util.cc File Reference

#include <core/scoring/fiber_diffraction/util.hh>
#include <core/scoring/fiber_diffraction/CentroidScatter.hh>
#include <core/scoring/fiber_diffraction/FAScatter.hh>
#include <core/pose/util.hh>
#include <core/pose/Pose.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/AtomType.hh>
#include <core/chemical/AtomTypeSet.hh>
#include <core/chemical/AA.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/conformation/symmetry/SymmetricConformation.hh>
#include <core/conformation/symmetry/SymmetryInfo.hh>
#include <core/pose/symmetry/util.hh>
#include <basic/datacache/BasicDataCache.hh>
#include <core/pose/datacache/CacheableDataType.hh>
#include <core/pose/PDBInfo.hh>
#include <core/id/AtomID.hh>
#include <core/id/NamedAtomID.hh>
#include <core/io/pdb/build_pose_as_is.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/OptionKeys.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <basic/options/keys/edensity.OptionKeys.gen.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <basic/Tracer.hh>
#include <utility/io/izstream.hh>
#include <utility/io/ozstream.hh>
#include <numeric/statistics/functions.hh>
#include <numeric/util.hh>

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

Functions
static basic::Tracer	core::scoring::fiber_diffraction::TR ("core.scoring.fiber_diffraction.util")
void	core::scoring::fiber_diffraction::setup_cylindrical_coords (pose::Pose const &pose, core::Size &natoms, utility::vector1< Size > &atom_type_number, std::map< core::id::AtomID, core::Size > &AtomID_to_atomnbr, utility::vector1< Real > &phi, utility::vector1< Real > &z, utility::vector1< Real > &r, utility::vector1< Real > &bfactors)
void	core::scoring::fiber_diffraction::find_pitch (pose::Pose const &pose, core::Real &pitch)
void	core::scoring::fiber_diffraction::find_min_xyz (pose::Pose const &pose, core::Real &minX, core::Real &minY, core::Real &minZ, core::Real &maxX, core::Real &maxY, core::Real &maxZ)
void	core::scoring::fiber_diffraction::find_max_r (pose::Pose const &pose, core::Real &maxR)
void	core::scoring::fiber_diffraction::find_num_scattering_atoms (pose::Pose &pose, core::Size &nscatterers)
void	core::scoring::fiber_diffraction::centroid_scatter (const std::string &res_name, OneGaussianScattering &sig_centroid)
utility::vector1 < OneGaussianScattering >	core::scoring::fiber_diffraction::setup_centroid_scatter (pose::Pose &pose)
bool	core::scoring::fiber_diffraction::isPowerOfTwo (int n)
utility::vector0 < utility::vector1 < utility::vector1< core::Real > > >	core::scoring::fiber_diffraction::setup_form_factors (pose::Pose &pose, core::Size const &lmax, utility::vector0< utility::vector1< core::Real > >::iterator const &layer_lines_R, core::Real const &c, core::Real const &B_factor, core::Real const &B_factor_solv, core::Real const &Ksolv)
void	core::scoring::fiber_diffraction::generate_shannon_points (core::Size const &lmax, core::Real const &dmax, utility::vector0< utility::vector1< core::Real > >::iterator const &layer_lines_R, utility::vector0< core::Size >::iterator &sampling_points_l, utility::vector0< utility::vector1< core::Real > >::iterator &shannon_points_lS, utility::vector0< core::Size >::iterator &lowest_bessel_orders_l, utility::vector0< utility::vector0< int > >::iterator const &nvals)
void	core::scoring::fiber_diffraction::bessel_roots (core::Size const &lmax, core::Real const &c, core::Real const &res_cutoff_high, core::Real const &res_cutoff_low, core::Real &structure_cutoff, utility::vector0< utility::vector1< core::Real > > &bessel_roots_lE_, utility::vector0< core::Size > &sampling_points_l_, utility::vector0< core::Size > &lowest_bessel_orders_l_, utility::vector0< core::Size > &highest_resolution_l_, utility::vector0< core::Size > &lowest_resolution_l_, utility::vector0< utility::vector1< core::Real > >::iterator const &layer_lines_R, utility::vector0< utility::vector0< int > >::iterator const &nvals)
void	core::scoring::fiber_diffraction::interpolate_sampled_to_grid (core::Size const &lmax, utility::vector0< utility::vector1< core::Real > > const &bessel_roots_lE, utility::vector0< core::Size > const &sampling_points_l, utility::vector0< core::Size > const &highest_resolution_l, utility::vector0< core::Size > const &lowest_resolution_l, utility::vector0< utility::vector1< core::Real > >::iterator const &layer_lines_R, utility::vector0< utility::vector1< core::Size > > &selected_R_l_, utility::vector0< utility::vector1< core::Real > > &selected_Rinv_l_)
void	core::scoring::fiber_diffraction::calculate_I_of_E (core::Size const &lmax, core::Size const &k_iteration, utility::vector0< utility::vector1< core::Real > > const &sampling_points_lE, core::Size const &natoms, core::Size const &c_, utility::vector0< utility::vector0< int > >::iterator const &nvals, utility::vector1< Size > const &atom_type_number, utility::vector1< Real > const &phi, utility::vector1< Real > const &z, utility::vector1< Real > const &r, utility::vector0< utility::vector1< utility::vector1< core::Real > > >::iterator const &form_factors, utility::vector0< utility::vector1< Real > > &I_E)
core::Real	core::scoring::fiber_diffraction::calculate_chi_k (core::Size const &lmax, core::Size const &k_iteration, utility::vector0< utility::vector1< core::Size > > const &selected_R_l, utility::vector0< utility::vector1< core::Real > > const &selected_Rinv_l, utility::vector0< utility::vector1< core::Real > >::iterator const &layer_lines_I, utility::vector0< utility::vector1< core::Real > > const &I_interpolated)
core::Real	core::scoring::fiber_diffraction::calculate_chi2_free (pose::Pose &pose, core::Size const &chi_free_iterations_, core::Size const &lmax, utility::vector0< utility::vector1< core::Real > >::iterator const &layer_lines_I, utility::vector0< utility::vector1< core::Real > >::iterator const &layer_lines_R, core::Size const &natoms, core::Size const &c_, utility::vector0< utility::vector0< int > >::iterator const &nvals, utility::vector1< Size > const &atom_type_number, utility::vector1< Real > const &phi, utility::vector1< Real > const &z, utility::vector1< Real > const &r, core::Real const b_factor_, core::Real const b_factor_solv, core::Real const b_factor_solv_K)
void	core::scoring::fiber_diffraction::sample_layer_lines_from_bins (core::Size const &lmax, core::Size const &k_iteration, utility::vector0< utility::vector1< core::Real > >::iterator const &layer_lines_R, utility::vector0< utility::vector1< core::Size > > &selected_R_l_, utility::vector0< utility::vector1< core::Real > > &selected_Rinv_l_)
void	core::scoring::fiber_diffraction::rootj (int const &N, core::Real const &CUTOFF, utility::vector1< core::Real > &zeros, core::Size &npoints)
void	core::scoring::fiber_diffraction::secant (int const &N, int const &nitmx, core::Real tol, core::Real *zeroJ, int *ier)