#include <MatchSet.hh>

Public Types
typedef core::Real	Real

typedef core::Size	Size

typedef core::Vector	Vector

typedef numeric::geometry::BoundingBox < Vector >	BoundingBox

typedef numeric::geometry::hashing::Bin6D	Bin6D

typedef std::list< Hit const * >	HitPtrList

typedef std::list< std::pair < core::Size, Hit const * > >	HitIndexList

typedef boost::unordered_map < boost::uint64_t, HitIndexList, numeric::geometry::hashing::bin_index_hasher >	HitHash

Public Member Functions
	HitNeighborFinder ()

virtual	~HitNeighborFinder ()

void	set_bounding_box (BoundingBox const &bb)
	Use the same bounding box as the HitHasher / OccupiedSpaceHash. More...

void	set_uniform_xyz_bin_width (Real bin_width)
	Give the same xyz bin witdh given to the HitHasher / OccupiedSpaceHash. More...

void	set_uniform_euler_angle_bin_width (Real bin_width_degrees)
	Give the same euler-angle bin witdh given to the HitHasher / OccupiedSpaceHash. More...

void	set_xyz_bin_widths (Vector const &bin_widths)
	Give the same xyz bin witdhs given to the HitHasher / OccupiedSpaceHash. More...

void	set_euler_bin_widths (Vector const &euler_bin_widths)
	Give the same euler-angle bin witdhs given to the HitHasher / OccupiedSpaceHash. More...

void	initialize ()
	Call this after the bounding-box and the bin-widths have been set up. Must be called before "add_hits" it called. This initializes the SixDCoordinateBinner. More...

void	add_hits (std::list< Hit > const &hitlist)
	Add all hits (using hit pointers!) from one list of hits. More...

void	add_hits (HitPtrList const &hitptrlist)
	Add hit pointers from the input list. More...

utility::vector1< HitPtrList >	connected_components () const
	Compute the set of connected components for the set of input hits. This search iterates across the 2^6 halfbin neighbors of each hit and creates an adjacency graph to determine the connected components (CCs). The CCs are returned in a vector where each element contains a list of hit pointers to the elements of each connected component. More...

HitPtrList	neighbor_hits (HitPtrList const &queryhits) const
	Find the neighbors of the given set of query hits. This search iterates across both the upper and the lower neighbors of the query hits (3^6 neighbors). More...

Private Member Functions
void	hash_hits ()
	Put the hits that have been added to "all_hits" into the hash_. More...

Size	find_next_bin (Real6 orig_point, Real6 offsets, utility::FixedSizeLexicographicalIterator< 6 > const &halfbin_lex, Bin6D &next_bin) const
	Find the neighbor bin for a point by taking a step along a certain offset vector for a subset of the dimensions as given by a lex iterator (the halfbin_lex). Returns 0 if successful, and the index of the euclidean dimension which is out-of-bounds if the step is not successful. More...

bool	within_reach (Bin6D const &query_halfbin, Bin6D const &nb_halfbin, Bin6D const &nbbin, utility::FixedSizeLexicographicalIterator< 6 > const &halfbin_lex) const

Private Attributes
BoundingBox	bb_

bool	initialized_

utility::fixedsizearray1< Real, 3 >	xyz_bin_widths_

utility::fixedsizearray1< Real, 3 >	euler_bin_widths_

HitIndexList	all_hits_

numeric::geometry::hashing::SixDCoordinateBinnerOP	binner_

HitHash	hash_

Detailed Description

Class for finding hit neighbors in 6D considering all 64 origin definitions (but without forming all 64 hashes).

Member Typedef Documentation

typedef numeric::geometry::hashing::Bin6D protocols::match::HitNeighborFinder::Bin6D

typedef numeric::geometry::BoundingBox< Vector > protocols::match::HitNeighborFinder::BoundingBox

typedef boost::unordered_map< boost::uint64_t, HitIndexList, numeric::geometry::hashing::bin_index_hasher > protocols::match::HitNeighborFinder::HitHash

typedef std::list< std::pair< core::Size, Hit const * > > protocols::match::HitNeighborFinder::HitIndexList

typedef std::list< Hit const * > protocols::match::HitNeighborFinder::HitPtrList

typedef core::Real protocols::match::HitNeighborFinder::Real

typedef core::Size protocols::match::HitNeighborFinder::Size

typedef core::Vector protocols::match::HitNeighborFinder::Vector

Constructor & Destructor Documentation

protocols::match::HitNeighborFinder::HitNeighborFinder ( )

protocols::match::HitNeighborFinder::~HitNeighborFinder ( )

virtual

Member Function Documentation

void protocols::match::HitNeighborFinder::add_hits ( std::list< Hit > const & hitlist )

Add all hits (using hit pointers!) from one list of hits.

References all_hits_, hash_hits(), and initialized_.

void protocols::match::HitNeighborFinder::add_hits ( HitPtrList const & hitptrlist )

Add hit pointers from the input list.

utility::vector1< HitNeighborFinder::HitPtrList > protocols::match::HitNeighborFinder::connected_components ( ) const

Compute the set of connected components for the set of input hits. This search iterates across the 2^6 halfbin neighbors of each hit and creates an adjacency graph to determine the connected components (CCs). The CCs are returned in a vector where each element contains a list of hit pointers to the elements of each connected component.

References all_hits_, utility::FixedSizeLexicographicalIterator< S >::at_end(), utility::FixedSizeLexicographicalIterator< S >::begin(), numeric::geometry::hashing::SixDCoordinateBinner::bin_index(), binner_, find_next_bin(), numeric::geometry::hashing::SixDCoordinateBinner::halfbin6(), numeric::geometry::hashing::SixDCoordinateBinner::halfbin_widths(), hash_, protocols::match::Hit::second(), and within_reach().

HitNeighborFinder::Size protocols::match::HitNeighborFinder::find_next_bin	(	Real6	orig_point,
		Real6	offsets,
		utility::FixedSizeLexicographicalIterator< 6 > const &	halfbin_lex,
		Bin6D &	next_bin
	)		const

private

Find the neighbor bin for a point by taking a step along a certain offset vector for a subset of the dimensions as given by a lex iterator (the halfbin_lex). Returns 0 if successful, and the index of the euclidean dimension which is out-of-bounds if the step is not successful.

References protocols::match::advance_to_neighbor_bin(), and binner_.

Referenced by connected_components(), and neighbor_hits().

void protocols::match::HitNeighborFinder::hash_hits ( )

private

Put the hits that have been added to "all_hits" into the hash_.

References all_hits_, numeric::geometry::hashing::SixDCoordinateBinner::bin_index(), binner_, and hash_.

Referenced by add_hits().

void protocols::match::HitNeighborFinder::initialize ( )

Call this after the bounding-box and the bin-widths have been set up. Must be called before "add_hits" it called. This initializes the SixDCoordinateBinner.

References bb_, binner_, euler_bin_widths_, initialized_, and xyz_bin_widths_.

HitNeighborFinder::HitPtrList protocols::match::HitNeighborFinder::neighbor_hits ( HitPtrList const & queryhits ) const

Find the neighbors of the given set of query hits. This search iterates across both the upper and the lower neighbors of the query hits (3^6 neighbors).

References utility::FixedSizeLexicographicalIterator< S >::at_end(), utility::FixedSizeLexicographicalIterator< S >::begin(), numeric::geometry::hashing::SixDCoordinateBinner::bin_index(), binner_, find_next_bin(), numeric::geometry::hashing::SixDCoordinateBinner::halfbin6(), numeric::geometry::hashing::SixDCoordinateBinner::halfbin_widths(), hash_, neighbors, protocols::match::Hit::second(), and within_reach().

void protocols::match::HitNeighborFinder::set_bounding_box ( BoundingBox const & bb )

Use the same bounding box as the HitHasher / OccupiedSpaceHash.

References bb_, and initialized_.

void protocols::match::HitNeighborFinder::set_euler_bin_widths ( Vector const & euler_bin_widths )

Give the same euler-angle bin witdhs given to the HitHasher / OccupiedSpaceHash.

References euler_bin_widths_, and initialized_.

void protocols::match::HitNeighborFinder::set_uniform_euler_angle_bin_width ( Real bin_width_degrees )

Give the same euler-angle bin witdh given to the HitHasher / OccupiedSpaceHash.

References euler_bin_widths_, and initialized_.

void protocols::match::HitNeighborFinder::set_uniform_xyz_bin_width ( Real bin_width )

Give the same xyz bin witdh given to the HitHasher / OccupiedSpaceHash.

References initialized_, and xyz_bin_widths_.

void protocols::match::HitNeighborFinder::set_xyz_bin_widths ( Vector const & bin_widths )

Give the same xyz bin witdhs given to the HitHasher / OccupiedSpaceHash.

References initialized_, and xyz_bin_widths_.

bool protocols::match::HitNeighborFinder::within_reach	(	Bin6D const &	query_halfbin,
		Bin6D const &	nb_halfbin,
		Bin6D const &	nbbin,
		utility::FixedSizeLexicographicalIterator< 6 > const &	halfbin_lex
	)		const