#include <MatchSet.hh>

Inheritance diagram for protocols::match::HitNeighborFinder:

Collaboration diagram for protocols::match::HitNeighborFinder:

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).

Definition at line 133 of file MatchSet.hh.

Member Typedef Documentation

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

Definition at line 140 of file MatchSet.hh.

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

Definition at line 139 of file MatchSet.hh.

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

Definition at line 144 of file MatchSet.hh.

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

Definition at line 143 of file MatchSet.hh.

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

Definition at line 142 of file MatchSet.hh.

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

Definition at line 136 of file MatchSet.hh.

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

Definition at line 137 of file MatchSet.hh.

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

Definition at line 138 of file MatchSet.hh.

Constructor & Destructor Documentation

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

Definition at line 244 of file MatchSet.cc.

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

virtual

Definition at line 245 of file MatchSet.cc.

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.

Definition at line 293 of file MatchSet.cc.

References all_hits_, hash_hits(), and initialized_.

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

Add hit pointers from the input list.

Definition at line 306 of file MatchSet.cc.

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.

Definition at line 330 of file MatchSet.cc.

References all_hits_, binner_, find_next_bin(), 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.

Definition at line 585 of file MatchSet.cc.

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_.

Definition at line 563 of file MatchSet.cc.

References all_hits_, 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.

Definition at line 311 of file MatchSet.cc.

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).

Definition at line 489 of file MatchSet.cc.

References binner_, find_next_bin(), hash_, 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.

Definition at line 248 of file MatchSet.cc.

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.

Definition at line 284 of file MatchSet.cc.

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.

Definition at line 265 of file MatchSet.cc.

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.

Definition at line 257 of file MatchSet.cc.

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.

Definition at line 273 of file MatchSet.cc.

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