numeric::geometry::hashing::xyzStripeHash Class Reference

#include <xyzStripeHash.hh>

Inheritance diagram for numeric::geometry::hashing::xyzStripeHash:

Classes
struct	const_iterator
struct	iter_base
struct	ushort2

Public Types
typedef unsigned short	ushort
typedef numeric::xyzVector< float >	Vec

Public Member Functions
	xyzStripeHash (float grid_size=0.0, utility::vector1< Ball > const &balls=utility::vector1< Ball >())
void	init (utility::vector1< Ball > const &balls)
	~xyzStripeHash () override
const_iterator	begin () const
const_iterator	end () const
bool	sanity_check () const
std::string	debug_pdb (Xform const &x=numeric::Xform::identity()) const
int	nbcount (Vec const &v_in) const
int	nbcount_raw (Vec const &v) const
bool	clash (Vec const &v_in) const
bool	clash_not_resid (Vec const &v_in, int const &resid, int const &resid2=0) const
bool	clash_raw (Vec const &v) const
float	clash_amount (Vec const &v_in) const
int	clash_check_ball (Ball const &b) const
bool	clash_check_residue_pairs (utility::vector1< Ball > const &test_balls, std::map< Size, Size > &residue_pairs) const
void	fill_pairs (xyzVector_float const &v, int const &ir, utility::vector1< std::pair< int, int > > &pairs, float maxd2=0.0) const
template<typename Visitor >
void	visit (Vec const &v_in, Visitor &visitor) const
template<typename Visitor >
void	visit_lax (Vec const &v_in, float const vr, Visitor &visitor) const
Ball const *	grid_atoms () const
Size	size () const
int	natom () const
int	xdim () const
int	ydim () const
int	zdim () const
float	grid_size () const
float	grid_size2 () const
xyzVector_float const &	translation () const
xyzVector< Real >	translation_real () const
ushort2 const *	grid_stripe () const
Ball const &	ball (Size const &ib) const
xyzVector_float	xyz (Size const &ib) const
Size	resi (Size const &ib) const
Public Member Functions inherited from utility::VirtualBase
	VirtualBase ()=default
	Default constructor. More...
virtual	~VirtualBase ()=default
	The virtual destructor is one of the main reasons for the VirtualBase class. More...
	VirtualBase (VirtualBase const &)=default
	VirtualBase (VirtualBase &&)=default
VirtualBase &	operator= (VirtualBase const &)=default
VirtualBase &	operator= (VirtualBase &&)=default

Private Member Functions
short	short_min (short const a, short const b)
short	short_max (short const a, short const b)
short	ushort_min (unsigned short const a, unsigned short const b)
short	ushort_max (unsigned short const a, unsigned short const b)

Private Attributes
float	grid_size_
float	grid_size2_
int	nballs_
Ball const *	grid_balls_
ushort2 const *	grid_stripe_
int	xdim_
int	ydim_
int	zdim_
float	xmx_
float	ymx_
float	zmx_
numeric::xyzVector< float >	translation_

Member Typedef Documentation

typedef unsigned short numeric::geometry::hashing::xyzStripeHash::ushort

typedef numeric::xyzVector<float> numeric::geometry::hashing::xyzStripeHash::Vec

Constructor & Destructor Documentation

numeric::geometry::hashing::xyzStripeHash::xyzStripeHash	(	float	grid_size = 0.0,
		utility::vector1< Ball > const &	balls = utility::vector1<Ball>()
	)

References init().

numeric::geometry::hashing::xyzStripeHash::~xyzStripeHash ( )

inlineoverride

References grid_balls_, and grid_stripe_.

Member Function Documentation

Ball const& numeric::geometry::hashing::xyzStripeHash::ball ( Size const &  ib ) const

inline

References grid_balls_, and nballs_.

Referenced by clash_check_residue_pairs().

const_iterator numeric::geometry::hashing::xyzStripeHash::begin ( ) const

inline

References grid_balls_.

bool numeric::geometry::hashing::xyzStripeHash::clash

(

Vec const &

v_in

)

const

References test.Workshop3test::a2, grid_balls_, grid_size2_, grid_size_, grid_stripe_, test.T150_PyMOL_Integration::i, numeric::max(), numeric::min(), translation_, test.T850_SubClassing::v, numeric::crick_equations::x(), numeric::geometry::hashing::Ball::x(), numeric::geometry::hashing::xyzStripeHash::ushort2::x, numeric::xyzVector< typename >::x(), xdim_, xmx_, numeric::geometry::hashing::Ball::y(), numeric::crick_equations::y(), numeric::geometry::hashing::xyzStripeHash::ushort2::y, numeric::xyzVector< typename >::y(), ydim_, ymx_, numeric::geometry::hashing::Ball::z(), numeric::crick_equations::z(), numeric::xyzVector< typename >::z(), zdim_, and zmx_.

float numeric::geometry::hashing::xyzStripeHash::clash_amount

(

Vec const &

v_in

)

const

References test.Workshop3test::a2, numeric::geometry::hashing::Ball::atomno(), utility::io::oc::cout, grid_balls_, grid_size2_, grid_size_, grid_stripe_, test.T150_PyMOL_Integration::i, numeric::max(), numeric::min(), numeric::geometry::hashing::Ball::resi(), translation_, test.T850_SubClassing::v, numeric::crick_equations::x(), numeric::geometry::hashing::Ball::x(), numeric::geometry::hashing::xyzStripeHash::ushort2::x, numeric::xyzVector< typename >::x(), xdim_, xmx_, numeric::geometry::hashing::Ball::y(), numeric::crick_equations::y(), numeric::geometry::hashing::xyzStripeHash::ushort2::y, numeric::xyzVector< typename >::y(), ydim_, ymx_, numeric::geometry::hashing::Ball::z(), numeric::crick_equations::z(), numeric::xyzVector< typename >::z(), zdim_, and zmx_.

int numeric::geometry::hashing::xyzStripeHash::clash_check_ball

(

Ball const &

b

)

const

References test.Workshop3test::a2, grid_balls_, grid_size_, grid_stripe_, test.T150_PyMOL_Integration::i, numeric::max(), numeric::min(), numeric::geometry::hashing::Ball::radius(), translation_, numeric::crick_equations::x(), numeric::geometry::hashing::Ball::x(), numeric::geometry::hashing::xyzStripeHash::ushort2::x, numeric::xyzVector< typename >::x(), xdim_, xmx_, numeric::geometry::hashing::Ball::xyz(), numeric::geometry::hashing::Ball::y(), numeric::crick_equations::y(), numeric::geometry::hashing::xyzStripeHash::ushort2::y, numeric::xyzVector< typename >::y(), ydim_, ymx_, numeric::geometry::hashing::Ball::z(), numeric::crick_equations::z(), numeric::xyzVector< typename >::z(), zdim_, and zmx_.

Referenced by clash_check_residue_pairs().

bool numeric::geometry::hashing::xyzStripeHash::clash_check_residue_pairs	(	utility::vector1< Ball > const &	test_balls,
		std::map< Size, Size > &	residue_pairs
	)		const

References ball(), clash_check_ball(), test.T150_PyMOL_Integration::i, and numeric::geometry::hashing::Ball::resi().

bool numeric::geometry::hashing::xyzStripeHash::clash_not_resid	(	Vec const &	v_in,
		int const &	resid,
		int const &	resid2 = 0
	)		const

References test.Workshop3test::a2, grid_balls_, grid_size2_, grid_size_, grid_stripe_, test.T150_PyMOL_Integration::i, numeric::max(), numeric::min(), numeric::geometry::hashing::Ball::resid_, translation_, test.T850_SubClassing::v, numeric::crick_equations::x(), numeric::geometry::hashing::Ball::x(), numeric::geometry::hashing::xyzStripeHash::ushort2::x, numeric::xyzVector< typename >::x(), xdim_, xmx_, numeric::geometry::hashing::Ball::y(), numeric::crick_equations::y(), numeric::geometry::hashing::xyzStripeHash::ushort2::y, numeric::xyzVector< typename >::y(), ydim_, ymx_, numeric::geometry::hashing::Ball::z(), numeric::crick_equations::z(), numeric::xyzVector< typename >::z(), zdim_, and zmx_.

bool numeric::geometry::hashing::xyzStripeHash::clash_raw

(

Vec const &

v

)

const

References test.Workshop3test::a2, grid_balls_, grid_size2_, grid_size_, grid_stripe_, test.T150_PyMOL_Integration::i, numeric::max(), numeric::min(), numeric::crick_equations::x(), numeric::geometry::hashing::Ball::x(), numeric::geometry::hashing::xyzStripeHash::ushort2::x, numeric::xyzVector< typename >::x(), xdim_, xmx_, numeric::geometry::hashing::Ball::y(), numeric::crick_equations::y(), numeric::geometry::hashing::xyzStripeHash::ushort2::y, numeric::xyzVector< typename >::y(), ydim_, ymx_, numeric::geometry::hashing::Ball::z(), numeric::crick_equations::z(), numeric::xyzVector< typename >::z(), zdim_, and zmx_.

std::string numeric::geometry::hashing::xyzStripeHash::debug_pdb

(

Xform const &

x = numeric::Xform::identity()

)

const

References basic::options::OptionKeys::score::fiber_diffraction::b, ObjexxFCL::format::F(), pyrosetta.tests.distributed.test_dask::format, grid_balls_, test.T110_numeric::I, test.T150_PyMOL_Integration::i, nballs_, erraser_single_res_analysis::out, translation_, test.T850_SubClassing::v, numeric::xyzVector< typename >::x(), numeric::geometry::hashing::Ball::xyz(), numeric::xyzVector< typename >::y(), and numeric::xyzVector< typename >::z().

const_iterator numeric::geometry::hashing::xyzStripeHash::end ( ) const

inline

References grid_balls_, and nballs_.

void numeric::geometry::hashing::xyzStripeHash::fill_pairs	(	xyzVector_float const &	v,
		int const &	ir,
		utility::vector1< std::pair< int, int > > &	pairs,
		float	maxd2 = 0.0
	)		const

References test.Workshop3test::a2, grid_balls_, grid_size2_, grid_size_, grid_stripe_, test.T150_PyMOL_Integration::i, numeric::max(), numeric::min(), numeric::geometry::hashing::Ball::resid_, translation_, test.T850_SubClassing::v, numeric::crick_equations::x(), numeric::geometry::hashing::Ball::x(), numeric::geometry::hashing::xyzStripeHash::ushort2::x, numeric::xyzVector< typename >::x(), xdim_, xmx_, numeric::geometry::hashing::Ball::y(), numeric::crick_equations::y(), numeric::geometry::hashing::xyzStripeHash::ushort2::y, numeric::xyzVector< typename >::y(), ydim_, ymx_, numeric::geometry::hashing::Ball::z(), numeric::crick_equations::z(), numeric::xyzVector< typename >::z(), zdim_, and zmx_.

Ball const* numeric::geometry::hashing::xyzStripeHash::grid_atoms ( ) const

inline

References grid_balls_.

float numeric::geometry::hashing::xyzStripeHash::grid_size ( ) const

inline

References grid_size_.

float numeric::geometry::hashing::xyzStripeHash::grid_size2 ( ) const

inline

References grid_size2_.

ushort2 const* numeric::geometry::hashing::xyzStripeHash::grid_stripe ( ) const

inline

References grid_stripe_.

void numeric::geometry::hashing::xyzStripeHash::init

(

utility::vector1< Ball > const &

balls

)

References basic::options::OptionKeys::score::fiber_diffraction::b, demo.D060_Folding::f, grid_balls_, grid_size2_, grid_size_, grid_stripe_, test.T150_PyMOL_Integration::i, numeric::max(), numeric::min(), nballs_, basic::options::OptionKeys::cluster::radius, translation_, utility_exit_with_message, numeric::crick_equations::x(), numeric::geometry::hashing::Ball::x(), numeric::xyzVector< typename >::x(), xdim_, xmx_, numeric::crick_equations::y(), numeric::geometry::hashing::xyzStripeHash::ushort2::y, numeric::xyzVector< typename >::y(), ydim_, ymx_, numeric::crick_equations::z(), numeric::xyzVector< typename >::z(), zdim_, and zmx_.

Referenced by xyzStripeHash().

int numeric::geometry::hashing::xyzStripeHash::natom ( ) const

inline

References nballs_.

int numeric::geometry::hashing::xyzStripeHash::nbcount

(

Vec const &

v_in

)

const

References test.Workshop3test::a2, clean_pdb_keep_ligand::count, grid_balls_, grid_size2_, grid_size_, grid_stripe_, test.T150_PyMOL_Integration::i, numeric::max(), numeric::min(), translation_, test.T850_SubClassing::v, numeric::crick_equations::x(), numeric::geometry::hashing::Ball::x(), numeric::geometry::hashing::xyzStripeHash::ushort2::x, numeric::xyzVector< typename >::x(), xdim_, xmx_, numeric::geometry::hashing::Ball::y(), numeric::crick_equations::y(), numeric::geometry::hashing::xyzStripeHash::ushort2::y, numeric::xyzVector< typename >::y(), ydim_, ymx_, numeric::geometry::hashing::Ball::z(), numeric::crick_equations::z(), numeric::xyzVector< typename >::z(), zdim_, and zmx_.

int numeric::geometry::hashing::xyzStripeHash::nbcount_raw

(

Vec const &

v

)

const

References test.Workshop3test::a2, clean_pdb_keep_ligand::count, grid_balls_, grid_size2_, grid_size_, grid_stripe_, test.T150_PyMOL_Integration::i, numeric::max(), numeric::min(), numeric::crick_equations::x(), numeric::geometry::hashing::Ball::x(), numeric::geometry::hashing::xyzStripeHash::ushort2::x, numeric::xyzVector< typename >::x(), xdim_, xmx_, numeric::geometry::hashing::Ball::y(), numeric::crick_equations::y(), numeric::geometry::hashing::xyzStripeHash::ushort2::y, numeric::xyzVector< typename >::y(), ydim_, ymx_, numeric::geometry::hashing::Ball::z(), numeric::crick_equations::z(), numeric::xyzVector< typename >::z(), zdim_, and zmx_.

Size numeric::geometry::hashing::xyzStripeHash::resi ( Size const &  ib ) const

inline

References grid_balls_, nballs_, and numeric::geometry::hashing::Ball::resi().

bool numeric::geometry::hashing::xyzStripeHash::sanity_check

(

)

const

References pyrosetta.tests.distributed.test_dask::format, grid_balls_, grid_size_, grid_stripe_, test.T150_PyMOL_Integration::i, utility_exit_with_message, numeric::geometry::hashing::xyzStripeHash::ushort2::x, xdim_, numeric::crick_equations::y(), numeric::geometry::hashing::xyzStripeHash::ushort2::y, ydim_, numeric::crick_equations::z(), and zdim_.

short numeric::geometry::hashing::xyzStripeHash::short_max ( short const  a, short const  b  )

inlineprivate

References basic::options::OptionKeys::score::fiber_diffraction::b.

short numeric::geometry::hashing::xyzStripeHash::short_min ( short const  a, short const  b  )

inlineprivate

References basic::options::OptionKeys::score::fiber_diffraction::b.

Size numeric::geometry::hashing::xyzStripeHash::size ( ) const

inline

References nballs_.

xyzVector_float const& numeric::geometry::hashing::xyzStripeHash::translation ( ) const

inline

References translation_.

xyzVector<Real> numeric::geometry::hashing::xyzStripeHash::translation_real ( ) const

inline

References translation_, numeric::xyzVector< typename >::x(), numeric::xyzVector< typename >::y(), and numeric::xyzVector< typename >::z().

short numeric::geometry::hashing::xyzStripeHash::ushort_max ( unsigned short const  a, unsigned short const  b  )

inlineprivate

References basic::options::OptionKeys::score::fiber_diffraction::b.

short numeric::geometry::hashing::xyzStripeHash::ushort_min ( unsigned short const  a, unsigned short const  b  )

inlineprivate

References basic::options::OptionKeys::score::fiber_diffraction::b.

template<typename Visitor >

void numeric::geometry::hashing::xyzStripeHash::visit ( Vec const &  v_in, Visitor &  visitor  ) const

inline

References grid_balls_, grid_size2_, grid_size_, grid_stripe_, test.T150_PyMOL_Integration::i, numeric::max(), numeric::min(), translation_, test.T850_SubClassing::v, numeric::crick_equations::x(), numeric::geometry::hashing::xyzStripeHash::ushort2::x, numeric::xyzVector< typename >::x(), xdim_, xmx_, numeric::crick_equations::y(), numeric::geometry::hashing::xyzStripeHash::ushort2::y, numeric::xyzVector< typename >::y(), ydim_, ymx_, numeric::crick_equations::z(), numeric::xyzVector< typename >::z(), zdim_, and zmx_.

template<typename Visitor >

void numeric::geometry::hashing::xyzStripeHash::visit_lax ( Vec const &  v_in, float const  vr, Visitor &  visitor  ) const

inline

References grid_balls_, grid_size_, grid_stripe_, test.T150_PyMOL_Integration::i, numeric::max(), numeric::min(), numeric::geometry::hashing::Ball::radius(), translation_, test.T850_SubClassing::v, numeric::crick_equations::x(), numeric::geometry::hashing::xyzStripeHash::ushort2::x, numeric::xyzVector< typename >::x(), xdim_, xmx_, numeric::crick_equations::y(), numeric::geometry::hashing::xyzStripeHash::ushort2::y, numeric::xyzVector< typename >::y(), ydim_, ymx_, numeric::crick_equations::z(), numeric::xyzVector< typename >::z(), zdim_, and zmx_.

int numeric::geometry::hashing::xyzStripeHash::xdim ( ) const

inline

References xdim_.

xyzVector_float numeric::geometry::hashing::xyzStripeHash::xyz ( Size const &  ib ) const

inline

References grid_balls_, nballs_, translation_, and numeric::geometry::hashing::Ball::xyz().

int numeric::geometry::hashing::xyzStripeHash::ydim ( ) const

inline

References ydim_.

int numeric::geometry::hashing::xyzStripeHash::zdim ( ) const

inline

References zdim_.

Member Data Documentation

Ball const* numeric::geometry::hashing::xyzStripeHash::grid_balls_

private

Referenced by ball(), begin(), clash(), clash_amount(), clash_check_ball(), clash_not_resid(), clash_raw(), debug_pdb(), end(), fill_pairs(), grid_atoms(), init(), nbcount(), nbcount_raw(), resi(), sanity_check(), visit(), visit_lax(), xyz(), and ~xyzStripeHash().

float numeric::geometry::hashing::xyzStripeHash::grid_size2_

private

Referenced by clash(), clash_amount(), clash_not_resid(), clash_raw(), fill_pairs(), grid_size2(), init(), nbcount(), nbcount_raw(), and visit().

float numeric::geometry::hashing::xyzStripeHash::grid_size_

private

Referenced by clash(), clash_amount(), clash_check_ball(), clash_not_resid(), clash_raw(), fill_pairs(), grid_size(), init(), nbcount(), nbcount_raw(), sanity_check(), visit(), and visit_lax().

ushort2 const* numeric::geometry::hashing::xyzStripeHash::grid_stripe_

private

Referenced by clash(), clash_amount(), clash_check_ball(), clash_not_resid(), clash_raw(), fill_pairs(), grid_stripe(), init(), nbcount(), nbcount_raw(), sanity_check(), visit(), visit_lax(), and ~xyzStripeHash().

int numeric::geometry::hashing::xyzStripeHash::nballs_

private

Referenced by ball(), debug_pdb(), end(), init(), natom(), resi(), size(), and xyz().

numeric::xyzVector<float> numeric::geometry::hashing::xyzStripeHash::translation_

private

Referenced by clash(), clash_amount(), clash_check_ball(), clash_not_resid(), debug_pdb(), fill_pairs(), init(), nbcount(), translation(), translation_real(), visit(), visit_lax(), and xyz().

int numeric::geometry::hashing::xyzStripeHash::xdim_

private

Referenced by clash(), clash_amount(), clash_check_ball(), clash_not_resid(), clash_raw(), fill_pairs(), init(), nbcount(), nbcount_raw(), sanity_check(), visit(), visit_lax(), and xdim().

float numeric::geometry::hashing::xyzStripeHash::xmx_

private

Referenced by clash(), clash_amount(), clash_check_ball(), clash_not_resid(), clash_raw(), fill_pairs(), init(), nbcount(), nbcount_raw(), visit(), and visit_lax().

int numeric::geometry::hashing::xyzStripeHash::ydim_

private

Referenced by clash(), clash_amount(), clash_check_ball(), clash_not_resid(), clash_raw(), fill_pairs(), init(), nbcount(), nbcount_raw(), sanity_check(), visit(), visit_lax(), and ydim().

float numeric::geometry::hashing::xyzStripeHash::ymx_

private

Referenced by clash(), clash_amount(), clash_check_ball(), clash_not_resid(), clash_raw(), fill_pairs(), init(), nbcount(), nbcount_raw(), visit(), and visit_lax().

int numeric::geometry::hashing::xyzStripeHash::zdim_

private

Referenced by clash(), clash_amount(), clash_check_ball(), clash_not_resid(), clash_raw(), fill_pairs(), init(), nbcount(), nbcount_raw(), sanity_check(), visit(), visit_lax(), and zdim().

float numeric::geometry::hashing::xyzStripeHash::zmx_

private

Referenced by clash(), clash_amount(), clash_check_ball(), clash_not_resid(), clash_raw(), fill_pairs(), init(), nbcount(), nbcount_raw(), visit(), and visit_lax().

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

• src/numeric/geometry/hashing/xyzStripeHash.hh
• src/numeric/geometry/hashing/xyzStripeHash.cc