core::scoring::nmr::rdc Namespace Reference

Classes
class	RDCData
class	RDCMultiSet
class	RDCSingle
class	RDCSingleSet
class	RDCTensor

Typedefs
typedef utility::pointer::shared_ptr < RDCData >	RDCDataOP
typedef utility::pointer::shared_ptr < RDCData const >	RDCDataCOP
typedef utility::pointer::weak_ptr < RDCData >	RDCDataAP
typedef utility::pointer::weak_ptr < RDCData const >	RDCDataCAP
typedef utility::pointer::shared_ptr < RDCMultiSet >	RDCMultiSetOP
typedef utility::pointer::shared_ptr < RDCMultiSet const >	RDCMultiSetCOP
typedef utility::pointer::weak_ptr < RDCMultiSet >	RDCMultiSetAP
typedef utility::pointer::weak_ptr < RDCMultiSet const >	RDCMultiSetCAP
typedef utility::pointer::shared_ptr < RDCSingle >	RDCSingleOP
typedef utility::pointer::shared_ptr < RDCSingle const >	RDCSingleCOP
typedef utility::pointer::weak_ptr < RDCSingle >	RDCSingleAP
typedef utility::pointer::weak_ptr < RDCSingle const >	RDCSingleCAP
typedef utility::pointer::shared_ptr < RDCSingleSet >	RDCSingleSetOP
typedef utility::pointer::shared_ptr < RDCSingleSet const >	RDCSingleSetCOP
typedef utility::pointer::weak_ptr < RDCSingleSet >	RDCSingleSetAP
typedef utility::pointer::weak_ptr < RDCSingleSet const >	RDCSingleSetCAP
typedef utility::pointer::shared_ptr < RDCTensor >	RDCTensorOP
typedef utility::pointer::shared_ptr < RDCTensor const >	RDCTensorCOP
typedef utility::pointer::weak_ptr < RDCTensor >	RDCTensorAP
typedef utility::pointer::weak_ptr < RDCTensor const >	RDCTensorCAP

Functions
Real	rdc_ideal_bond_length (RDC_TYPE const &type)
	returns the ideal bond length, in case this is not calculated from the pose More...
Real	rdc_scaling_factor_toNH (RDC_TYPE const &type)
	returns the ratio (gA * gB) / (r * r * r) relative to N-H this can be used to scale all RDC values relative to NH values in which case one general form of the RDC equation can be used Note that the 15N gyromagnetic ratio is treated as positive here. To account for the different signs of the NH and CH dipolar coupling constant, the option correct_sign can be used which changes the sign of Dconst. More...
Real	rdc_scaling_factor_toCH (RDC_TYPE const &type)
	returns the ratio (gA * gB) / (r * r * r) relative to CA-HA this can be used to scale all RDC values relative to CAHA values in which case one general form of the RDC equation can be used Note that the 15N gyromagnetic ratio is treated as positive here. To account for the different signs of the NH and CH dipolar coupling constant, the option correct_sign can be used which changes the sign of Dconst. More...
Real	rdc_D_const (RDC_TYPE const &type, bool correct_sign=false)
	returns the dipolar coupling constant for two spins A and B in Hz/Ang^3 D_const = -(gA * gB * mu0 * hbar)/(4 * pi * pi) where gA, gB are the gyromagnetic ratios of the two spins and mu0 and hbar are the vacuum permeability and Planck's constant / 2*pi From: Kramer et al. (2004) Concepts Magn Reson Part A, 21, 10-21 It is a common NMR convention to treat the sign of the 15N gyromagnetic ratio as positive. As a consequence the sign of dipolar couplings of experiments not involving 15N is flipped. To account for that, I flip here the sign of the CH and CC dipolar coupling constants. To turn this behavior off, the user can set the option "correct_sign" to true. More...
Real	rdc_D_max (RDC_TYPE const &type, bool correct_sign=false)
	returns the maximal dipolar coupling constant (in Hz) for a given spin pair A and B taking into account a predefined distance r between A and B D_max = -(gA * gB * mu0 * hbar)/(4 * pi * pi * r^3) where gA, gB are the gyromagnetic ratios of the two spins and mu0 and hbar are the vacuum permeability and Planck's constant / 2*pi From: Kramer et al. (2004) Concepts Magn Reson Part A, 21, 10-21 It is a common NMR convention to treat the sign of the 15N gyromagnetic ratio as positive. As a consequence the sign of dipolar couplings of experiments not involving 15N is flipped. To account for that, I flip here the sign of the CH and CC dipolar coupling constants. To turn this behavior off, the user can set the option "correct_sign" to true. More...
static basic::Tracer	TR ("core.scoring.nmr.rdc.RDCData")
static basic::Tracer	TR ("core.scoring.nmr.rdc.RDCMultiSet")
void	rdc_erf (Real const *par, int m_dat, void const *data, Real *fvec, int *)
	rdc error function used in the lmmin function More...
static basic::Tracer	TR ("core.scoring.nmr.rdc.RDCSingle")
bool	operator== (RDCSingle const &lhs, RDCSingle const &rhs)
bool	operator!= (RDCSingle const &lhs, RDCSingle const &rhs)
static basic::Tracer	TR ("core.scoring.nmr.rdc.RDCSingleSet")
static basic::Tracer	TR ("core.scoring.nmr.rdc.RDCTensor")

Typedef Documentation

typedef utility::pointer::weak_ptr< RDCData > core::scoring::nmr::rdc::RDCDataAP

typedef utility::pointer::weak_ptr< RDCData const > core::scoring::nmr::rdc::RDCDataCAP

typedef utility::pointer::shared_ptr< RDCData const > core::scoring::nmr::rdc::RDCDataCOP

typedef utility::pointer::shared_ptr< RDCData > core::scoring::nmr::rdc::RDCDataOP

typedef utility::pointer::weak_ptr< RDCMultiSet > core::scoring::nmr::rdc::RDCMultiSetAP

typedef utility::pointer::weak_ptr< RDCMultiSet const > core::scoring::nmr::rdc::RDCMultiSetCAP

typedef utility::pointer::shared_ptr< RDCMultiSet const > core::scoring::nmr::rdc::RDCMultiSetCOP

typedef utility::pointer::shared_ptr< RDCMultiSet > core::scoring::nmr::rdc::RDCMultiSetOP

typedef utility::pointer::weak_ptr< RDCSingle > core::scoring::nmr::rdc::RDCSingleAP

typedef utility::pointer::weak_ptr< RDCSingle const > core::scoring::nmr::rdc::RDCSingleCAP

typedef utility::pointer::shared_ptr< RDCSingle const > core::scoring::nmr::rdc::RDCSingleCOP

typedef utility::pointer::shared_ptr< RDCSingle > core::scoring::nmr::rdc::RDCSingleOP

typedef utility::pointer::weak_ptr< RDCSingleSet > core::scoring::nmr::rdc::RDCSingleSetAP

typedef utility::pointer::weak_ptr< RDCSingleSet const > core::scoring::nmr::rdc::RDCSingleSetCAP

typedef utility::pointer::shared_ptr< RDCSingleSet const > core::scoring::nmr::rdc::RDCSingleSetCOP

typedef utility::pointer::shared_ptr< RDCSingleSet > core::scoring::nmr::rdc::RDCSingleSetOP

typedef utility::pointer::weak_ptr< RDCTensor > core::scoring::nmr::rdc::RDCTensorAP

typedef utility::pointer::weak_ptr< RDCTensor const > core::scoring::nmr::rdc::RDCTensorCAP

typedef utility::pointer::shared_ptr< RDCTensor const > core::scoring::nmr::rdc::RDCTensorCOP

typedef utility::pointer::shared_ptr< RDCTensor > core::scoring::nmr::rdc::RDCTensorOP

Function Documentation

bool core::scoring::nmr::rdc::operator!=	(	RDCSingle const &	lhs,
		RDCSingle const &	rhs
	)

bool core::scoring::nmr::rdc::operator==	(	RDCSingle const &	lhs,
		RDCSingle const &	rhs
	)

References core::scoring::nmr::rdc::RDCSingle::spinsAB_.

Real core::scoring::nmr::rdc::rdc_D_const ( RDC_TYPE const &  type, bool  correct_sign = false  )

inline

returns the dipolar coupling constant for two spins A and B in Hz/Ang^3 D_const = -(gA * gB * mu0 * hbar)/(4 * pi * pi) where gA, gB are the gyromagnetic ratios of the two spins and mu0 and hbar are the vacuum permeability and Planck's constant / 2*pi From: Kramer et al. (2004) Concepts Magn Reson Part A, 21, 10-21 It is a common NMR convention to treat the sign of the 15N gyromagnetic ratio as positive. As a consequence the sign of dipolar couplings of experiments not involving 15N is flipped. To account for that, I flip here the sign of the CH and CC dipolar coupling constants. To turn this behavior off, the user can set the option "correct_sign" to true.

References core::scoring::nmr::RDC_TYPE_CACB, core::scoring::nmr::RDC_TYPE_CACO, core::scoring::nmr::RDC_TYPE_CAHA, core::scoring::nmr::RDC_TYPE_CAHN, core::scoring::nmr::RDC_TYPE_COHN, core::scoring::nmr::RDC_TYPE_NCA, core::scoring::nmr::RDC_TYPE_NCO, and core::scoring::nmr::RDC_TYPE_NH.

Real core::scoring::nmr::rdc::rdc_D_max ( RDC_TYPE const &  type, bool  correct_sign = false  )

inline

returns the maximal dipolar coupling constant (in Hz) for a given spin pair A and B taking into account a predefined distance r between A and B D_max = -(gA * gB * mu0 * hbar)/(4 * pi * pi * r^3) where gA, gB are the gyromagnetic ratios of the two spins and mu0 and hbar are the vacuum permeability and Planck's constant / 2*pi From: Kramer et al. (2004) Concepts Magn Reson Part A, 21, 10-21 It is a common NMR convention to treat the sign of the 15N gyromagnetic ratio as positive. As a consequence the sign of dipolar couplings of experiments not involving 15N is flipped. To account for that, I flip here the sign of the CH and CC dipolar coupling constants. To turn this behavior off, the user can set the option "correct_sign" to true.

References core::scoring::nmr::RDC_TYPE_CACB, core::scoring::nmr::RDC_TYPE_CACO, core::scoring::nmr::RDC_TYPE_CAHA, core::scoring::nmr::RDC_TYPE_CAHN, core::scoring::nmr::RDC_TYPE_COHN, core::scoring::nmr::RDC_TYPE_NCA, core::scoring::nmr::RDC_TYPE_NCO, and core::scoring::nmr::RDC_TYPE_NH.

Referenced by protocols::nmr::ParaNMRScoreMover::add_rdc_scores_to_scorefile(), core::scoring::nmr::rdc::RDCMultiSet::basic_rdc_equation(), core::scoring::nmr::rdc::RDCMultiSet::compute_rdc_values_and_score_from_tensor(), core::scoring::nmr::rdc::RDCData::init_rdc_data_from_file(), rdc_erf(), core::scoring::nmr::rdc::RDCMultiSet::set_atom_derivatives(), protocols::nmr::rdc::RDCEnergy::show_additional_info(), core::scoring::nmr::rdc::RDCMultiSet::solve_tensor_and_compute_score_by_nls(), and core::scoring::nmr::rdc::RDCMultiSet::update_matrix_A().

void core::scoring::nmr::rdc::rdc_erf	(	Real const *	par,
		int	m_dat,
		void const *	data,
		Real *	fvec,
		int *
	)

rdc error function used in the lmmin function

• par is an array of fit parameters [alpha, beta, gamma, (Da, R)]
• data is a pointer to the the RDCMultiSet object i.e. to all data needed for RDC calculation and NLS fitting
• fvc is an array holding the residuals of the fit calculation

References core::scoring::nmr::rdc::RDCMultiSet::computation_type_, core::scoring::nmr::rdc::RDCMultiSet::correct_sign_, core::scoring::nmr::rdc::RDCMultiSet::frdc(), core::scoring::nmr::rdc::RDCMultiSet::frdc_Da(), core::scoring::nmr::rdc::RDCMultiSet::frdc_Da_R(), core::scoring::nmr::rdc::RDCMultiSet::frdc_R(), core::scoring::nmr::rdc::RDCMultiSet::NLS, core::scoring::nmr::rdc::RDCMultiSet::NLSDA, core::scoring::nmr::rdc::RDCMultiSet::NLSDAR, core::scoring::nmr::rdc::RDCMultiSet::NLSR, core::scoring::nmr::rdc::RDCMultiSet::norm_type_, core::scoring::nmr::NORM_TYPE_CH, core::scoring::nmr::NORM_TYPE_NH, core::scoring::nmr::NORM_TYPE_NONE, core::scoring::nmr::rdc::RDCMultiSet::number_experiments_, rdc_D_max(), rdc_scaling_factor_toCH(), rdc_scaling_factor_toNH(), core::scoring::nmr::rdc::RDCMultiSet::rdc_single_weights_, core::scoring::nmr::rdc::RDCMultiSet::rdc_singleset_vec_, core::scoring::nmr::rdc::RDCMultiSet::rdc_values_, core::scoring::nmr::rotation_matrix_from_euler_angles(), core::scoring::nmr::rdc::RDCMultiSet::spin_coordinates_, core::scoring::nmr::rdc::RDCMultiSet::tensor_, and core::scoring::nmr::rdc::RDCMultiSet::total_number_rdc_.

Real core::scoring::nmr::rdc::rdc_ideal_bond_length ( RDC_TYPE const &  type )

inline

returns the ideal bond length, in case this is not calculated from the pose

References core::scoring::nmr::RDC_TYPE_CACB, core::scoring::nmr::RDC_TYPE_CACO, core::scoring::nmr::RDC_TYPE_CAHA, core::scoring::nmr::RDC_TYPE_CAHN, core::scoring::nmr::RDC_TYPE_COHN, core::scoring::nmr::RDC_TYPE_NCA, core::scoring::nmr::RDC_TYPE_NCO, and core::scoring::nmr::RDC_TYPE_NH.

Real core::scoring::nmr::rdc::rdc_scaling_factor_toCH ( RDC_TYPE const &  type )

inline

returns the ratio (gA * gB) / (r * r * r) relative to CA-HA this can be used to scale all RDC values relative to CAHA values in which case one general form of the RDC equation can be used Note that the 15N gyromagnetic ratio is treated as positive here. To account for the different signs of the NH and CH dipolar coupling constant, the option correct_sign can be used which changes the sign of Dconst.

References core::scoring::nmr::RDC_TYPE_CACB, core::scoring::nmr::RDC_TYPE_CACO, core::scoring::nmr::RDC_TYPE_CAHA, core::scoring::nmr::RDC_TYPE_CAHN, core::scoring::nmr::RDC_TYPE_COHN, core::scoring::nmr::RDC_TYPE_NCA, core::scoring::nmr::RDC_TYPE_NCO, and core::scoring::nmr::RDC_TYPE_NH.

Referenced by protocols::nmr::ParaNMRScoreMover::add_rdc_scores_to_scorefile(), core::scoring::nmr::rdc::RDCMultiSet::compute_rdc_values_and_score_from_tensor(), core::scoring::nmr::rdc::RDCMultiSet::init_from_rdc_filedata(), rdc_erf(), core::scoring::nmr::rdc::RDCMultiSet::set_atom_derivatives(), protocols::nmr::rdc::RDCEnergy::show_additional_info(), core::scoring::nmr::rdc::RDCMultiSet::solve_tensor_and_compute_score_by_nls(), and core::scoring::nmr::rdc::RDCMultiSet::update_matrix_A().

Real core::scoring::nmr::rdc::rdc_scaling_factor_toNH ( RDC_TYPE const &  type )

inline

returns the ratio (gA * gB) / (r * r * r) relative to N-H this can be used to scale all RDC values relative to NH values in which case one general form of the RDC equation can be used Note that the 15N gyromagnetic ratio is treated as positive here. To account for the different signs of the NH and CH dipolar coupling constant, the option correct_sign can be used which changes the sign of Dconst.

References core::scoring::nmr::RDC_TYPE_CACB, core::scoring::nmr::RDC_TYPE_CACO, core::scoring::nmr::RDC_TYPE_CAHA, core::scoring::nmr::RDC_TYPE_CAHN, core::scoring::nmr::RDC_TYPE_COHN, core::scoring::nmr::RDC_TYPE_NCA, core::scoring::nmr::RDC_TYPE_NCO, and core::scoring::nmr::RDC_TYPE_NH.

Referenced by protocols::nmr::ParaNMRScoreMover::add_rdc_scores_to_scorefile(), core::scoring::nmr::rdc::RDCMultiSet::compute_rdc_values_and_score_from_tensor(), core::scoring::nmr::rdc::RDCMultiSet::init_from_rdc_filedata(), rdc_erf(), core::scoring::nmr::rdc::RDCMultiSet::set_atom_derivatives(), protocols::nmr::rdc::RDCEnergy::show_additional_info(), core::scoring::nmr::rdc::RDCMultiSet::solve_tensor_and_compute_score_by_nls(), and core::scoring::nmr::rdc::RDCMultiSet::update_matrix_A().

static basic::Tracer core::scoring::nmr::rdc::TR ( "core.scoring.nmr.rdc.RDCTensor"  )

static

static basic::Tracer core::scoring::nmr::rdc::TR ( "core.scoring.nmr.rdc.RDCSingle"  )

static

static basic::Tracer core::scoring::nmr::rdc::TR ( "core.scoring.nmr.rdc.RDCSingleSet"  )

static

static basic::Tracer core::scoring::nmr::rdc::TR ( "core.scoring.nmr.rdc.RDCData"  )

static

Referenced by core::scoring::nmr::rdc::RDCSingleSet::init_from_rdc_filedata(), core::scoring::nmr::rdc::RDCData::init_rdc_data_from_file(), core::scoring::nmr::rdc::RDCSingle::RDCSingle(), core::scoring::nmr::rdc::RDCTensor::reorder_tensor(), core::scoring::nmr::rdc::RDCMultiSet::solve_tensor_and_compute_score_by_nls(), and core::scoring::nmr::rdc::RDCMultiSet::solve_tensor_and_compute_score_by_svd().

static basic::Tracer core::scoring::nmr::rdc::TR ( "core.scoring.nmr.rdc.RDCMultiSet"  )

static