#include <protocols/toolbox/superimpose.hh>
#include <core/kinematics/Stub.hh>
#include <core/kinematics/Jump.hh>
#include <core/conformation/Conformation.hh>
#include <core/pose/Pose.hh>
#include <core/types.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <basic/Tracer.hh>
#include <core/chemical/ResidueType.hh>
#include <utility/io/ozstream.hh>
#include <utility/exit.hh>
#include <numeric/xyz.functions.hh>
#include <string>
#include <iostream>
#include <core/id/AtomID.hh>
#include <core/id/NamedAtomID.hh>
#include <utility/vector1.hh>
#include <numeric/model_quality/RmsData.hh>

Namespaces
	protocols
	The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.

	protocols::toolbox

Macros
#define	DIM 3
	#define dump_matrix( nr, a ) {} More...

#define	ROTATE(a, i, j, k, l)

#define	DIM6 6

#define	XX 0

#define	YY 1

#define	ZZ 2

#define	ROTATE(a, i, j, k, l)

#define	DIM6 6

#define	XX 0

#define	YY 1

#define	ZZ 2

Functions
static thread_local basic::Tracer	protocols::toolbox::tr ("protocols.evaluation.PCA", basic::t_info)

template<typename T >
void	protocols::toolbox::vector_vector_to_FArray2 (utility::vector1< numeric::xyzVector< T > > &from, ObjexxFCL::FArray2D< T > &to)

void	protocols::toolbox::superposition_transform (utility::vector1< numeric::xyzVector< core::Real > > &init_coords, utility::vector1< numeric::xyzVector< core::Real > > &ref_coords, numeric::xyzMatrix< core::Real > &rotation, numeric::xyzVector< core::Real > &to_init_center, numeric::xyzVector< core::Real > &to_fit_center)

void	protocols::toolbox::superposition_transform (utility::vector1< numeric::xyzVector< core::Real > > &init_coords, utility::vector1< numeric::xyzVector< core::Real > > &ref_coords, utility::vector1< core::Real > &coord_weights, numeric::xyzMatrix< core::Real > &rotation, numeric::xyzVector< core::Real > &to_init_center, numeric::xyzVector< core::Real > &to_fit_center)

void	protocols::toolbox::apply_superposition_transform_to_jump (core::pose::Pose &pose, core::Size jump_id, Matrix rotation, Vector to_init_center, Vector to_fit_center)

void	protocols::toolbox::apply_superposition_transform (core::pose::Pose &pose, Matrix rotation, Vector to_init_center, Vector to_fit_center)

void	protocols::toolbox::fill_CA_coords (core::pose::Pose const &pose, FArray2_double &coords)

void	protocols::toolbox::fill_CA_coords (core::pose::Pose const &pose, Size n_atoms, FArray2_double &coords)

void	protocols::toolbox::CA_superimpose (FArray1_double const &weights, core::pose::Pose const &ref_pose, core::pose::Pose &fit_pose)

void	protocols::toolbox::superposition_transform (core::Size natoms, ObjexxFCL::FArray1_double const &weights, ObjexxFCL::FArray2_double &ref_coords, ObjexxFCL::FArray2_double &coords, Matrix &R, Vector &toCenter, Vector &toFitCenter)

void	protocols::toolbox::superimpose (Size natoms, FArray1_double const &weights, FArray2_double &ref_coords, FArray2_double &coords)
	compute projections for given pose More...

void	protocols::toolbox::superimpose (Size natoms, FArray1_double const &weights, FArray2_double &ref_coords, FArray2_double &coords, Matrix &R)
	compute projections for given pose More...

void	protocols::toolbox::CA_superimpose (core::pose::Pose const &ref_pose, core::pose::Pose &fit_pose)

void	protocols::toolbox::calc_fit_R (int natoms, Real const weights, rvec const xp, rvec const *x, matrix R)

void	protocols::toolbox::jacobi (double a[6][6], double d[], double v[6][6], int *nrot)

template<class T >
void	protocols::toolbox::dump_matrix (Size, T const &, basic::Tracer &)
	A function (not a macro) that will not print a square matrix to tr.Debug. More...

template<class T >
void	protocols::toolbox::dump_matrix_no (Size nr, T const &a, basic::Tracer &tr)
	A function (not a macro) that will print a square matrix to tr.Debug. More...

void	protocols::toolbox::rotate_vec (int natoms, rvec *x, matrix R)

void	protocols::toolbox::add_vec (int natoms, rvec *x, rvec transvec)

void	protocols::toolbox::reset_x (Size n, FArray2_double &x, FArray1_double const &wts, FArray1_double &transvec)

void	protocols::toolbox::dump_as_pdb (std::string filename, Size n, FArray2_double &x, FArray1D_double transvec)

void	protocols::toolbox::fit_centered_coords (Size natoms, FArray1_double const &weights, FArray2_double const &ref_coords, FArray2_double &coords, Matrix &R)

void	protocols::toolbox::oprod (const rvec a, const rvec b, rvec c)