compute_sasa.cc File Reference

#include <cmath>
#include <basic/database/open.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/io/StructFileRepOptions.hh>
#include <basic/options/keys/packstat.OptionKeys.gen.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/scoring/packstat/compute_sasa.hh>
#include <core/scoring/packstat/packing_score_params.hh>
#include <core/scoring/packstat/sasa_dot_locations.hh>
#include <core/scoring/packstat/SimplePDB.hh>
#include <core/scoring/packstat/util.hh>
#include <core/types.hh>
#include <basic/Tracer.hh>
#include <cstdlib>
#include <fstream>
#include <iostream>
#include <numeric/numeric.functions.hh>
#include <numeric/NumericTraits.hh>
#include <ObjexxFCL/FArray1D.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <ObjexxFCL/FArray3D.hh>
#include <ObjexxFCL/ubyte.hh>
#include <set>
#include <sstream>
#include <utility/exit.hh>
#include <utility/io/izstream.hh>
#include <utility/io/ozstream.hh>
#include <core/scoring/packstat/AtomRadiusMap.hh>
#include <utility/vector1.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/xyzVector.io.hh>
#include <numeric/random/random.fwd.hh>
#include <ObjexxFCL/format.hh>
#include <core/pose/util.tmpl.hh>

Classes
struct	core::scoring::packstat::OrderSphereOnX
struct	core::scoring::packstat::OrderSphereOnID
struct	core::scoring::packstat::OrderCavBallOnX
struct	core::scoring::packstat::OrderCavBallOnRmE
struct	core::scoring::packstat::OrderCavBallOnR
struct	core::scoring::packstat::OrderCavBallOnRmAnb

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

Typedefs
using	core::scoring::packstat::Rot = numeric::xyzMatrix< PackstatReal >
typedef std::pair < numeric::xyzMatrix < PackstatReal > , numeric::xyzMatrix < PackstatReal > >	core::scoring::packstat::RotPair

Functions
static basic::Tracer	core::scoring::packstat::TRcs ("protocols.packstat")
FArray2D_int	core::scoring::packstat::old::angles (nphi, ntheta)
FArray2D_ubyte	core::scoring::packstat::old::masks (nbytes, nolp *nori)
void	core::scoring::packstat::old::input_sasa_dats ()
	cj Reads in sampling/SASA-angles.dat sampling/SASA-masks.dat More...
RotPair	core::scoring::packstat::rand_rot ()
PosePackData	core::scoring::packstat::pose_to_pack_data (Pose const &pose, int include_water)
SasaResultOP	core::scoring::packstat::compute_sasa (Spheres &spheres, SasaOptions const &opts)
void	core::scoring::packstat::compute_cav_ball_volumes (CavBalls &cavballs, SasaOptions const &)
CavBalls	core::scoring::packstat::prune_hidden_cavity_balls (CavBalls &cavballs, SasaOptions const &opts)
size_t	core::scoring::packstat::prune_1pass (Spheres &spheres, CavBalls &cavballs, PackstatReal pr)
CavBalls	core::scoring::packstat::prune_cavity_balls (Spheres &spheres, CavBalls &cavballs, SasaOptions const &opts)
void	core::scoring::packstat::compute_cav_ball_neighbor_count (Spheres &spheres, CavBalls &cavballs, PackstatReal dis)
CavBalls	core::scoring::packstat::select_cav_balls (CavBalls cavballs, PackstatReal spacing)
Real	core::scoring::packstat::overlap (CavityBall const &cb1, CavityBall const &cb2)
vector1< CavityBallCluster >	core::scoring::packstat::compute_cav_ball_clusters (CavBalls &cavballs, SasaOptions const &opts)
PackingScoreResDataOP	core::scoring::packstat::compute_surrounding_sasa (XYZ const &xyz, Spheres &spheres, SasaResultOP result, SasaOptions const &opts)
core::Real	core::scoring::packstat::compute_packing_score (PosePackData &pd, core::Size oversample)
vector1< core::Real >	core::scoring::packstat::compute_residue_packing_scores (PosePackData &pd, core::Size oversample)
vector1< core::Real >	core::scoring::packstat::compute_atom_packing_scores (PosePackData &pd, core::Size oversample)
core::Real	core::scoring::packstat::compute_packing_score (Pose const &pose, core::Size oversample)
vector1< core::Real >	core::scoring::packstat::compute_residue_packing_scores (Pose const &pose, core::Size oversample)
core::Real	core::scoring::packstat::compute_residue_packing_score (Pose const &pose, int const seqpos, core::Size oversample)
core::Real	core::scoring::packstat::compute_residue_packing_score (PosePackData &pd, int const seqpos, core::Size oversample)
core::id::AtomID_Map< core::Real >	core::scoring::packstat::compute_atom_packing_scores (Pose const &pose, core::Size oversample)
Real	core::scoring::packstat::weight_func (Real d0, Real d)
vector1< std::map< id::AtomID, Real > >	core::scoring::packstat::cavity_distance_constraint (core::pose::Pose &pose, utility::vector1< core::Size > rois, core::pose::PoseOP native)
void	core::scoring::packstat::output_packstat_pdb (core::pose::Pose &pose, std::ostream &out)

Variables
short const	core::scoring::packstat::old::bit_count []
int const	core::scoring::packstat::old::nbytes = { 21 }
int const	core::scoring::packstat::old::nphi = { 64 }
int const	core::scoring::packstat::old::ntheta = { 64 }
int const	core::scoring::packstat::old::nolp = { 100 }
int const	core::scoring::packstat::old::nori = { 162 }
int const	core::scoring::packstat::old::maskbits = { 162 }