#include <BumpGrid.hh>

Inheritance diagram for protocols::match::Bool3DGrid:

Collaboration diagram for protocols::match::Bool3DGrid:

Public Types
typedef core::Real	Real

typedef core::Vector	Vector

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

typedef numeric::geometry::hashing::Bin3D	Bin3D

typedef utility::fixedsizearray1 < Vector, 8 >	CornerPoints

typedef std::pair < Bool3DGrid::Size, unsigned char >	index_mask_pair

Public Member Functions
	Bool3DGrid ()
	Creation and initialization. More...

virtual	~Bool3DGrid ()

void	set_bounding_box (BoundingBox const &bb)

void	set_bin_width (Real width)

Bool3DGrid	create_grid_for_sphere (Vector const &center, Real radius) const
	create a grid for the input sphere that aligns to this grid, such that it is large enough to hold a particular sphere. More...

Bool3DGrid	create_grid_for_bb (BoundingBox const &bb)
	create a grid for the input bounding box that aligns to this grid More...

Bin3D	dimsizes () const
	Accessors. More...

Real	bin_width () const

CornerPoints	corners (Bin3D const &bin) const

BoundingBox	bin_extrema (Bin3D const &bin) const
	bounding box points for a bin. More...

Vector	bin_center (Bin3D const &bin) const

bool	occupied (Vector const &) const

bool	occupied (Bin3D const &bin) const

BoundingBox	actual_bb () const

void	set_value_for_bin (Bin3D const &bin, bool setting)
	set the boolean value for a particular bin. The bin dimensions are indexed from 0 to nbins-1. More...

void	or_by_sphere_conservative (Vector const &center, Real radius)
	Set the value to true for any voxel that is wholy contained by the given sphere. A voxel is wholy contained iff all 8 corners of the voxel are within the sphere. More...

void	or_by_sphere_liberal (Vector const &center, Real radius)
	Set the value to true for any voxel that is partially contained by a given sphere. A voxel is partially contained iff any of the 8 corners of the voxel are within the sphere. More...

void	or_by_spheres_conservative (utility::vector1< std::pair< Vector, Real > > const &spheres)
	Consider a voxel filled if each of its corners are covered, even if they are covered by seperate spheres. Dangerous, in that some voxels will be counted as being fully occupied when they are only partially occupied. More...

void	or_by_box_liberal (BoundingBox const &bb)
	Turn the values of all the bins that overlap with the volume in this bounding box to true. More...

void	or_with (Bool3DGrid const &other)
	Performs a boolean OR on the voxels shared by the two grids, and ignores all voxels that are not shared by the two grids. These grids must be "compatible", in that the lower corner of other must lie on a grid point of this. More...

void	and_with (Bool3DGrid const &other)
	Performs a boolean AND on the voxels shared by the two grids, and ignores all voxels that are not shared by the two grids. These grids must be "compatible", in that the lower corner of other must lie on a grid point of this. More...

void	subtract (Bool3DGrid const &other)
	Sets any voxel on this grid to "false" which is true on the other grid. but does not set any voxel to "true" on this grid – even if the other voxel is "false". More...

void	clear ()
	Set all values in all bins to false. More...

Private Member Functions
index_mask_pair	index_and_mask_for_point (Vector const &point) const

index_mask_pair	index_and_mask_for_bin (Bin3D const &bin) const

Bin3D	bin_for_point (Vector const &point) const

void	reset_grid ()

unsigned char	mask_from_offsets (Size xmod2, Size ymod2, Size zmod2) const

unsigned char	negmask_from_offsets (Size xmod2, Size ymod2, Size zmod2) const

Size	byte_index_from_doublebin (Bin3D const &halfbin) const

Private Attributes
BoundingBox	bb_

BoundingBox	bb_extended_

Real	bin_width_

Real	bin_width_2x_

Real	half_bin_width_root_three_

Bin3D	dimsizes_

Bin3D	dimprods_

Bin3D	halfdimsizes_

Bin3D	halfdimprods_

Bin3D	supervoxel_dimsizes_

Bin3D	supervoxel_dimprods_

utility::vector0< unsigned char >	grid_

Static Private Attributes
static const Size	n_doublebins_per_supervoxel = 4

Detailed Description

Definition at line 52 of file BumpGrid.hh.

Member Typedef Documentation

typedef numeric::geometry::hashing::Bin3D protocols::match::Bool3DGrid::Bin3D

Definition at line 58 of file BumpGrid.hh.

typedef numeric::geometry::BoundingBox< core::Vector > protocols::match::Bool3DGrid::BoundingBox

Definition at line 57 of file BumpGrid.hh.

typedef utility::fixedsizearray1< Vector, 8 > protocols::match::Bool3DGrid::CornerPoints

Definition at line 59 of file BumpGrid.hh.

typedef std::pair< Bool3DGrid::Size, unsigned char > protocols::match::Bool3DGrid::index_mask_pair

Definition at line 60 of file BumpGrid.hh.

typedef core::Real protocols::match::Bool3DGrid::Real

Definition at line 55 of file BumpGrid.hh.

typedef core::Vector protocols::match::Bool3DGrid::Vector

Definition at line 56 of file BumpGrid.hh.

Constructor & Destructor Documentation

protocols::match::Bool3DGrid::Bool3DGrid ( )

Creation and initialization.

Definition at line 36 of file BumpGrid.cc.

protocols::match::Bool3DGrid::~Bool3DGrid ( )

virtual

Definition at line 47 of file BumpGrid.cc.

Member Function Documentation

BoundingBox protocols::match::Bool3DGrid::actual_bb ( ) const

inline

Definition at line 97 of file BumpGrid.hh.

References bb_extended_.

void protocols::match::Bool3DGrid::and_with ( Bool3DGrid const & other)

Performs a boolean AND on the voxels shared by the two grids, and ignores all voxels that are not shared by the two grids. These grids must be "compatible", in that the lower corner of other must lie on a grid point of this.

Definition at line 575 of file BumpGrid.cc.

References bb_, bin_width_, grid_, and index_and_mask_for_bin().

Bool3DGrid::Vector protocols::match::Bool3DGrid::bin_center ( Bin3D const & bin) const

Definition at line 428 of file BumpGrid.cc.

References bb_extended_, and bin_width_.

Referenced by or_by_sphere_conservative(), and or_by_sphere_liberal().

Bool3DGrid::BoundingBox protocols::match::Bool3DGrid::bin_extrema ( Bin3D const & bin) const

bounding box points for a bin.

Definition at line 415 of file BumpGrid.cc.

References bb_, and bin_width_.

Bool3DGrid::Bin3D protocols::match::Bool3DGrid::bin_for_point ( Vector const & point) const

private

Definition at line 779 of file BumpGrid.cc.

References bb_, bin_width_, and dimsizes_.

Referenced by or_by_box_liberal().

Real protocols::match::Bool3DGrid::bin_width ( ) const

inline

Definition at line 83 of file BumpGrid.hh.

References bin_width_.

Referenced by protocols::match::Bool3DGridKinemageWriter::write_grid_to_kinemage().

Bool3DGrid::Size protocols::match::Bool3DGrid::byte_index_from_doublebin ( Bin3D const & halfbin) const

private

Definition at line 902 of file BumpGrid.cc.

References halfdimsizes_, n_doublebins_per_supervoxel, and supervoxel_dimprods_.

Referenced by index_and_mask_for_bin(), index_and_mask_for_point(), and set_value_for_bin().

void protocols::match::Bool3DGrid::clear ( )

Set all values in all bins to false.

Definition at line 723 of file BumpGrid.cc.

References grid_.

Bool3DGrid::CornerPoints protocols::match::Bool3DGrid::corners ( Bin3D const & bin) const

Definition at line 372 of file BumpGrid.cc.

References bb_, and bin_width_.

Referenced by or_by_sphere_conservative(), or_by_sphere_liberal(), or_by_spheres_conservative(), and protocols::match::Bool3DGridKinemageWriter::write_grid_to_kinemage().

Bool3DGrid protocols::match::Bool3DGrid::create_grid_for_bb ( BoundingBox const & bb)

create a grid for the input bounding box that aligns to this grid

Definition at line 89 of file BumpGrid.cc.

References bb_, bin_width_, set_bin_width(), and set_bounding_box().

Bool3DGrid protocols::match::Bool3DGrid::create_grid_for_sphere	(	Vector const &	center,
		Real	radius
	)		const

create a grid for the input sphere that aligns to this grid, such that it is large enough to hold a particular sphere.

Definition at line 61 of file BumpGrid.cc.

References bb_, bin_width_, bin_width_2x_, set_bin_width(), and set_bounding_box().

Bool3DGrid::Bin3D protocols::match::Bool3DGrid::dimsizes ( ) const

Accessors.

Definition at line 367 of file BumpGrid.cc.

References dimsizes_.

Referenced by protocols::match::Bool3DGridKinemageWriter::write_grid_to_kinemage().

Bool3DGrid::index_mask_pair protocols::match::Bool3DGrid::index_and_mask_for_bin ( Bin3D const & bin) const

private

Definition at line 756 of file BumpGrid.cc.

References byte_index_from_doublebin(), and mask_from_offsets().

Referenced by and_with(), occupied(), or_with(), and subtract().

Bool3DGrid::index_mask_pair protocols::match::Bool3DGrid::index_and_mask_for_point ( Vector const & point) const

private

Definition at line 732 of file BumpGrid.cc.

References bb_, bin_width_, bin_width_2x_, byte_index_from_doublebin(), and mask_from_offsets().

Referenced by occupied().

unsigned char protocols::match::Bool3DGrid::mask_from_offsets	(	Size	xmod2,
		Size	ymod2,
		Size	zmod2
	)		const

private

Definition at line 857 of file BumpGrid.cc.

Referenced by index_and_mask_for_bin(), index_and_mask_for_point(), and set_value_for_bin().

unsigned char protocols::match::Bool3DGrid::negmask_from_offsets	(	Size	xmod2,
		Size	ymod2,
		Size	zmod2
	)		const

private

Definition at line 879 of file BumpGrid.cc.

Referenced by set_value_for_bin().

bool protocols::match::Bool3DGrid::occupied ( Vector const & point) const

Definition at line 436 of file BumpGrid.cc.

References bb_extended_, grid_, and index_and_mask_for_point().

Referenced by protocols::match::Bool3DGridKinemageWriter::write_grid_to_kinemage().

bool protocols::match::Bool3DGrid::occupied ( Bin3D const & bin) const

Definition at line 445 of file BumpGrid.cc.

References dimsizes_, grid_, and index_and_mask_for_bin().

void protocols::match::Bool3DGrid::or_by_box_liberal ( BoundingBox const & bb)

Turn the values of all the bins that overlap with the volume in this bounding box to true.

Definition at line 342 of file BumpGrid.cc.

References bb_, bin_for_point(), and set_value_for_bin().

void protocols::match::Bool3DGrid::or_by_sphere_conservative	(	Vector const &	center,
		Real	radius
	)

Set the value to true for any voxel that is wholy contained by the given sphere. A voxel is wholy contained iff all 8 corners of the voxel are within the sphere.

Sets the value of a voxel to true if all eight corners of the voxel are contained by the sphere.

Definition at line 115 of file BumpGrid.cc.

References bb_extended_, bin_center(), bin_width_, corners(), dimsizes_, half_bin_width_root_three_, and set_value_for_bin().

void protocols::match::Bool3DGrid::or_by_sphere_liberal	(	Vector const &	center,
		Real	radius
	)

Set the value to true for any voxel that is partially contained by a given sphere. A voxel is partially contained iff any of the 8 corners of the voxel are within the sphere.

Sets the value of a voxel to true if any volume of a voxel is inside the sphere. Handles edge cases properly where a voxel is glanced by a sphere at a face, but where the corners of the voxel are not contained by the sphere, and when a sphere is entirely contained within a voxel.

Definition at line 184 of file BumpGrid.cc.

References bb_extended_, bin_center(), bin_width_, corners(), dimsizes_, half_bin_width_root_three_, and set_value_for_bin().

void protocols::match::Bool3DGrid::or_by_spheres_conservative ( utility::vector1< std::pair< Vector, Real > > const & spheres)

Consider a voxel filled if each of its corners are covered, even if they are covered by seperate spheres. Dangerous, in that some voxels will be counted as being fully occupied when they are only partially occupied.

The sphere list should describe spheres by the centers and by their square radii, not by their radii.

Definition at line 306 of file BumpGrid.cc.

References corners(), dimsizes_, and set_value_for_bin().

void protocols::match::Bool3DGrid::or_with ( Bool3DGrid const & other)

Performs a boolean OR on the voxels shared by the two grids, and ignores all voxels that are not shared by the two grids. These grids must be "compatible", in that the lower corner of other must lie on a grid point of this.

Definition at line 503 of file BumpGrid.cc.

References bb_, bin_width_, grid_, and index_and_mask_for_bin().

void protocols::match::Bool3DGrid::reset_grid ( )

private

Definition at line 794 of file BumpGrid.cc.

References bb_, bb_extended_, bin_width_, bin_width_2x_, dimprods_, dimsizes_, grid_, half_bin_width_root_three_, halfdimprods_, halfdimsizes_, n_doublebins_per_supervoxel, supervoxel_dimprods_, and supervoxel_dimsizes_.

Referenced by set_bin_width(), and set_bounding_box().

void protocols::match::Bool3DGrid::set_bin_width ( Real width)

Definition at line 55 of file BumpGrid.cc.

References bin_width_, and reset_grid().

Referenced by create_grid_for_bb(), and create_grid_for_sphere().

void protocols::match::Bool3DGrid::set_bounding_box ( BoundingBox const & bb)

Definition at line 50 of file BumpGrid.cc.

References bb_, and reset_grid().

Referenced by create_grid_for_bb(), and create_grid_for_sphere().

void protocols::match::Bool3DGrid::set_value_for_bin	(	Bin3D const &	bin,
		bool	setting
	)

set the boolean value for a particular bin. The bin dimensions are indexed from 0 to nbins-1.

Definition at line 458 of file BumpGrid.cc.

References byte_index_from_doublebin(), grid_, mask_from_offsets(), and negmask_from_offsets().

Referenced by or_by_box_liberal(), or_by_sphere_conservative(), or_by_sphere_liberal(), and or_by_spheres_conservative().

void protocols::match::Bool3DGrid::subtract ( Bool3DGrid const & other)

Sets any voxel on this grid to "false" which is true on the other grid. but does not set any voxel to "true" on this grid – even if the other voxel is "false".

Set all the values in this grid to "false" that are true in the other grid.

Definition at line 648 of file BumpGrid.cc.

References bb_, bin_width_, grid_, and index_and_mask_for_bin().

Member Data Documentation

BoundingBox protocols::match::Bool3DGrid::bb_

private

Definition at line 176 of file BumpGrid.hh.

Referenced by and_with(), bin_extrema(), bin_for_point(), corners(), create_grid_for_bb(), create_grid_for_sphere(), index_and_mask_for_point(), or_by_box_liberal(), or_with(), reset_grid(), set_bounding_box(), and subtract().

BoundingBox protocols::match::Bool3DGrid::bb_extended_

private

Definition at line 177 of file BumpGrid.hh.

Referenced by actual_bb(), bin_center(), occupied(), or_by_sphere_conservative(), or_by_sphere_liberal(), and reset_grid().

Real protocols::match::Bool3DGrid::bin_width_

private

Definition at line 179 of file BumpGrid.hh.

Referenced by and_with(), bin_center(), bin_extrema(), bin_for_point(), bin_width(), corners(), create_grid_for_bb(), create_grid_for_sphere(), index_and_mask_for_point(), or_by_sphere_conservative(), or_by_sphere_liberal(), or_with(), reset_grid(), set_bin_width(), and subtract().

Real protocols::match::Bool3DGrid::bin_width_2x_

private

Definition at line 180 of file BumpGrid.hh.

Referenced by create_grid_for_sphere(), index_and_mask_for_point(), and reset_grid().

Bin3D protocols::match::Bool3DGrid::dimprods_

private

Definition at line 183 of file BumpGrid.hh.

Referenced by reset_grid().

Bin3D protocols::match::Bool3DGrid::dimsizes_

private

Definition at line 182 of file BumpGrid.hh.

Referenced by bin_for_point(), dimsizes(), occupied(), or_by_sphere_conservative(), or_by_sphere_liberal(), or_by_spheres_conservative(), and reset_grid().

utility::vector0< unsigned char > protocols::match::Bool3DGrid::grid_

private

Each byte represents the boolean "covered" status for 8 voxels in a double-voxel. The double voxel

Definition at line 199 of file BumpGrid.hh.

Referenced by and_with(), clear(), occupied(), or_with(), reset_grid(), set_value_for_bin(), and subtract().

Real protocols::match::Bool3DGrid::half_bin_width_root_three_

private

Definition at line 181 of file BumpGrid.hh.

Referenced by or_by_sphere_conservative(), or_by_sphere_liberal(), and reset_grid().

Bin3D protocols::match::Bool3DGrid::halfdimprods_

private

Definition at line 186 of file BumpGrid.hh.

Referenced by reset_grid().

Bin3D protocols::match::Bool3DGrid::halfdimsizes_

private

Definition at line 185 of file BumpGrid.hh.

Referenced by byte_index_from_doublebin(), and reset_grid().

const Size protocols::match::Bool3DGrid::n_doublebins_per_supervoxel = 4

staticprivate

creates super voxels of size 8x8x8 = 512 bits -> 64 bytes = cache line size on Core2 Duo, though this size should not have a very large effect for caches of larger or smaller size. The main point of the super voxel is to allow data locality as it's very often the same region of space that's being queried repeatedly during rotamer building.

Definition at line 195 of file BumpGrid.hh.

Referenced by byte_index_from_doublebin(), and reset_grid().

Bin3D protocols::match::Bool3DGrid::supervoxel_dimprods_

private

Definition at line 189 of file BumpGrid.hh.

Referenced by byte_index_from_doublebin(), and reset_grid().

Bin3D protocols::match::Bool3DGrid::supervoxel_dimsizes_

private

Definition at line 188 of file BumpGrid.hh.

Referenced by reset_grid().

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

src/protocols/match/BumpGrid.hh
src/protocols/match/BumpGrid.cc

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Static Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation