ResidualDipolarCoupling.cc File Reference

Uses NMR RDC for scoring. More...

#include <core/scoring/ResidualDipolarCoupling.hh>
#include <core/conformation/Residue.hh>
#include <core/kinematics/FoldTree.hh>
#include <basic/options/option.hh>
#include <basic/datacache/BasicDataCache.hh>
#include <core/pose/datacache/CacheableDataType.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <basic/Tracer.hh>
#include <ObjexxFCL/format.hh>
#include <iostream>
#include <fstream>
#include <string>
#include <utility/excn/Exceptions.hh>
#include <utility/io/izstream.hh>
#include <utility/io/ozstream.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/rdc.OptionKeys.gen.hh>
#include <numeric/nls/lmmin.hh>
#include <utility/vector1.hh>
#include <numeric/random/random.fwd.hh>
#include <numeric/NumericTraits.hh>

Classes
struct	core::scoring::data_struct
struct	core::scoring::data_structDa
struct	core::scoring::data_structR
struct	core::scoring::data_structDaR

Namespaces
	core
	A class for defining atom parameters, known as atom_types.
	core::scoring

Macros
#define	XX   0
#define	YY   1
#define	ZZ   2
#define	ROTATE(a, i, j, k, l)

Typedefs
typedef core::Real	core::scoring::Tensor [3][3]
typedef core::Real	core::scoring::Tensor5 [5][5]
typedef core::Real	core::scoring::rvec [3]
typedef core::Real	core::scoring::matrix [3][3]
typedef core::Real	core::scoring::rvec5 [5]

Functions
Real	core::scoring::sqr (Real x)
void	core::scoring::store_RDC_in_pose (ResidualDipolarCouplingOP rdc_info, core::pose::Pose &pose)
ResidualDipolarCouplingCOP	core::scoring::retrieve_RDC_from_pose (core::pose::Pose const &pose)
ResidualDipolarCouplingOP	core::scoring::retrieve_RDC_from_pose (core::pose::Pose &pose)
std::ostream &	core::scoring::operator<< (std::ostream &out, RDC const &rdc)
std::ostream &	core::scoring::operator<< (std::ostream &out, ResidualDipolarCoupling const &rdc)
std::string	core::scoring::element_string (std::string atom)
int	core::scoring::m_inv_gen (Tensor5 m, int n, Tensor5 minv)
void	core::scoring::jacobi (Real a[5][5], Real d[], Real v[5][5], int *nrot)
void	core::scoring::jacobi3 (Real a[3][3], Real d[], Real v[3][3], int *nrot)
Real	core::scoring::iprod (const rvec a, const rvec b)
void	core::scoring::mvmul (matrix a, const rvec src, rvec dest)
int	core::scoring::compare_by_abs (const void *a, const void *b)
double	core::scoring::frdc (double r0, double r1, double r2, double rdcconst, const double *par)
double	core::scoring::frdcDa (double r0, double r1, double r2, double rdcconst, double const tensorDa, const double *par)
double	core::scoring::frdcR (double r0, double r1, double r2, double rdcconst, double const tensorR, const double *par)
double	core::scoring::frdcDaR (double r0, double r1, double r2, double rdcconst, double const tensorDa, double const tensorR, const double *par)
void	core::scoring::evaluaterdc (const double *par, int m_dat, const void *data, double *fvec, int *)
void	core::scoring::evaluaterdcDa (const double *par, int m_dat, const void *data, double *fvec, int *)
void	core::scoring::evaluaterdcR (const double *par, int m_dat, const void *data, double *fvec, int *)
void	core::scoring::evaluaterdcDaR (const double *par, int m_dat, const void *data, double *fvec, int *)

Variables
static basic::Tracer	tr ("core.scoring.ResidualDipolarCoupling")
	Utility headers. More...

Detailed Description

Uses NMR RDC for scoring.

Author

Oliver Lange

Srivatsan Raman

Nikolas Sgourakis

Lei Shi (nls and modifications to original code)

Macro Definition Documentation

#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);

Referenced by core::scoring::jacobi(), and core::scoring::jacobi3().

#define XX   0

Referenced by core::scoring::iprod(), core::scoring::mvmul(), core::optimization::BrentLineMinimization::operator()(), core::scoring::rna::RNA_FullAtomStackingEnergy::setup_for_minimizing(), core::scoring::geometric_solvation::GeometricSolEnergy::setup_for_minimizing(), core::scoring::methods::LK_PolarNonPolarEnergy::setup_for_minimizing(), core::scoring::elec::FA_ElecEnergy::setup_for_minimizing(), core::scoring::etable::BaseEtableEnergy< Derived >::setup_for_minimizing(), core::scoring::rna::StackElecEnergy::setup_for_minimizing(), core::scoring::etable::BaseEtableEnergy< Derived >::setup_for_minimizing_for_residue(), and core::scoring::etable::BaseEtableEnergy< Derived >::setup_for_minimizing_for_residue_pair().

#define YY   1

Referenced by core::scoring::iprod(), and core::scoring::mvmul().

#define ZZ   2

Referenced by core::scoring::iprod(), and core::scoring::mvmul().

Variable Documentation

basic::Tracer tr("core.scoring.ResidualDipolarCoupling")

static

Utility headers.