util.hh File Reference

routines which calculate solvent accessible surface area More...

#include <core/types.hh>
#include <core/conformation/Residue.fwd.hh>
#include <core/id/AtomID_Map.fwd.hh>
#include <core/scoring/sasa/SasaMethod.hh>
#include <core/scoring/sasa/SasaMethodFactory.hh>
#include <ObjexxFCL/FArray2D.fwd.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <ObjexxFCL/ubyte.hh>

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

Functions
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 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...
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...
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...

Detailed Description

routines which calculate solvent accessible surface area

Author

Jeff Gray, Jerry Tsai (Fortran)

Ron Jacak, Jared Adolf-Bryfogle