RDCTest.cc File Reference

#include <core/types.hh>
#include <devel/init.hh>
#include <core/conformation/Residue.hh>
#include <core/pose/Pose.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <basic/Tracer.hh>
#include <core/scoring/ResidualDipolarCoupling.hh>
#include <basic/options/option.hh>
#include <basic/options/option_macros.hh>
#include <basic/options/keys/OptionKeys.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/rdc.OptionKeys.gen.hh>
#include <utility/vector1.hh>
#include <utility/io/izstream.hh>
#include <core/import_pose/import_pose.hh>
#include <utility/excn/Exceptions.hh>

Macros
#define	XX   0
#define	YY   1
#define	ZZ   2
#define	ROTATE(a, i, j, k, l)   g=a[i][j];h=a[k][l];a[i][j]=g-s*(h+g*tau); a[k][l]=h+s*(g-h*tau);

Functions
void	evaluate_score (core::pose::PoseOP, utility::vector1< core::scoring::RDC > &)
void	read_RDC_file (std::string const &, utility::vector1< core::scoring::RDC > &, Size)
Real	referenceRDC (core::pose::PoseOP p)
int	m_inv_gen (Real m[5][5], int n, Real minv[5][5])
void	jacobi (Real a[5][5], Real d[], Real v[5][5], int *nrot)
void	register_options ()
ResidualDipolarCouplingOP	filter_rdcs (Size first_pos, Size last_pos, ResidualDipolarCoupling const &orig_rdcs)
int	main (int argc, char *argv[])
Real	sqr (Real x)
Real	iprod (const Real a[3], const Real b[3])
void	mvmul (Real a[3][3], const Real src[3], Real dest[3])

Variables
static basic::Tracer	trace ("RDCTest")

Macro Definition Documentation

ROTATE

#define ROTATE	(		a,
			i,
			j,
			k,
			l
	)		g=a[i][j];h=a[k][l];a[i][j]=g-s*(h+g*tau); a[k][l]=h+s*(g-h*tau);

XX

#define XX   0

YY

#define YY   1

ZZ

#define ZZ   2

Function Documentation

evaluate_score()

void evaluate_score	(	core::pose::PoseOP	pose,
		utility::vector1< core::scoring::RDC > &	data
	)

References basic::options::OptionKeys::rdc::correct_NH_length, data, basic::Tracer::Debug, create_a3b_hbs::i, iprod(), create_a3b_hbs::j, m_inv_gen(), mvmul(), basic::options::option, beta_nonlocal::pose, docking::Q, create_a3b_hbs::r, basic::options::OptionKeys::motifs::r2, basic::options::OptionKeys::rdc::reduced_couplings, sqr(), trace, basic::Tracer::Trace, and basic::options::OptionKeys::sc::weight.

filter_rdcs()

ResidualDipolarCouplingOP filter_rdcs	(	Size	first_pos,
		Size	last_pos,
		ResidualDipolarCoupling const &	orig_rdcs
	)

Referenced by main().

iprod()

Real iprod ( const Real  a[3], const Real  b[3]  )

inline

References a, compute_difference::b, XX, YY, and ZZ.

Referenced by evaluate_score().

jacobi()

void jacobi	(	Real	a[5][5],
		Real	d[],
		Real	v[5][5],
		int *	nrot
	)

References a, compute_difference::b, kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, CREATE_EXCEPTION, g(), h, create_a3b_hbs::i, create_a3b_hbs::j, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, kmeans_bb_dependent_rotlib::nrot, ROTATE, docking::s, sm, predPRE::t, kmeans_adaptive_kernel_density_bb_dependent_rotlib::v, and predPRE::z.

Referenced by m_inv_gen().

m_inv_gen()

int m_inv_gen	(	Real	m[5][5],
		int	n,
		Real	minv[5][5]
	)

References test.T009_Exceptions::e, create_a3b_hbs::i, create_a3b_hbs::j, jacobi(), create_a3b_hbs::k, kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, kmeans_bb_dependent_rotlib::nrot, docking::s, loops_kic::tol, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

Referenced by evaluate_score().

main()

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

References argv, utility::io::oc::cout, test.T009_Exceptions::e, filter_rdcs(), basic::init(), and register_options().

mvmul()

void mvmul ( Real  a[3][3], const Real  src[3], Real  dest[3]  )

inline

References a, solution_counts::dest, XX, YY, and ZZ.

Referenced by evaluate_score().

read_RDC_file()

void read_RDC_file	(	std::string const &	filename,
		utility::vector1< core::scoring::RDC > &	data_sink,
		Size	exp_id
	)

References CREATE_EXCEPTION, basic::Tracer::Debug, basic::Tracer::Error, lactamize::filename, getline(), basic::Tracer::Info, line, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, erraser_analysis::res1, erraser_analysis::res2, trace, and basic::options::OptionKeys::sc::weight.

referenceRDC()

Real referenceRDC

(

core::pose::PoseOP

p

)

References utility::io::oc::cerr, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, and create_a3b_hbs::r.

register_options()

void register_options

(

)

References rdc::correct_NH_length(), in::file::native(), OPT, in::file::rdc(), rdc::reduced_couplings(), and in::file::s().

Referenced by main().

sqr()

Real sqr ( Real  x )

inline

References x.

Referenced by clash(), contacts(), numeric::expression_parser::DivideExpression::differentiate(), evaluate_score(), TCDock::get_contacts_by_component(), TCDock::precompute_intra(), numeric::linear_algebra::qzval(), sicdock_thread_num(), and MatchSet::sigmoidish_neighbor().

Variable Documentation

trace

basic::Tracer trace("RDCTest") ( "RDCTest"  )

static

Referenced by evaluate_score(), msd_base_doublet(), and read_RDC_file().