util.cc File Reference

function definitions for util.hh More...

#include <core/scoring/nmr/util.hh>
#include <core/io/nmr/AtomSelection.hh>
#include <core/id/AtomID.hh>
#include <core/id/NamedAtomID.hh>
#include <core/id/Exceptions.hh>
#include <core/types.hh>
#include <core/pose/Pose.hh>
#include <core/pose/symmetry/util.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/symmetry/SymmetryInfo.hh>
#include <core/conformation/symmetry/SymmetricConformation.hh>
#include <core/pose/util.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/AA.hh>
#include <numeric/xyzVector.hh>
#include <numeric/xyzMatrix.hh>
#include <numeric/HomogeneousTransform.hh>
#include <numeric/constants.hh>
#include <numeric/conversions.hh>
#include <numeric/xyz.functions.hh>
#include <utility/exit.hh>
#include <utility/vector1.hh>
#include <utility/string_util.hh>
#include <ObjexxFCL/string.functions.hh>
#include <basic/Tracer.hh>
#include <string>
#include <cmath>

Namespaces
	core
	A class for reading in the atom type properties.
	core::scoring
	core::scoring::nmr

Functions
static basic::Tracer	core::scoring::nmr::TR ("core.scoring.nmr.util")
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 More...
SINGLE_NMR_VALUE_WEIGHTING	core::scoring::nmr::convert_string_to_weighting_scheme (std::string const &weighting_scheme)
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)
std::string	core::scoring::nmr::convert_rdc_type_to_string (RDC_TYPE const &type)
std::string	core::scoring::nmr::convert_pre_spin_type_to_string (PRE_SPIN_TYPE const &type)
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 More...
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 More...
PRE_SPIN_TYPE	core::scoring::nmr::pre_spin_type_from_atom_name (core::io::nmr::AtomSelection const &atom)
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 More...
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 More...
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 More...
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. More...
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. More...
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. More...
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. More...
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. More...

Detailed Description

function definitions for util.hh

last Modified: 05/11/16

Author

Georg Kuenze (georg.nosp@m..kue.nosp@m.nze@v.nosp@m.ande.nosp@m.rbilt.nosp@m..edu)