a low-resolution density map by placing a single Gaussian at each CA.
core::Real	matchPose (core::pose::Pose const &pose, const core::conformation::symmetry::SymmetryInfo *symmInfo=NULL, bool cacheCCs=false)
	Quickly matches a centroid pose into a low-resolution density map by placing a single Gaussian at each atom.
core::Real	matchPoseToPatterson (core::pose::Pose const &pose, bool cacheCCs=false)
	Match a pose to a patterson map.
core::Real	rematchResToPatterson (core::conformation::Residue const &rsd) const
	Rematch the pose to a patterson map, using previous rho_calc with only rsd changed.
void	updateCachedDensity (core::conformation::Residue const &rsd)
	Update cached rho_calc by changing residue 'rsd'.
core::Real	matchRes (int resid, core::conformation::Residue const &rsd, core::pose::Pose const &pose, const core::conformation::symmetry::SymmetryInfo *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.
core::Real	matchResFast (int resid, core::conformation::Residue const &rsd, core::pose::Pose const &pose, const core::conformation::symmetry::SymmetryInfo *symmInfo=NULL)
	Match a residue's conformation to the density map. Same as matchRes, but using a fast approximation to the match function.
void	compute_symm_rotations (core::pose::Pose const &pose, const core::conformation::symmetry::SymmetryInfo *symmInfo=NULL)
	Computes the symmatric rotation matrices.
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.
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.
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.
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.
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.
void	clear_dCCdx_res_cache (core::pose::Pose const &pose)
	Resets the counters used for derivative computation in sliding-window/fast scoring.
numeric::xyzVector< core::Real >	getTransform ()
	Get the transformation from indices to Cartesian coords using 'real' origin.
void	set_nres (int nres)
	set # of residues
void	showCachedScores (utility::vector1< int > const &reses)
	Print cached CCs.
core::Real	getCCs (int resid)
void	setUseDensityInMinimizer (bool newVal)
bool	getUseDensityInMinimizer () const
void	setUseExactDerivatives (bool newVal)
bool	getUseExactDerivatives () 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
bool	isMapLoaded () const
numeric::xyzVector< core::Real >	getCoM () const
numeric::xyzVector< core::Real >	getOrigin () const
numeric::xyzVector< core::Real >	getEffOrigin () const
utility::vector1 < core::kinematics::RT >	getsymmOps () const
void	maskResidues (int scoring_mask)
void	maskResidues (utility::vector1< int > const &scoring_mask)
void	clearMask ()
ObjexxFCL::FArray3D< float > const &	data () const
void	cart2idx (numeric::xyzVector< core::Real > const &cartX, numeric::xyzVector< core::Real > &idxX) const
template<class Q >
void	idx2cart (numeric::xyzVector< Q > const &idxX, numeric::xyzVector< core::Real > &cartX) const
template<class Q >
void	idxoffset2cart (numeric::xyzVector< Q > const &idxX, numeric::xyzVector< core::Real > &cartX) const
void	cart2frac (numeric::xyzVector< core::Real > const &cartX, numeric::xyzVector< core::Real > &fracX) const
void	frac2cart (numeric::xyzVector< core::Real > const &fracX, numeric::xyzVector< core::Real > &cartX) const
numeric::xyzVector< core::Real >	delt_cart (numeric::xyzVector< core::Real > const &cartX1, numeric::xyzVector< core::Real > const &cartX2)
numeric::xyzVector< core::Real >	get_cart_unitCell (numeric::xyzVector< core::Real > const &cartX)
numeric::xyzVector< core::Real >	get_nearest_UC (numeric::xyzVector< core::Real > const &cartX_in, numeric::xyzVector< core::Real > const &cartX_ref)
numeric::xyzVector< core::Real >	dens_grad (numeric::xyzVector< core::Real > const &idxX) const
void	resize (core::Real approxGridSpacing)
	resize the map via FFT
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)

---

Constructor & Destructor Documentation

core::scoring::electron_density::ElectronDensity::ElectronDensity

(

)

constructor

null constructor

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

template<class T >

core::scoring::electron_density::ElectronDensity::ElectronDensity	(	ObjexxFCL::FArray3D< T > const &	map,
		core::Real	apix = 1.0,
		numeric::xyzVector< core::Real >	new_origin = numeric::xyzVector< core::Real >(0,0,0),
		bool	fftshift = false
	)		[inline]

constructor from an FArray3D (debugging only)

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

---

Member Function Documentation

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

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

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, make_table_of_pilot_apps::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]

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

Computes the symmatric rotation matrices.

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

References core::conformation::Residue::atom(), core::conformation::symmetry::SymmetryInfo::bb_follows(), core::conformation::symmetry::SymmetryInfo::bb_is_independent(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::get_outgoing_edges(), core::conformation::symmetry::SymmetryInfo::num_independent_residues(), core::pose::Pose::residue(), core::conformation::symmetry::SymmetryInfo::subunit_index(), core::conformation::symmetry::SymmetryInfo::subunits(), core::pose::Pose::total_residue(), core::scoring::electron_density::TR(), and core::conformation::Atom::xyz().

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

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

(

)

const [inline]

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

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

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

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

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

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

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

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

References core::conformation::Residue::atom(), core::scoring::electron_density::getDensityMap(), matchRes(), 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::frac2cart	(	numeric::xyzVector< core::Real > const &	fracX,
		numeric::xyzVector< core::Real > &	cartX
	)		const [inline]

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

(

numeric::xyzVector< core::Real > const &

cartX

)

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

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

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

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

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

core::Real core::scoring::electron_density::ElectronDensity::getCCs

(

int

resid

)

[inline]

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

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

(

)

const [inline]

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

(

)

const [inline]

core::Real core::scoring::electron_density::ElectronDensity::getMax

(

)

const [inline]

core::Real core::scoring::electron_density::ElectronDensity::getMean

(

)

const [inline]

core::Real core::scoring::electron_density::ElectronDensity::getMin

(

)

const [inline]

core::Real core::scoring::electron_density::ElectronDensity::getNumDerivH

(

)

const [inline]

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

(

)

const [inline]

core::Real core::scoring::electron_density::ElectronDensity::getResolution

(

)

const [inline]

core::Real core::scoring::electron_density::ElectronDensity::getStdev

(

)

const [inline]

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

(

)

const [inline]

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

(

)

[inline]

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

References idx2cart().

bool core::scoring::electron_density::ElectronDensity::getUseDensityInMinimizer

(

)

const [inline]

bool core::scoring::electron_density::ElectronDensity::getUseExactDerivatives

(

)

const [inline]

template<class Q >

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

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]

bool core::scoring::electron_density::ElectronDensity::isMapLoaded

(

)

const [inline]

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

void core::scoring::electron_density::ElectronDensity::maskResidues

(

int

scoring_mask

)

[inline]

void core::scoring::electron_density::ElectronDensity::maskResidues

(

utility::vector1< int > const &

scoring_mask

)

[inline]

core::Real core::scoring::electron_density::ElectronDensity::matchCentroidPose	(	core::pose::Pose const &	pose,
		const core::conformation::symmetry::SymmetryInfo *	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 core::conformation::symmetry::SymmetryInfo::bb_is_independent(), protocols::forge::build::SegmentInsertConnectionScheme::C, make_table_of_pilot_apps::f, core::scoring::electron_density::is_missing_density(), core::chemical::ResidueType::is_protein(), core::scoring::electron_density::pos_mod(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::scoring::electron_density::square(), core::pose::Pose::total_residue(), core::scoring::electron_density::TR(), and core::conformation::Atom::xyz().

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

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

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

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

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

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

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

Match a pose to a patterson map.

Match pose to patterson map

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(), make_table_of_pilot_apps::begin, core::scoring::electron_density::OneGaussianScattering::C(), core::pack::interaction_graph::debug, core::sequence::end, core::pose::Pose::energies(), make_table_of_pilot_apps::f, core::scoring::electron_density::get_A(), core::scoring::electron_density::interp_linear(), core::scoring::electron_density::interp_spline(), core::scoring::electron_density::is_missing_density(), 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::scoring::electron_density::spline_coeffs(), core::scoring::electron_density::square(), core::pose::Pose::total_residue(), core::scoring::electron_density::TR(), core::scoring::Energies::use_nblist(), writeMRC(), and core::conformation::Atom::xyz().

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,
		const core::conformation::symmetry::SymmetryInfo *	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::conformation::symmetry::SymmetryInfo::bb_is_independent(), core::scoring::electron_density::OneGaussianScattering::C(), protocols::forge::build::SegmentInsertConnectionScheme::C, core::pack::interaction_graph::debug, core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), make_table_of_pilot_apps::f, core::pose::Pose::fold_tree(), core::scoring::electron_density::get_A(), core::graph::Edge::get_first_node_ind(), core::graph::Edge::get_second_node_ind(), core::kinematics::FoldTree::is_cutpoint(), core::scoring::electron_density::is_missing_density(), core::conformation::Residue::is_polymer(), core::scoring::electron_density::OneGaussianScattering::k(), core::conformation::Residue::last_backbone_atom(), core::scoring::electron_density::MAX_FLT, core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), core::scoring::electron_density::TR(), writeMRC(), and core::conformation::Atom::xyz().

Referenced by 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,
		const core::conformation::symmetry::SymmetryInfo *	symmInfo = NULL
	)

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

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

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

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

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

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

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

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

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(), core::scoring::electron_density::get_A(), core::scoring::electron_density::is_missing_density(), core::scoring::electron_density::OneGaussianScattering::k(), core::conformation::Residue::nheavyatoms(), core::conformation::Residue::seqpos(), and core::scoring::electron_density::square().

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

void core::scoring::electron_density::ElectronDensity::resize

(

core::Real

approxGridSpacing

)

resize the map via FFT

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

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

Align a pose about a 2D rotation axis.

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

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

void core::scoring::electron_density::ElectronDensity::set_nres

(

int

nres

)

[inline]

set # of residues

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

void core::scoring::electron_density::ElectronDensity::setUseDensityInMinimizer

(

bool

newVal

)

[inline]

void core::scoring::electron_density::ElectronDensity::setUseExactDerivatives

(

bool

newVal

)

[inline]

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::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(), core::scoring::electron_density::is_missing_density(), core::scoring::electron_density::OneGaussianScattering::k(), core::conformation::Residue::nheavyatoms(), core::conformation::Residue::seqpos(), and core::scoring::electron_density::square().

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

bool core::scoring::electron_density::ElectronDensity::writeMAT

(

std::string

mapfilestem

)

(debugging) Write MATLAB v5 mapfile

bool core::scoring::electron_density::ElectronDensity::writeMRC

(

std::string

mapfilestem

)

(debugging) Write MRC mapfile

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

Referenced by matchPoseToPatterson(), matchRes(), and rotAlign2DPose().

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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