core::scoring::packstat Namespace Reference

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
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 utility::pointer::shared_ptr< PosePackData >	PosePackDataOP
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

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 (std::string const &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

AccumulatorOP

typedef utility::pointer::shared_ptr<Accumulator> core::scoring::packstat::AccumulatorOP

Arc

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

ArcIter

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

Arcs

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

AreaAccumulatorOP

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

CavBallCIter

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

CavBallIter

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

CavBalls

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

CircleIter

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

Circles

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

EventIter

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

Events

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

FloatCIter

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

FloatIter

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

Floats

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

MultiProbePerSphereAccumulatorOP

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

MultiProbePoseAccumulatorOP

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

P

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

PackingScoreCOP

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

PackingScoreOP

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

PackingScoreResDataCOP

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

PackingScoreResDataOP

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

PackstatReal

typedef core::Real core::scoring::packstat::PackstatReal

PerSphereAccumulatorOP

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

PosePackDataOP

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

RealCIter

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

RealIter

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

Reals

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

Rot

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

RotPair

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

SasaOptionsOP

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

SasaResultOP

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

SliceIter

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

Slices

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

SPAtomCIter

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

SPAtomIter

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

SPAtoms

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

SphereCIter

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

SphereIter

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

Spheres

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

traceIter

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

traces

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

XYZ

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

XYZCIter

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

XYZIter

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

XYZs

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

Enumeration Type Documentation

EventType

enum core::scoring::packstat::EventType

Enumerator
ENTER
EXIT
ISECT

Function Documentation

cavity_distance_constraint()

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 core::scoring::packstat::SasaOptions::area_cav_ball_required_exposed, core::scoring::packstat::SasaOptions::cluster_min_volume, 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::scoring::packstat::SasaOptions::frac_cav_ball_required_exposed, core::chemical::element::I, core::scoring::packstat::SasaOptions::min_cav_ball_radius, core::scoring::packstat::SasaOptions::min_cluster_overlap, core::conformation::Residue::nheavyatoms(), core::scoring::packstat::SasaOptions::num_cav_ball_layers, core::conformation::membrane::out, pose_to_pack_data(), core::scoring::packstat::SasaOptions::probe_radii, prune_cavity_balls(), core::scoring::packstat::SasaOptions::prune_cavity_burial_probe_radii, prune_hidden_cavity_balls(), core::scoring::packstat::SasaOptions::prune_max_delta, core::scoring::packstat::SasaOptions::prune_max_iters, core::pose::Pose::residue(), core::pose::Pose::size(), core::scoring::packstat::PosePackData::spheres, core::scoring::packstat::SasaOptions::surrounding_sasa_smoothing_window, TRcs(), weight_func(), core::pose::Pose::xyz(), protocols::kinmatch::xyz(), and core::conformation::Residue::xyz().

check_surface_area_leerichards_deriv()

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::scoring::csa, core::id::D, protocols::mean_field::min(), and core::chemical::element::N.

compute_atom_packing_scores() [1/2]

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(), pose_to_pack_data(), core::pose::Pose::residue(), and core::pose::Pose::size().

compute_atom_packing_scores() [2/2]

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

References core::scoring::packstat::SasaOptions::area_cav_ball_required_exposed, core::scoring::packstat::PosePackData::centers, compute_sasa(), compute_surrounding_sasa(), core::scoring::packstat::SasaOptions::frac_cav_ball_required_exposed, init_packing_score_discrim(), core::scoring::packstat::SasaOptions::num_cav_ball_layers, core::scoring::packstat::SasaOptions::num_surrounding_sasa_bins, core::scoring::packstat::SasaOptions::probe_radii, core::scoring::packstat::SasaOptions::prune_max_delta, core::scoring::packstat::SasaOptions::prune_max_iters, core::scoring::packstat::PackingScore::score(), core::scoring::packstat::PosePackData::spheres, and core::scoring::packstat::SasaOptions::surrounding_sasa_smoothing_window.

Referenced by compute_atom_packing_scores(), and compute_residue_packing_scores().

compute_cav_ball_clusters()

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

References core::scoring::packstat::CavityBall::area, 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(), output_packstat_pdb(), and protocols::denovo_design::calculators::CavityCalculator::recompute().

compute_cav_ball_neighbor_count()

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().

compute_cav_ball_volumes()

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::packstat::old::maskbits, core::scoring::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(), output_packstat_pdb(), and protocols::denovo_design::calculators::CavityCalculator::recompute().

compute_packing_score() [1/2]

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

References compute_packing_score(), and pose_to_pack_data().

compute_packing_score() [2/2]

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

References core::scoring::packstat::SasaOptions::area_cav_ball_required_exposed, core::scoring::packstat::PosePackData::centers, compute_sasa(), compute_surrounding_sasa(), core::scoring::packstat::SasaOptions::frac_cav_ball_required_exposed, init_packing_score_discrim(), core::scoring::packstat::SasaOptions::num_cav_ball_layers, core::scoring::packstat::SasaOptions::num_surrounding_sasa_bins, core::scoring::packstat::SasaOptions::probe_radii, core::scoring::packstat::SasaOptions::prune_max_delta, core::scoring::packstat::SasaOptions::prune_max_iters, core::scoring::packstat::PackingScore::score(), core::scoring::packstat::PosePackData::spheres, and core::scoring::packstat::SasaOptions::surrounding_sasa_smoothing_window.

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

compute_packing_score_leerichards() [1/2]

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

compute_packing_score_leerichards() [2/2]

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().

compute_residue_packing_score() [1/2]

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

References pose_to_pack_data().

compute_residue_packing_score() [2/2]

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

References core::scoring::packstat::SasaOptions::area_cav_ball_required_exposed, core::scoring::packstat::PosePackData::centers, compute_sasa(), compute_surrounding_sasa(), core::scoring::packstat::SasaOptions::frac_cav_ball_required_exposed, init_packing_score_discrim(), core::scoring::packstat::SasaOptions::num_cav_ball_layers, core::scoring::packstat::SasaOptions::num_surrounding_sasa_bins, core::scoring::packstat::SasaOptions::probe_radii, core::scoring::packstat::SasaOptions::prune_max_delta, core::scoring::packstat::SasaOptions::prune_max_iters, core::scoring::packstat::PackingScore::score(), core::scoring::packstat::PosePackData::spheres, and core::scoring::packstat::SasaOptions::surrounding_sasa_smoothing_window.

compute_residue_packing_scores() [1/2]

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().

compute_residue_packing_scores() [2/2]

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().

compute_sasa()

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

References core::scoring::angles(), core::scoring::bit_count, core::pack::guidance_scoreterms::lk_dome::bit_test(), 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().

compute_sasa_generic()

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, core::chemical::element::S, protocols::analysis::total, and protocols::kinmatch::xyz().

compute_surface_area_leerichards() [1/2]

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(), and core::scoring::csa.

compute_surface_area_leerichards() [2/2]

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
	)

References core::scoring::csa.

Referenced by check_surface_area_leerichards_deriv(), and compute_surface_area_leerichards().

compute_surface_area_leerichards_deriv()

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

References core::scoring::csa.

compute_surrounding_sasa()

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, core::scoring::packstat::Sphere::xyz, and protocols::kinmatch::xyz().

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

get_sasa_dot_locations()

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

inline

Referenced by compute_sasa().

init_packing_score_discrim()

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().

init_packing_score_respred()

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().

max_rad() [1/2]

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

inline

max_rad() [2/2]

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

inline

Referenced by prune_1pass(), and prune_hidden_cavity_balls().

operator<<() [1/5]

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.

operator<<() [2/5]

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.

operator<<() [3/5]

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

operator<<() [4/5]

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

operator<<() [5/5]

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.

operator>>() [1/2]

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

operator>>() [2/2]

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.

output_packstat_pdb()

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

References core::scoring::packstat::SasaOptions::area_cav_ball_required_exposed, core::scoring::packstat::SasaOptions::cluster_min_volume, compute_cav_ball_clusters(), compute_cav_ball_volumes(), compute_sasa(), core::scoring::packstat::SasaOptions::frac_cav_ball_required_exposed, core::scoring::packstat::SasaOptions::min_cav_ball_radius, core::scoring::packstat::SasaOptions::min_cluster_overlap, core::scoring::packstat::SasaOptions::num_cav_ball_layers, core::conformation::membrane::out, pose_to_pack_data(), core::scoring::packstat::SasaOptions::probe_radii, prune_cavity_balls(), core::scoring::packstat::SasaOptions::prune_cavity_burial_probe_radii, prune_hidden_cavity_balls(), core::scoring::packstat::SasaOptions::prune_max_delta, core::scoring::packstat::SasaOptions::prune_max_iters, core::pose::Pose::size(), core::scoring::packstat::SasaOptions::surrounding_sasa_smoothing_window, and TRcs().

overlap()

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().

pose_to_pack_data()

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

References core::scoring::packstat::PosePackData::centers, core::io::pdb::dump_pdb(), core::scoring::packstat::SimplePDB::get_res_centers(), core::scoring::packstat::SimplePDB::get_spheres(), core::scoring::packstat::PosePackData::labels, core::scoring::packstat::SimplePDB::res_labels(), 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().

prune_1pass()

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::CavityBall::radius(), core::scoring::packstat::Sphere::radius, core::scoring::packstat::CavityBall::radius_, search_x(), core::scoring::packstat::CavityBall::xyz(), and core::scoring::packstat::Sphere::xyz.

Referenced by prune_cavity_balls().

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().

prune_hidden_cavity_balls()

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::packstat::old::maskbits, core::scoring::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().

rand_rot()

RotPair core::scoring::packstat::rand_rot

(

)

References protocols::rigid::random.

Referenced by compute_sasa().

read_stoopid()

template<class T >

void core::scoring::packstat::read_stoopid	(	std::string const &	buf,
		size_t	start,
		size_t	end,
		T &	field
	)

References core::sequence::end, and protocols::loops::start.

search_x() [1/4]

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

inline

References search_x().

search_x() [2/4]

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

inline

References core::sequence::end, search_x(), and protocols::kinmatch::xyz().

search_x() [3/4]

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

inline

References search_x().

search_x() [4/4]

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

inline

References core::sequence::end, and protocols::kinmatch::xyz().

Referenced by prune_1pass(), and search_x().

select_cav_balls()

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

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

ToUpper()

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

(

std::string

s

)

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

TRcs()

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

static

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

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().

weight_func()

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

References protocols::hybridization::d0.

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

HYDROGEN_RADIUS

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

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

N_PROBES

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

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