BALL::RSComputer Class Reference
[Molecular Surface Computation]

#include <BALL/STRUCTURE/reducedSurface.h>

List of all members.

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::list< Index > >	neighbours_
std::vector< AtomStatus >	atom_status_
HashMap< Position, HashMap < Position, std::list< Index > > >	neighbours_of_two_
HashMap< Position, HashMap < Position, HashMap< Position, 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::list< Index > &third, std::list< std::pair< Index, TSphere3< double > > > &atoms)
void	neighboursOfTwoAtoms (Index atom1, Index atom2)
void	neighboursOfThreeAtoms (Index atom1, Index atom2, Index atom3, std::list< 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 (Index a1, Index a2, Index a3, TVector3< double > &c1, TVector3< double > &c2)
bool	checkProbe (const TSphere3< double > &probe, Index atom1, Index atom2, Index atom3)
void	correctProbePosition (Position atom)
void	sort (Index u1, Index u2, Index u3, Index &s1, Index &s2, Index &s3)
void	correctProbePosition (Position a1, Position a2, Position a3)
void	insert (RSVertex *vertex)
void	insert (RSEdge *edge)
void	insert (RSFace *face)

---

Detailed Description

Generic RSComputer Class.

---

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

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

---

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	(	Index	a1,
		Index	a2,
		Index	a3,
		TVector3< double > &	c1,
		TVector3< double > &	c2
	)			[private]

bool BALL::RSComputer::checkProbe	(	const TSphere3< double > &	probe,
		Index	atom1,
		Index	atom2,
		Index	atom3
	)			[private]

void BALL::RSComputer::correct

(

Index

atom

)

[private]

void BALL::RSComputer::correctProbePosition	(	Position	a1,
		Position	a2,
		Position	a3
	)			[private]

void BALL::RSComputer::correctProbePosition

(

Position

atom

)

[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::list< Index > &	third,
		std::list< 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

(

RSFace *

face

)

[private]

void BALL::RSComputer::insert

(

RSEdge *

edge

)

[private]

void BALL::RSComputer::insert

(

RSVertex *

vertex

)

[private]

void BALL::RSComputer::neighboursOfThreeAtoms	(	Index	atom1,
		Index	atom2,
		Index	atom3,
		std::list< Index > &	output_list
	)			[private]

void BALL::RSComputer::neighboursOfTwoAtoms	(	Index	atom1,
		Index	atom2
	)			[private]

void BALL::RSComputer::preProcessing

(

)

[private]

void BALL::RSComputer::run

(

)

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

Compute the reduced surface

void BALL::RSComputer::sort	(	Index	u1,
		Index	u2,
		Index	u3,
		Index &	s1,
		Index &	s2,
		Index &	s3
	)			[private]

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]

std::vector< std::list<Index> > BALL::RSComputer::neighbours_ [protected]

HashMap< Position, HashMap< Position, std::list<Index> > > BALL::RSComputer::neighbours_of_two_ [protected]

HashSet<RSFace*> BALL::RSComputer::new_faces_ [protected]

HashSet<RSVertex*> BALL::RSComputer::new_vertices_ [protected]

HashMap< Position, HashMap< Position, HashMap< Position, ProbePosition* > > > BALL::RSComputer::probe_positions_ [protected]

ReducedSurface* BALL::RSComputer::rs_ [protected]

std::vector< std::list<RSVertex*> > BALL::RSComputer::vertices_ [protected]