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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 
)
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 *   
)
Real core::scoring::nmr::rdc::rdc_ideal_bond_length ( RDC_TYPE const &  type)
inline
Real core::scoring::nmr::rdc::rdc_scaling_factor_toCH ( RDC_TYPE const &  type)
inline
Real core::scoring::nmr::rdc::rdc_scaling_factor_toNH ( RDC_TYPE const &  type)
inline
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
static basic::Tracer core::scoring::nmr::rdc::TR ( "core.scoring.nmr.rdc.RDCMultiSet"  )
static