Rosetta 3.4
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src/core/scoring/sasa.hh File Reference

routines which calculate solvent accessible surface area More...

#include <core/types.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/conformation/Residue.fwd.hh>
#include <core/id/AtomID_Map.fwd.hh>
#include <utility/vector1.hh>
#include <ObjexxFCL/FArray2D.fwd.hh>

Namespaces

namespace  core
 

A class for defining atom parameters, known as atom_types.


namespace  core::scoring

Functions

void core::scoring::input_sasa_dats ()
 Reads in the SASA database files sampling/SASA-angles.dat and sampling/SASA-masks.dat into FArrays above.
void core::scoring::get_overlap (Real const radius_a, Real const radius_b, Real const distance_ijxyz, int &degree_of_overlap)
void core::scoring::get_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)
void core::scoring::get_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)
Real core::scoring::calc_per_atom_sasa (pose::Pose const &pose, id::AtomID_Map< Real > &atom_sasa, utility::vector1< Real > &rsd_sasa, Real const probe_radius, bool const use_big_polar_H=false)
 returns total sasa
Real core::scoring::calc_per_atom_sasa (pose::Pose const &pose, id::AtomID_Map< Real > &atom_sasa, utility::vector1< Real > &rsd_sasa, Real const probe_radius, bool const use_big_polar_H, id::AtomID_Map< bool > &atom_subset, bool const use_naccess_sasa_radii=false, bool const expand_polar_radii=false, Real const polar_expansion_radius=1.0)
 returns total sasa
void core::scoring::calc_atom_masks (core::conformation::Residue const &irsd, core::conformation::Residue const &jrsd, Real const probe_radius, Real const cutoff_distance, utility::vector1< Real > const &radii, id::AtomID_Map< bool > const &atom_subset, core::id::AtomID_Map< utility::vector1< ObjexxFCL::ubyte > > &atom_masks)
Real core::scoring::calc_total_sasa (pose::Pose const &pose, Real const probe_radius)
 returns total sasa
int core::scoring::get_num_bytes ()
 Returns the number of bytes the overlap arrays use for tracking SASA. Adding this in so that the values in the SASA database files can be used in SASA-based scores. (ronj)
ObjexxFCL::FArray2D_int const & core::scoring::get_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)
ObjexxFCL::FArray2D_ubyte const & core::scoring::get_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)
Real core::scoring::calc_per_res_hydrophobic_sasa (pose::Pose const &pose, utility::vector1< Real > &rsd_sasa, utility::vector1< Real > &rsd_hydrophobic_sasa, Real const probe_radius, bool use_naccess_sasa_radii)
 Uses the method above to calculate total SASA and then only looks at the hydrophobic contribution. Returns the total hydrophobic SASA for the passed in pose. This method is being used for a protein surface score being developed by ronj. Note: Uses an atom id mask that ignores H's in the pose - only sees and computes the SASA for heavy atoms in the pose. This is done to keep things fast. Only computes the amount of hSASA per residue, not per atom. Doesn't make sense to calculate a per-atom hSASA. (ronj)
void core::scoring::print_dot_bit_string (utility::vector1< ObjexxFCL::ubyte > &values)
 helper method I was using to try to confirm that the dots are being overlapped and bits are being set correctly (ronj).

Detailed Description

routines which calculate solvent accessible surface area

Author:
Jeff Gray
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