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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< CavityBallClustercore::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::Realcore::scoring::packstat::compute_residue_packing_scores (PosePackData &pd, core::Size oversample)
 
vector1< core::Realcore::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::Realcore::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::Realcore::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 }