util.cc File Reference

#include <core/chemical/AtomType.hh>
#include <core/chemical/AtomTypeSet.hh>
#include <core/conformation/Residue.hh>
#include <core/id/AtomID.hh>
#include <core/id/AtomID_Map.hh>
#include <basic/database/open.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/scoring/sasa/SasaCalc.hh>
#include <core/scoring/sasa/util.hh>
#include <core/types.hh>
#include <basic/Tracer.hh>
#include <ObjexxFCL/ubyte.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <ObjexxFCL/Fmath.hh>
#include <ObjexxFCL/format.hh>
#include <numeric/constants.hh>
#include <numeric/trig.functions.hh>
#include <utility/io/izstream.hh>
#include <cmath>
#include <cstdlib>
#include <fstream>
#include <iostream>
#include <map>
#include <algorithm>
#include <utility/vector1.hh>
#include <core/pose/util.tmpl.hh>

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

Functions
static basic::Tracer	TR ("core.scoring.sasa")
utility::vector1< Real >	core::scoring::sasa::per_res_sc_sasa (const pose::Pose &pose)
	Absolute per residue sidechain SASA. More...
utility::vector1< Real >	core::scoring::sasa::rel_per_res_sc_sasa (const pose::Pose &pose)
	Relative per residue sidechain SASA. More...
bool	core::scoring::sasa::is_res_exposed (const pose::Pose &pose, core::Size resnum)
	Is residue exposed? More...
std::pair< Real, Real >	core::scoring::sasa::get_sc_bb_sasa (const pose::Pose &pose, const id::AtomID_Map< Real > &atom_sasa)
	Calculate the sidechain and backbone sasa from atom sasa. More...
std::pair< utility::vector1 < Real >, utility::vector1 < Real > >	core::scoring::sasa::get_sc_bb_sasa_per_res (const pose::Pose &pose, const id::AtomID_Map< Real > &atom_sasa)
SasaMethodEnum	core::scoring::sasa::get_sasa_method_from_string (std::string method)
	Gets sasa enum from string passed by options system. More...
std::string	core::scoring::sasa::get_sasa_radii_parameter_name (SasaRadii radii_set)
	Get string name of SASA radii used to obtain extra parameter index from atom_type_set. More...
SasaRadii	core::scoring::sasa::get_sasa_radii_set_from_string (std::string radii_set)
	Gets sasa radii enum from string passed by options system. More...
ObjexxFCL::FArray2D_int	core::scoring::sasa::angles (num_phi, num_theta)
ObjexxFCL::FArray2D_ubyte	core::scoring::sasa::masks (num_bytes, num_overlaps *num_orientations)
ObjexxFCL::FArray2D_ubyte const &	core::scoring::sasa::get_legrand_sasa_masks ()
	Returns const access to the masks FArray, which contains the information in the SASA database file sampling/SASA-masks.dat. Adding this in so that the values in the SASA database files can be used in SASA-based scores. (ronj) More...
ObjexxFCL::FArray2D_int const &	core::scoring::sasa::get_legrand_sasa_angles ()
	Returns const access to the angles FArray, which contains the information in the SASA database file sampling/SASA-angles.dat. Adding this in so that the values in the SASA database files can be used in SASA-based scores. (ronj) More...
void	core::scoring::sasa::input_legrand_sasa_dats ()
	Reads in the SASA database files sampling/SASA-angles.dat and sampling/SASA-masks.dat into FArrays above. More...
void	core::scoring::sasa::get_legrand_atomic_overlap (Real const radius_a, Real const radius_b, Real const distance_ijxyz, int &degree_of_overlap)
void	core::scoring::sasa::get_legrand_orientation (Vector const &a_xyz, Vector const &b_xyz, int &phi_index, int &theta_index, Real distance_ijxyz)
	Gets the orientation of a to b (i to j, see below). Does this by calculating two angles, aphi and theta. (j) More...
void	core::scoring::sasa::get_legrand_2way_orientation (Vector const &a_xyz, Vector const &b_xyz, int &phi_a2b_index, int &theta_a2b_index, int &phi_b2a_index, int &theta_b2a_index, Real distance_ijxyz)
	Gets the orientation of a to b (i to j, see below). Does this by calculating two angles, aphi and theta. (j) More...

Variables
int const	core::scoring::sasa::num_bytes = 21
int const	core::scoring::sasa::num_phi = 64
int const	core::scoring::sasa::num_theta = 64
int const	core::scoring::sasa::num_overlaps = 100
int const	core::scoring::sasa::num_orientations = 162

Function Documentation

static basic::Tracer TR ( "core.scoring.sasa"  )

static