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
typedef numeric::xyzMatrix < PackstatReal >	Rot
typedef std::pair < numeric::xyzMatrix < PackstatReal > , numeric::xyzMatrix < PackstatReal > >	RotPair
typedef utility::pointer::owning_ptr < SasaResult >	SasaResultOP
typedef utility::pointer::owning_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::owning_ptr < Accumulator >	AccumulatorOP
typedef utility::pointer::owning_ptr < AreaAccumulator >	AreaAccumulatorOP
typedef utility::pointer::owning_ptr < PerSphereAccumulator >	PerSphereAccumulatorOP
typedef utility::pointer::owning_ptr < MultiProbePoseAccumulator >	MultiProbePoseAccumulatorOP
typedef utility::pointer::owning_ptr < MultiProbePerSphereAccumulator >	MultiProbePerSphereAccumulatorOP
typedef utility::pointer::owning_ptr < PackingScoreResData >	PackingScoreResDataOP
typedef utility::pointer::owning_ptr < PackingScoreResData const >	PackingScoreResDataCOP
typedef utility::pointer::owning_ptr < PackingScore >	PackingScoreOP
typedef utility::pointer::owning_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 double	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::owning_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)
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))
core::Real	compute_surface_area_leerichards (Real &buried_area_out, PosePackDataOP pd, Real slicesize, Real pr, bool csa=false, numeric::xyzVector< Real > plane=numeric::xyzVector< Real >(0, 0, 0))
core::Real	compute_surface_area_leerichards (PosePackDataOP pd, Real slicesize, Real pr, bool csa=false, numeric::xyzVector< Real > plane=numeric::xyzVector< Real >(0, 0, 0))
XYZs	compute_surface_area_leerichards_deriv (PosePackDataOP pd, Real slicesize, Real pr, bool csa=false)
XYZs	check_surface_area_leerichards_deriv (PosePackDataOP pd, Real slicesize, Real pr, bool csa=false, Size max_num=10)
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
basic::Tracer	TRcs ("protocols.packstat")
core::Size const	N_PROBES = 20

Typedef Documentation

typedef utility::pointer::owning_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::owning_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::owning_ptr<MultiProbePerSphereAccumulator> core::scoring::packstat::MultiProbePerSphereAccumulatorOP

typedef utility::pointer::owning_ptr<MultiProbePoseAccumulator> core::scoring::packstat::MultiProbePoseAccumulatorOP

typedef pair<string const,string const> core::scoring::packstat::P

typedef utility::pointer::owning_ptr< PackingScore const > core::scoring::packstat::PackingScoreCOP

typedef utility::pointer::owning_ptr< PackingScore > core::scoring::packstat::PackingScoreOP

typedef utility::pointer::owning_ptr< PackingScoreResData const > core::scoring::packstat::PackingScoreResDataCOP

typedef utility::pointer::owning_ptr< PackingScoreResData > core::scoring::packstat::PackingScoreResDataOP

typedef double core::scoring::packstat::PackstatReal

typedef utility::pointer::owning_ptr<PerSphereAccumulator> core::scoring::packstat::PerSphereAccumulatorOP

typedef utility::pointer::owning_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

typedef numeric::xyzMatrix<PackstatReal> core::scoring::packstat::Rot

typedef std::pair< numeric::xyzMatrix<PackstatReal>, numeric::xyzMatrix<PackstatReal> > core::scoring::packstat::RotPair

typedef utility::pointer::owning_ptr< SasaOptions > core::scoring::packstat::SasaOptionsOP

typedef utility::pointer::owning_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 utility::io::ozstream::close(), compute_cav_ball_clusters(), compute_cav_ball_neighbor_count(), compute_cav_ball_volumes(), compute_sasa(), constraints, numeric::xyzVector< class >::distance(), numeric::xyzVector< class >::distance_squared(), core::pose::Pose::dump_pdb(), j, core::pose::Pose::n_residue(), core::conformation::Residue::nheavyatoms(), out, pose_to_pack_data(), prune_cavity_balls(), prune_hidden_cavity_balls(), core::scoring::packstat::SasaOptions::prune_max_iters, core::pose::Pose::residue(), TRcs, utility_exit_with_message, w(), weight_func(), numeric::xyzVector< class >::x(), xyz, core::conformation::Residue::xyz(), core::pose::Pose::xyz(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

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, and min.

XYZs core::scoring::packstat::check_surface_area_leerichards_deriv	(	PosePackDataOP	pd,
		Real	slicesize,
		Real	pr,
		bool	csa = false,
		Size	max_num = 10
	)

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(), core::scoring::packstat::PosePackData::spheres, and ss.

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 atom_scores, 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::total_residue().

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, j, numeric::max(), numeric::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, numeric::xyzVector< class >::x(), 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
	)

References core::pack::dunbrack::c, and s.

Referenced by cavity_distance_constraint().

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

References core::scoring::angles(), core::scoring::bit_count, numeric::xyzVector< class >::distance_squared(), core::scoring::get_orientation(), core::scoring::get_overlap(), l, core::scoring::maskbits, core::scoring::packstat::old::maskbits, core::scoring::masks(), core::scoring::packstat::old::nbytes, radius, core::scoring::packstat::CavityBall::radius(), core::scoring::packstat::CavityBall::radius_, numeric::xyzVector< class >::x(), 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 compute_packing_score(), and core::scoring::methods::PackStatEnergy::finalize_total_energy().

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(), j, core::scoring::packstat::SasaOptions::prune_max_iters, core::scoring::packstat::PackingScore::score(), core::scoring::packstat::PosePackData::spheres, and ss.

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

References compute_atom_packing_scores().

Referenced by compute_residue_packing_scores().

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, center(), numeric::xyzVector< class >::distance_squared(), core::scoring::packstat::SasaOptions::dont_compute_cav_balls, dot(), core::scoring::get_orientation(), core::scoring::get_overlap(), get_sasa_dot_locations(), core::scoring::input_sasa_dats(), j, l, core::scoring::maskbits, core::scoring::masks(), median(), 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, probe_radius, radius, rand_rot(), rots, core::scoring::packstat::SasaResult::sphere_sasa, and xyz.

Referenced by cavity_distance_constraint(), compute_atom_packing_scores(), compute_packing_score(), compute_residue_packing_score(), 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(), j, l, core::scoring::packstat::old::maskbits, core::scoring::packstat::old::masks, core::scoring::packstat::old::nbytes, numeric::constants::d::pi, and xyz.

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

References numeric::xyzVector< class >::length().

Referenced by check_surface_area_leerichards_deriv(), and compute_surface_area_leerichards().

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().

core::Real core::scoring::packstat::compute_surface_area_leerichards	(	Real &	buried_area_out,
		PosePackDataOP	pd,
		Real	slicesize,
		Real	pr,
		bool	csa = false,
		numeric::xyzVector< Real >	plane = numeric::xyzVector< Real >(0, 0, 0)
	)

core::Real core::scoring::packstat::compute_surface_area_leerichards	(	PosePackDataOP	pd,
		Real	slicesize,
		Real	pr,
		bool	csa = false,
		numeric::xyzVector< Real >	plane = numeric::xyzVector< Real >(0, 0, 0)
	)

XYZs core::scoring::packstat::compute_surface_area_leerichards_deriv	(	PosePackDataOP	pd,
		Real	slicesize,
		Real	pr,
		bool	csa
	)

XYZs core::scoring::packstat::compute_surface_area_leerichards_deriv	(	PosePackDataOP	pd,
		Real	slicesize,
		Real	pr,
		bool	csa = false
	)

PackingScoreResDataOP core::scoring::packstat::compute_surrounding_sasa	(	XYZ const &	xyz,
		Spheres &	spheres,
		SasaResultOP	result,
		SasaOptions const &	opts
	)

References begin, numeric::xyzVector< class >::distance(), 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

References radius.

Referenced by prune_1pass(), and prune_hidden_cavity_balls().

PackstatReal core::scoring::packstat::max_rad ( CavBalls const &  s )

inline

References radius.

std::ostream & core::scoring::packstat::operator<<	(	std::ostream &	out,
		PackingScoreResData const &	dat
	)

References j, core::scoring::packstat::PackingScoreResData::msa(), core::scoring::packstat::PackingScoreResData::npr(), and core::scoring::packstat::PackingScoreResData::nrad().

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

References core::scoring::packstat::SimplePDB::atoms_.

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::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::scoring::packstat::Sphere::radius, and core::scoring::packstat::Sphere::xyz.

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

References 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::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(), j, option, pose_to_pack_data(), prune_cavity_balls(), prune_hidden_cavity_balls(), core::scoring::packstat::SasaOptions::prune_max_iters, radius, surface_accessibility, core::pose::Pose::total_residue(), and TRcs.

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

References numeric::xyzVector< class >::distance_squared(), numeric::NumericTraits< class >::pi(), r1, r2, core::scoring::packstat::CavityBall::radius(), and core::scoring::packstat::CavityBall::xyz().

Referenced by compute_cav_ball_clusters(), core::pack::interaction_graph::RotamerDots::get_res_res_overlap(), and core::scoring::electron_density::ElectronDensity::rescale_fastscoring_temp_bins().

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

References core::io::pdb::dump_pdb(), basic::options::option, basic::options::OptionKeys::out::file::output_virtual, pdb, and core::scoring::packstat::PosePackData::spheres.

Referenced by cavity_distance_constraint(), compute_atom_packing_scores(), compute_packing_score(), compute_residue_packing_score(), compute_residue_packing_scores(), and output_packstat_pdb().

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

References core::scoring::angles(), begin, core::scoring::bit_count, numeric::xyzVector< class >::distance_squared(), core::scoring::packstat::CavityBall::exposed_radius, core::scoring::get_orientation(), core::scoring::get_overlap(), l, 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_, s, search_x(), numeric::xyzVector< class >::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(), 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, numeric::xyzVector< class >::distance_squared(), core::scoring::packstat::SasaOptions::frac_cav_ball_required_exposed, core::scoring::get_orientation(), core::scoring::get_overlap(), l, 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_, numeric::xyzVector< class >::x(), and core::scoring::packstat::CavityBall::xyz().

Referenced by cavity_distance_constraint(), and output_packstat_pdb().

RotPair core::scoring::packstat::rand_rot

(

)

References numeric::xyzVector< class >::length(), numeric::NumericTraits< class >::pi(), and uniform().

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 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 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
	)

References j.

std::string core::scoring::packstat::ToUpper

(

std::string

s

)

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

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
	)

References w().

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().

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

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