util.cc File Reference

#include <core/scoring/electron_density/util.hh>
#include <core/scoring/electron_density/SplineInterp.hh>
#include <core/conformation/Residue.hh>
#include <core/scoring/ScoreFunction.hh>
#include <basic/options/option.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoreTypeManager.hh>
#include <core/scoring/ScoreType.hh>
#include <core/scoring/EnergyMap.hh>
#include <core/scoring/Energies.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/symmetry/util.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <core/scoring/EnergyGraph.hh>
#include <core/scoring/electron_density/ElectronDensity.hh>
#include <core/conformation/symmetry/SymmetricConformation.hh>
#include <core/conformation/symmetry/SymmetryInfo.hh>
#include <core/scoring/symmetry/SymmetricScoreFunction.hh>
#include <iostream>
#include <basic/options/keys/edensity.OptionKeys.gen.hh>
#include <basic/options/keys/patterson.OptionKeys.gen.hh>
#include <utility/vector1.hh>
#include <basic/Tracer.hh>

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

Functions
static basic::Tracer	core::scoring::electron_density::TR ("protocols.scoring.electron_density.util")
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)
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::Real >	core::scoring::electron_density::interp_dspline (ObjexxFCL::FArray3D< core::Real > &coeffs, numeric::xyzVector< core::Real > const &idxX, bool mirrored)
	spline interpolation with periodic boundaries 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::Real >	core::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< core::Real > const &data, ObjexxFCL::FArray3D< core::Real > &coeffs, bool mirrored=false)
	precompute spline coefficients (float array => core::Real coeffs) 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::Real >	core::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_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::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::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...

Detailed Description

Author