#include <DensSkeleton.hh>

Public Member Functions
	DensSkeleton ()

	DensSkeleton (std::string filename, core::Real mapreso, core::Real gridspace)

void	load_density (std::string filename, core::Real mapreso, core::Real gridspace)

utility::vector1 < utility::vector1 < numeric::xyzVector< int > > >	breadth_first_connect (numeric::xyzVector< int > const &start_point, numeric::xyzVector< int >const &end_point, core::Real max_length, bool &hit_max, core::Size max_que=1e5)

utility::vector1 < utility::vector1 < numeric::xyzVector< int > > >	breadth_first_connect (numeric::xyzVector< core::Real > const &start_cart, numeric::xyzVector< core::Real > const &end_cart, core::Real max_length, core::Size maxque, bool &hit_max, core::Size max_grid)

core::Real	shortest_path (utility::vector1< utility::vector1< numeric::xyzVector< int > > > paths)

numeric::xyzVector< int >	find_closest_occupied_point (numeric::xyzVector< core::Real >const &coord, core::Size max_grid)

core::Real	shortest_path_bfs (numeric::xyzVector< core::Real >const &start, numeric::xyzVector< core::Real >const &end, core::Real max_length, core::Size max_que, bool hit_max, core::Size max_grid)

bool	has_density ()

std::map< core::Size, numeric::xyzVector< int > >	assign_neighbors (numeric::xyzVector< int > point)

bool	breaks_skeleton (utility::vector1< numeric::xyzVector< int > > accepted_points, std::map< core::Size, numeric::xyzVector< int > > neighbors)

core::Real	path_length (utility::vector1< numeric::xyzVector< int > > path, numeric::xyzVector< int > end_point)

core::scoring::electron_density::ElectronDensity const &	get_density () const

core::Real	matchAtomFast (core::Size resid, core::Size atomid, core::conformation::Residue &res, core::pose::Pose &pose)

Private Attributes
bool	density_loaded_

core::scoring::electron_density::ElectronDensity	density_

Constructor & Destructor Documentation

protocols::loop_grower::DensSkeleton::DensSkeleton ( )

inline

protocols::loop_grower::DensSkeleton::DensSkeleton	(	std::string	filename,
		core::Real	mapreso,
		core::Real	gridspace
	)

inline

References density_, density_loaded_, and core::scoring::electron_density::ElectronDensity::readMRCandResize().

Member Function Documentation

std::map< core::Size, numeric::xyzVector< int > > protocols::loop_grower::DensSkeleton::assign_neighbors ( numeric::xyzVector< int > point )

utility::vector1< utility::vector1< numeric::xyzVector< int > > > protocols::loop_grower::DensSkeleton::breadth_first_connect	(	numeric::xyzVector< int > const &	start_point,
		numeric::xyzVector< int >const &	end_point,
		core::Real	max_length,
		bool &	hit_max,
		core::Size	max_que = `1e5`
	)

References core::kinematics::distance(), protocols::hybridization::path, core::chemical::rings::q, and protocols::loop_grower::TR().

utility::vector1< utility::vector1< numeric::xyzVector< int > > > protocols::loop_grower::DensSkeleton::breadth_first_connect	(	numeric::xyzVector< core::Real > const &	start_cart,
		numeric::xyzVector< core::Real > const &	end_cart,
		core::Real	max_length,
		core::Size	maxque,
		bool &	hit_max,
		core::Size	max_grid
	)

References protocols::loop_grower::TR().

bool protocols::loop_grower::DensSkeleton::breaks_skeleton	(	utility::vector1< numeric::xyzVector< int > >	accepted_points,
		std::map< core::Size, numeric::xyzVector< int > >	neighbors
	)

numeric::xyzVector< int > protocols::loop_grower::DensSkeleton::find_closest_occupied_point	(	numeric::xyzVector< core::Real >const &	coord,
		core::Size	max_grid
	)

References core::kinematics::distance().

core::scoring::electron_density::ElectronDensity const& protocols::loop_grower::DensSkeleton::get_density ( ) const

inline

References density_.

bool protocols::loop_grower::DensSkeleton::has_density ( )

inline

References density_loaded_.

void protocols::loop_grower::DensSkeleton::load_density	(	std::string	filename,
		core::Real	mapreso,
		core::Real	gridspace
	)

inline

References density_, density_loaded_, and core::scoring::electron_density::ElectronDensity::readMRCandResize().

core::Real protocols::loop_grower::DensSkeleton::matchAtomFast	(	core::Size	resid,
		core::Size	atomid,
		core::conformation::Residue &	res,
		core::pose::Pose &	pose
	)

core::Real protocols::loop_grower::DensSkeleton::path_length	(	utility::vector1< numeric::xyzVector< int > >	path,
		numeric::xyzVector< int >	end_point
	)

References core::kinematics::distance(), core::scoring::electron_density::getDensityMap(), core::scoring::electron_density::ElectronDensity::idx2cart(), and protocols::hybridization::path.

core::Real protocols::loop_grower::DensSkeleton::shortest_path ( utility::vector1< utility::vector1< numeric::xyzVector< int > > > paths )

References core::chemical::shortest_path().

core::Real protocols::loop_grower::DensSkeleton::shortest_path_bfs	(	numeric::xyzVector< core::Real >const &	start,
		numeric::xyzVector< core::Real >const &	end,
		core::Real	max_length,
		core::Size	max_que,
		bool	hit_max,
		core::Size	max_grid
	)

References core::chemical::shortest_path().

Referenced by protocols::loop_grower::LoopPartialSolutionStore::skeleton_filter().

Member Data Documentation

core::scoring::electron_density::ElectronDensity protocols::loop_grower::DensSkeleton::density_

private

Referenced by DensSkeleton(), get_density(), and load_density().

bool protocols::loop_grower::DensSkeleton::density_loaded_

private

Referenced by DensSkeleton(), has_density(), and load_density().

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

src/protocols/loop_grower/DensSkeleton.hh
src/protocols/loop_grower/DensSkeleton.cc

Public Member Functions

Private Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation