#include <ShapeComplementarityCalculator.hh>

Inheritance diagram for core::scoring::sc::ShapeComplementarityCalculator:

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

	~ShapeComplementarityCalculator () override

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

int	Calc (core::pose::Pose const &pose, core::Size jump_id) override
	Run the SC calculation on a Pose, partitionied by jump_id. 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...

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 ()

Static Public Member Functions
static core::Real	CalcSc (core::pose::Pose const &pose, core::Size jump_id=1, int quick=0)
	Run the SC calculation on Pose and return just the sc statistic or -1 on error. More...

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 @defailed 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)

int	TrimPeripheralBandCheckDot (DOT const &dot, std::vector< DOT > const &sdots)

int	CalcNeighborDistance (int const molecule, std::vector< const DOT * > const &my_dots, std::vector< const DOT * > const &their_dots)

DOT const *	CalcNeighborDistanceFindClosestNeighbor (DOT const &dot1, std::vector< const DOT * > const &their_dots)

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

typedef numeric::xyzVector< float >	Vec3

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 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

◆ ShapeComplementarityCalculator()

core::scoring::sc::ShapeComplementarityCalculator::ShapeComplementarityCalculator ( )

ShapeComplementarityCalculator constructor, initializes default settings.

◆ ~ShapeComplementarityCalculator()

core::scoring::sc::ShapeComplementarityCalculator::~ShapeComplementarityCalculator ( )

overridedefault

Member Function Documentation

◆ AssignAttentionNumbers()

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

overrideprotectedvirtual

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

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

Referenced by Calc().

◆ Calc() [1/2]

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

overridevirtual

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

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

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

References AssignAttentionNumbers(), CalcNeighborDistance(), core::scoring::sc::ShapeComplementarityCalculatorException::error, core::scoring::sc::MolecularSurfaceCalculator::GenerateMolecularSurfaces(), core::scoring::sc::MolecularSurfaceCalculator::run_, core::scoring::sc::MolecularSurfaceCalculator::settings, core::id::to_string(), core::scoring::TR(), and TrimPeripheralBand().

Referenced by protocols::pose_sewing::movers::BlockwiseAnalysisMover::apply(), core::scoring::sc::ElectrostaticComplementarityCalculator::Calc(), CalcSc(), protocols::simple_filters::ShapeComplementarityFilter::compute(), and protocols::analysis::InterfaceAnalyzerMover::compute_interface_sc().

◆ Calc() [2/2]

int core::scoring::sc::ShapeComplementarityCalculator::Calc	(	core::pose::Pose const &	pose,
		core::Size	jump_id
	)

overridevirtual

Run the SC calculation on a Pose, partitionied by jump_id.

This non-static function requires an instance of the ShapeComplementarityCalculator class. The jump_id is used to partition the pose into two molecular surfaces. To control what residues make up either surface, use the AddResidue() or even add_atom() function instead. Returns true on success. Results are retrieved with GetResults().

Example: core::scoring::sc::ShapeComplementarityCalculator calc; core::Real sc; if(calc.Calc( pose )) sc = calc.GetResults().sc;

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

References core::scoring::sc::MolecularSurfaceCalculator::Calc(), core::pose::Pose::num_jump(), and core::scoring::TR().

◆ CalcNeighborDistance()

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

private

References CalcNeighborDistanceFindClosestNeighbor(), core::scoring::sc::_DOT::coor, MAX, 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 Calc().

◆ CalcNeighborDistanceFindClosestNeighbor()

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

private

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

Referenced by CalcNeighborDistance().

◆ CalcSc()

core::Real core::scoring::sc::ShapeComplementarityCalculator::CalcSc	(	core::pose::Pose const &	pose,
		core::Size	jump_id = `1`,
		int	quick = `0`
	)

static

Run the SC calculation on Pose and return just the sc statistic or -1 on error.

This is a static function and can be called without instantiating ShapeComplementarityCalculator. The jump_id is used to partition the pose into two molecular surfaces; the first jump (1) is used is no jump_id is explicity specified. Those desiring more control as to what residues make up either surface should use the AddResidue() or even add_atom() function instead. 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::ShapeComplementarityCalculator( pose );

References Calc(), core::scoring::sc::MolecularSurfaceCalculator::density, core::scoring::sc::MolecularSurfaceCalculator::GetResults(), core::scoring::sc::_RESULTS::sc, and core::scoring::sc::MolecularSurfaceCalculator::settings.

Referenced by protocols::docking::membrane::MPFindInterfaceMover::apply().

◆ TrimPeripheralBand()

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

private

References core::scoring::sc::_DOT::area, core::scoring::sc::_DOT::buried, core::scoring::sc::MolecularSurfaceCalculator::settings, core::scoring::sc::MolecularSurfaceCalculator::trimmed_dots, and TrimPeripheralBandCheckDot().

Referenced by Calc().

◆ TrimPeripheralBandCheckDot()

int core::scoring::sc::ShapeComplementarityCalculator::TrimPeripheralBandCheckDot	(	DOT const &	dot,
		std::vector< DOT > const &	sdots
	)

private

References core::scoring::sc::_DOT::buried, core::scoring::sc::_DOT::coor, protocols::hybridization::r2, and core::scoring::sc::MolecularSurfaceCalculator::settings.

Referenced by TrimPeripheralBand().

The documentation for this class was generated from the following files:

src/core/scoring/sc/ShapeComplementarityCalculator.hh
src/core/scoring/sc/ShapeComplementarityCalculator.cc

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

◆ ShapeComplementarityCalculator()

◆ ~ShapeComplementarityCalculator()

Member Function Documentation

◆ AssignAttentionNumbers()

◆ Calc() [1/2]

◆ Calc() [2/2]

◆ CalcNeighborDistance()

◆ CalcNeighborDistanceFindClosestNeighbor()

◆ CalcSc()

◆ TrimPeripheralBand()

◆ TrimPeripheralBandCheckDot()