core::scoring::nmr Namespace Reference

Namespaces
	pcs
	pre
	rdc

Classes
class	NMRDataFactory
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	VoxelGridPoint
	Base class of a point object from which the voxel grid is created. More...
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	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...
class	NMRDummySpinlabelVoxelGrid
	Derived class of VoxelGrid to create a grid of VoxelGridPoint objects. More...
class	NMRGridSearch
class	NMRSpinlabel
class	NMRTensor

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::AtomID >	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 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 @params 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

AtomNamePosMap

typedef boost::unordered_map< std::string, Vector > core::scoring::nmr::AtomNamePosMap

AtomPairKey

typedef std::pair< std::string, std::string > core::scoring::nmr::AtomPairKey

HT

typedef numeric::HomogeneousTransform<core::Real> core::scoring::nmr::HT

Matrix

typedef numeric::xyzMatrix<core::Real> core::scoring::nmr::Matrix

NMRDataFactoryCOP

typedef utility::pointer::shared_ptr< NMRDataFactory const > core::scoring::nmr::NMRDataFactoryCOP

NMRDataFactoryOP

typedef utility::pointer::shared_ptr< NMRDataFactory > core::scoring::nmr::NMRDataFactoryOP

NMRDummySpinlabelAtomAP

typedef utility::pointer::weak_ptr< NMRDummySpinlabelAtom > core::scoring::nmr::NMRDummySpinlabelAtomAP

NMRDummySpinlabelAtomCAP

typedef utility::pointer::weak_ptr< NMRDummySpinlabelAtom const > core::scoring::nmr::NMRDummySpinlabelAtomCAP

NMRDummySpinlabelAtomCOP

typedef utility::pointer::shared_ptr< NMRDummySpinlabelAtom const > core::scoring::nmr::NMRDummySpinlabelAtomCOP

NMRDummySpinlabelAtomOP

typedef utility::pointer::shared_ptr< NMRDummySpinlabelAtom > core::scoring::nmr::NMRDummySpinlabelAtomOP

NMRDummySpinlabelAtomTable

typedef boost::unordered_map< std::string, NMRDummySpinlabelAtom > core::scoring::nmr::NMRDummySpinlabelAtomTable

NMRDummySpinlabelAtomTableCOIter

typedef boost::unordered_map< std::string, NMRDummySpinlabelAtom >::const_iterator core::scoring::nmr::NMRDummySpinlabelAtomTableCOIter

NMRDummySpinlabelAtomTableIter

typedef boost::unordered_map< std::string, NMRDummySpinlabelAtom >::iterator core::scoring::nmr::NMRDummySpinlabelAtomTableIter

NMRDummySpinlabelConformerAP

typedef utility::pointer::weak_ptr< NMRDummySpinlabelConformer > core::scoring::nmr::NMRDummySpinlabelConformerAP

NMRDummySpinlabelConformerCAP

typedef utility::pointer::weak_ptr< NMRDummySpinlabelConformer const > core::scoring::nmr::NMRDummySpinlabelConformerCAP

NMRDummySpinlabelConformerCOP

typedef utility::pointer::shared_ptr< NMRDummySpinlabelConformer const > core::scoring::nmr::NMRDummySpinlabelConformerCOP

NMRDummySpinlabelConformerOP

typedef utility::pointer::shared_ptr< NMRDummySpinlabelConformer > core::scoring::nmr::NMRDummySpinlabelConformerOP

NMRDummySpinlabelEnsembleAP

typedef utility::pointer::weak_ptr< NMRDummySpinlabelEnsemble > core::scoring::nmr::NMRDummySpinlabelEnsembleAP

NMRDummySpinlabelEnsembleCAP

typedef utility::pointer::weak_ptr< NMRDummySpinlabelEnsemble const > core::scoring::nmr::NMRDummySpinlabelEnsembleCAP

NMRDummySpinlabelEnsembleCOP

typedef utility::pointer::shared_ptr< NMRDummySpinlabelEnsemble const > core::scoring::nmr::NMRDummySpinlabelEnsembleCOP

NMRDummySpinlabelEnsembleOP

typedef utility::pointer::shared_ptr< NMRDummySpinlabelEnsemble > core::scoring::nmr::NMRDummySpinlabelEnsembleOP

NMRDummySpinlabelVoxelGridAP

typedef utility::pointer::weak_ptr< NMRDummySpinlabelVoxelGrid > core::scoring::nmr::NMRDummySpinlabelVoxelGridAP

NMRDummySpinlabelVoxelGridCAP

typedef utility::pointer::weak_ptr< NMRDummySpinlabelVoxelGrid const > core::scoring::nmr::NMRDummySpinlabelVoxelGridCAP

NMRDummySpinlabelVoxelGridCOP

typedef utility::pointer::shared_ptr< NMRDummySpinlabelVoxelGrid const > core::scoring::nmr::NMRDummySpinlabelVoxelGridCOP

NMRDummySpinlabelVoxelGridOP

typedef utility::pointer::shared_ptr< NMRDummySpinlabelVoxelGrid > core::scoring::nmr::NMRDummySpinlabelVoxelGridOP

NMRGridSearchAP

typedef utility::pointer::weak_ptr< NMRGridSearch > core::scoring::nmr::NMRGridSearchAP

NMRGridSearchCAP

typedef utility::pointer::weak_ptr< NMRGridSearch const > core::scoring::nmr::NMRGridSearchCAP

NMRGridSearchCOP

typedef utility::pointer::shared_ptr< NMRGridSearch const > core::scoring::nmr::NMRGridSearchCOP

NMRGridSearchOP

typedef utility::pointer::shared_ptr< NMRGridSearch > core::scoring::nmr::NMRGridSearchOP

NMRSpinlabelAP

typedef utility::pointer::weak_ptr< NMRSpinlabel > core::scoring::nmr::NMRSpinlabelAP

NMRSpinlabelCAP

typedef utility::pointer::weak_ptr< NMRSpinlabel const > core::scoring::nmr::NMRSpinlabelCAP

NMRSpinlabelCOP

typedef utility::pointer::shared_ptr< NMRSpinlabel const > core::scoring::nmr::NMRSpinlabelCOP

NMRSpinlabelOP

typedef utility::pointer::shared_ptr< NMRSpinlabel > core::scoring::nmr::NMRSpinlabelOP

NMRTensorAP

typedef utility::pointer::weak_ptr< NMRTensor > core::scoring::nmr::NMRTensorAP

NMRTensorCAP

typedef utility::pointer::weak_ptr< NMRTensor const > core::scoring::nmr::NMRTensorCAP

NMRTensorCOP

typedef utility::pointer::shared_ptr< NMRTensor const > core::scoring::nmr::NMRTensorCOP

NMRTensorOP

typedef utility::pointer::shared_ptr< NMRTensor > core::scoring::nmr::NMRTensorOP

ResidueCOP

typedef core::conformation::ResidueCOP core::scoring::nmr::ResidueCOP

ResidueOP

typedef core::conformation::ResidueOP core::scoring::nmr::ResidueOP

Vec5

typedef utility::fixedsizearray1<core::Real,5> core::scoring::nmr::Vec5

VoxelGridPoint_AAAP

typedef utility::pointer::weak_ptr< VoxelGridPoint_AA > core::scoring::nmr::VoxelGridPoint_AAAP

VoxelGridPoint_AACAP

typedef utility::pointer::weak_ptr< VoxelGridPoint_AA const > core::scoring::nmr::VoxelGridPoint_AACAP

VoxelGridPoint_AACOP

typedef utility::pointer::shared_ptr< VoxelGridPoint_AA const > core::scoring::nmr::VoxelGridPoint_AACOP

VoxelGridPoint_AAOP

typedef utility::pointer::shared_ptr< VoxelGridPoint_AA > core::scoring::nmr::VoxelGridPoint_AAOP

VoxelGridPointAP

typedef utility::pointer::weak_ptr< VoxelGridPoint > core::scoring::nmr::VoxelGridPointAP

VoxelGridPointCAP

typedef utility::pointer::weak_ptr< VoxelGridPoint const > core::scoring::nmr::VoxelGridPointCAP

VoxelGridPointCOP

typedef utility::pointer::shared_ptr< VoxelGridPoint const > core::scoring::nmr::VoxelGridPointCOP

VoxelGridPointOP

typedef utility::pointer::shared_ptr< VoxelGridPoint > core::scoring::nmr::VoxelGridPointOP

Enumeration Type Documentation

EULER_CONVENTION

enum core::scoring::nmr::EULER_CONVENTION

possible sequences of euler rotation axes

Enumerator
ZXZ_CONVENTION
ZYZ_CONVENTION
ZYX_CONVENTION

NMR_VALUE_AVERAGING_TYPE

enum core::scoring::nmr::NMR_VALUE_AVERAGING_TYPE

the type how equivalent, ambiguous spins are averaged

Enumerator
SUM
MEAN

PRE_RATE_TYPE

enum core::scoring::nmr::PRE_RATE_TYPE

type of the paramagnetic relaxation rate

Enumerator
R2_PARA
R1_PARA

PRE_SPIN_TYPE

enum core::scoring::nmr::PRE_SPIN_TYPE

type of PRE nuclear spin

Enumerator
PRE_SPIN_TYPE_H
PRE_SPIN_TYPE_N
PRE_SPIN_TYPE_C

RDC_NORM_TYPE

enum core::scoring::nmr::RDC_NORM_TYPE

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

RDC_TYPE

enum core::scoring::nmr::RDC_TYPE

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

SINGLE_NMR_VALUE_WEIGHTING

enum core::scoring::nmr::SINGLE_NMR_VALUE_WEIGHTING

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

apply_tensor_transformation()

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::pose::symmetry::is_symmetric(), and core::pose::symmetry::symmetry_info().

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

apply_vector_rotation()

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::pose::symmetry::is_symmetric(), and core::pose::symmetry::symmetry_info().

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

apply_vector_transformation()

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::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().

convert_pre_spin_type_to_string()

std::string core::scoring::nmr::convert_pre_spin_type_to_string

(

PRE_SPIN_TYPE const &

type

)

References PRE_SPIN_TYPE_H, and PRE_SPIN_TYPE_N.

Referenced by protocols::nmr::ParaNMRScoreMover::add_pre_scores_to_scorefile().

convert_rdc_type_to_string()

std::string core::scoring::nmr::convert_rdc_type_to_string

(

RDC_TYPE const &

type

)

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

Referenced by protocols::nmr::ParaNMRScoreMover::add_pcs_scores_to_scorefile(), protocols::nmr::ParaNMRScoreMover::add_rdc_scores_to_scorefile(), and core::scoring::nmr::rdc::RDCMultiSet::show().

convert_string_to_averaging_type()

NMR_VALUE_AVERAGING_TYPE core::scoring::nmr::convert_string_to_averaging_type

(

std::string const &

averaging_type

)

the type how equivalent, ambiguous spins are averaged

References MEAN, protocols::kinmatch::str(), and SUM.

Referenced by core::scoring::nmr::pcs::PCSSingleSet::set_averaging_type(), core::scoring::nmr::pre::PREMultiSet::set_averaging_type(), and core::scoring::nmr::rdc::RDCMultiSet::set_averaging_type().

convert_string_to_normalization_type()

RDC_NORM_TYPE core::scoring::nmr::convert_string_to_normalization_type

(

std::string const &

computation_type

)

References NORM_TYPE_CH, NORM_TYPE_NH, NORM_TYPE_NONE, and protocols::kinmatch::str().

Referenced by core::scoring::nmr::rdc::RDCMultiSet::init_from_cml(), and core::scoring::nmr::rdc::RDCData::init_rdc_data_from_file().

convert_string_to_rate_type()

PRE_RATE_TYPE core::scoring::nmr::convert_string_to_rate_type

(

std::string const &

rate_type

)

References R1_PARA, R2_PARA, and protocols::kinmatch::str().

Referenced by core::scoring::nmr::pre::PRESingleSet::PRESingleSet().

convert_string_to_weighting_scheme()

SINGLE_NMR_VALUE_WEIGHTING core::scoring::nmr::convert_string_to_weighting_scheme

(

std::string const &

weighting_scheme

)

References CONST, OBSIG, SIGMA, and protocols::kinmatch::str().

Referenced by core::scoring::nmr::pcs::PCSSingleSet::PCSSingleSet(), core::scoring::nmr::pre::PRESingleSet::PRESingleSet(), core::scoring::nmr::rdc::RDCSingleSet::RDCSingleSet(), core::scoring::nmr::pre::PRESingleSet::set_single_pre_weighting_scheme(), and core::scoring::nmr::rdc::RDCSingleSet::set_single_rdc_weighting_scheme().

define_local_frame()

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.

References core::chemical::element::C, protocols::frag_picker::CA, and protocols::frag_picker::CB.

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().

euler_angles_from_rotation_matrix()

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().

lookup_pseudoprotons()

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().

order_tensor_parameters()

void core::scoring::nmr::order_tensor_parameters	(	utility::vector1< Real > &	params,
		EULER_CONVENTION	convention
	)

orders the three eigenvalues of NMRTensor and brings NMRTensor in unique tensor representation

References core::scoring::angles(), euler_angles_from_rotation_matrix(), rotation_matrix_from_euler_angles(), and core::id::swap().

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

pcs_func()

Real core::scoring::nmr::pcs_func	(	Vec5 const &	par,
		Matrix const &	rotM,
		Vector const &	spin_coord,
		Real const &	scal
	)

Auxiliary PCS function @params 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(), and protocols::qsar::scoring_grid::PCSSingleGrid::refresh().

pre_spin_type_from_atom_name()

PRE_SPIN_TYPE core::scoring::nmr::pre_spin_type_from_atom_name

(

core::io::nmr::AtomSelection const &

atom

)

References core::io::nmr::AtomSelection::get_atom(), PRE_SPIN_TYPE_C, PRE_SPIN_TYPE_H, and PRE_SPIN_TYPE_N.

Referenced by core::scoring::nmr::pre::PRESingle::PRESingle().

rdc_type_from_atom_names()

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().

rotation_matrix_from_euler_angles()

Matrix core::scoring::nmr::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

creates a rotation matrix given three Euler angles and a convention as determined at runtime

References core::scoring::angles(), ZXZ_CONVENTION, ZYX_CONVENTION, and ZYZ_CONVENTION.

Referenced by core::scoring::nmr::pcs::PCSSingleSet::compute_pcs_values_and_score_from_tensor(), core::scoring::nmr::rdc::RDCMultiSet::compute_rdc_values_and_score_from_tensor(), protocols::nmr::pcs::PCSLigandTransformMover::find_best_ligand_pose_with_grid_search(), order_tensor_parameters(), protocols::qsar::scoring_grid::PCSSingleGrid::refresh(), core::scoring::nmr::pcs::PCSSingleSet::set_atom_derivatives(), core::scoring::nmr::rdc::RDCMultiSet::set_atom_derivatives(), protocols::nmr::pcs::PCSEnergy::show_additional_info(), protocols::nmr::rdc::RDCEnergy::show_additional_info(), core::scoring::nmr::rdc::RDCMultiSet::solve_tensor_and_compute_score_by_nls(), and core::scoring::nmr::pcs::PCSSingleSet::solve_tensor_and_compute_score_by_nls().

TR() [1/6]

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

static

Referenced by core::scoring::nmr::NMRDummySpinlabelEnsemble::clash_check(), core::scoring::nmr::NMRSpinlabel::cluster_conformers_and_set_weights_and_coordinates(), core::scoring::nmr::NMRSpinlabel::filter_spinlabel_ensemble_by_distance_check(), core::scoring::nmr::NMRSpinlabel::filter_spinlabel_ensemble_by_mask(), core::scoring::nmr::NMRDummySpinlabelEnsemble::init_from_database_file(), lookup_pseudoprotons(), and core::scoring::nmr::NMRDummySpinlabelConformer::NMRDummySpinlabelConformer().

TR() [2/6]

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

static

TR() [3/6]

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

static

TR() [4/6]

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

static

TR() [5/6]

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

static

TR() [6/6]

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

static