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core::scoring::nmr Namespace Reference

Namespaces

 pcs
 
 pre
 
 rdc
 

Classes

class  NMRDataFactory
 
class  NMRDummySpinlabelAtom
 Derived class of VoxelGridPoint to store the 3D coordinates of one atom of a NMRDummySpinlabelConformer. NMRDummySpinlabelAtom is also a member of NMRDummySpinlabelConformer and holds a const pointer to its outer class. More...
 
class  NMRDummySpinlabelConformer
 Class that stores information about one dummy spinlabel conformer (e.g. atom names and xyz coordinates, and whether it clashes with neighboring amino acid residues or not). A vector of NMRDummySpinlabelConformer objects is member of class NMRDummySpinlabelEnsemble. More...
 
class  NMRDummySpinlabelEnsemble
 Class that represents a "dummy" spinlabel ensemble. It holds information about each individual conformer member (atom coordinates, number of observations) and data to score those based on atom clashes with the neighborhood of the ensemble. To speed up the clash score calculation, this class holds also an object of type NMRDummySpinlabelVoxelGrid which gets filled with constant pointers to NMRDummySpinlabelAtoms. More...
 
class  NMRDummySpinlabelVoxelGrid
 Derived class of VoxelGrid to create a grid of VoxelGridPoint objects. More...
 
class  NMRGridSearch
 
class  NMRSpinlabel
 
class  NMRTensor
 
class  VoxelGridPoint
 Base class of a point object from which the voxel grid is created. More...
 
class  VoxelGridPoint_AA
 Derived class of VoxelGridPoint to store the 3D coordinates of one atom of an amino acid residue. In addition, it holds a const pointer to the residue object to which it refers to. More...
 

Typedefs

typedef
utility::pointer::shared_ptr
< NMRDataFactory
NMRDataFactoryOP
 
typedef
utility::pointer::shared_ptr
< NMRDataFactory const > 
NMRDataFactoryCOP
 
typedef
utility::pointer::shared_ptr
< NMRDummySpinlabelConformer
NMRDummySpinlabelConformerOP
 
typedef
utility::pointer::shared_ptr
< NMRDummySpinlabelConformer
const > 
NMRDummySpinlabelConformerCOP
 
typedef
utility::pointer::weak_ptr
< NMRDummySpinlabelConformer
NMRDummySpinlabelConformerAP
 
typedef
utility::pointer::weak_ptr
< NMRDummySpinlabelConformer
const > 
NMRDummySpinlabelConformerCAP
 
typedef
utility::pointer::shared_ptr
< NMRDummySpinlabelEnsemble
NMRDummySpinlabelEnsembleOP
 
typedef
utility::pointer::shared_ptr
< NMRDummySpinlabelEnsemble
const > 
NMRDummySpinlabelEnsembleCOP
 
typedef
utility::pointer::weak_ptr
< NMRDummySpinlabelEnsemble
NMRDummySpinlabelEnsembleAP
 
typedef
utility::pointer::weak_ptr
< NMRDummySpinlabelEnsemble
const > 
NMRDummySpinlabelEnsembleCAP
 
typedef boost::unordered_map
< std::string, Vector
AtomNamePosMap
 
typedef boost::unordered_map
< std::string,
NMRDummySpinlabelAtom
NMRDummySpinlabelAtomTable
 
typedef boost::unordered_map
< std::string,
NMRDummySpinlabelAtom >
::iterator 
NMRDummySpinlabelAtomTableIter
 
typedef boost::unordered_map
< std::string,
NMRDummySpinlabelAtom >
::const_iterator 
NMRDummySpinlabelAtomTableCOIter
 
typedef std::pair< std::string,
std::string > 
AtomPairKey
 
typedef
core::conformation::ResidueOP 
ResidueOP
 
typedef
core::conformation::ResidueCOP 
ResidueCOP
 
typedef
utility::pointer::shared_ptr
< VoxelGridPoint
VoxelGridPointOP
 
typedef
utility::pointer::shared_ptr
< VoxelGridPoint const > 
VoxelGridPointCOP
 
typedef
utility::pointer::weak_ptr
< VoxelGridPoint
VoxelGridPointAP
 
typedef
utility::pointer::weak_ptr
< VoxelGridPoint const > 
VoxelGridPointCAP
 
typedef
utility::pointer::shared_ptr
< NMRDummySpinlabelAtom
NMRDummySpinlabelAtomOP
 
typedef
utility::pointer::shared_ptr
< NMRDummySpinlabelAtom const > 
NMRDummySpinlabelAtomCOP
 
typedef
utility::pointer::weak_ptr
< NMRDummySpinlabelAtom
NMRDummySpinlabelAtomAP
 
typedef
utility::pointer::weak_ptr
< NMRDummySpinlabelAtom const > 
NMRDummySpinlabelAtomCAP
 
typedef
utility::pointer::shared_ptr
< VoxelGridPoint_AA
VoxelGridPoint_AAOP
 
typedef
utility::pointer::shared_ptr
< VoxelGridPoint_AA const > 
VoxelGridPoint_AACOP
 
typedef
utility::pointer::weak_ptr
< VoxelGridPoint_AA
VoxelGridPoint_AAAP
 
typedef
utility::pointer::weak_ptr
< VoxelGridPoint_AA const > 
VoxelGridPoint_AACAP
 
typedef
utility::pointer::shared_ptr
< NMRDummySpinlabelVoxelGrid
NMRDummySpinlabelVoxelGridOP
 
typedef
utility::pointer::shared_ptr
< NMRDummySpinlabelVoxelGrid
const > 
NMRDummySpinlabelVoxelGridCOP
 
typedef
utility::pointer::weak_ptr
< NMRDummySpinlabelVoxelGrid
NMRDummySpinlabelVoxelGridAP
 
typedef
utility::pointer::weak_ptr
< NMRDummySpinlabelVoxelGrid
const > 
NMRDummySpinlabelVoxelGridCAP
 
typedef
utility::pointer::shared_ptr
< NMRGridSearch
NMRGridSearchOP
 
typedef
utility::pointer::shared_ptr
< NMRGridSearch const > 
NMRGridSearchCOP
 
typedef
utility::pointer::weak_ptr
< NMRGridSearch
NMRGridSearchAP
 
typedef
utility::pointer::weak_ptr
< NMRGridSearch const > 
NMRGridSearchCAP
 
typedef
utility::pointer::shared_ptr
< NMRSpinlabel
NMRSpinlabelOP
 
typedef
utility::pointer::shared_ptr
< NMRSpinlabel const > 
NMRSpinlabelCOP
 
typedef
utility::pointer::weak_ptr
< NMRSpinlabel
NMRSpinlabelAP
 
typedef
utility::pointer::weak_ptr
< NMRSpinlabel const > 
NMRSpinlabelCAP
 
typedef
utility::pointer::shared_ptr
< NMRTensor
NMRTensorOP
 
typedef
utility::pointer::shared_ptr
< NMRTensor const > 
NMRTensorCOP
 
typedef
utility::pointer::weak_ptr
< NMRTensor
NMRTensorAP
 
typedef
utility::pointer::weak_ptr
< NMRTensor const > 
NMRTensorCAP
 
typedef numeric::xyzMatrix
< core::Real
Matrix
 
typedef
numeric::HomogeneousTransform
< core::Real
HT
 
typedef
utility::fixedsizearray1
< core::Real, 5 > 
Vec5
 

Enumerations

enum  EULER_CONVENTION { ZXZ_CONVENTION = 1, ZYZ_CONVENTION = 2, ZYX_CONVENTION = 3 }
 possible sequences of euler rotation axes More...
 
enum  SINGLE_NMR_VALUE_WEIGHTING { CONST = 1, SIGMA = 2, OBSIG = 3 }
 type of weighting of single PCS/RDC/PRE values More...
 
enum  NMR_VALUE_AVERAGING_TYPE { SUM = 1, MEAN = 2 }
 the type how equivalent, ambiguous spins are averaged More...
 
enum  RDC_TYPE {
  RDC_TYPE_NH = 1, RDC_TYPE_NCO = 2, RDC_TYPE_CAHA = 3, RDC_TYPE_CACO = 4,
  RDC_TYPE_CACB = 5, RDC_TYPE_NCA = 6, RDC_TYPE_CAHN = 7, RDC_TYPE_COHN = 8
}
 the type of the residual dipolar coupling measured between two nuclei More...
 
enum  RDC_NORM_TYPE { NORM_TYPE_NH = 1, NORM_TYPE_CH = 2, NORM_TYPE_NONE = 3 }
 type of RDC normalization NORM_TYPE_NH = relative to N-H RDCs NORM_TYPE_CH = relative to CA-HA RDCs NORM_TYPE_NONE = it is assumed that input RDCs have been normalized to N-H RDCs in beforehand (which is the NMR convention). Thus no additional scaling will be applied here More...
 
enum  PRE_SPIN_TYPE { PRE_SPIN_TYPE_H = 1, PRE_SPIN_TYPE_N = 2, PRE_SPIN_TYPE_C = 3 }
 type of PRE nuclear spin More...
 
enum  PRE_RATE_TYPE { R2_PARA = 1, R1_PARA = 2 }
 type of the paramagnetic relaxation rate More...
 

Functions

static basic::Tracer TR ("core.scoring.nmr.NMRDataFactory")
 
static basic::Tracer TR ("core.scoring.nmr.NMRDummySpinlabelEnsemble")
 
static basic::Tracer TR ("core.scoring.nmr.NMRDummySpinlabelVoxelGrid")
 
static basic::Tracer TR ("core.scoring.nmr.NMRGridSearch")
 
static basic::Tracer TR ("core.scoring.nmr.NMRSpinlabel")
 
static basic::Tracer TR ("core.scoring.nmr.util")
 
NMR_VALUE_AVERAGING_TYPE convert_string_to_averaging_type (std::string const &averaging_type)
 the type how equivalent, ambiguous spins are averaged More...
 
SINGLE_NMR_VALUE_WEIGHTING convert_string_to_weighting_scheme (std::string const &weighting_scheme)
 
RDC_NORM_TYPE convert_string_to_normalization_type (std::string const &computation_type)
 
PRE_RATE_TYPE convert_string_to_rate_type (std::string const &rate_type)
 
std::string convert_rdc_type_to_string (RDC_TYPE const &type)
 
std::string convert_pre_spin_type_to_string (PRE_SPIN_TYPE const &type)
 
utility::vector1< id::AtomIDlookup_pseudoprotons (Size const rsd, std::string const &atomname, pose::Pose const &pose)
 : function that handles conversion from pseudoatom identifier for degenerate protons to fullatom name More...
 
RDC_TYPE rdc_type_from_atom_names (std::pair< core::io::nmr::AtomSelection, core::io::nmr::AtomSelection > const &spinsAB)
 determine the RDC type from the spins atom names More...
 
PRE_SPIN_TYPE pre_spin_type_from_atom_name (core::io::nmr::AtomSelection const &atom)
 
Matrix rotation_matrix_from_euler_angles (Vector const &angles, EULER_CONVENTION convention)
 : creates a rotation matrix given three Euler angles and a convention as determined at runtime More...
 
Vector euler_angles_from_rotation_matrix (Matrix const &rotM, EULER_CONVENTION convention)
 : determines the three Euler angles given a rotation matrix and the respective Euler convention as determined at runtime More...
 
void order_tensor_parameters (utility::vector1< Real > &params, EULER_CONVENTION convention)
 orders the three eigenvalues of NMRTensor and brings NMRTensor in unique tensor representation More...
 
Matrix apply_tensor_transformation (pose::Pose &pose, Matrix const &Min, Size resid_from, Size resid_to)
 Utility function that transforms an NMR tensor from the frame of residue_from into the coordinate frame of the symmetric residue_to given a symmetric pose. Returns the original matrix if the pose is not symmetric or if residue_from and residue_to belong to the same subunit residue_to. More...
 
Vector apply_vector_transformation (pose::Pose &pose, Vector const &Vin, Size resid_from, Size resid_to)
 Utility function that transforms a vector of metal (or spinlabel) coordinates from the frame of residue_from into the coordinate frame of the symmetric residue_to given a symmetric pose. Returns the original vector if the pose is not symmetric or if residue_from and residue_to belong to the same subunit residue_to. More...
 
Vector apply_vector_rotation (pose::Pose &pose, Vector const &Vin, Size resid_from, Size resid_to)
 Utility function that rotates a vector from the frame of residue_from into the coordinate frame of the symmetric residue_to given a symmetric pose. Returns the original vector if the pose is not symmetric or if residue_from and residue_to belong to the same subunit residue_to. More...
 
HT define_local_frame (Vector const &CA, Vector const &CB, Vector const &C)
 Create a local coordinate frame from backbone coordinates. The local frame is defined by a homogeneous transform object which can be created from three axes and one point. The center is located at CA. The z'-axis is along CA - CB. The x'-axis is within the CA-CB - CA-C plane and the y'-axis is perpendicular to the CB - CA - C plane. More...
 
Real pcs_func (Vec5 const &par, Matrix const &rotM, Vector const &spin_coord, Real const &scal)
 Auxiliary PCS function par: Tensor values [xM, yM, zM, Xax, Xrh] rotM: Rotation matrix to transform spin coordinates in tensor frame spin_coord: Spin xyz coordinates scal: optional scaling factor. More...
 

Typedef Documentation

typedef boost::unordered_map< std::string, Vector > core::scoring::nmr::AtomNamePosMap
typedef std::pair< std::string, std::string > core::scoring::nmr::AtomPairKey
typedef numeric::HomogeneousTransform<core::Real> core::scoring::nmr::HT
typedef numeric::xyzMatrix<core::Real> core::scoring::nmr::Matrix
typedef utility::pointer::shared_ptr< NMRDataFactory const > core::scoring::nmr::NMRDataFactoryCOP
typedef utility::pointer::shared_ptr< NMRDataFactory > core::scoring::nmr::NMRDataFactoryOP
typedef utility::pointer::weak_ptr< NMRDummySpinlabelAtom const > core::scoring::nmr::NMRDummySpinlabelAtomCAP
typedef utility::pointer::shared_ptr< NMRDummySpinlabelAtom const > core::scoring::nmr::NMRDummySpinlabelAtomCOP
typedef utility::pointer::shared_ptr< NMRDummySpinlabelAtom > core::scoring::nmr::NMRDummySpinlabelAtomOP
typedef boost::unordered_map< std::string, NMRDummySpinlabelAtom > core::scoring::nmr::NMRDummySpinlabelAtomTable
typedef boost::unordered_map< std::string, NMRDummySpinlabelAtom >::const_iterator core::scoring::nmr::NMRDummySpinlabelAtomTableCOIter
typedef boost::unordered_map< std::string, NMRDummySpinlabelAtom >::iterator core::scoring::nmr::NMRDummySpinlabelAtomTableIter
typedef utility::pointer::shared_ptr< NMRDummySpinlabelEnsemble const > core::scoring::nmr::NMRDummySpinlabelEnsembleCOP
typedef utility::pointer::weak_ptr< NMRGridSearch > core::scoring::nmr::NMRGridSearchAP
typedef utility::pointer::weak_ptr< NMRGridSearch const > core::scoring::nmr::NMRGridSearchCAP
typedef utility::pointer::shared_ptr< NMRGridSearch const > core::scoring::nmr::NMRGridSearchCOP
typedef utility::pointer::shared_ptr< NMRGridSearch > core::scoring::nmr::NMRGridSearchOP
typedef utility::pointer::weak_ptr< NMRSpinlabel > core::scoring::nmr::NMRSpinlabelAP
typedef utility::pointer::weak_ptr< NMRSpinlabel const > core::scoring::nmr::NMRSpinlabelCAP
typedef utility::pointer::shared_ptr< NMRSpinlabel const > core::scoring::nmr::NMRSpinlabelCOP
typedef utility::pointer::shared_ptr< NMRSpinlabel > core::scoring::nmr::NMRSpinlabelOP
typedef utility::pointer::weak_ptr< NMRTensor > core::scoring::nmr::NMRTensorAP
typedef utility::pointer::weak_ptr< NMRTensor const > core::scoring::nmr::NMRTensorCAP
typedef utility::pointer::shared_ptr< NMRTensor const > core::scoring::nmr::NMRTensorCOP
typedef utility::pointer::shared_ptr< NMRTensor > core::scoring::nmr::NMRTensorOP
typedef utility::fixedsizearray1<core::Real,5> core::scoring::nmr::Vec5
typedef utility::pointer::weak_ptr< VoxelGridPoint_AA > core::scoring::nmr::VoxelGridPoint_AAAP
typedef utility::pointer::weak_ptr< VoxelGridPoint_AA const > core::scoring::nmr::VoxelGridPoint_AACAP
typedef utility::pointer::shared_ptr< VoxelGridPoint_AA const > core::scoring::nmr::VoxelGridPoint_AACOP
typedef utility::pointer::shared_ptr< VoxelGridPoint_AA > core::scoring::nmr::VoxelGridPoint_AAOP
typedef utility::pointer::weak_ptr< VoxelGridPoint > core::scoring::nmr::VoxelGridPointAP
typedef utility::pointer::weak_ptr< VoxelGridPoint const > core::scoring::nmr::VoxelGridPointCAP
typedef utility::pointer::shared_ptr< VoxelGridPoint const > core::scoring::nmr::VoxelGridPointCOP
typedef utility::pointer::shared_ptr< VoxelGridPoint > core::scoring::nmr::VoxelGridPointOP

Enumeration Type Documentation

possible sequences of euler rotation axes

Enumerator
ZXZ_CONVENTION 
ZYZ_CONVENTION 
ZYX_CONVENTION 

the type how equivalent, ambiguous spins are averaged

Enumerator
SUM 
MEAN 

type of the paramagnetic relaxation rate

Enumerator
R2_PARA 
R1_PARA 

type of PRE nuclear spin

Enumerator
PRE_SPIN_TYPE_H 
PRE_SPIN_TYPE_N 
PRE_SPIN_TYPE_C 

type of RDC normalization NORM_TYPE_NH = relative to N-H RDCs NORM_TYPE_CH = relative to CA-HA RDCs NORM_TYPE_NONE = it is assumed that input RDCs have been normalized to N-H RDCs in beforehand (which is the NMR convention). Thus no additional scaling will be applied here

Enumerator
NORM_TYPE_NH 
NORM_TYPE_CH 
NORM_TYPE_NONE 

the type of the residual dipolar coupling measured between two nuclei

Enumerator
RDC_TYPE_NH 
RDC_TYPE_NCO 
RDC_TYPE_CAHA 
RDC_TYPE_CACO 
RDC_TYPE_CACB 
RDC_TYPE_NCA 
RDC_TYPE_CAHN 
RDC_TYPE_COHN 

type of weighting of single PCS/RDC/PRE values

CONST = constant weighting, 1.0 for every value SIGMA = weighting based on error, 1.0/(error * error) OBSIG = weighting based on observed NMR value and error val_obs/val_max/ (error * error)

Enumerator
CONST 
SIGMA 
OBSIG 

Function Documentation

Matrix core::scoring::nmr::apply_tensor_transformation ( pose::Pose pose,
Matrix const &  Min,
Size  resid_from,
Size  resid_to 
)

Utility function that transforms an NMR tensor from the frame of residue_from into the coordinate frame of the symmetric residue_to given a symmetric pose. Returns the original matrix if the pose is not symmetric or if residue_from and residue_to belong to the same subunit residue_to.

References core::pose::Pose::conformation(), core::conformation::symmetry::SymmetricConformation::get_transformation(), core::pose::symmetry::is_symmetric(), and core::pose::symmetry::symmetry_info().

Referenced by core::scoring::nmr::pcs::PCSSingleSet::set_atom_derivatives().

Vector core::scoring::nmr::apply_vector_rotation ( pose::Pose pose,
Vector const &  Vin,
Size  resid_from,
Size  resid_to 
)

Utility function that rotates a vector from the frame of residue_from into the coordinate frame of the symmetric residue_to given a symmetric pose. Returns the original vector if the pose is not symmetric or if residue_from and residue_to belong to the same subunit residue_to.

References core::pose::Pose::conformation(), core::conformation::symmetry::SymmetricConformation::get_transformation(), core::pose::symmetry::is_symmetric(), and core::pose::symmetry::symmetry_info().

Referenced by protocols::nmr::rdc::RDCEnergy::setup_for_minimizing(), protocols::nmr::pcs::PCSEnergy::setup_for_minimizing(), and protocols::nmr::pre::PREEnergy::setup_for_minimizing().

Vector core::scoring::nmr::apply_vector_transformation ( pose::Pose pose,
Vector const &  Vin,
Size  resid_from,
Size  resid_to 
)

Utility function that transforms a vector of metal (or spinlabel) coordinates from the frame of residue_from into the coordinate frame of the symmetric residue_to given a symmetric pose. Returns the original vector if the pose is not symmetric or if residue_from and residue_to belong to the same subunit residue_to.

References core::pose::Pose::conformation(), core::conformation::symmetry::SymmetricConformation::get_transformation(), core::pose::symmetry::is_symmetric(), and core::pose::symmetry::symmetry_info().

Referenced by core::scoring::nmr::pcs::PCSSingleSet::set_atom_derivatives(), and core::scoring::nmr::pre::PREMultiSet::set_atom_derivatives().

std::string core::scoring::nmr::convert_pre_spin_type_to_string ( PRE_SPIN_TYPE const &  type)
std::string core::scoring::nmr::convert_rdc_type_to_string ( RDC_TYPE const &  type)
NMR_VALUE_AVERAGING_TYPE core::scoring::nmr::convert_string_to_averaging_type ( std::string const &  averaging_type)
RDC_NORM_TYPE core::scoring::nmr::convert_string_to_normalization_type ( std::string const &  computation_type)
PRE_RATE_TYPE core::scoring::nmr::convert_string_to_rate_type ( std::string const &  rate_type)
SINGLE_NMR_VALUE_WEIGHTING core::scoring::nmr::convert_string_to_weighting_scheme ( std::string const &  weighting_scheme)
HT core::scoring::nmr::define_local_frame ( Vector const &  CA,
Vector const &  CB,
Vector const &  C 
)

Create a local coordinate frame from backbone coordinates. The local frame is defined by a homogeneous transform object which can be created from three axes and one point. The center is located at CA. The z'-axis is along CA - CB. The x'-axis is within the CA-CB - CA-C plane and the y'-axis is perpendicular to the CB - CA - C plane.

Referenced by core::scoring::nmr::NMRDummySpinlabelEnsemble::coordinate_transform_from_target_site(), core::scoring::nmr::NMRDummySpinlabelEnsemble::define_ensemble_frame(), and core::scoring::nmr::NMRDummySpinlabelEnsemble::init_from_database_file().

Vector core::scoring::nmr::euler_angles_from_rotation_matrix ( Matrix const &  rotM,
EULER_CONVENTION  convention 
)

: determines the three Euler angles given a rotation matrix and the respective Euler convention as determined at runtime

determines the three Euler angles given a rotation matrix and the respective Euler convention as determined at runtime

References ZXZ_CONVENTION, ZYX_CONVENTION, and ZYZ_CONVENTION.

Referenced by core::scoring::nmr::pcs::PCSTensor::diagonalize_tensor(), core::scoring::nmr::rdc::RDCTensor::diagonalize_tensor(), and order_tensor_parameters().

utility::vector1< id::AtomID > core::scoring::nmr::lookup_pseudoprotons ( Size const  rsd,
std::string const &  atomname,
pose::Pose const &  pose 
)

: function that handles conversion from pseudoatom identifier for degenerate protons to fullatom name

function that handles conversion from pseudoatom identifier for degenerate protons to fullatom name

References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_ala, core::chemical::aa_arg, core::chemical::aa_asn, core::chemical::aa_asp, core::chemical::aa_cys, core::chemical::aa_dal, core::chemical::aa_dan, core::chemical::aa_dar, core::chemical::aa_das, core::chemical::aa_dcs, core::chemical::aa_dgn, core::chemical::aa_dgu, core::chemical::aa_dhi, core::chemical::aa_dil, core::chemical::aa_dle, core::chemical::aa_dly, core::chemical::aa_dme, core::chemical::aa_dph, core::chemical::aa_dpr, core::chemical::aa_dse, core::chemical::aa_dth, core::chemical::aa_dtr, core::chemical::aa_dty, core::chemical::aa_dva, core::chemical::aa_gln, core::chemical::aa_glu, core::chemical::aa_gly, core::chemical::aa_his, core::chemical::aa_ile, core::chemical::aa_leu, core::chemical::aa_lys, core::chemical::aa_met, core::chemical::aa_phe, core::chemical::aa_pro, core::chemical::aa_ser, core::chemical::aa_thr, core::chemical::aa_trp, core::chemical::aa_tyr, core::chemical::aa_val, core::pose::Pose::is_fullatom(), core::pose::named_atom_id_to_atom_id(), core::pose::Pose::residue_type(), core::pose::Pose::total_residue(), and TR().

Referenced by core::scoring::nmr::pcs::PCSSingle::PCSSingle(), core::scoring::nmr::pre::PRESingle::PRESingle(), and core::scoring::nmr::rdc::RDCSingle::RDCSingle().

void core::scoring::nmr::order_tensor_parameters ( utility::vector1< Real > &  params,
EULER_CONVENTION  convention 
)
Real core::scoring::nmr::pcs_func ( Vec5 const &  par,
Matrix const &  rotM,
Vector const &  spin_coord,
Real const &  scal 
)

Auxiliary PCS function par: Tensor values [xM, yM, zM, Xax, Xrh] rotM: Rotation matrix to transform spin coordinates in tensor frame spin_coord: Spin xyz coordinates scal: optional scaling factor.

References core::scoring::pcs, and protocols::hybridization::r2.

Referenced by protocols::nmr::pcs::PCSLigandTransformMover::find_best_ligand_pose_with_grid_search(), protocols::nmr::pcs::pcs_lmmin(), and protocols::qsar::scoring_grid::PCSSingleGrid::refresh().

PRE_SPIN_TYPE core::scoring::nmr::pre_spin_type_from_atom_name ( core::io::nmr::AtomSelection const &  atom)
RDC_TYPE core::scoring::nmr::rdc_type_from_atom_names ( std::pair< core::io::nmr::AtomSelection, core::io::nmr::AtomSelection > const &  spinsAB)

determine the RDC type from the spins atom names

determine the RDC type from the spins' atom names

References RDC_TYPE_CACB, RDC_TYPE_CACO, RDC_TYPE_CAHA, RDC_TYPE_CAHN, RDC_TYPE_COHN, RDC_TYPE_NCA, RDC_TYPE_NCO, and RDC_TYPE_NH.

Referenced by core::scoring::nmr::rdc::RDCSingle::RDCSingle().

Matrix core::scoring::nmr::rotation_matrix_from_euler_angles ( Vector const &  angles,
EULER_CONVENTION  convention 
)
static basic::Tracer core::scoring::nmr::TR ( "core.scoring.nmr.NMRDummySpinlabelVoxelGrid"  )
static
static basic::Tracer core::scoring::nmr::TR ( "core.scoring.nmr.NMRDataFactory"  )
static
static basic::Tracer core::scoring::nmr::TR ( "core.scoring.nmr.NMRGridSearch"  )
static
static basic::Tracer core::scoring::nmr::TR ( "core.scoring.nmr.NMRSpinlabel"  )
static
static basic::Tracer core::scoring::nmr::TR ( "core.scoring.nmr.util"  )
static
static basic::Tracer core::scoring::nmr::TR ( "core.scoring.nmr.NMRDummySpinlabelEnsemble"  )
static