Namespaces
	old

Classes
class	AtomRadiusMap

class	CavityBall

struct	OrderSphereOnX

struct	OrderSphereOnID

struct	OrderCavBallOnX

struct	OrderCavBallOnRmE

struct	OrderCavBallOnR

struct	OrderCavBallOnRmAnb

struct	SasaResult

struct	SasaOptions

struct	CavityBallCluster

struct	OrderCBC

struct	HTL_EventX

struct	Accumulator

struct	AreaAccumulator

struct	LR_AtomData

struct	PerSphereAccumulator

struct	LR_MP_AtomData

struct	MultiProbePoseAccumulator

struct	MultiProbePerSphereAccumulator

struct	Point

struct	PointPair

struct	Circle

struct	Event

struct	Slice

struct	trace

struct	Array2D

struct	Octree2D

struct	LeeRichards

struct	PackingScoreResData

struct	PackingScore

class	SimplePDB

struct	SimplePDB_Atom

struct	Sphere

struct	PosePackData

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)

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 ()

size_t	search_x (Spheres const &spheres, PackstatReal const x, size_t begin, size_t end)

size_t	search_x (Spheres const &spheres, PackstatReal const x)

size_t	search_x (CavBalls const &cbs, PackstatReal const x, size_t begin, size_t end)

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::owning_ptr<Accumulator> core::scoring::packstat::AccumulatorOP

Definition at line 71 of file LeeRichards.hh.

typedef std::pair< core::id::AtomID,Real > core::scoring::packstat::Arc

Definition at line 62 of file LeeRichards.hh.

typedef utility::vector1< Arc >::iterator core::scoring::packstat::ArcIter

Definition at line 64 of file LeeRichards.hh.

typedef utility::vector1< Arc > core::scoring::packstat::Arcs

Definition at line 63 of file LeeRichards.hh.

typedef utility::pointer::owning_ptr<AreaAccumulator> core::scoring::packstat::AreaAccumulatorOP

Definition at line 87 of file LeeRichards.hh.

typedef utility::vector1< CavityBall >::const_iterator core::scoring::packstat::CavBallCIter

Definition at line 115 of file CavityBall.hh.

typedef utility::vector1< CavityBall >::iterator core::scoring::packstat::CavBallIter

Definition at line 114 of file CavityBall.hh.

typedef utility::vector1< CavityBall > core::scoring::packstat::CavBalls

Definition at line 113 of file CavityBall.hh.

typedef utility::vector1< Circle* >::iterator core::scoring::packstat::CircleIter

Definition at line 58 of file LeeRichards.hh.

typedef utility::vector1< Circle* > core::scoring::packstat::Circles

Definition at line 56 of file LeeRichards.hh.

typedef utility::vector1< Event* >::iterator core::scoring::packstat::EventIter

Definition at line 57 of file LeeRichards.hh.

typedef utility::vector1< Event* > core::scoring::packstat::Events

Definition at line 52 of file LeeRichards.hh.

typedef Floats::const_iterator core::scoring::packstat::FloatCIter

Definition at line 40 of file types.hh.

typedef Floats::iterator core::scoring::packstat::FloatIter

Definition at line 39 of file types.hh.

typedef utility::vector1<PackstatReal> core::scoring::packstat::Floats

Definition at line 38 of file types.hh.

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

Definition at line 182 of file LeeRichards.hh.

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

Definition at line 141 of file LeeRichards.hh.

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

Definition at line 38 of file AtomRadiusMap.cc.

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

Definition at line 76 of file PackingScore.hh.

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

Definition at line 75 of file PackingScore.hh.

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

Definition at line 47 of file PackingScore.hh.

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

Definition at line 46 of file PackingScore.hh.

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

Definition at line 36 of file types.hh.

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

Definition at line 111 of file LeeRichards.hh.

typedef utility::pointer::owning_ptr<PosePackData> core::scoring::packstat::PosePackDataOP

Definition at line 70 of file types.hh.

typedef Reals::const_iterator core::scoring::packstat::RealCIter

Definition at line 44 of file types.hh.

typedef Reals::iterator core::scoring::packstat::RealIter

Definition at line 43 of file types.hh.

typedef utility::vector1<core::Real> core::scoring::packstat::Reals

Definition at line 42 of file types.hh.

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

Definition at line 76 of file compute_sasa.cc.

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

Definition at line 77 of file compute_sasa.cc.

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

Definition at line 231 of file compute_sasa.hh.

typedef utility::pointer::owning_ptr< SasaResult > core::scoring::packstat::SasaResultOP

Definition at line 230 of file compute_sasa.hh.

typedef utility::vector1< Slice* >::iterator core::scoring::packstat::SliceIter

Definition at line 59 of file LeeRichards.hh.

typedef utility::vector1< Slice* > core::scoring::packstat::Slices

Definition at line 54 of file LeeRichards.hh.

typedef utility::vector1<SimplePDB_Atom>::const_iterator core::scoring::packstat::SPAtomCIter

Definition at line 37 of file SimplePDB.hh.

typedef utility::vector1<SimplePDB_Atom>::iterator core::scoring::packstat::SPAtomIter

Definition at line 36 of file SimplePDB.hh.

typedef utility::vector1<SimplePDB_Atom> core::scoring::packstat::SPAtoms

Definition at line 35 of file SimplePDB.hh.

typedef Spheres::const_iterator core::scoring::packstat::SphereCIter

Definition at line 63 of file types.hh.

typedef Spheres::iterator core::scoring::packstat::SphereIter

Definition at line 62 of file types.hh.

typedef utility::vector1<Sphere> core::scoring::packstat::Spheres

Definition at line 61 of file types.hh.

typedef utility::vector1< trace* >::iterator core::scoring::packstat::traceIter

Definition at line 60 of file LeeRichards.hh.

typedef utility::vector1< trace* > core::scoring::packstat::traces

Definition at line 55 of file LeeRichards.hh.

typedef numeric::xyzVector<PackstatReal> core::scoring::packstat::XYZ

Definition at line 46 of file types.hh.

typedef XYZs::const_iterator core::scoring::packstat::XYZCIter

Definition at line 49 of file types.hh.

typedef XYZs::iterator core::scoring::packstat::XYZIter

Definition at line 48 of file types.hh.

typedef utility::vector1<XYZ> core::scoring::packstat::XYZs

Definition at line 47 of file types.hh.

Enumeration Type Documentation

enum core::scoring::packstat::EventType

Enumerator
ENTER
EXIT
ISECT

Definition at line 238 of file LeeRichards.hh.

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
	)

Definition at line 1134 of file compute_sasa.cc.

References compute_cav_ball_clusters(), compute_cav_ball_neighbor_count(), compute_cav_ball_volumes(), compute_sasa(), core::pose::Pose::dump_pdb(), core::pose::Pose::n_residue(), core::conformation::Residue::nheavyatoms(), pose_to_pack_data(), prune_cavity_balls(), prune_hidden_cavity_balls(), core::scoring::packstat::SasaOptions::prune_max_iters, core::pose::Pose::residue(), 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
	)

Definition at line 549 of file LeeRichards.cc.

References compute_surface_area_leerichards(), core::id::D, and protocols::forge::build::SegmentInsertConnectionScheme::N.

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

Definition at line 998 of file compute_sasa.cc.

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
	)

Definition at line 1105 of file compute_sasa.cc.

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::total_residue().

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

Definition at line 747 of file compute_sasa.cc.

Referenced by cavity_distance_constraint(), and output_packstat_pdb().

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

Definition at line 699 of file compute_sasa.cc.

References core::pack::dunbrack::c.

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

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

Definition at line 416 of file compute_sasa.cc.

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
	)

Definition at line 941 of file compute_sasa.cc.

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::toolbox::pose_metric_calculators::PackstatCalculator::recompute().

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

Definition at line 1034 of file compute_sasa.cc.

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
	)

Definition at line 595 of file LeeRichards.cc.

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
	)

Definition at line 1053 of file compute_sasa.cc.

References pose_to_pack_data().

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

Definition at line 1064 of file compute_sasa.cc.

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
	)

Definition at line 991 of file compute_sasa.cc.

References compute_atom_packing_scores().

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

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

Definition at line 1044 of file compute_sasa.cc.

References compute_residue_packing_scores(), and pose_to_pack_data().

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

Definition at line 244 of file compute_sasa.cc.

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`
	)

Definition at line 370 of file compute_sasa.hh.

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, 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
	)

Definition at line 456 of file LeeRichards.cc.

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
	)

Definition at line 498 of file LeeRichards.cc.

References compute_surface_area_leerichards().

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

Definition at line 510 of file LeeRichards.cc.

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

Definition at line 888 of file compute_sasa.cc.

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

Definition at line 26 of file sasa_dot_locations.hh.

Referenced by compute_sasa().

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

Definition at line 239 of file packing_score_params.cc.

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)

Definition at line 21 of file packing_score_params.cc.

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

Definition at line 59 of file util.hh.

Referenced by prune_1pass(), and prune_hidden_cavity_balls().

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

inline

Definition at line 67 of file util.hh.

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

Definition at line 33 of file PackingScore.cc.

References 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
	)

Definition at line 55 of file io.cc.

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

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

Definition at line 123 of file io.cc.

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

Definition at line 144 of file io.cc.

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

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

Definition at line 266 of file LeeRichards.cc.

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
	)

Definition at line 35 of file io.cc.

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
	)

Definition at line 87 of file io.cc.

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

Definition at line 1285 of file compute_sasa.cc.

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::total_residue(), and TRcs().

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

Definition at line 733 of file compute_sasa.cc.

References core::scoring::packstat::CavityBall::radius(), and core::scoring::packstat::CavityBall::xyz().

Referenced by protocols::comparative_modeling::AlignmentClustering::AlignmentClustering(), compute_cav_ball_clusters(), protocols::simple_filters::SymmetricMotifFilter::compute_d2(), core::pack::interaction_graph::RotamerDots::get_res_res_overlap(), and protocols::hybridization::DomainAssembly::run().

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

Definition at line 222 of file compute_sasa.cc.

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
	)

Definition at line 558 of file compute_sasa.cc.

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
	)

Definition at line 640 of file compute_sasa.cc.

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
	)

Definition at line 492 of file compute_sasa.cc.

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 ( )

Definition at line 180 of file compute_sasa.cc.

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
	)

Definition at line 67 of file io.cc.

References protocols::loops::start.

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

inline

Definition at line 31 of file util.hh.

References protocols::kinmatch::xyz().

Referenced by prune_1pass(), and search_x().

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

inline

Definition at line 41 of file util.hh.

References search_x().

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

inline

Definition at line 45 of file util.hh.

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

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

inline

Definition at line 55 of file util.hh.

References search_x().

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

Definition at line 715 of file compute_sasa.cc.

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

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

Definition at line 40 of file AtomRadiusMap.cc.

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

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

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
	)

Definition at line 50 of file AtomRadiusMap.cc.

References ToUpper().

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

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

Definition at line 1126 of file compute_sasa.cc.

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

Definition at line 36 of file AtomRadiusMap.cc.

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

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

Definition at line 49 of file LeeRichards.cc.

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

Namespaces

Classes

Typedefs

Enumerations

Functions

Variables

Typedef Documentation

Enumeration Type Documentation

Function Documentation

Variable Documentation