superimpose.cc File Reference

#include <protocols/toolbox/superimpose.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>

Go to the source code of this file.

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

Constant Groups
	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 basic::Tracer	protocols::toolbox::tr ("protocols.evaluation.PCA", basic::t_info)
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::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)

Macro Definition Documentation

#define DIM   3

#define dump_matrix( nr, a ) {}

some low-level helper routines

Definition at line 189 of file superimpose.cc.

Referenced by protocols::toolbox::add_vec(), protocols::toolbox::calc_fit_R(), and protocols::toolbox::rotate_vec().

#define DIM6   6

Definition at line 410 of file superimpose.cc.

#define DIM6   6

Definition at line 410 of file superimpose.cc.

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

Value:

g=a[i][j];h=a[k][l];a[i][j]=g-s*(h+g*tau);  \
  a[k][l]=h+s*(g-h*tau);

Definition at line 408 of file superimpose.cc.

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

Value:

g=a[i][j];h=a[k][l];a[i][j]=g-s*(h+g*tau);  \
  a[k][l]=h+s*(g-h*tau);

Definition at line 408 of file superimpose.cc.

#define XX   0

Definition at line 411 of file superimpose.cc.

#define XX   0

Definition at line 411 of file superimpose.cc.

#define YY   1

Definition at line 412 of file superimpose.cc.

#define YY   1

Definition at line 412 of file superimpose.cc.

#define ZZ   2

Definition at line 413 of file superimpose.cc.

#define ZZ   2

Definition at line 413 of file superimpose.cc.