#include <BALL/STRUCTURE/reducedSurface.h>

Classes
struct	ProbePosition

Public Types
Enums
enum	ProbeStatus { STATUS_OK = 0, STATUS_NOT_OK, STATUS_NOT_TESTED }

enum	AtomStatus { STATUS_ON_SURFACE = 0, STATUS_INSIDE, STATUS_UNKNOWN }

Public Member Functions
Constructors and Destructors
	RSComputer ()

	RSComputer (ReducedSurface *rs)

virtual	~RSComputer ()

Accessors
void	run () throw (Exception::GeneralException, Exception::DivisionByZero, Exception::IndexOverflow)

Protected Attributes
ReducedSurface *	rs_

std::vector< std::deque< Index > >	neighbours_

std::vector< AtomStatus >	atom_status_

HashMap< SortedPosition2, std::deque< Index > >	neighbours_of_two_

HashMap< SortedPosition3, ProbePosition * >	probe_positions_

HashSet< RSVertex * >	new_vertices_

HashSet< RSFace * >	new_faces_

std::vector< std::list < RSVertex * > >	vertices_

Private Member Functions

void	preProcessing ()

void	getRSComponent () throw (Exception::GeneralException, Exception::DivisionByZero, Exception::IndexOverflow)

bool	treatFace (RSFace *face) throw (Exception::GeneralException, Exception::DivisionByZero, Exception::IndexOverflow)

bool	treatEdge (RSEdge *edge) throw (Exception::GeneralException, Exception::DivisionByZero, Exception::IndexOverflow)

void	correct (Index atom)

void	extendComponent () throw (Exception::GeneralException, Exception::DivisionByZero, Exception::IndexOverflow)

Index	thirdAtom (RSVertex vertex1, RSVertex vertex2, RSFace *face, TSphere3< double > &probe, TAngle< double > &phi) throw (Exception::GeneralException, Exception::DivisionByZero, Exception::IndexOverflow)


Position	getStartPosition () throw (Exception::DivisionByZero)


RSFace *	findFirstFace () throw (Exception::DivisionByZero)

RSFace *	findFace (Position direction, Position extrem) throw (Exception::DivisionByZero)


RSEdge *	findFirstEdge ()

RSEdge *	findEdge (Position direction, Position extrem)


RSVertex *	findFirstVertex ()

Index	findFirstAtom (Position direction, Position extrem)

Index	findSecondAtom (Index atom, Position direction, Position extrem)

void	findThirdAtom (Index atom1, Index atom2, const std::deque< Index > &third, std::deque< std::pair< Index, TSphere3< double > > > &atoms)


const std::deque< Index > &	neighboursOfTwoAtoms (const SortedPosition2 &pos)

void	neighboursOfThreeAtoms (Index atom1, Index atom2, Index atom3, std::deque< Index > &output_list)

double	getCircleExtremum (const TCircle3< double > &circle, Position direction, Position extrem)


RSEdge *	createFreeEdge (RSVertex vertex1, RSVertex vertex2)

bool	getCircles (Index atom1, Index atom2, TCircle3< double > &circle1, TCircle3< double > &circle2, TCircle3< double > &circle3)

TVector3< double >	getFaceNormal (const TSphere3< double > &atom1, const TSphere3< double > &atom2, const TSphere3< double > &atom3, const TSphere3< double > &probe)

void	updateFaceAndEdges (RSVertex v1, RSVertex v2, RSVertex v3, RSEdge e1, RSEdge e2, RSEdge e3, RSFace *f, const TSphere3< double > &probe)

RSFace *	faceExists (RSFace face, const std::list< RSVertex > &vertices)


bool	centerOfProbe (const SortedPosition3 &pos, TVector3< double > &c1, TVector3< double > &c2)

bool	checkProbe (const TSphere3< double > &probe, const SortedPosition3 &pos)

void	correctProbePosition (Position atom)

void	correctProbePosition (const SortedPosition3 &pos)

void	insert (RSVertex *vertex)

void	insert (RSEdge *edge)

void	insert (RSFace *face)

Detailed Description

Generic RSComputer Class.

Definition at line 476 of file reducedSurface.h.

Member Enumeration Documentation

enum BALL::RSComputer::AtomStatus

status of an atom 0 on surface 1 inside 2 outside

Enumerator
STATUS_ON_SURFACE
STATUS_INSIDE
STATUS_UNKNOWN

Definition at line 503 of file reducedSurface.h.

enum BALL::RSComputer::ProbeStatus

status of the probe positions of three atoms: 0 ok 1 not ok 2 not tested

Enumerator
STATUS_OK
STATUS_NOT_OK
STATUS_NOT_TESTED

Definition at line 491 of file reducedSurface.h.

Constructor & Destructor Documentation

BALL::RSComputer::RSComputer ( )

Default constructor. All components are initialized to (T)0 or NULL, respectivly.

BALL::RSComputer::RSComputer ( ReducedSurface * rs )

Detailed constructor.

virtual BALL::RSComputer::~RSComputer ( )

virtual

Destructor.

Member Function Documentation

bool BALL::RSComputer::centerOfProbe	(	const SortedPosition3 &	pos,
		TVector3< double > &	c1,
		TVector3< double > &	c2
	)

private

bool BALL::RSComputer::checkProbe	(	const TSphere3< double > &	probe,
		const SortedPosition3 &	pos
	)

private

void BALL::RSComputer::correct ( Index atom )

private

void BALL::RSComputer::correctProbePosition ( Position atom )

private

void BALL::RSComputer::correctProbePosition ( const SortedPosition3 & pos )

private

RSEdge* BALL::RSComputer::createFreeEdge	(	RSVertex *	vertex1,
		RSVertex *	vertex2
	)

private

void BALL::RSComputer::extendComponent ( ) throw (Exception::GeneralException, Exception::DivisionByZero, Exception::IndexOverflow)

private

RSFace* BALL::RSComputer::faceExists	(	RSFace *	face,
		const std::list< RSVertex * > &	vertices
	)

private

RSEdge* BALL::RSComputer::findEdge	(	Position	direction,
		Position	extrem
	)

private

RSFace* BALL::RSComputer::findFace	(	Position	direction,
		Position	extrem
	)		throw (Exception::DivisionByZero)

private

Index BALL::RSComputer::findFirstAtom	(	Position	direction,
		Position	extrem
	)

private

RSEdge* BALL::RSComputer::findFirstEdge ( )

private

RSFace* BALL::RSComputer::findFirstFace ( ) throw (Exception::DivisionByZero)

private

RSVertex* BALL::RSComputer::findFirstVertex ( )

private

Index BALL::RSComputer::findSecondAtom	(	Index	atom,
		Position	direction,
		Position	extrem
	)

private

void BALL::RSComputer::findThirdAtom	(	Index	atom1,
		Index	atom2,
		const std::deque< Index > &	third,
		std::deque< std::pair< Index, TSphere3< double > > > &	atoms
	)

private

double BALL::RSComputer::getCircleExtremum	(	const TCircle3< double > &	circle,
		Position	direction,
		Position	extrem
	)

private

bool BALL::RSComputer::getCircles	(	Index	atom1,
		Index	atom2,
		TCircle3< double > &	circle1,
		TCircle3< double > &	circle2,
		TCircle3< double > &	circle3
	)

private

TVector3<double> BALL::RSComputer::getFaceNormal	(	const TSphere3< double > &	atom1,
		const TSphere3< double > &	atom2,
		const TSphere3< double > &	atom3,
		const TSphere3< double > &	probe
	)

private

void BALL::RSComputer::getRSComponent ( ) throw (Exception::GeneralException, Exception::DivisionByZero, Exception::IndexOverflow)

private

Position BALL::RSComputer::getStartPosition ( ) throw (Exception::DivisionByZero)

private

void BALL::RSComputer::insert ( RSVertex * vertex )

private

void BALL::RSComputer::insert ( RSEdge * edge )

private

void BALL::RSComputer::insert ( RSFace * face )

private

void BALL::RSComputer::neighboursOfThreeAtoms	(	Index	atom1,
		Index	atom2,
		Index	atom3,
		std::deque< Index > &	output_list
	)

private

const std::deque<Index>& BALL::RSComputer::neighboursOfTwoAtoms ( const SortedPosition2 & pos )

private

void BALL::RSComputer::preProcessing ( )

private

void BALL::RSComputer::run ( ) throw (Exception::GeneralException, Exception::DivisionByZero, Exception::IndexOverflow)

Compute the reduced surface

Index BALL::RSComputer::thirdAtom	(	RSVertex *	vertex1,
		RSVertex *	vertex2,
		RSFace *	face,
		TSphere3< double > &	probe,
		TAngle< double > &	phi
	)		throw (Exception::GeneralException, Exception::DivisionByZero, Exception::IndexOverflow)

private

bool BALL::RSComputer::treatEdge ( RSEdge * edge ) throw (Exception::GeneralException, Exception::DivisionByZero, Exception::IndexOverflow)

private

bool BALL::RSComputer::treatFace ( RSFace * face ) throw (Exception::GeneralException, Exception::DivisionByZero, Exception::IndexOverflow)

private

void BALL::RSComputer::updateFaceAndEdges	(	RSVertex *	v1,
		RSVertex *	v2,
		RSVertex *	v3,
		RSEdge *	e1,
		RSEdge *	e2,
		RSEdge *	e3,
		RSFace *	f,
		const TSphere3< double > &	probe
	)

private

Member Data Documentation

std::vector< AtomStatus > BALL::RSComputer::atom_status_

protected

Definition at line 874 of file reducedSurface.h.

std::vector< std::deque<Index> > BALL::RSComputer::neighbours_

protected

Definition at line 870 of file reducedSurface.h.

HashMap< SortedPosition2, std::deque<Index> > BALL::RSComputer::neighbours_of_two_

protected

Definition at line 878 of file reducedSurface.h.

HashSet<RSFace*> BALL::RSComputer::new_faces_

protected

Definition at line 890 of file reducedSurface.h.

HashSet<RSVertex*> BALL::RSComputer::new_vertices_

protected

Definition at line 886 of file reducedSurface.h.

HashMap< SortedPosition3, ProbePosition* > BALL::RSComputer::probe_positions_

protected

Definition at line 882 of file reducedSurface.h.

ReducedSurface* BALL::RSComputer::rs_

protected

Definition at line 866 of file reducedSurface.h.

std::vector< std::list<RSVertex*> > BALL::RSComputer::vertices_

protected

Definition at line 894 of file reducedSurface.h.

Classes

Public Types

Public Member Functions

Protected Attributes

Private Member Functions

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation