header file for ThreadingJob classes, part of August 2008 job distributor as planned at RosettaCon08. This file is responsible for three ideas: "inner" jobs, "outer" jobs (with which the job distributor works) and job container (currently just typdefed in the .fwd.hh) More...

#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)

Detailed Description

header file for ThreadingJob classes, part of August 2008 job distributor as planned at RosettaCon08. This file is responsible for three ideas: "inner" jobs, "outer" jobs (with which the job distributor works) and job container (currently just typdefed in the .fwd.hh)