gpu_mat_vec.hh File Reference

#include <numeric/IOTraits.hh>
#include <iosfwd>

Classes
struct	VEC
struct	MAT
struct	XFORM

Typedefs
typedef cl_float16	float16
typedef cl_float8	float8
typedef cl_float4	float4
typedef cl_float3	float3
typedef cl_float2	float2
typedef cl_ushort2	ushort2
typedef cl_uint8	uint8

Functions
float	native_sin (float x)
float	native_cos (float x)
float	native_divide (float a, float b)
float	native_sqrt (float a)
float	mad (float a, float b, float c)
float	sqr (float const &x)
struct VEC	vec (float x, float y, float z)
struct MAT	rows (float xx, float xy, float xz, float yx, float yy, float yz, float zx, float zy, float zz)
struct MAT	cols (float xx, float yx, float zx, float xy, float yy, float zy, float xz, float yz, float zz)
struct MAT	rows (struct VEC const rx, struct VEC const ry, struct VEC const rz)
struct MAT	cols (struct VEC const cx, struct VEC const cy, struct VEC const cz)
struct XFORM	xform (struct MAT const R, struct VEC const t)
struct MAT	multmm (struct MAT const a, struct MAT const b)
struct VEC	multmv (struct MAT const a, struct VEC const b)
struct VEC	multfv (float const a, struct VEC const v)
struct MAT	multfm (float const a, struct MAT const m)
struct VEC	crossvv (struct VEC const a, struct VEC const b)
struct VEC	addvv (struct VEC const a, struct VEC const b)
struct VEC	subvv (struct VEC const a, struct VEC const b)
float	dotvv (struct VEC const a, struct VEC const b)
float	length2v (struct VEC v)
float	length2f (float const x, float const y, float const z)
float	lengthv (struct VEC v)
float	lengthf (float const x, float const y, float const z)
struct VEC	normalizedv (struct VEC v)
struct VEC	normalizedf (float const x, float const y, float const z)
struct VEC	proj (struct VEC const a, struct VEC const v)
struct VEC	pproj (struct VEC const a, struct VEC const v)
void	rotx (struct VEC *v, float const sin, float const cos)
void	roty (struct VEC *v, float const sin, float const cos)
void	rotz (struct VEC *v, float const sin, float const cos)
struct MAT	projectionMAT (struct VEC const a)
struct MAT	projectionMAT (float const x, float const y, float const z)
struct MAT	rotationMAT (struct VEC const a, float const t)
struct MAT	rotationMAT (float const x, float const y, float const z, float const t)
struct MAT	transposed (struct MAT const m)
struct XFORM	multxx (struct XFORM const x2, struct XFORM const x1)
struct XFORM	xrev (struct XFORM const x)
struct VEC	multxv (struct XFORM const x, struct VEC const v)
struct XFORM const	vvcxform (struct VEC const _x1, struct VEC const _x2, struct VEC const _y1, struct VEC const _y2, struct VEC const _c1, struct VEC const _c2)
struct XFORM const	stub (struct VEC const a, struct VEC const b, struct VEC const c)
struct XFORM const	stubrev (struct VEC const a, struct VEC const b, struct VEC const c)
struct XFORM const	stubc (struct VEC const cen, struct VEC const a, struct VEC const b, struct VEC const c)
struct XFORM const	stubcrev (struct VEC const cen, struct VEC const a, struct VEC const b, struct VEC const c)
bool	eq (float u, float v)
bool	eq (struct VEC u, struct VEC v)
bool	eq (struct MAT u, struct MAT v)
bool	eq (Vec u, struct VEC v)
bool	eq (struct VEC u, Vec v)
bool	eq (Mat u, struct MAT v)
bool	eq (struct MAT u, Mat v)
std::ostream &	operator<< (std::ostream &out, struct MAT m)
std::ostream &	operator<< (std::ostream &out, struct VEC v)
void	myasserteq (float u, float v, string s)
void	myasserteq (struct VEC u, struct VEC v, string s)
bool	myasserteq (Vec u, struct VEC v, string s)
bool	myasserteq (struct VEC u, Vec v, string s)
void	myasserteq (struct MAT u, struct MAT v, string s)
bool	myasserteq (Mat u, struct MAT v, string s)
bool	myasserteq (struct MAT u, Mat v, string s)
void	test_MAT_VEC ()
void	test_chi_xform ()

Typedef Documentation

float16

typedef cl_float16 float16

float2

typedef cl_float2 float2

float3

typedef cl_float3 float3

float4

typedef cl_float4 float4

float8

typedef cl_float8 float8

uint8

typedef cl_uint8 uint8

ushort2

typedef cl_ushort2 ushort2

Function Documentation

addvv()

struct VEC addvv ( struct VEC const  a, struct VEC const  b  )

inline

References x.

cols() [1/2]

struct MAT cols ( float  xx, float  yx, float  zx, float  xy, float  yy, float  zy, float  xz, float  yz, float  zz  )

inline

Referenced by numeric::xyzTransform< T >::BAD_XFORM(), get_base_coordinate_system(), get_coordinate_system(), get_ncac(), get_phosphate_stub(), numeric::kinematic_closure::multMatrix(), numeric::kinematic_closure::multTransMatrix(), randomly_shift_and_tilt_pose(), randomly_shift_and_tilt_poses(), refold_second(), test_chi_xform(), and test_MAT_VEC().

cols() [2/2]

struct MAT cols ( struct VEC const  cx, struct VEC const  cy, struct VEC const  cz  )

inline

crossvv()

struct VEC crossvv ( struct VEC const  a, struct VEC const  b  )

inline

Referenced by refold_second(), test_chi_xform(), and test_MAT_VEC().

dotvv()

float dotvv ( struct VEC const  a, struct VEC const  b  )

inline

References a, compute_difference::b, and mad().

Referenced by test_MAT_VEC().

eq() [1/7]

bool eq ( float  u, float  v  )

inline

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::u, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

Referenced by eq(), and myasserteq().

eq() [2/7]

bool eq ( Mat  u, struct MAT  v  )

inline

References eq(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::u, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

eq() [3/7]

bool eq ( struct MAT  u, Mat  v  )

inline

References eq(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::u, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

eq() [4/7]

bool eq ( struct MAT  u, struct MAT  v  )

inline

References eq(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::u, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

eq() [5/7]

bool eq ( struct VEC  u, struct VEC  v  )

inline

References eq(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::u, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

eq() [6/7]

bool eq ( struct VEC  u, Vec  v  )

inline

References eq(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::u, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

eq() [7/7]

bool eq ( Vec  u, struct VEC  v  )

inline

References eq(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::u, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

length2f()

float length2f ( float const  x, float const  y, float const  z  )

inline

References mad(), x, predPRE::y, and predPRE::z.

length2v()

float length2v ( struct VEC  v )

inline

References mad(), and kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

Referenced by test_MAT_VEC().

lengthf()

float lengthf ( float const  x, float const  y, float const  z  )

inline

References mad(), native_sqrt(), x, predPRE::y, and predPRE::z.

lengthv()

float lengthv ( struct VEC  v )

inline

References mad(), native_sqrt(), and kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

mad()

float mad ( float  a, float  b, float  c  )

inline

References a, compute_difference::b, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::c.

Referenced by clash(), contacts(), dotvv(), length2f(), length2v(), lengthf(), lengthv(), and refold_first().

multfm()

struct MAT multfm ( float const  a, struct MAT const  m  )

inline

multfv()

struct VEC multfv ( float const  a, struct VEC const  v  )

inline

multmm()

struct MAT multmm ( struct MAT const  a, struct MAT const  b  )

inline

Referenced by refold_second(), test_chi_xform(), and test_MAT_VEC().

multmv()

struct VEC multmv ( struct MAT const  a, struct VEC const  b  )

inline

Referenced by refold_second(), and test_chi_xform().

multxv()

struct VEC multxv ( struct XFORM const  x, struct VEC const  v  )

inline

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

Referenced by refold_third().

multxx()

struct XFORM multxx ( struct XFORM const  x2, struct XFORM const  x1  )

inline

myasserteq() [1/7]

void myasserteq	(	float	u,
		float	v,
		string	s
	)

References utility::io::oc::cout, eq(), docking::s, kmeans_adaptive_kernel_density_bb_dependent_rotlib::u, utility_exit_with_message, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

Referenced by myasserteq(), test_chi_xform(), and test_MAT_VEC().

myasserteq() [2/7]

bool myasserteq ( Mat  u, struct MAT  v, string  s  )

inline

References myasserteq(), docking::s, kmeans_adaptive_kernel_density_bb_dependent_rotlib::u, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

myasserteq() [3/7]

bool myasserteq ( struct MAT  u, Mat  v, string  s  )

inline

References myasserteq(), docking::s, kmeans_adaptive_kernel_density_bb_dependent_rotlib::u, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

myasserteq() [4/7]

void myasserteq	(	struct MAT	u,
		struct MAT	v,
		string	s
	)

References utility::io::oc::cerr, eq(), docking::s, kmeans_adaptive_kernel_density_bb_dependent_rotlib::u, utility_exit_with_message, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

myasserteq() [5/7]

void myasserteq	(	struct VEC	u,
		struct VEC	v,
		string	s
	)

References utility::io::oc::cerr, eq(), docking::s, kmeans_adaptive_kernel_density_bb_dependent_rotlib::u, utility_exit_with_message, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

myasserteq() [6/7]

bool myasserteq ( struct VEC  u, Vec  v, string  s  )

inline

References myasserteq(), docking::s, kmeans_adaptive_kernel_density_bb_dependent_rotlib::u, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

myasserteq() [7/7]

bool myasserteq ( Vec  u, struct VEC  v, string  s  )

inline

References myasserteq(), docking::s, kmeans_adaptive_kernel_density_bb_dependent_rotlib::u, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

native_cos()

float native_cos ( float  x )

inline

References x.

native_divide()

float native_divide ( float  a, float  b  )

inline

References a, and compute_difference::b.

native_sin()

float native_sin ( float  x )

inline

References x.

native_sqrt()

float native_sqrt ( float  a )

inline

References a.

Referenced by lengthf(), and lengthv().

normalizedf()

struct VEC normalizedf ( float const  x, float const  y, float const  z  )

inline

normalizedv()

struct VEC normalizedv ( struct VEC  v )

inline

Referenced by refold_second(), test_chi_xform(), and test_MAT_VEC().

operator<<() [1/2]

std::ostream& operator<<	(	std::ostream &	out,
		struct MAT	m
	)

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, and erraser_single_res_analysis::out.

operator<<() [2/2]

std::ostream& operator<<	(	std::ostream &	out,
		struct VEC	v
	)

References erraser_single_res_analysis::out, basic::options::OptionKeys::ufv::right, ObjexxFCL::uppercase(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::v, w, and basic::options::OptionKeys::mp::visualize::width.

pproj()

struct VEC pproj ( struct VEC const  a, struct VEC const  v  )

inline

Referenced by refold_second(), test_chi_xform(), and test_MAT_VEC().

proj()

struct VEC proj ( struct VEC const  a, struct VEC const  v  )

inline

Referenced by protocols::abinitio::PcaEvaluator::apply(), project_line(), and test_MAT_VEC().

projectionMAT() [1/2]

struct MAT projectionMAT ( float const  x, float const  y, float const  z  )

inline

projectionMAT() [2/2]

struct MAT projectionMAT ( struct VEC const  a )

inline

Referenced by test_MAT_VEC().

rotationMAT() [1/2]

struct MAT rotationMAT ( float const  x, float const  y, float const  z, float const  t  )

inline

rotationMAT() [2/2]

struct MAT rotationMAT ( struct VEC const  a, float const  t  )

inline

Referenced by test_chi_xform(), and test_MAT_VEC().

rotx()

void rotx ( struct VEC *  v, float const  sin, float const  cos  )

inline

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

Referenced by main().

roty()

void roty ( struct VEC *  v, float const  sin, float const  cos  )

inline

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

Referenced by main().

rotz()

void rotz ( struct VEC *  v, float const  sin, float const  cos  )

inline

Referenced by main().

rows() [1/2]

struct MAT rows ( float  xx, float  xy, float  xz, float  yx, float  yy, float  yz, float  zx, float  zy, float  zz  )

inline

Referenced by ui::task::TaskSubmit::backspace_pressed_on_files(), numeric::linear_algebra::GeneralizedEigenSolver< _MatrixType >::extract_eigenvalues(), ui::task::ProjectView::get_selection(), numeric::kinematic_closure::multMatrix(), numeric::kinematic_closure::multTransMatrix(), ui::task::ProjectView::on_clone_task_clicked(), refold_second(), test_chi_xform(), and test_MAT_VEC().

rows() [2/2]

struct MAT rows ( struct VEC const  rx, struct VEC const  ry, struct VEC const  rz  )

inline

sqr()

float sqr ( float const &  x )

inline

stub()

struct XFORM const stub ( struct VEC const  a, struct VEC const  b, struct VEC const  c  )

inline

Referenced by brt_clash(), MatchSet::c2_iface_check(), ClashCheck::clash_check(), MatchSet::clash_check(), MatchSet::clash_check_inv(), get_repl_xyz(), grd_clash(), ifc_clash(), main(), phosphate_stats(), place_water_acceptor(), place_water_donor(), print_tree(), refold_third(), ReportStubTargetEnergy(), rotate_into_nucleobase_frame(), run(), run_diiron_glu(), run_m8(), run_tyr_his(), run_zn2his(), and toXform().

stubc()

struct XFORM const stubc ( struct VEC const  cen, struct VEC const  a, struct VEC const  b, struct VEC const  c  )

inline

stubcrev()

struct XFORM const stubcrev ( struct VEC const  cen, struct VEC const  a, struct VEC const  b, struct VEC const  c  )

inline

stubrev()

struct XFORM const stubrev ( struct VEC const  a, struct VEC const  b, struct VEC const  c  )

inline

Referenced by main().

subvv()

struct VEC subvv ( struct VEC const  a, struct VEC const  b  )

inline

test_chi_xform()

void test_chi_xform

(

)

References CHI1, CHI2, cols(), numeric::xyzMatrix< Real >::cols(), numeric::xyzVector< T >::cross(), crossvv(), multmm(), multmv(), myasserteq(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, numeric::xyzVector< T >::normalized(), normalizedv(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, pproj(), projperp(), create_a3b_hbs::r, docking::R, numeric::conversions::radians(), rot_pose(), numeric::rotation_matrix_degrees(), rotationMAT(), rows(), numeric::xyzMatrix< Real >::rows(), docking::s, tr, trans_pose(), TZ, utility_exit_with_message, and xform_pose_rev().

test_MAT_VEC()

void test_MAT_VEC

(

)

References cols(), numeric::xyzMatrix< Real >::cols(), crossvv(), dotvv(), length2v(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, multmm(), myasserteq(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, N, normalizedv(), pproj(), proj(), numeric::projection_matrix(), projectionMAT(), projperp(), numeric::rotation_matrix(), rotationMAT(), rows(), numeric::xyzMatrix< Real >::rows(), docking::U, kmeans_adaptive_kernel_density_bb_dependent_rotlib::u, numeric::random::uniform(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::v, w, and numeric::xyzMatrix< T >::xyzMatrix.

transposed()

struct MAT transposed ( struct MAT const  m )

inline

Referenced by utility::options::OptionCollection::add_edits(), and numeric::MathMatrix< T >::inverse_rectangular_matrix().

vec()

struct VEC vec ( float  x, float  y, float  z  )

inline

Referenced by binder::cpp_python_operator(), SimpleDGBindAggregateFunction::evaluate(), myspace::find_best_projection(), find_index(), gpu_refold_test(), in_set(), main(), utility::nmers_of(), utility::nmers_worker(), print_res_ids(), myspace::project(), put_it_in_list(), numeric::random::random_point_on_unit_sphere(), basic::read_metric_value_vector1(), utility::io::read_vector(), refold_second(), refold_third(), numeric::VoxelGrid< T >::RemoveObject(), numeric::random::reservoir_sample(), numeric::rotation_axis_angle(), core::pack::annealer::FixbbSimAnnealer::run(), updateSSAtoms(), vec2str(), basic::write_metric_value_vector1(), and utility::io::write_vector().

vvcxform()

struct XFORM const vvcxform ( struct VEC const  _x1, struct VEC const  _x2, struct VEC const  _y1, struct VEC const  _y2, struct VEC const  _c1, struct VEC const  _c2  )

inline

xform()

struct XFORM xform ( struct MAT const  R, struct VEC const  t  )

inline

Referenced by numeric::XformHash64::operator()(), and numeric::XformHash32::operator()().

xrev()

struct XFORM xrev ( struct XFORM const  x )

inline