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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< ArcArcs
 
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< XYZXYZs
 
typedef XYZs::iterator XYZIter
 
typedef XYZs::const_iterator XYZCIter
 
typedef utility::vector1< SphereSpheres
 
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< CavityBallClustercompute_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::Realcompute_residue_packing_scores (PosePackData &pd, core::Size oversample)
 
vector1< core::Realcompute_atom_packing_scores (PosePackData &pd, core::Size oversample)
 
core::Real compute_packing_score (Pose const &pose, core::Size oversample)
 
vector1< core::Realcompute_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::Realcompute_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 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 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<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 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

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 
)
XYZs core::scoring::packstat::check_surface_area_leerichards_deriv ( PosePackDataOP  pd,
Real  slicesize,
Real  pr,
bool  csa,
Size  max_num 
)
utility::vector1< core::Real > core::scoring::packstat::compute_atom_packing_scores ( PosePackData pd,
core::Size  oversample 
)
core::id::AtomID_Map< core::Real > core::scoring::packstat::compute_atom_packing_scores ( Pose const &  pose,
core::Size  oversample 
)
utility::vector1< CavityBallCluster > core::scoring::packstat::compute_cav_ball_clusters ( CavBalls cavballs,
SasaOptions const &  opts 
)
void core::scoring::packstat::compute_cav_ball_neighbor_count ( Spheres spheres,
CavBalls cavballs,
PackstatReal  dis 
)
void core::scoring::packstat::compute_cav_ball_volumes ( CavBalls cavballs,
SasaOptions const &   
)
core::Real core::scoring::packstat::compute_packing_score ( PosePackData pd,
core::Size  oversample 
)
core::Real core::scoring::packstat::compute_packing_score ( Pose const &  pose,
core::Size  oversample 
)
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 
)
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 
)
utility::vector1< core::Real > core::scoring::packstat::compute_residue_packing_scores ( PosePackData pd,
core::Size  oversample 
)
utility::vector1< core::Real > core::scoring::packstat::compute_residue_packing_scores ( Pose const &  pose,
core::Size  oversample 
)
SasaResultOP core::scoring::packstat::compute_sasa ( Spheres spheres,
SasaOptions const &  opts 
)
template<class T >
PackstatReal core::scoring::packstat::compute_sasa_generic ( utility::vector1< T > &  S,
PackstatReal  probe,
bool  csa = true 
)
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 
)
core::Real core::scoring::packstat::compute_surface_area_leerichards ( PosePackDataOP  pd,
Real  slicesize,
Real  pr,
bool  csa,
numeric::xyzVector< Real >  plane 
)
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 
)
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)
void core::scoring::packstat::init_packing_score_respred ( PackingScore &  p)
PackstatReal core::scoring::packstat::max_rad ( Spheres const &  s)
inline
PackstatReal core::scoring::packstat::max_rad ( CavBalls const &  s)
inline
std::ostream & core::scoring::packstat::operator<< ( std::ostream &  out,
PackingScoreResData const &  dat 
)
std::ostream & core::scoring::packstat::operator<< ( std::ostream &  out,
SimplePDB const &  pdb 
)
std::ostream & core::scoring::packstat::operator<< ( std::ostream &  out,
SimplePDB_Atom const &  atom 
)
std::ostream & core::scoring::packstat::operator<< ( std::ostream &  out,
Sphere const &  sphere 
)
std::ostream & core::scoring::packstat::operator<< ( std::ostream &  out,
Circle &  circle 
)
std::istream & core::scoring::packstat::operator>> ( std::istream &  in,
SimplePDB &  pdb 
)
std::istream & core::scoring::packstat::operator>> ( std::istream &  in_raw,
SimplePDB_Atom &  atom 
)
void core::scoring::packstat::output_packstat_pdb ( core::pose::Pose pose,
std::ostream &  out 
)
Real core::scoring::packstat::overlap ( CavityBall const &  cb1,
CavityBall const &  cb2 
)
PosePackData core::scoring::packstat::pose_to_pack_data ( Pose const &  pose,
int  include_water 
)
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 
)
CavBalls core::scoring::packstat::prune_hidden_cavity_balls ( CavBalls cavballs,
SasaOptions const &  opts 
)
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 
)
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
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 
)
std::string core::scoring::packstat::ToUpper ( std::string  s)
static basic::Tracer core::scoring::packstat::TRcs ( "protocols.packstat"  )
static
void core::scoring::packstat::type_map_add ( map< P, PackstatReal > &  type_map,
string  type,
string  res,
PackstatReal  rad 
)
Real core::scoring::packstat::weight_func ( Real  d0,
Real  d 
)

Variable Documentation

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