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util.hh File Reference
#include <core/types.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/conformation/symmetry/SymmetryInfo.fwd.hh>
#include <core/scoring/ScoreType.hh>
#include <numeric/xyzMatrix.fwd.hh>
#include <numeric/xyzVector.hh>
#include <numeric/fourier/FFT.hh>
#include <ObjexxFCL/FArray3D.hh>
#include <ObjexxFCL/FArray4D.hh>
#include <basic/Tracer.hh>
#include <iosfwd>
#include <complex>
#include <map>

Classes

struct  core::scoring::electron_density::poseCoord
 

Namespaces

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

Typedefs

typedef utility::vector1
< poseCoord > 
core::scoring::electron_density::poseCoords
 

Functions

void core::scoring::electron_density::add_dens_scores_from_cmdline_to_scorefxn (core::scoring::ScoreFunction &scorefxn)
 read density weights from the cmd line into the scorefunction More...
 
bool core::scoring::electron_density::pose_has_nonzero_Bs (core::pose::Pose const &pose)
 helper function quickly guesses if a pose has non-zero B factors More...
 
bool core::scoring::electron_density::pose_has_nonzero_Bs (poseCoords const &pose)
 
template<class S >
core::Real core::scoring::electron_density::interp_linear (ObjexxFCL::FArray3D< S > const &data, numeric::xyzVector< core::Real > const &idxX)
 trilinear interpolation with periodic boundaries More...
 
core::Real core::scoring::electron_density::interp_spline (ObjexxFCL::FArray3D< core::Real > &coeffs, numeric::xyzVector< core::Real > const &idxX, bool mirrored)
 spline interpolation with periodic boundaries More...
 
numeric::xyzVector< core::Realcore::scoring::electron_density::interp_dspline (ObjexxFCL::FArray3D< core::Real > &coeffs, numeric::xyzVector< core::Real > const &idxX, bool mirrored)
 spline interpolation with periodic boundaries More...
 
void core::scoring::electron_density::spline_coeffs (ObjexxFCL::FArray3D< core::Real > const &data, ObjexxFCL::FArray3D< core::Real > &coeffs, bool mirrored=false)
 precompute spline coefficients (float array => core::Real coeffs) More...
 
core::Real core::scoring::electron_density::interp_spline (ObjexxFCL::FArray3D< float > &coeffs, numeric::xyzVector< core::Real > const &idxX, bool mirrored)
 spline interpolation with periodic boundaries, single precision More...
 
numeric::xyzVector< core::Realcore::scoring::electron_density::interp_dspline (ObjexxFCL::FArray3D< float > &coeffs, numeric::xyzVector< core::Real > const &idxX, bool mirrored)
 spline interpolation with periodic boundaries, single precision More...
 
void core::scoring::electron_density::spline_coeffs (ObjexxFCL::FArray3D< float > const &data, ObjexxFCL::FArray3D< core::Real > &coeffs, bool mirrored=false)
 precompute spline coefficients (core::Real array => core::Real coeffs) More...
 
void core::scoring::electron_density::conj_map_times (ObjexxFCL::FArray3D< std::complex< core::Real > > &map_product, ObjexxFCL::FArray3D< std::complex< core::Real > > const &mapA, ObjexxFCL::FArray3D< std::complex< core::Real > > const &mapB)
 
ObjexxFCL::FArray3D< core::Realcore::scoring::electron_density::convolute_maps (ObjexxFCL::FArray3D< core::Real > const &mapA, ObjexxFCL::FArray3D< core::Real > const &mapB)
 
core::Real core::scoring::electron_density::interp_spline (ObjexxFCL::FArray4D< core::Real > &coeffs, core::Real slab, numeric::xyzVector< core::Real > const &idxX)
 4D interpolants More...
 
void core::scoring::electron_density::interp_dspline (ObjexxFCL::FArray4D< core::Real > &coeffs, numeric::xyzVector< core::Real > const &idxX, core::Real slab, numeric::xyzVector< core::Real > &gradX, core::Real &gradSlab)
 spline interpolation with periodic boundaries More...
 
void core::scoring::electron_density::spline_coeffs (ObjexxFCL::FArray4D< core::Real > const &data, ObjexxFCL::FArray4D< core::Real > &coeffs)
 
void core::scoring::electron_density::spline_coeffs (ObjexxFCL::FArray4D< float > const &data, ObjexxFCL::FArray4D< core::Real > &coeffs)
 
void core::scoring::electron_density::calculate_density_nbr (pose::Pose &pose, std::map< Size, Real > &per_rsd_dens, std::map< Size, Real > &per_rsd_nbrdens, core::conformation::symmetry::SymmetryInfoCOP syminfo, bool mixed_sliding_window=false, Size sliding_window_size=3)
 Calculate the density and relative neighbor density score. Map must be initialized to number of calculation residues. More...
 
void core::scoring::electron_density::calculate_geometry (pose::Pose &pose, std::map< Size, Real > &geometry, Size n_symm_subunit, Real weight=1.0)
 Calculate the geometry score using cartesian scoring. Map must be initialized to number of calculation residues. More...
 
void core::scoring::electron_density::calculate_rama (pose::Pose &pose, std::map< Size, Real > &rama, Size n_symm_subunit, Real weight=0.2)
 Calculate the geometry score using rama or sugar_bb Map must be initialized to number of calculation residues. More...
 
void core::scoring::electron_density::calc_per_rsd_score (pose::Pose &pose, scoring::ScoreType const &score_type, std::map< Size, Real > &per_rsd_score, Size n_symm_subunit, Real weight)
 Fill the weighted per-residue weighted score of a particular score type Note, does not decompose pair-energies, but does work with symmetry. More...
 
template<class S , class T >
void core::scoring::electron_density::resample (ObjexxFCL::FArray3D< S > const &density, ObjexxFCL::FArray3D< T > &newDensity, numeric::xyzVector< int > newDims)
 templated helper function to FFT resample a map More...
 

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