ResidualDipolarCouplings are mainly handled by this class related classed: RDC — a single line in an RDC file - representing a single dipolar coupling ResidualDipolarCouplingEnergy – an energy method which triggers computations handled by this class. More...

#include <ResidualDipolarCoupling.hh>

Inheritance diagram for core::scoring::ResidualDipolarCoupling:

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Public Types
typedef core::Real	Real

typedef core::Size	Size

typedef utility::vector1 < core::scoring::RDC >	RDC_lines

typedef utility::fixedsizearray0 < core::Real, 3 >	rvec

typedef utility::fixedsizearray0< rvec, 3 >	Tensor

typedef utility::fixedsizearray0 < core::Real, 5 >	rvec5

typedef utility::fixedsizearray0 < rvec5, 5 >	Tensor5

Public Member Functions
	ResidualDipolarCoupling (std::string const &filename="")
	standard c'stor – will access option -in:file:rdc to read RDC data More...

	ResidualDipolarCoupling (RDC_lines data_in)
	alternative c'stor if you have a list of RDC lines More...

	ResidualDipolarCoupling (ResidualDipolarCoupling const &other)

ResidualDipolarCoupling &	operator= (ResidualDipolarCoupling const &other)

	~ResidualDipolarCoupling () override

basic::datacache::CacheableDataOP	clone () const override

core::Real	compute_dipscore (core::pose::Pose const &pose)
	compute dipolar score for given pose will set alignment tensor and force-fields in RDC More...

core::Real	compute_dipscore_nls (core::pose::Pose const &pose)
	fit rdc using RDC data More...

core::Real	compute_dipscore_nlsDa (core::pose::Pose const &pose, utility::vector1< Real > const &tensorDa)

core::Real	compute_dipscore_nlsR (core::pose::Pose const &pose, utility::vector1< Real > const &tensorR)

core::Real	compute_dipscore_nlsDaR (core::pose::Pose const &pose, utility::vector1< Real > const &tensorDa, utility::vector1< Real > const &tensorR)

core::Real	compute_dipscore_nls (core::pose::Pose const &pose, utility::vector1< Real > const &tensorDa, utility::vector1< Real > const &tensorR)

Real	iterate_tensor_weights (core::pose::Pose const &pose, core::Real sigma2, core::Real tolerance, bool reset)

void	show (std::ostream &) const

void	read_RDC_file ()
	read RDC data from file More...

void	preprocess_data ()
	fill internal buffers... call always when RDC lines change. More...

void	release_buffers ()
	free memory of buffers More...

void	reserve_buffers ()
	get memory for buffers More...

RDC_lines const &	get_RDC_data () const
	get the raw RDC data More...

Real	Q () const
	return the Q value ( cornilescu ) — only valid after compute_dipscore More...

Real	R () const
	return the R value ( M Clore ) — only valid after compute_dipscore More...

core::Size	get_n_alignments () const

utility::vector0< Tensor > &	tensor ()
	return tensor of certain experiment... exp_id starts at 1 More...

core::Real	get_al_tensor_trace (core::Size ex) const

core::Real	get_al_tensor_max_z (core::Size ex) const

void	compute_tensor_stats ()

void	show_tensor_stats (std::ostream &, core::Size ex) const

void	show_tensor_matrix (std::ostream &, core::Size ex) const

void	show_rdc_values (std::ostream &, core::Size ex) const

void	show_tensor_stats_nls (std::ostream &, core::Size ex, const core::Real *par) const

void	do_correct_NH (utility::vector1< core::scoring::RDC >::const_iterator it, numeric::xyzVector< Real > &r, core::Real &r2, core::Real &invr)

Private Member Functions
void	read_RDC_file (Size nex, std::string const &filename)
	read RDC data from file More...

RDC_lines &	get_RDC_data_ref ()
	non-const reference to RDC data private use only. More...

Private Attributes
RDC_lines	All_RDC_lines_
	some internal buffers in More...

utility::vector0< rvec >	EV_

utility::vector0< rvec5 >	D_

utility::vector0< rvec5 >	rhs_

utility::vector0< Tensor >	S_

utility::vector0< Tensor5 >	T_

core::Size	nex_

core::Size	nrows_

core::Real	R_

core::Real	rmsd_

utility::vector0< Tensor >	SD_

utility::vector0< Tensor >	EIG_

utility::vector0< core::Real >	FA_

utility::vector0< core::Real >	trace_

utility::vector0< core::Real >	maxz_

utility::vector0< core::Real >	r0_

utility::vector0< core::Real >	r1_

utility::vector0< core::Real >	r2_

utility::vector0< core::Real >	exprdc_

utility::vector0< core::Real >	rdcconst_

utility::vector0< core::Real >	rdcweight_

utility::vector0< core::Size >	lenex_

Static Private Attributes
static Real const	COMMON_DENOMINATOR = 36.5089/1.041/1.041/1.041

Detailed Description

ResidualDipolarCouplings are mainly handled by this class related classed: RDC — a single line in an RDC file - representing a single dipolar coupling ResidualDipolarCouplingEnergy – an energy method which triggers computations handled by this class.

Member Typedef Documentation

typedef utility::vector1< core::scoring::RDC > core::scoring::ResidualDipolarCoupling::RDC_lines

typedef core::Real core::scoring::ResidualDipolarCoupling::Real

typedef utility::fixedsizearray0< core::Real, 3 > core::scoring::ResidualDipolarCoupling::rvec

typedef utility::fixedsizearray0< core::Real, 5 > core::scoring::ResidualDipolarCoupling::rvec5

typedef core::Size core::scoring::ResidualDipolarCoupling::Size

typedef utility::fixedsizearray0< rvec, 3 > core::scoring::ResidualDipolarCoupling::Tensor

typedef utility::fixedsizearray0< rvec5, 5 > core::scoring::ResidualDipolarCoupling::Tensor5

Constructor & Destructor Documentation

core::scoring::ResidualDipolarCoupling::ResidualDipolarCoupling ( std::string const & filename = "" )

inline

standard c'stor – will access option -in:file:rdc to read RDC data

References protocols::abinitio::filename(), preprocess_data(), read_RDC_file(), release_buffers(), and reserve_buffers().

core::scoring::ResidualDipolarCoupling::ResidualDipolarCoupling ( RDC_lines data_in )

inline

alternative c'stor if you have a list of RDC lines

References preprocess_data(), and reserve_buffers().

core::scoring::ResidualDipolarCoupling::ResidualDipolarCoupling ( ResidualDipolarCoupling const & other )

References All_RDC_lines_, preprocess_data(), and reserve_buffers().

core::scoring::ResidualDipolarCoupling::~ResidualDipolarCoupling ( )

override

References release_buffers().

Member Function Documentation

basic::datacache::CacheableDataOP core::scoring::ResidualDipolarCoupling::clone ( ) const

inlineoverride

Real core::scoring::ResidualDipolarCoupling::compute_dipscore ( core::pose::Pose const & pose )

compute dipolar score for given pose will set alignment tensor and force-fields in RDC

References All_RDC_lines_, core::scoring::RDC::atom1(), core::scoring::RDC::atom2(), COMMON_DENOMINATOR, compute_tensor_stats(), D_, core::scoring::RDC::Dconst(), core::pose::Pose::dump_pdb(), core::scoring::RDC::fij_, protocols::abinitio::filename(), core::pose::Pose::fold_tree(), core::scoring::m_inv_gen(), protocols::mean_field::min(), nex_, nrows_, core::conformation::membrane::out, Q(), protocols::hybridization::r2, R_, core::scoring::rdc, core::scoring::RDC::RDC_TYPE_NH, core::scoring::RDC::res1(), core::scoring::RDC::res2(), core::pose::Pose::residue(), rhs_, rmsd_, S_, show_rdc_values(), show_tensor_matrix(), show_tensor_stats(), core::pose::Pose::size(), core::scoring::sqr(), T_, core::scoring::tr(), and protocols::kinmatch::xyz().

Referenced by core::energy_methods::ResidualDipolarCouplingEnergy::eval_dipolar(), and iterate_tensor_weights().

Real core::scoring::ResidualDipolarCoupling::compute_dipscore_nls ( core::pose::Pose const & pose )

fit rdc using RDC data

Referenced by compute_dipscore_nlsDa(), compute_dipscore_nlsDaR(), compute_dipscore_nlsR(), and core::energy_methods::ResidualDipolarCouplingEnergy::eval_dipolar().

Real core::scoring::ResidualDipolarCoupling::compute_dipscore_nls	(	core::pose::Pose const &	pose,
		utility::vector1< Real > const &	tensorDa,
		utility::vector1< Real > const &	tensorR
	)

References core::pose::motif::a(), All_RDC_lines_, core::scoring::RDC::atom1(), core::scoring::RDC::atom2(), protocols::match::upstream::b, core::pack::dunbrack::c, COMMON_DENOMINATOR, core::scoring::RDC::Dconst(), do_correct_NH(), core::scoring::evaluaterdc(), exprdc_, core::scoring::RDC::fij_, protocols::abinitio::filename(), core::pose::Pose::fold_tree(), core::scoring::frdc(), core::scoring::frdcDa(), core::scoring::frdcDaR(), core::scoring::frdcR(), core::scoring::RDC::Jdipolar(), lenex_, protocols::mean_field::max(), protocols::mean_field::min(), nex_, NLS, NLSDA, NLSDAR, NLSR, nrows_, core::conformation::membrane::out, Q(), r0_, r1_, protocols::hybridization::r2, r2_, R_, core::scoring::rdc, rdcconst_, rdcweight_, core::scoring::RDC::res1(), core::scoring::RDC::res2(), core::pose::Pose::residue(), rmsd_, show_rdc_values(), core::pose::Pose::size(), core::scoring::sqr(), core::scoring::tr(), and protocols::kinmatch::xyz().

Real core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsDa	(	core::pose::Pose const &	pose,
		utility::vector1< Real > const &	tensorDa
	)

References compute_dipscore_nls().

Referenced by core::energy_methods::ResidualDipolarCouplingEnergy::eval_dipolar().

Real core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsDaR	(	core::pose::Pose const &	pose,
		utility::vector1< Real > const &	tensorDa,
		utility::vector1< Real > const &	tensorR
	)

References compute_dipscore_nls().

Referenced by core::energy_methods::ResidualDipolarCouplingEnergy::eval_dipolar().

Real core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsR	(	core::pose::Pose const &	pose,
		utility::vector1< Real > const &	tensorR
	)

References compute_dipscore_nls().

Referenced by core::energy_methods::ResidualDipolarCouplingEnergy::eval_dipolar().

void core::scoring::ResidualDipolarCoupling::compute_tensor_stats ( )

References core::scoring::compare_by_abs(), EIG_, EV_, core::scoring::jacobi3(), maxz_, nex_, S_, SD_, and trace_.

Referenced by compute_dipscore().

void core::scoring::ResidualDipolarCoupling::do_correct_NH	(	utility::vector1< core::scoring::RDC >::const_iterator	it,
		numeric::xyzVector< Real > &	r,
		core::Real &	r2,
		core::Real &	invr
	)

References core::scoring::RDC::RDC_TYPE_CC, core::scoring::RDC::RDC_TYPE_CH, core::scoring::RDC::RDC_TYPE_CHN, core::scoring::RDC::RDC_TYPE_NC, core::scoring::RDC::RDC_TYPE_NCA, core::scoring::RDC::RDC_TYPE_NH, and core::scoring::tr().

Referenced by compute_dipscore_nls().

core::Real core::scoring::ResidualDipolarCoupling::get_al_tensor_max_z ( core::Size ex ) const

inline

References maxz_.

core::Real core::scoring::ResidualDipolarCoupling::get_al_tensor_trace ( core::Size ex ) const

inline

References trace_.

core::Size core::scoring::ResidualDipolarCoupling::get_n_alignments ( ) const

inline

References nex_.

RDC_lines const& core::scoring::ResidualDipolarCoupling::get_RDC_data ( ) const

inline

get the raw RDC data

References All_RDC_lines_.

Referenced by core::energy_methods::ResidualDipolarCouplingEnergy::eval_atom_derivative(), core::energy_methods::ResidualDipolarCouplingEnergy::eval_dipolar(), protocols::simple_filters::SelectRDC_Evaluator::init_rdcs(), protocols::scoring::ResidualDipolarCouplingRigidSegments::read_RDCs_from_cmdline(), and core::energy_methods::ResidualDipolarCouplingEnergy::setup_for_minimizing().

RDC_lines& core::scoring::ResidualDipolarCoupling::get_RDC_data_ref ( )

private

non-const reference to RDC data private use only.

Real core::scoring::ResidualDipolarCoupling::iterate_tensor_weights	(	core::pose::Pose const &	pose,
		core::Real	sigma2,
		core::Real	tolerance,
		bool	reset
	)