protocols::electron_density Namespace Reference

Classes
class	BfactorMultifunc
	Bfactor multifunc. More...
class	BfactorFittingMover
	mover to fit B factors More...
class	BfactorFittingMoverCreator
class	DensitySymmInfo
	scale density map intensities to match a pose's More...
class	DensityZscores
	protocol to score local density-fit More...
class	DensityZscoresCreator
class	DockFragmentsIntoDensityMover
	The workhorse. More...
class	RBfitResult
	CLASSES. More...
class	RefinementResult
class	RBfitResultComparitor
class	RefinementResultComparitor
class	RevRefinementResultComparitor
class	PointScoreComparator
class	ResultDB
struct	PoseSphericalSamplesOptions
struct	SelectDensityPointsOptions
struct	DensityGridSearchOptions
struct	MinimizePoseIntoDensityOptions
class	DockPDBIntoDensityMover
class	ReportFSC
	scale density map intensities to match a pose's More...
class	ReportFSCCreator
class	ScaleMapIntensities
	scale density map intensities to match a pose's More...
class	ScaleMapIntensitiesCreator
class	SetupForDensityScoringMover
class	SetupForDensityScoringMoverCreator
class	VoxelSpacingMultifunc
	Bfactor multifunc. More...
class	VoxelSpacingRefinementMover
	mover to fit B factors More...
class	VoxelSpacingRefinementMoverCreator

Typedefs
using	DensityZscoresOP = utility::pointer::shared_ptr< DensityZscores >
using	DensityZscoresCOP = utility::pointer::shared_ptr< DensityZscores const >
typedef utility::pointer::shared_ptr< DockFragmentsIntoDensityMover >	DockFragmentsIntoDensityMoverOP
typedef ResultDB< RBfitResult, RBfitResultComparitor >	RBfitResultDB
typedef ResultDB< RefinementResult, RefinementResultComparitor >	RefinementResultDB
typedef ResultDB< RefinementResult, RevRefinementResultComparitor >	RevRefinementResultDB
typedef utility::pointer::shared_ptr< DockPDBIntoDensityMover >	DockPDBIntoDensityMoverOP
typedef utility::pointer::shared_ptr< SetupForDensityScoringMover >	SetupForDensityScoringMoverOP

Functions
void	symmetrizeBfactors (core::pose::Pose &pose)
	helper function More...
std::ostream &	operator<< (std::ostream &os, DensityZscores const &mover)
static basic::Tracer	TR ("protocols.electron_density.DockFragmentsIntoDensityMover")
std::ostream &	operator<< (std::ostream &out, const RBfitResult &result)
template<typename T >
void	write_RBfitResultDB (RBfitResultDB fit_result_DB, T &outresults)
	FUNCTIONS. More...
template void	write_RBfitResultDB< std::ofstream > (RBfitResultDB fit_result_DB, std::ofstream &outresults)
template void	write_RBfitResultDB< std::stringstream > (RBfitResultDB fit_result_DB, std::stringstream &outresults)
template<typename T >
void	dump_RefinementDB_to_silent (T resultDB, std::string const &outfile, std::string const &tag_prefix, std::string const &final_chain, bool const centroid_output, bool const append_to_outfile, utility::vector1< core::pose::PoseCOP > const &natives, DensitySymmInfo const &symminfo, bool const legacy_rms)
template void	dump_RefinementDB_to_silent< RevRefinementResultDB > (RevRefinementResultDB resultDB, std::string const &outfile, std::string const &tag_prefix, std::string const &final_chain, bool const centroid_output, bool const append_to_outfile, utility::vector1< core::pose::PoseCOP > const &natives, DensitySymmInfo const &symminfo, bool const legacy_rms)
template void	dump_RefinementDB_to_silent< RefinementResultDB > (RefinementResultDB resultDB, std::string const &outfile, std::string const &tag_prefix, std::string const &final_chain, bool const centroid_output, bool const append_to_outfile, utility::vector1< core::pose::PoseCOP > const &natives, DensitySymmInfo const &symminfo, bool const legacy_rms)
void	compare_RBfitDB_to_native (RBfitResultDB resultDB, core::pose::Pose const &pose, core::pose::PoseCOPs const &natives, utility::vector1< numeric::xyzVector< core::Real > > const &native_coms, utility::vector1< numeric::xyzVector< core::Real > > const &native_middle_cas, DensitySymmInfo const &symminfo, bool const rot_middle_ca, core::Real const rms_cutoff)
core::Real	get_rms (core::pose::Pose const &r1, core::pose::Pose const &r2, DensitySymmInfo const &d)
template<typename T >
void	dump_and_raise_bad_pose_alignment (core::pose::Pose const &r1, char const r1_chain, core::Size const r1_resnum, core::Size const r1_posenum, core::pose::Pose const &r2, core::Size const r2_posenum, T &out)
template<typename T >
void	dump_and_raise_no_pose_alignment (core::pose::Pose const &r1, core::pose::Pose const &r2, T &out)
core::Real	get_rms (core::pose::Pose const &r1, core::pose::Pose const &r2, DensitySymmInfo const &d, bool const native)
core::Real	get_rms (RefinementResult const &r1, RefinementResult const &r2, DensitySymmInfo const &d)
core::Real	get_gdt (core::pose::Pose const &r1, core::pose::Pose const &r2, DensitySymmInfo const &d, bool native)
void	apply_transform (core::pose::Pose &pose, RBfitResult const &transform)
	FUNCTIONS. More...
core::Real	get_rot_angle (numeric::xyzMatrix< core::Real > const &R)
void	pose_spherical_samples (core::pose::Pose const &pose, ObjexxFCL::FArray3D< core::Real > &sigR, ObjexxFCL::FArray3D< core::Real > &epsR, PoseSphericalSamplesOptions const &params)
	Step 0: map pose to spherically sampled density + mask. More...
core::Real	get_radius (core::pose::Pose const &pose, numeric::xyzVector< core::Real > &com, bool const center_on_middle_ca)
	Get max extent of pose. More...
core::Real	get_spectrum (core::pose::Pose const &pose, utility::vector1< core::Real > &pose_1dspec, core::Real const delR, core::Real const fragDens, bool const convolute_single_residue, bool const center_on_middle_ca)
	Get 1d power spectrum of a pose. More...
void	map_from_spectrum (utility::vector1< core::Real > const &pose_1dspec, ObjexxFCL::FArray3D< core::Real > &rot, core::Real const delR)
utility::vector1< std::pair< numeric::xyzVector< core::Real >, core::Real > >	create_and_sort_point_score_pairs (ObjexxFCL::FArray3D< float > const &densdata, ObjexxFCL::FArray3D< core::Real > const &rot, core::Size const grid_step)
void	dump_points_to_search_to_pdb_or_txt (utility::vector1< numeric::xyzVector< core::Real > > const &points_to_search, std::string const &pdb_filename, std::string const &txt_filename)
utility::vector1< numeric::xyzVector< core::Real > >	select_density_points (core::pose::Pose const &pose, SelectDensityPointsOptions const &params, core::Size &nRsteps)
void	cluster_RefinementDB (RefinementResultDB &results, DensitySymmInfo const &symminfo, core::Real const cluster_radius, core::Size const target_size=0)
	cluster a RefinementResultDB based on a specific cluster_radius. If target_size is unset or More...
void	do_filter (utility::vector1< core::pose::PoseOP > const &poses, RBfitResultDB &results, bool const rescore, DensitySymmInfo const &symminfo, core::Real const cluster_radius)
void	cluster_RBfitResultDB_fast (RBfitResultDB &results, core::Size const delR, core::Size const nRsteps, core::Real const cluster_radius, core::Size const max_results, bool const include_distance, core::scoring::electron_density::ElectronDensity const &dens)
void	density_grid_search (core::Size pose_idx, core::pose::Pose const &pose, RBfitResultDB &results, utility::vector1< numeric::xyzVector< core::Real > > const &points_to_search, DensityGridSearchOptions const &params)
	do the main search over the map More...
static basic::Tracer	TR ("protocols.electron_density.DockPDBIntoDensityMover")
MinimizePoseIntoDensityOptions	create_minimize_pose_into_density_options (core::pose::Pose const &pose, core::Real const dens_wt)
void	dump_to_silent (core::pose::Pose const &pose, std::string const &fname, std::string tag, bool overwrite)
bool	check_if_file_exists (const std::string &name)
static basic::Tracer	TR ("protocols.electron_density.util")
void	set_pose_and_scorefxn_for_edens_scoring (core::pose::Pose &pose, core::scoring::ScoreFunction &scorefxn)
static basic::Tracer	TR ("protocols.electron_density.util")
protocols::loops::Loops	findLoopFromDensity (core::pose::Pose &pose, core::Real frac, int max_helix_melt, int max_strand_melt)
core::Real	dockPoseIntoMap (core::pose::Pose &pose, std::string const &align_in)
void	remove_occupied_density_from_density (core::pose::Pose const &pose, core::scoring::electron_density::ElectronDensity &dens, core::Size const edge_trim, core::Real const mask_radius)

Typedef Documentation

DensityZscoresCOP

using protocols::electron_density::DensityZscoresCOP = typedef utility::pointer::shared_ptr< DensityZscores const >

DensityZscoresOP

using protocols::electron_density::DensityZscoresOP = typedef utility::pointer::shared_ptr< DensityZscores >

DockFragmentsIntoDensityMoverOP

typedef utility::pointer::shared_ptr< DockFragmentsIntoDensityMover > protocols::electron_density::DockFragmentsIntoDensityMoverOP

DockPDBIntoDensityMoverOP

typedef utility::pointer::shared_ptr< DockPDBIntoDensityMover > protocols::electron_density::DockPDBIntoDensityMoverOP

RBfitResultDB

typedef ResultDB<RBfitResult, RBfitResultComparitor> protocols::electron_density::RBfitResultDB

RefinementResultDB

typedef ResultDB<RefinementResult, RefinementResultComparitor> protocols::electron_density::RefinementResultDB

RevRefinementResultDB

typedef ResultDB<RefinementResult, RevRefinementResultComparitor> protocols::electron_density::RevRefinementResultDB

SetupForDensityScoringMoverOP

typedef utility::pointer::shared_ptr< SetupForDensityScoringMover > protocols::electron_density::SetupForDensityScoringMoverOP

Function Documentation

apply_transform()

void protocols::electron_density::apply_transform	(	core::pose::Pose &	pose,
		RBfitResult const &	transform
	)

FUNCTIONS.

References core::pose::Pose::batch_set_xyz(), protocols::electron_density::RBfitResult::post_trans_, protocols::electron_density::RBfitResult::pre_trans_, core::pose::Pose::residue_type(), protocols::electron_density::RBfitResult::rotation_, core::pose::Pose::size(), and core::pose::Pose::xyz().

Referenced by protocols::hybridization::CartesianSampler::apply_frame(), compare_RBfitDB_to_native(), do_filter(), protocols::electron_density::DockFragmentsIntoDensityMover::do_refinement(), protocols::electron_density::DockPDBIntoDensityMover::dump_RBfitDB_to_pdbs(), protocols::electron_density::DockFragmentsIntoDensityMover::print_best_rms(), and protocols::electron_density::DockPDBIntoDensityMover::refine_RBfitResultDB().

check_if_file_exists()

bool protocols::electron_density::check_if_file_exists ( const std::string &  name )

inline

Referenced by protocols::electron_density::DockPDBIntoDensityMover::check_for_existing_output_file(), and protocols::electron_density::DockPDBIntoDensityMover::read_in_points_to_search().

cluster_RBfitResultDB_fast()

void protocols::electron_density::cluster_RBfitResultDB_fast	(	RBfitResultDB &	results,
		core::Size const	delR,
		core::Size const	nRsteps,
		core::Real const	cluster_radius,
		core::Size const	max_results,
		bool const	include_distance,
		core::scoring::electron_density::ElectronDensity const &	dens
	)

References protocols::electron_density::ResultDB< T, Tcomp >::add_element(), core::kinematics::distance(), get_rot_angle(), core::scoring::electron_density::ElectronDensity::idx2cart(), protocols::electron_density::ResultDB< T, Tcomp >::pop(), and protocols::electron_density::ResultDB< T, Tcomp >::size().

Referenced by protocols::electron_density::DockPDBIntoDensityMover::combine_search(), and density_grid_search().

cluster_RefinementDB()

void protocols::electron_density::cluster_RefinementDB	(	RefinementResultDB &	results,
		DensitySymmInfo const &	symminfo,
		core::Real const	cluster_radius,
		core::Size const	target_size
	)

cluster a RefinementResultDB based on a specific cluster_radius. If target_size is unset or

References protocols::electron_density::ResultDB< T, Tcomp >::add_element(), get_rms(), protocols::electron_density::ResultDB< T, Tcomp >::pop(), and protocols::electron_density::ResultDB< T, Tcomp >::size().

Referenced by protocols::electron_density::DockFragmentsIntoDensityMover::apply_multi().

compare_RBfitDB_to_native()

void protocols::electron_density::compare_RBfitDB_to_native	(	RBfitResultDB	resultDB,
		core::pose::Pose const &	pose,
		core::pose::PoseCOPs const &	natives,
		utility::vector1< numeric::xyzVector< core::Real > > const &	native_coms,
		utility::vector1< numeric::xyzVector< core::Real > > const &	native_middle_cas,
		DensitySymmInfo const &	symminfo,
		bool const	rot_middle_ca,
		core::Real const	rms_cutoff
	)

References core::pose::addVirtualResAsRoot(), apply_transform(), get_gdt(), get_rms(), protocols::electron_density::DensitySymmInfo::min_symm_dist2(), protocols::electron_density::ResultDB< T, Tcomp >::pop(), protocols::electron_density::RBfitResult::post_trans_, core::scoring::rms, protocols::electron_density::RBfitResult::score_, protocols::electron_density::ResultDB< T, Tcomp >::size(), and TR().

Referenced by protocols::electron_density::DockPDBIntoDensityMover::combine_search(), and density_grid_search().

create_and_sort_point_score_pairs()

utility::vector1< std::pair< numeric::xyzVector< core::Real >, core::Real > > protocols::electron_density::create_and_sort_point_score_pairs	(	ObjexxFCL::FArray3D< float > const &	densdata,
		ObjexxFCL::FArray3D< core::Real > const &	rot,
		core::Size const	grid_step
	)

References rot().

Referenced by select_density_points().

create_minimize_pose_into_density_options()

MinimizePoseIntoDensityOptions protocols::electron_density::create_minimize_pose_into_density_options	(	core::pose::Pose const &	pose,
		core::Real const	dens_wt
	)

References core::scoring::coordinate_constraint, core::scoring::elec_dens_fast, core::scoring::elec_dens_whole_structure_allatom, core::pose::Pose::fold_tree(), core::kinematics::FoldTree::get_outgoing_edges(), core::scoring::get_score_function(), and core::kinematics::FoldTree::root().

Referenced by protocols::electron_density::DockPDBIntoDensityMover::manual_refine_pdb(), and protocols::electron_density::DockPDBIntoDensityMover::refine_RBfitResultDB().

density_grid_search()

void protocols::electron_density::density_grid_search	(	core::Size const	pose_idx,
		core::pose::Pose const &	pose,
		RBfitResultDB &	results,
		utility::vector1< numeric::xyzVector< core::Real > > const &	points_to_search,
		DensityGridSearchOptions const &	params
	)

do the main search over the map

References protocols::electron_density::ResultDB< T, Tcomp >::add_element(), protocols::electron_density::DensityGridSearchOptions::B_, protocols::electron_density::DensityGridSearchOptions::center_on_middle_ca_, protocols::electron_density::DensityGridSearchOptions::cluster_radius_, cluster_RBfitResultDB_fast(), compare_RBfitDB_to_native(), core::pack::interaction_graph::debug, protocols::electron_density::DensityGridSearchOptions::delRSteps_, get_radius(), core::scoring::electron_density::getDensityMap(), core::scoring::electron_density::ElectronDensity::idx2cart(), protocols::electron_density::DensityGridSearchOptions::include_distance_during_fast_cluster_, protocols::electron_density::DensityGridSearchOptions::laplacian_offset_, core::scoring::electron_density::ElectronDensity::mapSphericalSamples(), protocols::electron_density::DensityGridSearchOptions::max_rot_per_trans_, protocols::mean_field::min(), protocols::electron_density::DensityGridSearchOptions::native_coms_, protocols::electron_density::DensityGridSearchOptions::native_middle_cas_, protocols::electron_density::DensityGridSearchOptions::natives_, protocols::electron_density::DensityGridSearchOptions::nRsteps_, protocols::electron_density::DensityGridSearchOptions::output_fn_, protocols::electron_density::DensityGridSearchOptions::point_search_end_, protocols::electron_density::DensityGridSearchOptions::point_search_start_, protocols::electron_density::ResultDB< T, Tcomp >::pop(), pose_spherical_samples(), protocols::electron_density::DensityGridSearchOptions::rms_cutoff_, rot(), protocols::electron_density::ResultDB< T, Tcomp >::size(), core::scoring::electron_density::square(), protocols::electron_density::DensityGridSearchOptions::symminfo_, protocols::hybridization::t, protocols::electron_density::ResultDB< T, Tcomp >::to_add_element(), core::id::to_string(), protocols::electron_density::ResultDB< T, Tcomp >::top(), TR(), write_RBfitResultDB(), and core::scoring::electron_density::ElectronDensity::writeMRC().

Referenced by protocols::electron_density::DockFragmentsIntoDensityMover::apply_multi(), and protocols::electron_density::DockPDBIntoDensityMover::apply_search().

do_filter()

void protocols::electron_density::do_filter	(	utility::vector1< core::pose::PoseOP > const &	poses,
		RBfitResultDB &	results,
		bool const	rescore,
		DensitySymmInfo const &	symminfo,
		core::Real const	cluster_radius
	)

References protocols::electron_density::ResultDB< T, Tcomp >::add_element(), core::pose::addVirtualResAsRoot(), apply_transform(), core::scoring::elec_dens_whole_structure_allatom, get_rms(), protocols::electron_density::ResultDB< T, Tcomp >::pop(), protocols::electron_density::ResultDB< T, Tcomp >::size(), and TR().

Referenced by protocols::electron_density::DockFragmentsIntoDensityMover::apply_multi().

dockPoseIntoMap()

core::Real protocols::electron_density::dockPoseIntoMap	(	core::pose::Pose &	pose,
		std::string const &	align_in
	)

References core::scoring::electron_density::add_dens_scores_from_cmdline_to_scorefxn(), core::scoring::elec_dens_fast, core::scoring::elec_dens_whole_structure_allatom, core::scoring::elec_dens_whole_structure_ca, core::scoring::elec_dens_window, core::pose::Pose::fold_tree(), core::kinematics::FoldTree::get_outgoing_edges(), core::scoring::get_score_function(), core::pose::symmetry::is_symmetric(), core::pose::symmetry::make_symmetric_movemap(), core::kinematics::FoldTree::root(), and TR().

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

dump_and_raise_bad_pose_alignment()

template<typename T >

void protocols::electron_density::dump_and_raise_bad_pose_alignment	(	core::pose::Pose const &	r1,
		char const	r1_chain,
		core::Size const	r1_resnum,
		core::Size const	r1_posenum,
		core::pose::Pose const &	r2,
		core::Size const	r2_posenum,
		T &	out
	)

References core::conformation::membrane::out, protocols::hybridization::r1, and protocols::hybridization::r2.

Referenced by get_gdt(), and get_rms().

dump_and_raise_no_pose_alignment()

template<typename T >

void protocols::electron_density::dump_and_raise_no_pose_alignment	(	core::pose::Pose const &	r1,
		core::pose::Pose const &	r2,
		T &	out
	)

References core::conformation::membrane::out, protocols::hybridization::r1, and protocols::hybridization::r2.

Referenced by get_gdt(), and get_rms().

dump_points_to_search_to_pdb_or_txt()

void protocols::electron_density::dump_points_to_search_to_pdb_or_txt	(	utility::vector1< numeric::xyzVector< core::Real > > const &	points_to_search,
		std::string const &	pdb_filename,
		std::string const &	txt_filename
	)

References core::io::AtomInformation::chainID, core::io::StructFileRep::chains(), core::io::pdb::create_pdb_contents_from_sfr(), core::io::AtomInformation::element, core::scoring::electron_density::getDensityMap(), core::scoring::electron_density::ElectronDensity::idx2cart(), core::io::AtomInformation::name, core::io::AtomInformation::occupancy, core::conformation::membrane::out, protocols::denovo_design::movers::pdb_filename(), core::io::AtomInformation::resName, core::io::AtomInformation::serial, core::id::to_string(), core::io::AtomInformation::x, core::io::AtomInformation::y, and core::io::AtomInformation::z.

Referenced by protocols::electron_density::DockPDBIntoDensityMover::get_points_to_search(), and select_density_points().

dump_RefinementDB_to_silent()

template<typename T >

void protocols::electron_density::dump_RefinementDB_to_silent	(	T	resultDB,
		std::string const &	outfile,
		std::string const &	tag_prefix,
		std::string const &	final_chain,
		bool const	centroid_output,
		bool const	append_to_outfile,
		utility::vector1< core::pose::PoseCOP > const &	natives,
		DensitySymmInfo const &	symminfo,
		bool const	legacy_rms
	)

References core::io::silent::SilentStruct::add_energy(), protocols::simple_moves::SwitchResidueTypeSetMover::apply(), core::io::silent::SilentStruct::clear_energies(), get_gdt(), get_rms(), core::pose::Pose::pdb_info(), protocols::electron_density::RefinementResult::pose_, protocols::electron_density::RefinementResult::prerefine_score_, core::scoring::rms, protocols::electron_density::RefinementResult::score_, core::pose::Pose::size(), protocols::electron_density::RefinementResult::spharm_score_, and core::io::silent::SilentFileData::write_silent_struct().

Referenced by protocols::electron_density::DockFragmentsIntoDensityMover::apply_multi(), protocols::electron_density::DockPDBIntoDensityMover::apply_refinement(), protocols::electron_density::DockPDBIntoDensityMover::cluster_silent(), and protocols::electron_density::DockPDBIntoDensityMover::combine_refinement().

dump_RefinementDB_to_silent< RefinementResultDB >()

template void protocols::electron_density::dump_RefinementDB_to_silent< RefinementResultDB >	(	RefinementResultDB	resultDB,
		std::string const &	outfile,
		std::string const &	tag_prefix,
		std::string const &	final_chain,
		bool const	centroid_output,
		bool const	append_to_outfile,
		utility::vector1< core::pose::PoseCOP > const &	natives,
		DensitySymmInfo const &	symminfo,
		bool const	legacy_rms
	)

dump_RefinementDB_to_silent< RevRefinementResultDB >()

template void protocols::electron_density::dump_RefinementDB_to_silent< RevRefinementResultDB >	(	RevRefinementResultDB	resultDB,
		std::string const &	outfile,
		std::string const &	tag_prefix,
		std::string const &	final_chain,
		bool const	centroid_output,
		bool const	append_to_outfile,
		utility::vector1< core::pose::PoseCOP > const &	natives,
		DensitySymmInfo const &	symminfo,
		bool const	legacy_rms
	)

dump_to_silent()

void protocols::electron_density::dump_to_silent	(	core::pose::Pose const &	pose,
		std::string const &	fname,
		std::string	tag,
		bool	overwrite
	)

References core::io::silent::SilentFileData::write_silent_struct().

Referenced by protocols::electron_density::DockPDBIntoDensityMover::minimize_poseOP_into_density(), and protocols::electron_density::DockPDBIntoDensityMover::refine_RBfitResultDB().

findLoopFromDensity()

protocols::loops::Loops protocols::electron_density::findLoopFromDensity	(	core::pose::Pose &	pose,
		core::Real	frac,
		int	max_helix_melt,
		int	max_strand_melt
	)

References core::conformation::Residue::atom(), core::kinematics::FoldTree::cutpoints(), core::scoring::dssp::Dssp::dssp_reduced(), core::pose::Pose::fold_tree(), core::scoring::electron_density::getDensityMap(), core::kinematics::FoldTree::is_cutpoint(), core::conformation::Residue::is_polymer(), protocols::mean_field::max(), protocols::mean_field::min(), core::conformation::Residue::natoms(), protocols::loops::Loops::push_back(), core::pose::Pose::residue(), core::scoring::electron_density::ElectronDensity::set_nres(), core::pose::Pose::size(), and core::conformation::Atom::xyz().

get_gdt()

core::Real protocols::electron_density::get_gdt	(	core::pose::Pose const &	r1,
		core::pose::Pose const &	r2,
		DensitySymmInfo const &	d,
		bool	native
	)

References core::kinematics::distance(), dump_and_raise_bad_pose_alignment(), dump_and_raise_no_pose_alignment(), protocols::electron_density::DensitySymmInfo::min_symm_dist2(), core::chemical::element::N, protocols::hybridization::r1, protocols::hybridization::r2, and TR().

Referenced by compare_RBfitDB_to_native(), dump_RefinementDB_to_silent(), and protocols::electron_density::DockPDBIntoDensityMover::refine_RBfitResultDB().

get_radius()

core::Real protocols::electron_density::get_radius	(	core::pose::Pose const &	pose,
		numeric::xyzVector< core::Real > &	com,
		bool const	center_on_middle_ca
	)

Get max extent of pose.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::conformation::Residue::atom(), protocols::membrane::com(), protocols::mean_field::max(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Atom::xyz().

Referenced by density_grid_search(), core::scoring::packstat::AtomRadiusMap::get_radius(), and get_spectrum().

get_rms() [1/3]

core::Real protocols::electron_density::get_rms	(	core::pose::Pose const &	r1,
		core::pose::Pose const &	r2,
		DensitySymmInfo const &	d
	)

References protocols::electron_density::DensitySymmInfo::min_symm_dist2(), core::chemical::element::N, protocols::hybridization::r1, protocols::hybridization::r2, and core::scoring::rms.

Referenced by protocols::electron_density::DockPDBIntoDensityMover::analyze_RefinementDB(), cluster_RefinementDB(), protocols::electron_density::DockPDBIntoDensityMover::cluster_RevRefinementDB(), compare_RBfitDB_to_native(), do_filter(), protocols::electron_density::DockFragmentsIntoDensityMover::do_refinement(), dump_RefinementDB_to_silent(), get_rms(), protocols::electron_density::DockFragmentsIntoDensityMover::print_best_rms(), and protocols::electron_density::DockPDBIntoDensityMover::refine_RBfitResultDB().

get_rms() [2/3]

core::Real protocols::electron_density::get_rms	(	core::pose::Pose const &	r1,
		core::pose::Pose const &	r2,
		DensitySymmInfo const &	d,
		bool const	native
	)

References core::kinematics::distance(), dump_and_raise_bad_pose_alignment(), dump_and_raise_no_pose_alignment(), protocols::electron_density::DensitySymmInfo::min_symm_dist2(), core::chemical::element::N, protocols::hybridization::r1, protocols::hybridization::r2, core::scoring::rms, and TR().

get_rms() [3/3]

core::Real protocols::electron_density::get_rms	(	RefinementResult const &	r1,
		RefinementResult const &	r2,
		DensitySymmInfo const &	d
	)

References get_rms(), protocols::hybridization::r1, and protocols::hybridization::r2.

get_rot_angle()

core::Real protocols::electron_density::get_rot_angle

(

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

R

)

References protocols::mean_field::max(), and protocols::mean_field::min().

Referenced by cluster_RBfitResultDB_fast().

get_spectrum()

core::Real protocols::electron_density::get_spectrum	(	core::pose::Pose const &	pose,
		utility::vector1< core::Real > &	pose_1dspec,
		core::Real const	delR,
		core::Real const	fragDens,
		bool const	convolute_single_residue,
		bool const	center_on_middle_ca
	)

Get 1d power spectrum of a pose.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::conformation::Residue::atom(), protocols::membrane::com(), get_radius(), core::conformation::Residue::is_virtual_residue(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), core::pose::Pose::size(), TR(), and core::conformation::Atom::xyz().

Referenced by protocols::electron_density::DockPDBIntoDensityMover::apply_search(), and select_density_points().

map_from_spectrum()

void protocols::electron_density::map_from_spectrum	(	utility::vector1< core::Real > const &	pose_1dspec,
		ObjexxFCL::FArray3D< core::Real > &	rot,
		core::Real const	delR
	)

References core::scoring::electron_density::getDensityMap(), core::scoring::electron_density::ElectronDensity::idxoffset2cart(), and rot().

Referenced by select_density_points().

operator<<() [1/2]

std::ostream & protocols::electron_density::operator<<	(	std::ostream &	os,
		DensityZscores const &	mover
	)

References protocols::electron_density::DensityZscores::show().

operator<<() [2/2]

std::ostream& protocols::electron_density::operator<<	(	std::ostream &	out,
		const RBfitResult &	result
	)

pose_spherical_samples()

void protocols::electron_density::pose_spherical_samples	(	core::pose::Pose const &	pose,
		ObjexxFCL::FArray3D< core::Real > &	sigR,
		ObjexxFCL::FArray3D< core::Real > &	epsR,
		protocols::electron_density::PoseSphericalSamplesOptions const &	params
	)

Step 0: map pose to spherically sampled density + mask.

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(), protocols::electron_density::PoseSphericalSamplesOptions::B_, core::chemical::element::C, core::scoring::electron_density::OneGaussianScattering::C(), protocols::electron_density::PoseSphericalSamplesOptions::center_on_middle_ca_, protocols::electron_density::PoseSphericalSamplesOptions::delRsteps_, core::scoring::electron_density::get_A(), core::scoring::electron_density::getDensityMap(), core::scoring::electron_density::ElectronDensity::getEffectiveBfactor(), core::scoring::electron_density::OneGaussianScattering::k(), protocols::electron_density::PoseSphericalSamplesOptions::laplacian_offset_, core::conformation::Residue::nheavyatoms(), protocols::electron_density::PoseSphericalSamplesOptions::nRsteps_, core::pose::Pose::residue(), core::pose::Pose::size(), protocols::hybridization::t, TR(), core::conformation::Atom::xyz(), and protocols::kinmatch::xyz().

Referenced by density_grid_search().

remove_occupied_density_from_density()

void protocols::electron_density::remove_occupied_density_from_density	(	core::pose::Pose const &	pose,
		core::scoring::electron_density::ElectronDensity &	dens,
		core::Size const	edge_trim,
		core::Real const	mask_radius
	)

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::conformation::Residue::atom_type_index(), core::conformation::Residue::atom_type_set(), core::scoring::electron_density::poseCoord::B_, core::scoring::electron_density::ElectronDensity::calcRhoC(), core::pack::interaction_graph::debug, core::scoring::electron_density::poseCoord::elt_, core::pose::Pose::fold_tree(), core::scoring::electron_density::ElectronDensity::get_data(), core::scoring::electron_density::getDensityMap(), core::scoring::electron_density::ElectronDensity::getEffectiveBfactor(), core::kinematics::FoldTree::is_cutpoint(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), core::scoring::electron_density::ElectronDensity::set_data(), core::pose::Pose::size(), core::scoring::electron_density::ElectronDensity::writeMRC(), core::scoring::electron_density::poseCoord::x_, and core::conformation::Residue::xyz().

Referenced by protocols::electron_density::DockPDBIntoDensityMover::get_points_to_search().

select_density_points()

utility::vector1< numeric::xyzVector< core::Real > > protocols::electron_density::select_density_points	(	core::pose::Pose const &	pose,
		SelectDensityPointsOptions const &	params,
		core::Size &	nRsteps
	)

References protocols::electron_density::SelectDensityPointsOptions::center_on_middle_ca_, protocols::electron_density::SelectDensityPointsOptions::convolute_single_residue_, create_and_sort_point_score_pairs(), core::pack::interaction_graph::debug, protocols::electron_density::SelectDensityPointsOptions::delRsteps_, core::kinematics::distance(), dump_points_to_search_to_pdb_or_txt(), protocols::electron_density::DensitySymmInfo::enabled(), protocols::electron_density::SelectDensityPointsOptions::fragDens_, core::scoring::electron_density::ElectronDensity::get_data(), get_spectrum(), core::scoring::electron_density::getDensityMap(), protocols::electron_density::SelectDensityPointsOptions::gridStep_, core::scoring::electron_density::ElectronDensity::idx2cart(), map_from_spectrum(), protocols::electron_density::DensitySymmInfo::mask_asu(), protocols::electron_density::DensitySymmInfo::min_symm_dist2(), protocols::electron_density::SelectDensityPointsOptions::native_coms_, protocols::electron_density::SelectDensityPointsOptions::native_middle_cas_, protocols::electron_density::SelectDensityPointsOptions::natives_, protocols::electron_density::SelectDensityPointsOptions::point_radius_, rot(), core::scoring::electron_density::ElectronDensity::set_data(), protocols::electron_density::SelectDensityPointsOptions::symminfo_, protocols::electron_density::SelectDensityPointsOptions::topNtrans_, TR(), and core::scoring::electron_density::ElectronDensity::writeMRC().

Referenced by protocols::electron_density::DockFragmentsIntoDensityMover::apply_multi(), and protocols::electron_density::DockPDBIntoDensityMover::get_points_to_search().

set_pose_and_scorefxn_for_edens_scoring()

void protocols::electron_density::set_pose_and_scorefxn_for_edens_scoring	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunction &	scorefxn
	)

References core::scoring::electron_density::add_dens_scores_from_cmdline_to_scorefxn(), and core::pose::addVirtualResAsRoot().

symmetrizeBfactors()

void protocols::electron_density::symmetrizeBfactors

(

core::pose::Pose &

pose

)

helper function

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::chemical::element::B, core::pose::Pose::conformation(), core::pose::symmetry::is_symmetric(), core::conformation::Residue::natoms(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), and core::pose::Pose::size().

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

TR() [1/4]

static basic::Tracer protocols::electron_density::TR ( "protocols.electron_density.DockFragmentsIntoDensityMover"  )

static

Referenced by protocols::electron_density::DockPDBIntoDensityMover::analyze_RefinementDB(), protocols::electron_density::BfactorFittingMover::apply(), protocols::electron_density::DockPDBIntoDensityMover::apply(), protocols::electron_density::ReportFSC::apply(), protocols::electron_density::ScaleMapIntensities::apply(), protocols::electron_density::DockFragmentsIntoDensityMover::apply_multi(), protocols::electron_density::DensitySymmInfo::autocorrelate(), protocols::electron_density::DockPDBIntoDensityMover::cluster_silent(), protocols::electron_density::DockPDBIntoDensityMover::combine_refinement(), protocols::electron_density::DockPDBIntoDensityMover::combine_search(), protocols::electron_density::DockPDBIntoDensityMover::compare_and_align_poses(), compare_RBfitDB_to_native(), density_grid_search(), protocols::electron_density::DensitySymmInfo::detect_axes(), do_filter(), protocols::electron_density::DockFragmentsIntoDensityMover::do_refinement(), dockPoseIntoMap(), get_gdt(), protocols::electron_density::DockPDBIntoDensityMover::get_points_to_search(), get_rms(), get_spectrum(), protocols::electron_density::DockPDBIntoDensityMover::import_refinement_silent_files(), protocols::electron_density::DockPDBIntoDensityMover::minimize_poseOP_into_density(), protocols::electron_density::SetupForDensityScoringMover::parse_my_tag(), pose_spherical_samples(), protocols::electron_density::DockFragmentsIntoDensityMover::print_best_rms(), protocols::electron_density::DockPDBIntoDensityMover::refine_RBfitResultDB(), select_density_points(), protocols::electron_density::DockPDBIntoDensityMover::set_refinement_responsibilities(), protocols::electron_density::DockPDBIntoDensityMover::set_search_responsibilities(), and protocols::electron_density::DockPDBIntoDensityMover::setMultiNative().

TR() [2/4]

static basic::Tracer protocols::electron_density::TR ( "protocols.electron_density.DockPDBIntoDensityMover"  )

static

TR() [3/4]

static basic::Tracer protocols::electron_density::TR ( "protocols.electron_density.util"  )

static

TR() [4/4]

static basic::Tracer protocols::electron_density::TR ( "protocols.electron_density.util"  )

static

write_RBfitResultDB()

template<typename T >

void protocols::electron_density::write_RBfitResultDB	(	RBfitResultDB	fit_result_DB,
		T &	outresults
	)

FUNCTIONS.

References protocols::electron_density::ResultDB< T, Tcomp >::pop(), protocols::electron_density::RBfitResult::pose_idx_, protocols::electron_density::RBfitResult::post_trans_, protocols::electron_density::RBfitResult::pre_trans_, protocols::electron_density::RBfitResult::rotation_, protocols::electron_density::RBfitResult::score_, and protocols::electron_density::ResultDB< T, Tcomp >::size().

Referenced by protocols::electron_density::DockPDBIntoDensityMover::combine_search(), and density_grid_search().

write_RBfitResultDB< std::ofstream >()

template void protocols::electron_density::write_RBfitResultDB< std::ofstream >	(	RBfitResultDB	fit_result_DB,
		std::ofstream &	outresults
	)

write_RBfitResultDB< std::stringstream >()

template void protocols::electron_density::write_RBfitResultDB< std::stringstream >	(	RBfitResultDB	fit_result_DB,
		std::stringstream &	outresults
	)