#include <ShapeSimilarityCalculator.hh>

Inheritance diagram for core::scoring::sc::ShapeSimilarityCalculator:

Public Member Functions
	ShapeSimilarityCalculator ()
	ShapeSimilarityCalculator constructor, initializes default settings. More...

	~ShapeSimilarityCalculator () override

int	Calc () override
	Run the SS calculation for previously defined molecules (via AddResidue or add_atom calls) More...

core::Real	CalcSs (core::pose::Pose const &pose, core::pose::Pose const &native, core::select::residue_selector::ResidueSelectorCOP selector_pose, core::select::residue_selector::ResidueSelectorCOP selector_native)
	Run the SS calculation on Pose and Reference and return the ss statistic or -1 on error. More...

Public Member Functions inherited from core::scoring::sc::MolecularSurfaceCalculator
	MolecularSurfaceCalculator ()
	MolecularSurfaceCalculator constructor, initializes default settings. More...

	~MolecularSurfaceCalculator () override

virtual int	Init ()
	Initializes calculation and GPU (if used) Init() is also called implicitly by the static CalcSc() function. More...

void	Reset ()
	Reset calculator for another calculation. Must be used when the MolecularSurfaceCalculator instance is re-used. More...

int	AddAtom (int molecule, Atom &atom)
	Add an atom to a molecule for computation. More...

core::Size	AddResidue (int molecule, core::conformation::Residue const &residue, bool apolar_only=false)
	Add a rosetta residue to a specific molecule. More...

virtual int	Calc (core::pose::Pose const &pose, core::Size jump_id=0)
	Generate molecular surfaces for the given pose. //. More...

std::vector< Atom > const &	GetAtoms ()

std::vector< DOT > const &	GetDots (int const moleculeid)

std::vector< const DOT * > const &	GetTrimmedDots (int const moleculeid)

RESULTS const &	GetResults ()

Public Attributes
bool	median

Public Attributes inherited from core::scoring::sc::MolecularSurfaceCalculator
struct {
core::Real rp

core::Real density

core::Real band

core::Real sep

core::Real weight

core::Real binwidth_dist

core::Real binwidth_norm

core::Real near_squared_size

bool use_rosetta_radii

}	settings

Protected Member Functions
int	AssignAttentionNumbers (std::vector< Atom > &atom) override

Protected Member Functions inherited from core::scoring::sc::MolecularSurfaceCalculator
void	GenerateMolecularSurfaces ()
	Generate untrimmed surfaces for the defined molecules. More...

int	AssignAtomRadius (Atom &atom)

int	WildcardMatch (char const query, char const pattern, int const l)

int	ReadScRadii ()
	Read atom radius definitions from file This function is implicitly called, but can be overloaded or called explicitly for custom handling of the atom radii library. Returns true on success. More...

void	AddDot (int const molecule, int const type, Vec3 const &coor, ScValue const area, Vec3 const &pcen, Atom const &atom)

Private Member Functions
ScValue	TrimPeripheralBand (std::vector< DOT > const &sdots, std::vector< const DOT * > &trimmed_dots)
	SS molecular dot trimming, vector dot product calculation and statistics. More...

int	TrimPeripheralBandCheckDot (DOT const &dot, std::vector< DOT > const &sdots)
	Test a dot against a set of dots for collision NOTE: ~75% of time is spent in this function. More...

core::Real	CalcNeighborDistance (int const molecule, std::vector< const DOT * > const &my_dots, std::vector< const DOT * > const &their_dots)
	Evaluate similarity of two points of the surface. More...

DOT const *	CalcNeighborDistanceFindClosestNeighbor (DOT const &dot1, std::vector< const DOT * > const &their_dots)
	Find closest neighbor dot for a given dot NOTE: ~20% of time is spent in this function. More...

Additional Inherited Members
Public Types inherited from core::scoring::sc::MolecularSurfaceCalculator
typedef float	ScValue

typedef numeric::xyzVector< float >	Vec3

Protected Attributes inherited from core::scoring::sc::MolecularSurfaceCalculator
struct {
ScValue radmax

RESULTS results

std::vector< Atom > atoms

std::vector< DOT > dots [2]

std::vector< const DOT * > trimmed_dots [2]

std::vector< PROBE > probes

Vec3 prevp

int prevburied

}	run_

Static Protected Attributes inherited from core::scoring::sc::MolecularSurfaceCalculator
static std::vector< ATOM_RADIUS >	radii_

Constructor & Destructor Documentation

core::scoring::sc::ShapeSimilarityCalculator::ShapeSimilarityCalculator ( )

ShapeSimilarityCalculator constructor, initializes default settings.

core::scoring::sc::ShapeSimilarityCalculator::~ShapeSimilarityCalculator ( )

overridedefault

Member Function Documentation

int core::scoring::sc::ShapeSimilarityCalculator::AssignAttentionNumbers ( std::vector< Atom > & atom )

overrideprotectedvirtual

Reimplemented from core::scoring::sc::MolecularSurfaceCalculator.

References core::scoring::sc::ATTEN_BURIED_FLAGGED, and core::scoring::sc::MolecularSurfaceCalculator::run_.

Referenced by Calc().

int core::scoring::sc::ShapeSimilarityCalculator::Calc ( )

overridevirtual

Run the SS calculation for previously defined molecules (via AddResidue or add_atom calls)

This function is called for residues / atoms making up the two molecular surfaces have been explicitly defined. Returns true on success.

Reimplemented from core::scoring::sc::MolecularSurfaceCalculator.

References AssignAttentionNumbers(), core::scoring::sc::MolecularSurfaceCalculator::GenerateMolecularSurfaces(), core::scoring::sc::MolecularSurfaceCalculator::run_, and core::scoring::TR().

Referenced by core::scoring::sc::ElectrostaticSimilarityCalculator::Calc(), and CalcSs().

core::Real core::scoring::sc::ShapeSimilarityCalculator::CalcNeighborDistance	(	int const	molecule,
		std::vector< const DOT * > const &	my_dots,
		std::vector< const DOT * > const &	their_dots
	)

private

Evaluate similarity of two points of the surface.

Identify the closes points of the two provided surfaces and compute the distance between the points and their normal vectors. The normal vectors are used to evaluate the shape of the points via the normal vector dot product. This operation is performed for all points of the specified surfaces and the mean of all values represent the overall shape similarity.

References core::pack::dunbrack::c, CalcNeighborDistanceFindClosestNeighbor(), core::scoring::sc::_DOT::coor, MAX, median, MIN, core::scoring::sc::_DOT::outnml, core::scoring::sc::MolecularSurfaceCalculator::run_, core::scoring::sc::MolecularSurfaceCalculator::settings, protocols::analysis::total, and core::scoring::TR().

Referenced by CalcSs().

DOT const * core::scoring::sc::ShapeSimilarityCalculator::CalcNeighborDistanceFindClosestNeighbor	(	DOT const &	dot1,
		std::vector< const DOT * > const &	their_dots
	)

private

Find closest neighbor dot for a given dot NOTE: ~20% of time is spent in this function.

References core::scoring::sc::_DOT::buried, and core::scoring::sc::_DOT::coor.

Referenced by CalcNeighborDistance().

core::Real core::scoring::sc::ShapeSimilarityCalculator::CalcSs	(	core::pose::Pose const &	pose,
		core::pose::Pose const &	native,
		core::select::residue_selector::ResidueSelectorCOP	selector_pose,
		core::select::residue_selector::ResidueSelectorCOP	selector_native
	)

Run the SS calculation on Pose and Reference and return the ss statistic or -1 on error.

This is a static function and can be called without instantiating ShapeSimilarityCalculator. The residue selectors for the pose and reference are used to select two surfaces to compare. Setting quick to true will perform a much faster calculation (~5-10 times faster) at the expense of accuracy (about 0.05 units).

Example: core::Real sc = core::scoring::sc::ShapeSimilarityCalculator( pose );

References core::scoring::sc::MolecularSurfaceCalculator::AddResidue(), Calc(), CalcNeighborDistance(), core::conformation::Residue::chain(), core::sequence::end, core::scoring::sc::MolecularSurfaceCalculator::GetDots(), protocols::hybridization::r1, protocols::hybridization::r2, core::pose::Pose::residue(), core::pose::Pose::split_by_chain(), and core::scoring::TR().

Referenced by core::simple_metrics::metrics::ShapeSimilarityMetric::calculate().

ShapeSimilarityCalculator::ScValue core::scoring::sc::ShapeSimilarityCalculator::TrimPeripheralBand	(	std::vector< DOT > const &	sdots,
		std::vector< const DOT * > &	trimmed_dots
	)