Bin the six degrees of freedom that describe the downstream geometry of a hit. These degrees of freedom are, in order, the x, y and z coordinates of orientation atom3, and the phi, psi, and theta euler angles that describe the orientation of the coordinate frame at orientation atom 3. The binner is responsible for maintaining the lower corner of the 6-d space – the first two Euler angles wrap at 360; the third Euler angle, theta, does not wrap in the same way. See the comments for the bin6 method. More...

#include <SixDHasher.hh>

Inheritance diagram for numeric::geometry::hashing::SixDCoordinateBinner:

[legend]

Public Types
typedef numeric::Real	Real

typedef numeric::Size	Size

typedef numeric::xyzVector < numeric::Real >	Vector

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

Public Types inherited from utility::pointer::ReferenceCount
typedef platform::Size	Size

typedef platform::Size	size_type

Public Member Functions
	~SixDCoordinateBinner () override
	Automatically generated virtual destructor for class deriving directly from ReferenceCount. More...

	SixDCoordinateBinner (BoundingBox const &bounding_box, Size3 const &euler_offsets, utility::fixedsizearray1< Real, 6 > bin_widths)

bool	contains (Real6 const &point) const

void	tree_init (Size max_radius)

Bin6D	bin6 (Real6 const &values) const
	Construct the discrete representation of a six-dimensional vector of reals representing an xyz coordinate in its first three dimensions and a set of three Euler angles in the last three dimensions. Precondition: The xyz coordinate must be inside the bounding box of this binner. Precondition: The euler angles should be in degrees; the first two should be in the range between 0 and 360, the third should be in the range from 0 to 180. More...

Bin6D	halfbin6 (Real6 const &values) const
	Determine halfbin index for a point in 6D i.e., how far from the lower corner of the point's containing 6D voxel is the point – is it more than halfway to the next 6D voxel? Each dimension returned will hold a 0 or a 1. More...

boost::uint64_t	bin_index (Bin6D const &bin) const
	functor used by boost (and sgi's stl) hash classes. More...

boost::uint64_t	bin_index (Real6 const &values) const
	compute the bin index (64-bit int) for a 6D point. More...

std::vector< boost::uint64_t >	radial_bin_index (numeric::Size radius, Real6 const &center) const

Bin6D	bin_from_index (boost::uint64_t index) const

Real6	bin_center_point (Bin6D const &bin) const

BoundingBox	bounding_volume_from_index (boost::uint64_t index) const

BoundingBox const &	bounding_box () const

Real3 const &	euler_offsets () const

Real6 const &	bin_widths () const

Real6 const &	halfbin_widths () const

Size6 const &	dimsizes () const

Public Member Functions inherited from utility::pointer::ReferenceCount
	ReferenceCount ()
	Default constructor. More...

virtual	~ReferenceCount ()

Private Member Functions
	SixDCoordinateBinner ()

Real3	wrap_euler_angles (Real6 const &values) const

Private Attributes
BoundingBox	bounding_box_

Size6	dimsizes_

Size6	dimprods_

Real6	bin_widths_

Real6	halfbin_widths_

Real3	euler_offsets_

SixDOffsetTree	offset_tree_

Detailed Description

Bin the six degrees of freedom that describe the downstream geometry of a hit. These degrees of freedom are, in order, the x, y and z coordinates of orientation atom3, and the phi, psi, and theta euler angles that describe the orientation of the coordinate frame at orientation atom 3. The binner is responsible for maintaining the lower corner of the 6-d space – the first two Euler angles wrap at 360; the third Euler angle, theta, does not wrap in the same way. See the comments for the bin6 method.

Member Typedef Documentation

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

typedef numeric::Real numeric::geometry::hashing::SixDCoordinateBinner::Real

typedef numeric::Size numeric::geometry::hashing::SixDCoordinateBinner::Size

typedef numeric::xyzVector< numeric::Real > numeric::geometry::hashing::SixDCoordinateBinner::Vector

Constructor & Destructor Documentation

numeric::geometry::hashing::SixDCoordinateBinner::~SixDCoordinateBinner ( )

overridedefault

Automatically generated virtual destructor for class deriving directly from ReferenceCount.

Auto-generated virtual destructor

numeric::geometry::hashing::SixDCoordinateBinner::SixDCoordinateBinner ( )

privatedefault

numeric::geometry::hashing::SixDCoordinateBinner::SixDCoordinateBinner	(	BoundingBox const &	bounding_box,
		Size3 const &	euler_offsets,
		utility::fixedsizearray1< Real, 6 >	bin_widths
	)

References bin_widths_, bounding_box_, dimprods_, dimsizes_, euler_offsets_, halfbin_widths_, test.T200_Scoring::ii, numeric::geometry::BoundingBox< typename >::lower(), numeric::geometry::BoundingBox< typename >::set_upper(), and numeric::geometry::BoundingBox< typename >::upper().

Member Function Documentation

Bin6D numeric::geometry::hashing::SixDCoordinateBinner::bin6 ( Real6 const & values ) const

Construct the discrete representation of a six-dimensional vector of reals representing an xyz coordinate in its first three dimensions and a set of three Euler angles in the last three dimensions. Precondition: The xyz coordinate must be inside the bounding box of this binner. Precondition: The euler angles should be in degrees; the first two should be in the range between 0 and 360, the third should be in the range from 0 to 180.

When floating point comparison breaks down, it is possible to have a point hash outside of the bounding volume: 359.999999 / 10.0 -> 36 instead of 35. For this reason, it's important to mod the resulting bin index by the number of bins.

References bin_widths_, bounding_box_, numeric::geometry::BoundingBox< typename >::contains(), dimsizes_, numeric::geometry::BoundingBox< typename >::lower(), wrap_euler_angles(), numeric::xyzVector< typename >::x(), numeric::xyzVector< typename >::y(), and numeric::xyzVector< typename >::z().

Referenced by bin_index(), halfbin6(), and radial_bin_index().

Real6 numeric::geometry::hashing::SixDCoordinateBinner::bin_center_point ( Bin6D const & bin ) const

References bin_widths_, bounding_box_, numeric::center(), euler_offsets_, halfbin_widths_, test.T200_Scoring::ii, and numeric::geometry::BoundingBox< typename >::lower().

Bin6D numeric::geometry::hashing::SixDCoordinateBinner::bin_from_index ( boost::uint64_t index ) const

inline

References basic::options::OptionKeys::lh::fragpdb::bin, dimprods_, and test.T200_Scoring::ii.

Referenced by bounding_volume_from_index().

boost::uint64_t numeric::geometry::hashing::SixDCoordinateBinner::bin_index ( Bin6D const & bin ) const

inline

functor used by boost (and sgi's stl) hash classes.

References ObjexxFCL::format::A(), dimprods_, and dimsizes_.

Referenced by bin_index(), and radial_bin_index().

boost::uint64_t numeric::geometry::hashing::SixDCoordinateBinner::bin_index ( Real6 const & values ) const

inline

compute the bin index (64-bit int) for a 6D point.

References basic::options::OptionKeys::lh::fragpdb::bin, bin6(), and bin_index().

Real6 const& numeric::geometry::hashing::SixDCoordinateBinner::bin_widths ( ) const

inline

References bin_widths_.

BoundingBox const& numeric::geometry::hashing::SixDCoordinateBinner::bounding_box ( ) const

inline

References bounding_box_.

BoundingBox numeric::geometry::hashing::SixDCoordinateBinner::bounding_volume_from_index ( boost::uint64_t index ) const

inline

References basic::options::OptionKeys::lh::fragpdb::bin, bin_from_index(), bin_widths_, bounding_box_, numeric::geometry::BoundingBox< typename >::lower(), utility::lower(), and utility::upper().

bool numeric::geometry::hashing::SixDCoordinateBinner::contains ( Real6 const & point ) const

inline

References bounding_box_, and numeric::geometry::BoundingBox< typename >::contains().

Size6 const& numeric::geometry::hashing::SixDCoordinateBinner::dimsizes ( ) const

inline

References dimsizes_.

Real3 const& numeric::geometry::hashing::SixDCoordinateBinner::euler_offsets ( ) const

inline

References euler_offsets_.

Bin6D numeric::geometry::hashing::SixDCoordinateBinner::halfbin6 ( Real6 const & values ) const

Determine halfbin index for a point in 6D i.e., how far from the lower corner of the point's containing 6D voxel is the point – is it more than halfway to the next 6D voxel? Each dimension returned will hold a 0 or a 1.

References basic::options::OptionKeys::lh::fragpdb::bin, bin6(), bin_widths_, bounding_box_, halfbin_widths_, test.T200_Scoring::ii, numeric::geometry::BoundingBox< typename >::lower(), and wrap_euler_angles().

Real6 const& numeric::geometry::hashing::SixDCoordinateBinner::halfbin_widths ( ) const

inline

References halfbin_widths_.

std::vector< boost::uint64_t > numeric::geometry::hashing::SixDCoordinateBinner::radial_bin_index	(	numeric::Size	radius,
		Real6 const &	center
	)		const

References bin6(), bin_index(), dimsizes_, numeric::geometry::hashing::SixDOffsetTree::lookup(), basic::options::OptionKeys::rna::denovo::offset, and offset_tree_.

void numeric::geometry::hashing::SixDCoordinateBinner::tree_init ( Size max_radius )

inline

References numeric::geometry::hashing::SixDOffsetTree::init(), and offset_tree_.

Real3 numeric::geometry::hashing::SixDCoordinateBinner::wrap_euler_angles ( Real6 const & values ) const

private

When using a particular set of offsets, make sure that the euler angles wrap so that neighboring points in 6D actually fall into the same bins. The logic here is tested thuroughly in Hasher.cxxtest.hh

References euler_offsets_.

Referenced by bin6(), and halfbin6().