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core::scoring::packstat Namespace Reference

Namespaces

 old
 

Classes

struct  Accumulator
 
struct  AreaAccumulator
 
struct  Array2D
 
class  AtomRadiusMap
 
class  CavityBall
 
struct  CavityBallCluster
 
struct  Circle
 
struct  Event
 
struct  HTL_EventX
 
struct  LeeRichards
 
struct  LR_AtomData
 
struct  LR_MP_AtomData
 
struct  MultiProbePerSphereAccumulator
 
struct  MultiProbePoseAccumulator
 
struct  Octree2D
 
struct  OrderCavBallOnR
 
struct  OrderCavBallOnRmAnb
 
struct  OrderCavBallOnRmE
 
struct  OrderCavBallOnX
 
struct  OrderCBC
 
struct  OrderSphereOnID
 
struct  OrderSphereOnX
 
struct  PackingScore
 
struct  PackingScoreResData
 
struct  PerSphereAccumulator
 
struct  Point
 
struct  PointPair
 
struct  PosePackData
 
struct  SasaOptions
 
struct  SasaResult
 
class  SimplePDB
 
struct  SimplePDB_Atom
 
struct  Slice
 
struct  Sphere
 
struct  trace
 

Typedefs

typedef pair< string const,
string const > 		P
 
typedef utility::vector1
< CavityBall > 		CavBalls
 
typedef utility::vector1
< CavityBall >::iterator 		CavBallIter
 
typedef utility::vector1
< CavityBall >::const_iterator 		CavBallCIter
 
using Rot = numeric::xyzMatrix< PackstatReal >
 
typedef std::pair
< numeric::xyzMatrix
< PackstatReal >
, numeric::xyzMatrix
< PackstatReal > > 		RotPair
 
typedef
utility::pointer::shared_ptr
< SasaResult > 		SasaResultOP
 
typedef
utility::pointer::shared_ptr
< SasaOptions > 		SasaOptionsOP
 
typedef utility::vector1< Event * > Events
 
typedef utility::vector1< Slice * > Slices
 
typedef utility::vector1< trace * > traces
 
typedef utility::vector1
< Circle * > 		Circles
 
typedef utility::vector1
< Event * >::iterator 		EventIter
 
typedef utility::vector1
< Circle * >::iterator 		CircleIter
 
typedef utility::vector1
< Slice * >::iterator 		SliceIter
 
typedef utility::vector1
< trace * >::iterator 		traceIter
 
typedef std::pair
< core::id::AtomID, Real > 		Arc
 
typedef utility::vector1< Arc > Arcs
 
typedef utility::vector1< Arc >
::iterator 		ArcIter
 
typedef
utility::pointer::shared_ptr
< Accumulator > 		AccumulatorOP
 
typedef
utility::pointer::shared_ptr
< AreaAccumulator > 		AreaAccumulatorOP
 
typedef
utility::pointer::shared_ptr
< PerSphereAccumulator > 		PerSphereAccumulatorOP
 
typedef
utility::pointer::shared_ptr
< MultiProbePoseAccumulator > 		MultiProbePoseAccumulatorOP
 
typedef
utility::pointer::shared_ptr
< MultiProbePerSphereAccumulator > 		MultiProbePerSphereAccumulatorOP
 
typedef
utility::pointer::shared_ptr
< PackingScoreResData > 		PackingScoreResDataOP
 
typedef
utility::pointer::shared_ptr
< PackingScoreResData const > 		PackingScoreResDataCOP
 
typedef
utility::pointer::shared_ptr
< PackingScore > 		PackingScoreOP
 
typedef
utility::pointer::shared_ptr
< PackingScore const > 		PackingScoreCOP
 
typedef utility::vector1
< SimplePDB_Atom > 		SPAtoms
 
typedef utility::vector1
< SimplePDB_Atom >::iterator 		SPAtomIter
 
typedef utility::vector1
< SimplePDB_Atom >
::const_iterator 		SPAtomCIter
 
typedef core::Real PackstatReal
 
typedef utility::vector1
< PackstatReal > 		Floats
 
typedef Floats::iterator FloatIter
 
typedef Floats::const_iterator FloatCIter
 
typedef utility::vector1
< core::Real > 		Reals
 
typedef Reals::iterator RealIter
 
typedef Reals::const_iterator RealCIter
 
typedef numeric::xyzVector
< PackstatReal > 		XYZ
 
typedef utility::vector1< XYZ > XYZs
 
typedef XYZs::iterator XYZIter
 
typedef XYZs::const_iterator XYZCIter
 
typedef utility::vector1< Sphere > Spheres
 
typedef Spheres::iterator SphereIter
 
typedef Spheres::const_iterator SphereCIter
 
typedef
utility::pointer::shared_ptr
< PosePackData > 		PosePackDataOP
 

Enumerations

enum  EventType { ENTER, EXIT, ISECT }
 

Functions

std::string ToUpper (std::string s)
 
void type_map_add (map< P, PackstatReal > &type_map, string type, string res, PackstatReal rad)
 
static basic::Tracer TRcs ("protocols.packstat")
 
RotPair rand_rot ()
 
PosePackData pose_to_pack_data (Pose const &pose, int include_water)
 
SasaResultOP compute_sasa (Spheres &spheres, SasaOptions const &opts)
 
void compute_cav_ball_volumes (CavBalls &cavballs, SasaOptions const &)
 
CavBalls prune_hidden_cavity_balls (CavBalls &cavballs, SasaOptions const &opts)
 
size_t prune_1pass (Spheres &spheres, CavBalls &cavballs, PackstatReal pr)
 
CavBalls prune_cavity_balls (Spheres &spheres, CavBalls &cavballs, SasaOptions const &opts)
 
void compute_cav_ball_neighbor_count (Spheres &spheres, CavBalls &cavballs, PackstatReal dis)
 
CavBalls select_cav_balls (CavBalls cavballs, PackstatReal spacing)
 
Real overlap (CavityBall const &cb1, CavityBall const &cb2)
 
vector1< CavityBallCluster > compute_cav_ball_clusters (CavBalls &cavballs, SasaOptions const &opts)
 
PackingScoreResDataOP compute_surrounding_sasa (XYZ const &xyz, Spheres &spheres, SasaResultOP result, SasaOptions const &opts)
 
core::Real compute_packing_score (PosePackData &pd, core::Size oversample)
 
vector1< core::Real > compute_residue_packing_scores (PosePackData &pd, core::Size oversample)
 
vector1< core::Real > compute_atom_packing_scores (PosePackData &pd, core::Size oversample)
 
core::Real compute_packing_score (Pose const &pose, core::Size oversample)
 
vector1< core::Real > compute_residue_packing_scores (Pose const &pose, core::Size oversample)
 
core::Real compute_residue_packing_score (Pose const &pose, int const seqpos, core::Size oversample)
 
core::Real compute_residue_packing_score (PosePackData &pd, int const seqpos, core::Size oversample)
 
core::id::AtomID_Map< core::Real > compute_atom_packing_scores (Pose const &pose, core::Size oversample)
 
Real weight_func (Real d0, Real d)
 
vector1< std::map< id::AtomID,
Real > > 		cavity_distance_constraint (core::pose::Pose &pose, utility::vector1< core::Size > rois, core::pose::PoseOP native)
 
void output_packstat_pdb (core::pose::Pose &pose, std::ostream &out)
 
template<class T >
PackstatReal compute_sasa_generic (utility::vector1< T > &S, PackstatReal probe, bool csa=true)
 
std::istream & operator>> (std::istream &in, SimplePDB &pdb)
 
std::ostream & operator<< (std::ostream &out, SimplePDB const &pdb)
 
template<class T >
void read_stoopid (char *buf, size_t start, size_t end, T &field)
 
std::istream & operator>> (std::istream &in_raw, SimplePDB_Atom &atom)
 
std::ostream & operator<< (std::ostream &out, SimplePDB_Atom const &atom)
 
std::ostream & operator<< (std::ostream &out, Sphere const &sphere)
 
std::ostream & operator<< (std::ostream &out, Circle &circle)
 
Real compute_surface_area_leerichards (Real &buried_area_out, PosePackDataOP pd, Real slicesize, Real pr, bool csa, numeric::xyzVector< Real > plane)
 
Real compute_surface_area_leerichards (PosePackDataOP pd, Real slicesize, Real pr, bool csa, numeric::xyzVector< Real > plane)
 
XYZs compute_surface_area_leerichards_deriv (PosePackDataOP pd, Real slicesize, Real pr, bool csa)
 
XYZs check_surface_area_leerichards_deriv (PosePackDataOP pd, Real slicesize, Real pr, bool csa, Size max_num)
 
Real compute_packing_score_leerichards (PosePackDataOP pd, Real slicesize, numeric::xyzVector< Real > plane)
 
core::Real compute_packing_score_leerichards (PosePackDataOP pd, core::Real slicesize, numeric::xyzVector< Real > plane=numeric::xyzVector< Real >(0, 0, 1))
 
void init_packing_score_respred (PackingScore &p)
 
void init_packing_score_discrim (PackingScore &p)
 
std::ostream & operator<< (std::ostream &out, PackingScoreResData const &dat)
 
utility::vector1
< numeric::xyzVector
< PackstatReal > > const 		get_sasa_dot_locations ()
 
std::size_t search_x (Spheres const &spheres, PackstatReal const x, std::size_t begin, std::size_t end)
 
std::size_t search_x (Spheres const &spheres, PackstatReal const x)
 
std::size_t search_x (CavBalls const &cbs, PackstatReal const x, std::size_t begin, std::size_t end)
 
std::size_t search_x (CavBalls const &cbs, PackstatReal const x)
 
PackstatReal max_rad (Spheres const &s)
 
PackstatReal max_rad (CavBalls const &s)
 

Variables

core::Real HYDROGEN_RADIUS = 0.0
 
core::Size const N_PROBES = 20
 

Typedef Documentation

typedef utility::pointer::shared_ptr<Accumulator> core::scoring::packstat::AccumulatorOP
typedef std::pair< core::id::AtomID,Real > core::scoring::packstat::Arc
typedef utility::vector1< Arc >::iterator core::scoring::packstat::ArcIter
typedef utility::vector1< Arc > core::scoring::packstat::Arcs
typedef utility::pointer::shared_ptr<AreaAccumulator> core::scoring::packstat::AreaAccumulatorOP
typedef utility::vector1< CavityBall >::const_iterator core::scoring::packstat::CavBallCIter
typedef utility::vector1< CavityBall >::iterator core::scoring::packstat::CavBallIter
typedef utility::vector1< CavityBall > core::scoring::packstat::CavBalls
typedef utility::vector1< Circle* >::iterator core::scoring::packstat::CircleIter
typedef utility::vector1< Circle* > core::scoring::packstat::Circles
typedef utility::vector1< Event* >::iterator core::scoring::packstat::EventIter
typedef utility::vector1< Event* > core::scoring::packstat::Events
typedef Floats::const_iterator core::scoring::packstat::FloatCIter
typedef Floats::iterator core::scoring::packstat::FloatIter
typedef utility::vector1<PackstatReal> core::scoring::packstat::Floats
typedef utility::pointer::shared_ptr<MultiProbePerSphereAccumulator> core::scoring::packstat::MultiProbePerSphereAccumulatorOP
typedef utility::pointer::shared_ptr<MultiProbePoseAccumulator> core::scoring::packstat::MultiProbePoseAccumulatorOP
typedef pair<string const,string const> core::scoring::packstat::P
typedef utility::pointer::shared_ptr< PackingScore const > core::scoring::packstat::PackingScoreCOP
typedef utility::pointer::shared_ptr< PackingScore > core::scoring::packstat::PackingScoreOP
typedef utility::pointer::shared_ptr< PackingScoreResData const > core::scoring::packstat::PackingScoreResDataCOP
typedef utility::pointer::shared_ptr< PackingScoreResData > core::scoring::packstat::PackingScoreResDataOP
typedef core::Real core::scoring::packstat::PackstatReal
typedef utility::pointer::shared_ptr<PerSphereAccumulator> core::scoring::packstat::PerSphereAccumulatorOP
typedef utility::pointer::shared_ptr<PosePackData> core::scoring::packstat::PosePackDataOP
typedef Reals::const_iterator core::scoring::packstat::RealCIter
typedef Reals::iterator core::scoring::packstat::RealIter
typedef utility::vector1<core::Real> core::scoring::packstat::Reals
using core::scoring::packstat::Rot = typedef numeric::xyzMatrix<PackstatReal>
typedef std::pair< numeric::xyzMatrix<PackstatReal>, numeric::xyzMatrix<PackstatReal> > core::scoring::packstat::RotPair
typedef utility::pointer::shared_ptr< SasaOptions > core::scoring::packstat::SasaOptionsOP
typedef utility::pointer::shared_ptr< SasaResult > core::scoring::packstat::SasaResultOP
typedef utility::vector1< Slice* >::iterator core::scoring::packstat::SliceIter
typedef utility::vector1< Slice* > core::scoring::packstat::Slices
typedef utility::vector1<SimplePDB_Atom>::const_iterator core::scoring::packstat::SPAtomCIter
typedef utility::vector1<SimplePDB_Atom>::iterator core::scoring::packstat::SPAtomIter
typedef utility::vector1<SimplePDB_Atom> core::scoring::packstat::SPAtoms
typedef Spheres::const_iterator core::scoring::packstat::SphereCIter
typedef Spheres::iterator core::scoring::packstat::SphereIter
typedef utility::vector1<Sphere> core::scoring::packstat::Spheres
typedef utility::vector1< trace* >::iterator core::scoring::packstat::traceIter
typedef utility::vector1< trace* > core::scoring::packstat::traces
typedef numeric::xyzVector<PackstatReal> core::scoring::packstat::XYZ
typedef XYZs::const_iterator core::scoring::packstat::XYZCIter
typedef XYZs::iterator core::scoring::packstat::XYZIter
typedef utility::vector1<XYZ> core::scoring::packstat::XYZs

Enumeration Type Documentation

enum core::scoring::packstat::EventType
Enumerator
ENTER 
EXIT 
ISECT 

Function Documentation

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 
)

References compute_cav_ball_clusters(), compute_cav_ball_neighbor_count(), compute_cav_ball_volumes(), compute_sasa(), protocols::hybridization::d0, core::pose::Pose::dump_pdb(), core::chemical::element::F, core::chemical::element::I, core::conformation::Residue::nheavyatoms(), core::conformation::membrane::out, pose_to_pack_data(), prune_cavity_balls(), prune_hidden_cavity_balls(), core::scoring::packstat::SasaOptions::prune_max_iters, core::pose::Pose::residue(), core::pose::Pose::size(), TRcs(), weight_func(), protocols::kinmatch::xyz(), core::conformation::Residue::xyz(), and core::pose::Pose::xyz().

XYZs core::scoring::packstat::check_surface_area_leerichards_deriv ( PosePackDataOP  pd,
Real  slicesize,
Real  pr,
bool  csa,
Size  max_num 
)

References compute_surface_area_leerichards(), core::id::D, protocols::mean_field::min(), and core::chemical::element::N.

utility::vector1< core::Real > core::scoring::packstat::compute_atom_packing_scores ( PosePackData &  pd,
core::Size  oversample 
)

References core::scoring::packstat::PosePackData::centers, compute_sasa(), compute_surrounding_sasa(), init_packing_score_discrim(), core::scoring::packstat::SasaOptions::prune_max_iters, core::scoring::packstat::PackingScore::score(), and core::scoring::packstat::PosePackData::spheres.

Referenced by compute_atom_packing_scores(), and compute_residue_packing_scores().

core::id::AtomID_Map< core::Real > core::scoring::packstat::compute_atom_packing_scores ( Pose const &  pose,
core::Size  oversample 
)

References compute_atom_packing_scores(), core::pose::initialize_atomid_map(), core::conformation::Residue::nheavyatoms(), pose_to_pack_data(), core::pose::Pose::residue(), and core::pose::Pose::size().

utility::vector1< CavityBallCluster > core::scoring::packstat::compute_cav_ball_clusters ( CavBalls &  cavballs,
SasaOptions const &  opts 
)

References core::scoring::packstat::CavityBall::area, core::pack::dunbrack::c, core::scoring::packstat::CavityBallCluster::cavballs, core::scoring::packstat::CavityBallCluster::center, core::scoring::packstat::CavityBall::cluster_, core::scoring::packstat::SasaOptions::cluster_min_volume, core::scoring::packstat::CavityBall::exposed_radius, protocols::mean_field::max(), protocols::mean_field::min(), core::scoring::packstat::SasaOptions::min_cluster_overlap, overlap(), core::scoring::packstat::CavityBallCluster::surface_accessibility, core::scoring::packstat::CavityBallCluster::surface_area, core::scoring::packstat::CavityBall::vol, core::scoring::packstat::CavityBallCluster::volume, and core::scoring::packstat::CavityBall::xyz().

Referenced by cavity_distance_constraint(), and output_packstat_pdb().

void core::scoring::packstat::compute_cav_ball_neighbor_count ( Spheres &  spheres,
CavBalls &  cavballs,
PackstatReal  dis 
)

Referenced by cavity_distance_constraint(), and protocols::simple_moves::AddCavitiesMover::get_cavities().

void core::scoring::packstat::compute_cav_ball_volumes ( CavBalls &  cavballs,
SasaOptions const &   
)

References core::scoring::angles(), core::scoring::bit_count, core::scoring::get_orientation(), core::scoring::get_overlap(), core::scoring::maskbits, core::scoring::packstat::old::maskbits, core::scoring::masks(), core::scoring::packstat::old::nbytes, core::scoring::packstat::CavityBall::radius(), core::scoring::packstat::CavityBall::radius_, and core::scoring::packstat::CavityBall::xyz().

Referenced by cavity_distance_constraint(), and output_packstat_pdb().

core::Real core::scoring::packstat::compute_packing_score ( PosePackData &  pd,
core::Size  oversample 
)

References core::scoring::packstat::PosePackData::centers, compute_sasa(), compute_surrounding_sasa(), init_packing_score_discrim(), core::scoring::packstat::SasaOptions::prune_max_iters, core::scoring::packstat::PackingScore::score(), and core::scoring::packstat::PosePackData::spheres.

Referenced by protocols::analysis::PackStatMover::apply(), protocols::flxbb::FlxbbDesign::apply(), protocols::flxbb::FilterStructs_Packstat::apply(), protocols::simple_filters::PackStatFilter::compute(), compute_packing_score(), core::scoring::methods::PackStatEnergy::finalize_total_energy(), and protocols::pose_metric_calculators::PackstatCalculator::recompute().

core::Real core::scoring::packstat::compute_packing_score ( Pose const &  pose,
core::Size  oversample 
)

References compute_packing_score(), and pose_to_pack_data().

core::Real core::scoring::packstat::compute_packing_score_leerichards ( PosePackDataOP  pd,
core::Real  slicesize,
numeric::xyzVector< Real >  plane = numeric::xyzVector< Real >(0, 0, 1) 
)
Real core::scoring::packstat::compute_packing_score_leerichards ( PosePackDataOP  pd,
Real  slicesize,
numeric::xyzVector< Real >  plane 
)

References init_packing_score_discrim(), core::scoring::packstat::MultiProbePerSphereAccumulator::MultiProbePerSphereAccumulator(), and core::scoring::packstat::PackingScore::score().

core::Real core::scoring::packstat::compute_residue_packing_score ( Pose const &  pose,
int const  seqpos,
core::Size  oversample 
)

References pose_to_pack_data().

core::Real core::scoring::packstat::compute_residue_packing_score ( PosePackData &  pd,
int const  seqpos,
core::Size  oversample 
)

References core::scoring::packstat::PosePackData::centers, compute_sasa(), compute_surrounding_sasa(), init_packing_score_discrim(), core::scoring::packstat::SasaOptions::prune_max_iters, core::scoring::packstat::PackingScore::score(), and core::scoring::packstat::PosePackData::spheres.

utility::vector1< core::Real > core::scoring::packstat::compute_residue_packing_scores ( PosePackData &  pd,
core::Size  oversample 
)

References compute_atom_packing_scores().

Referenced by protocols::analysis::PackStatMover::apply(), protocols::analysis::InterfaceAnalyzerMover::compute_interface_packstat(), compute_residue_packing_scores(), and protocols::pose_metric_calculators::PackstatCalculator::recompute().

utility::vector1< core::Real > core::scoring::packstat::compute_residue_packing_scores ( Pose const &  pose,
core::Size  oversample 
)

References compute_residue_packing_scores(), and pose_to_pack_data().

SasaResultOP core::scoring::packstat::compute_sasa ( Spheres &  spheres,
SasaOptions const &  opts 
)

References core::scoring::angles(), core::scoring::bit_count, core::scoring::packstat::SasaResult::cavballs, core::conformation::membrane::center, core::scoring::packstat::SasaOptions::dont_compute_cav_balls, core::scoring::get_orientation(), core::scoring::get_overlap(), get_sasa_dot_locations(), core::scoring::input_sasa_dats(), core::scoring::maskbits, core::scoring::masks(), protocols::mean_field::min(), core::scoring::packstat::SasaOptions::min_cav_ball_radius, core::scoring::packstat::SasaOptions::min_hole_radius, core::scoring::packstat::old::nbytes, core::scoring::packstat::SasaOptions::num_cav_ball_layers, core::scoring::packstat::SasaOptions::probe_radii, rand_rot(), rot(), core::scoring::packstat::SasaResult::sphere_sasa, and protocols::kinmatch::xyz().

Referenced by cavity_distance_constraint(), compute_atom_packing_scores(), compute_packing_score(), compute_residue_packing_score(), protocols::simple_moves::AddCavitiesMover::get_cavities(), and output_packstat_pdb().

template<class T >
PackstatReal core::scoring::packstat::compute_sasa_generic ( utility::vector1< T > &  S,
PackstatReal  probe,
bool  csa = true 
)

References core::scoring::packstat::old::angles, core::scoring::packstat::old::bit_count, core::scoring::csa, core::scoring::packstat::old::get_orientation(), core::scoring::packstat::old::get_overlap(), core::scoring::packstat::old::input_sasa_dats(), core::scoring::packstat::old::maskbits, core::scoring::packstat::old::masks, core::scoring::packstat::old::nbytes, protocols::analysis::total, and protocols::kinmatch::xyz().

core::Real core::scoring::packstat::compute_surface_area_leerichards ( Real &  buried_area_out,
PosePackDataOP  pd,
Real  slicesize,
Real  pr,
bool  csa,
numeric::xyzVector< Real >  plane 
)

Referenced by check_surface_area_leerichards_deriv(), and compute_surface_area_leerichards().

core::Real core::scoring::packstat::compute_surface_area_leerichards ( PosePackDataOP  pd,
Real  slicesize,
Real  pr,
bool  csa,
numeric::xyzVector< Real >  plane 
)

References compute_surface_area_leerichards().

XYZs core::scoring::packstat::compute_surface_area_leerichards_deriv ( PosePackDataOP  pd,
Real  slicesize,
Real  pr,
bool  csa 
)
PackingScoreResDataOP core::scoring::packstat::compute_surrounding_sasa ( XYZ const &  xyz,
Spheres &  spheres,
SasaResultOP  result,
SasaOptions const &  opts 
)

References core::scoring::packstat::SasaOptions::num_surrounding_sasa_bins, core::scoring::packstat::SasaOptions::probe_radii, core::scoring::packstat::SasaOptions::surrounding_sasa_smoothing_window, and core::scoring::packstat::Sphere::xyz.

Referenced by compute_atom_packing_scores(), compute_packing_score(), and compute_residue_packing_score().

utility::vector1<numeric::xyzVector<PackstatReal> > const core::scoring::packstat::get_sasa_dot_locations ( )
inline

Referenced by compute_sasa().

void core::scoring::packstat::init_packing_score_discrim ( PackingScore &  p)

References core::scoring::packstat::PackingScore::center(), core::scoring::packstat::PackingScore::compprob(), core::scoring::packstat::PackingScore::probA(), core::scoring::packstat::PackingScore::probB(), core::scoring::packstat::PackingScore::rho(), and core::scoring::packstat::PackingScore::weight().

Referenced by compute_atom_packing_scores(), compute_packing_score(), compute_packing_score_leerichards(), and compute_residue_packing_score().

void core::scoring::packstat::init_packing_score_respred ( PackingScore &  p)

References core::scoring::packstat::PackingScore::center(), core::scoring::packstat::PackingScore::compprob(), core::scoring::packstat::PackingScore::probA(), core::scoring::packstat::PackingScore::probB(), core::scoring::packstat::PackingScore::rho(), and core::scoring::packstat::PackingScore::weight().

PackstatReal core::scoring::packstat::max_rad ( Spheres const &  s)
inline

Referenced by prune_1pass(), and prune_hidden_cavity_balls().

PackstatReal core::scoring::packstat::max_rad ( CavBalls const &  s)
inline
std::ostream & core::scoring::packstat::operator<< ( std::ostream &  out,
PackingScoreResData const &  dat 
)

References core::scoring::packstat::PackingScoreResData::msa(), core::scoring::packstat::PackingScoreResData::npr(), core::scoring::packstat::PackingScoreResData::nrad(), and core::conformation::membrane::out.

std::ostream & core::scoring::packstat::operator<< ( std::ostream &  out,
SimplePDB const &  pdb 
)

References core::scoring::packstat::SimplePDB::atoms_, and core::conformation::membrane::out.

std::ostream & core::scoring::packstat::operator<< ( std::ostream &  out,
SimplePDB_Atom const &  atom 
)

References core::scoring::packstat::SimplePDB_Atom::ATOM, core::scoring::packstat::SimplePDB_Atom::bfac, core::scoring::packstat::SimplePDB_Atom::chain, core::scoring::packstat::SimplePDB_Atom::lastcol, core::scoring::packstat::SimplePDB_Atom::num, core::scoring::packstat::SimplePDB_Atom::occ, core::conformation::membrane::out, core::scoring::packstat::SimplePDB_Atom::res, core::scoring::packstat::SimplePDB_Atom::resnum, core::scoring::packstat::SimplePDB_Atom::type, core::scoring::packstat::SimplePDB_Atom::x, core::scoring::packstat::SimplePDB_Atom::y, and core::scoring::packstat::SimplePDB_Atom::z.

std::ostream & core::scoring::packstat::operator<< ( std::ostream &  out,
Sphere const &  sphere 
)

References core::conformation::membrane::out, core::scoring::packstat::Sphere::radius, and core::scoring::packstat::Sphere::xyz.

std::ostream & core::scoring::packstat::operator<< ( std::ostream &  out,
Circle &  circle 
)

References core::conformation::membrane::out, core::scoring::packstat::Circle::r, core::scoring::packstat::Circle::x, and core::scoring::packstat::Circle::y.

std::istream & core::scoring::packstat::operator>> ( std::istream &  in,
SimplePDB &  pdb 
)

References core::scoring::packstat::SimplePDB::atoms_, core::conformation::membrane::in, core::scoring::packstat::SimplePDB_Atom::num, and core::scoring::packstat::SimplePDB::remove_surface_waters().

std::istream & core::scoring::packstat::operator>> ( std::istream &  in_raw,
SimplePDB_Atom &  atom 
)

References core::scoring::packstat::SimplePDB_Atom::ATOM, core::scoring::packstat::SimplePDB_Atom::bfac, core::scoring::packstat::SimplePDB_Atom::chain, core::scoring::packstat::SimplePDB_Atom::icode, core::scoring::packstat::SimplePDB_Atom::lastcol, core::scoring::packstat::SimplePDB_Atom::num, core::scoring::packstat::SimplePDB_Atom::occ, core::scoring::packstat::SimplePDB_Atom::res, core::scoring::packstat::SimplePDB_Atom::resnum, core::scoring::packstat::SimplePDB_Atom::type, core::scoring::packstat::SimplePDB_Atom::whole_line, core::scoring::packstat::SimplePDB_Atom::x, core::scoring::packstat::SimplePDB_Atom::y, and core::scoring::packstat::SimplePDB_Atom::z.

void core::scoring::packstat::output_packstat_pdb ( core::pose::Pose &  pose,
std::ostream &  out 
)

References compute_cav_ball_clusters(), compute_cav_ball_volumes(), compute_sasa(), pose_to_pack_data(), prune_cavity_balls(), prune_hidden_cavity_balls(), core::scoring::packstat::SasaOptions::prune_max_iters, core::pose::Pose::size(), and TRcs().

Real core::scoring::packstat::overlap ( CavityBall const &  cb1,
CavityBall const &  cb2 
)

References protocols::hybridization::r1, protocols::hybridization::r2, core::scoring::packstat::CavityBall::radius(), and core::scoring::packstat::CavityBall::xyz().

Referenced by protocols::denovo_design::movers::add_overlap_to_loops(), protocols::comparative_modeling::AlignmentClustering::AlignmentClustering(), protocols::indexed_structure_store::append_pose_with_overlap(), compute_cav_ball_clusters(), protocols::simple_filters::SymmetricMotifFilter::compute_d2(), core::pack::interaction_graph::RotamerDots::get_res_res_overlap(), protocols::denovo_design::loop_start_without_overlap(), protocols::denovo_design::loop_stop_without_overlap(), core::scoring::electron_density::ElectronDensity::rescale_fastscoring_temp_bins(), and protocols::hybridization::DomainAssembly::run().

PosePackData core::scoring::packstat::pose_to_pack_data ( Pose const &  pose,
int  include_water 
)

References core::io::pdb::dump_pdb(), and core::scoring::packstat::PosePackData::spheres.

Referenced by protocols::analysis::PackStatMover::apply(), cavity_distance_constraint(), compute_atom_packing_scores(), compute_packing_score(), compute_residue_packing_score(), compute_residue_packing_scores(), protocols::simple_moves::AddCavitiesMover::get_cavities(), and output_packstat_pdb().

size_t core::scoring::packstat::prune_1pass ( Spheres &  spheres,
CavBalls &  cavballs,
PackstatReal  pr 
)

References core::scoring::angles(), core::scoring::bit_count, core::scoring::packstat::CavityBall::exposed_radius, core::scoring::get_orientation(), core::scoring::get_overlap(), core::scoring::packstat::old::maskbits, core::scoring::masks(), max_rad(), core::scoring::packstat::old::nbytes, core::scoring::packstat::Sphere::radius, core::scoring::packstat::CavityBall::radius(), core::scoring::packstat::CavityBall::radius_, search_x(), core::scoring::packstat::Sphere::xyz, and core::scoring::packstat::CavityBall::xyz().

Referenced by prune_cavity_balls().

CavBalls core::scoring::packstat::prune_cavity_balls ( Spheres &  spheres,
CavBalls &  cavballs,
SasaOptions const &  opts 
)

References prune_1pass(), core::scoring::packstat::SasaOptions::prune_cavity_burial_probe_radii, core::scoring::packstat::SasaOptions::prune_max_delta, core::scoring::packstat::SasaOptions::prune_max_iters, and TRcs().

Referenced by cavity_distance_constraint(), protocols::simple_moves::AddCavitiesMover::get_cavities(), and output_packstat_pdb().

CavBalls core::scoring::packstat::prune_hidden_cavity_balls ( CavBalls &  cavballs,
SasaOptions const &  opts 
)

References core::scoring::angles(), core::scoring::packstat::SasaOptions::area_cav_ball_required_exposed, core::scoring::bit_count, core::scoring::packstat::SasaOptions::frac_cav_ball_required_exposed, core::scoring::get_orientation(), core::scoring::get_overlap(), core::scoring::maskbits, core::scoring::packstat::old::maskbits, core::scoring::masks(), max_rad(), core::scoring::packstat::old::nbytes, core::scoring::packstat::CavityBall::radius(), core::scoring::packstat::CavityBall::radius_, and core::scoring::packstat::CavityBall::xyz().

Referenced by cavity_distance_constraint(), protocols::simple_moves::AddCavitiesMover::get_cavities(), and output_packstat_pdb().

RotPair core::scoring::packstat::rand_rot ( )

References protocols::rigid::random.

Referenced by compute_sasa().

template<class T >
void core::scoring::packstat::read_stoopid ( char *  buf,
size_t  start,
size_t  end,
T &  field 
)

References protocols::loops::start.

std::size_t core::scoring::packstat::search_x ( Spheres const &  spheres,
PackstatReal const  x,
std::size_t  begin,
std::size_t  end 
)
inline

References protocols::kinmatch::xyz().

Referenced by prune_1pass(), and search_x().

std::size_t core::scoring::packstat::search_x ( Spheres const &  spheres,
PackstatReal const  x 
)
inline

References search_x().

std::size_t core::scoring::packstat::search_x ( CavBalls const &  cbs,
PackstatReal const  x,
std::size_t  begin,
std::size_t  end 
)
inline

References search_x(), and protocols::kinmatch::xyz().

std::size_t core::scoring::packstat::search_x ( CavBalls const &  cbs,
PackstatReal const  x 
)
inline

References search_x().

CavBalls core::scoring::packstat::select_cav_balls ( CavBalls  cavballs,
PackstatReal  spacing 
)

Referenced by protocols::simple_moves::AddCavitiesMover::get_cavities().

std::string core::scoring::packstat::ToUpper ( std::string  s)

Referenced by core::scoring::packstat::AtomRadiusMap::get_radius(), and type_map_add().

static basic::Tracer core::scoring::packstat::TRcs ( "protocols.packstat"  )
static

Referenced by cavity_distance_constraint(), output_packstat_pdb(), and prune_cavity_balls().

void core::scoring::packstat::type_map_add ( map< P, PackstatReal > &  type_map,
string  type,
string  res,
PackstatReal  rad 
)

References ToUpper().

Referenced by core::scoring::packstat::AtomRadiusMap::AtomRadiusMap().

Real core::scoring::packstat::weight_func ( Real  d0,
Real  d 
)

Referenced by cavity_distance_constraint(), core::scoring::NeighborList::declare_atom_neighbor_1sided(), core::scoring::NeighborList::declare_atoms_neighbors(), and core::scoring::NeighborList::setup().

Variable Documentation

core::Real core::scoring::packstat::HYDROGEN_RADIUS = 0.0

Referenced by core::scoring::packstat::AtomRadiusMap::AtomRadiusMap(), and core::scoring::packstat::AtomRadiusMap::get_radius().

core::Size const core::scoring::packstat::N_PROBES = 20

Referenced by core::scoring::packstat::MultiProbePoseAccumulator::show().

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