#include <core/types.hh>
#include <protocols/cryst/spacegroup.hh>
#include <utility/vector1.hh>
#include <numeric/constants.hh>
#include <numeric/xyzMatrix.hh>
#include <numeric/xyzVector.hh>
#include <numeric/xyz.functions.hh>
#include <utility/excn/Exceptions.hh>
#include <basic/Tracer.hh>
#include <iostream>
#include <math.h>
#include <string>
#include <basic/options/keys/OptionKeys.hh>

Classes
class	pointGroupHit

struct	latticeHit

struct	fiberHit

Macros
#define	DEG2RAD 0.0174532925199433

#define	RAD2DEG 57.295779513082323

Functions
int	pos_mod (int x, int y)

Real	pos_mod (Real x, Real y)

int	min_mod (int x, int y)

double	min_mod (double x, double y)

double	sign (double x)

double	norm4 (double a, double b, double c, double d)

numeric::xyzMatrix< Real >	axis_angle (numeric::xyzVector< Real > u, Real theta)

void	get_axis_angle (numeric::xyzMatrix< Real > const &R, numeric::xyzVector< Real > &u, Real &theta, numeric::xyzVector< Real > const &suggest_axis=numeric::xyzVector< Real >(0, 0, 0))

numeric::xyzVector< Real >	get_rotation_axis (numeric::xyzMatrix< Real > const &R)

numeric::xyzVector< Real >	project_line (numeric::xyzVector< Real > const &line, numeric::xyzVector< Real > const &proj)

bool	transforms_equiv_mod1 (numeric::xyzMatrix< Real > const &S1, numeric::xyzVector< Real > const &T1, numeric::xyzMatrix< Real > const &S2, numeric::xyzVector< Real > const &T2)

bool	transforms_equiv (numeric::xyzMatrix< Real > const &S1, numeric::xyzVector< Real > const &T1, numeric::xyzMatrix< Real > const &S2, numeric::xyzVector< Real > const &T2)

bool	transforms_equiv (numeric::xyzMatrix< Real > const &S1, numeric::xyzMatrix< Real > const &S2)

bool	transforms_equiv (numeric::xyzVector< Real > const &T1, numeric::xyzVector< Real > const &T2)

void	disp_symmop (core::kinematics::RT const &rt)

numeric::xyzVector< Real >	get_reflection_axis (numeric::xyzMatrix< Real > const &R)

void	get_angle_and_offset (pointGroupHit hit_i, pointGroupHit hit_j, core::Real &angle, core::Real &offset, core::Real &shift)

void	dedup (utility::vector1< pointGroupHit > &hits)

void	remove_drift (utility::vector1< pointGroupHit > &hits)

pointGroupHit	get_primary_point_group (numeric::xyzMatrix< Real > const &Si, numeric::xyzVector< Real > const &Ti, numeric::xyzMatrix< core::Real > const &skewM)

utility::vector1< pointGroupHit >	get_point_groups (utility::vector1< core::kinematics::RT > const &rts, numeric::xyzMatrix< core::Real > const &skewM)

bool	expand_all_and_check_if_forms_lattice (utility::vector1< core::kinematics::RT > const &rts, utility::vector1< core::kinematics::RT > const &rts_all, bool verbose=false)

void	set_all_spacegroups (utility::vector1< std::string > &spacegroups)

void	set_achiral_spacegroups (utility::vector1< std::string > &spacegroups)

numeric::xyzMatrix< Real >	get_skew (std::string name)

utility::vector1< latticeHit >	generate_from_point (utility::vector1< pointGroupHit > const &pgs, utility::vector1< core::kinematics::RT > const &rts)

utility::vector1< fiberHit >	generate_from_fiber (utility::vector1< pointGroupHit > const &pgs, utility::vector1< core::kinematics::RT > const &rts, numeric::xyzMatrix< core::Real > const &skewM)

int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("cryst.gen")

Macro Definition Documentation

◆ DEG2RAD

#define DEG2RAD 0.0174532925199433

◆ RAD2DEG

#define RAD2DEG 57.295779513082323

Function Documentation

◆ axis_angle()

numeric::xyzMatrix<Real> axis_angle	(	numeric::xyzVector< Real >	u,
		Real	theta
	)

inline

References numeric::xyzMatrix< T >::rows(), and kmeans_adaptive_kernel_density_bb_dependent_rotlib::u.

Referenced by numeric::rotation_matrix().

◆ dedup()

void dedup ( utility::vector1< pointGroupHit > & hits )

References create_a3b_hbs::i, enumerate_junctions::int, create_a3b_hbs::j, and create_a3b_hbs::score.

Referenced by get_point_groups().

◆ disp_symmop()

void disp_symmop ( core::kinematics::RT const & rt )

References utility::io::oc::cout, and pyrosetta.distributed.cluster.exceptions::T.

Referenced by expand_all_and_check_if_forms_lattice().

◆ expand_all_and_check_if_forms_lattice()

bool expand_all_and_check_if_forms_lattice	(	utility::vector1< core::kinematics::RT > const &	rts,
		utility::vector1< core::kinematics::RT > const &	rts_all,
		bool	verbose = `false`
	)

References disp_symmop(), gpu_set_args::done, create_a3b_hbs::i, enumerate_junctions::int, create_a3b_hbs::j, create_a3b_hbs::k, basic::options::OptionKeys::lh::rounds, numeric::xyzMatrix< T >::rows(), beta_nonlocal::rts, transforms_equiv(), transforms_equiv_mod1(), ObjexxFCL::unique(), and basic::options::OptionKeys::sc::verbose.

Referenced by generate_from_fiber(), and generate_from_point().

◆ generate_from_fiber()

utility::vector1< fiberHit > generate_from_fiber	(	utility::vector1< pointGroupHit > const &	pgs,
		utility::vector1< core::kinematics::RT > const &	rts,
		numeric::xyzMatrix< core::Real > const &	skewM
	)

References pointGroupHit::append_symmops(), pointGroupHit::contains_symmop(), numeric::xyzVector< T >::cross(), measure_params::dot(), numeric::xyzVector< T >::dot(), test.T009_Exceptions::e, expand_all_and_check_if_forms_lattice(), get_axis_angle(), fiberHit::haxis, fiberHit::haxis_expansion, fiberHit::hit, create_a3b_hbs::i, enumerate_junctions::int, numeric::inverse(), pointGroupHit::isC(), pointGroupHit::isC1(), pointGroupHit::isD(), create_a3b_hbs::j, create_a3b_hbs::k, numeric::xyzVector< T >::length(), numeric::xyzVector< T >::length_squared(), min_mod(), numeric::xyzVector< T >::normalized(), pointGroupHit::order(), pointGroupHit::origin(), numeric::constants::d::pi, project_line(), fiberHit::rise, fiberHit::rotation, numeric::xyzMatrix< T >::rows(), beta_nonlocal::rts, docking::s, fiberHit::score(), transforms_equiv_mod1(), and ObjexxFCL::unique().

Referenced by main().

◆ generate_from_point()

utility::vector1< latticeHit > generate_from_point	(	utility::vector1< pointGroupHit > const &	pgs,
		utility::vector1< core::kinematics::RT > const &	rts
	)

References basic::options::OptionKeys::hotspot::angle, pointGroupHit::append_symmops(), test.T009_Exceptions::e, expand_all_and_check_if_forms_lattice(), get_angle_and_offset(), create_a3b_hbs::i, enumerate_junctions::int, create_a3b_hbs::j, pointGroupHit::name(), offset, pointGroupHit::order(), enumerate_junctions::q, beta_nonlocal::rts, and shift.

Referenced by main().

◆ get_angle_and_offset()

void get_angle_and_offset	(	pointGroupHit	hit_i,
		pointGroupHit	hit_j,
		core::Real &	angle,
		core::Real &	offset,
		core::Real &	shift
	)

Referenced by generate_from_point().

◆ get_axis_angle()

void get_axis_angle	(	numeric::xyzMatrix< Real > const &	R,
		numeric::xyzVector< Real > &	u,
		Real &	theta,
		numeric::xyzVector< Real > const &	suggest_axis = `numeric::xyzVector<Real>(0,0,0)`
	)

inline

References test.T009_Exceptions::e, numeric::constants::d::pi, docking::R, docking::s, kmeans_adaptive_kernel_density_bb_dependent_rotlib::u, x, xx, test.T110_numeric::xy, test.T110_numeric::xz, predPRE::y, yy, test.T110_numeric::yz, predPRE::z, and test.T110_numeric::zz.

Referenced by generate_from_fiber(), and get_rotation_axis().

◆ get_point_groups()

utility::vector1< pointGroupHit > get_point_groups	(	utility::vector1< core::kinematics::RT > const &	rts,
		numeric::xyzMatrix< core::Real > const &	skewM
	)

References pointGroupHit::add_symmop(), dedup(), pointGroupHit::expand(), get_primary_point_group(), create_a3b_hbs::i, enumerate_junctions::int, pointGroupHit::intersects(), pointGroupHit::isCs(), pointGroupHit::isCv(), create_a3b_hbs::j, pointGroupHit::name(), remove_drift(), numeric::xyzMatrix< T >::rows(), beta_nonlocal::rts, transforms_equiv(), x, predPRE::y, and predPRE::z.

Referenced by main().

◆ get_primary_point_group()

pointGroupHit get_primary_point_group	(	numeric::xyzMatrix< Real > const &	Si,
		numeric::xyzVector< Real > const &	Ti,
		numeric::xyzMatrix< core::Real > const &	skewM
	)

References numeric::xyzMatrix< T >::det(), get_reflection_axis(), get_rotation_axis(), numeric::inverse(), numeric::xyzMatrix< T >::rows(), transforms_equiv(), and TT.

Referenced by get_point_groups().

◆ get_reflection_axis()

numeric::xyzVector<Real> get_reflection_axis ( numeric::xyzMatrix< Real > const & R )

References numeric::xyzMatrix< T >::col(), utility::io::oc::cout, test.T009_Exceptions::e, numeric::eigenvector_jacobi(), numeric::xyzVector< T >::normalize(), docking::R, and utility_exit_with_message.

Referenced by get_primary_point_group().

◆ get_rotation_axis()

numeric::xyzVector<Real> get_rotation_axis ( numeric::xyzMatrix< Real > const & R )

References get_axis_angle(), and docking::R.

Referenced by get_primary_point_group().

◆ get_skew()

numeric::xyzMatrix<Real> get_skew ( std::string name )

References numeric::xyzMatrix< T >::rows().

Referenced by main().

◆ main()

int main	(	int	argc,
		char *	argv[]
	)

References argv, fiberHit::as_string(), utility::io::oc::cerr, utility::io::oc::cout, test.T009_Exceptions::e, utility::options::OptionKeys::options::exit, generate_from_fiber(), generate_from_point(), get_point_groups(), get_skew(), create_a3b_hbs::i, enumerate_junctions::int, SmotifHasher::mode, beta_nonlocal::rts, set_achiral_spacegroups(), and pointGroupHit::show().

◆ min_mod() [1/2]

double min_mod	(	double	x,
		double	y
	)

inline

References create_a3b_hbs::r, x, and predPRE::y.

◆ min_mod() [2/2]

int min_mod	(	int	x,
		int	y
	)

inline

References create_a3b_hbs::r, x, and predPRE::y.

Referenced by generate_from_fiber(), CrystFFTDock::get_interfaces_allatom(), CrystFFTDock::setup_maps(), and transforms_equiv_mod1().

◆ norm4()

double norm4	(	double	a,
		double	b,
		double	c,
		double	d
	)

inline

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

◆ pos_mod() [1/2]

int pos_mod	(	int	x,
		int	y
	)

inline

References create_a3b_hbs::r, x, and predPRE::y.

Referenced by CrystFFTDock::get_clash_score_exact(), CrystFFTDock::project_along_axis(), CrystFFTDock::transform_map(), CrystFFTDock::transform_map_offset0(), and CrystFFTDock::writeMRC().

◆ pos_mod() [2/2]

Real pos_mod	(	Real	x,
		Real	y
	)

inline

References create_a3b_hbs::r, x, and predPRE::y.

◆ project_line()

numeric::xyzVector<Real> project_line	(	numeric::xyzVector< Real > const &	line,
		numeric::xyzVector< Real > const &	proj
	)

inline

References numeric::xyzVector< T >::dot(), line, and proj().

Referenced by generate_from_fiber().

◆ remove_drift()

void remove_drift ( utility::vector1< pointGroupHit > & hits )

References create_a3b_hbs::i, and enumerate_junctions::int.

Referenced by get_point_groups().

◆ set_achiral_spacegroups()

void set_achiral_spacegroups ( utility::vector1< std::string > & spacegroups )

Referenced by main().

◆ set_all_spacegroups()

void set_all_spacegroups ( utility::vector1< std::string > & spacegroups )

◆ sign()

double sign ( double x )

inline

References x.

◆ transforms_equiv() [1/3]

bool transforms_equiv	(	numeric::xyzMatrix< Real > const &	S1,
		numeric::xyzMatrix< Real > const &	S2
	)

inline

References test.T009_Exceptions::e, numeric::xyzMatrix< T >::xx(), numeric::xyzMatrix< T >::xy(), numeric::xyzMatrix< T >::xz(), numeric::xyzMatrix< T >::yx(), numeric::xyzMatrix< T >::yy(), numeric::xyzMatrix< T >::yz(), numeric::xyzMatrix< T >::zx(), numeric::xyzMatrix< T >::zy(), and numeric::xyzMatrix< T >::zz().

◆ transforms_equiv() [2/3]

bool transforms_equiv	(	numeric::xyzMatrix< Real > const &	S1,
		numeric::xyzVector< Real > const &	T1,
		numeric::xyzMatrix< Real > const &	S2,
		numeric::xyzVector< Real > const &	T2
	)

inline

References test.T009_Exceptions::e, numeric::xyzMatrix< T >::xx(), numeric::xyzMatrix< T >::xy(), numeric::xyzMatrix< T >::xz(), numeric::xyzMatrix< T >::yx(), numeric::xyzMatrix< T >::yy(), numeric::xyzMatrix< T >::yz(), numeric::xyzMatrix< T >::zx(), numeric::xyzMatrix< T >::zy(), and numeric::xyzMatrix< T >::zz().

Referenced by pointGroupHit::construct_from_basis(), pointGroupHit::expand(), expand_all_and_check_if_forms_lattice(), get_point_groups(), get_primary_point_group(), and pointGroupHit::pointGroupHit().

◆ transforms_equiv() [3/3]

bool transforms_equiv	(	numeric::xyzVector< Real > const &	T1,
		numeric::xyzVector< Real > const &	T2
	)

inline

References test.T009_Exceptions::e.

◆ transforms_equiv_mod1()

bool transforms_equiv_mod1	(	numeric::xyzMatrix< Real > const &	S1,
		numeric::xyzVector< Real > const &	T1,
		numeric::xyzMatrix< Real > const &	S2,
		numeric::xyzVector< Real > const &	T2
	)

inline

References test.T009_Exceptions::e, min_mod(), numeric::xyzMatrix< T >::xx(), numeric::xyzMatrix< T >::xy(), numeric::xyzMatrix< T >::xz(), numeric::xyzMatrix< T >::yx(), numeric::xyzMatrix< T >::yy(), numeric::xyzMatrix< T >::yz(), numeric::xyzMatrix< T >::zx(), numeric::xyzMatrix< T >::zy(), and numeric::xyzMatrix< T >::zz().

Referenced by pointGroupHit::expand(), expand_all_and_check_if_forms_lattice(), generate_from_fiber(), and pointGroupHit::transform().

Variable Documentation

◆ TR

basic::Tracer TR("cryst.gen") ( "cryst.gen" )

static

Classes

Macros

Functions

Variables

Macro Definition Documentation

◆ DEG2RAD

◆ RAD2DEG

Function Documentation

◆ axis_angle()

◆ dedup()

◆ disp_symmop()

◆ expand_all_and_check_if_forms_lattice()

◆ generate_from_fiber()

◆ generate_from_point()

◆ get_angle_and_offset()

◆ get_axis_angle()

◆ get_point_groups()

◆ get_primary_point_group()

◆ get_reflection_axis()

◆ get_rotation_axis()

◆ get_skew()

◆ main()

◆ min_mod() [1/2]

◆ min_mod() [2/2]

◆ norm4()

◆ pos_mod() [1/2]

◆ pos_mod() [2/2]

◆ project_line()

◆ remove_drift()

◆ set_achiral_spacegroups()

◆ set_all_spacegroups()

◆ sign()

◆ transforms_equiv() [1/3]

◆ transforms_equiv() [2/3]

◆ transforms_equiv() [3/3]

◆ transforms_equiv_mod1()

Variable Documentation

◆ TR