BALL::SolventExcludedSurface Class Reference
[Molecular Surface Computation]

#include <BALL/STRUCTURE/solventExcludedSurface.h>

List of all members.

Public Types

Type definitions

typedef std::vector< SESVertex * >
::iterator 		VertexIterator
typedef std::vector< SESVertex * >
::const_iterator 		ConstVertexIterator
typedef std::vector< SESEdge * >
::iterator 		EdgeIterator
typedef std::vector< SESEdge * >
::const_iterator 		ConstEdgeIterator
typedef std::list< SESEdge * >
::iterator 		SingularEdgeIterator
typedef std::list< SESEdge * >
::const_iterator 		ConstSingularEdgeIterator
typedef std::vector< SESFace * >
::iterator 		ContactFaceIterator
typedef std::vector< SESFace * >
::const_iterator 		ConstContactFaceIterator
typedef std::vector< SESFace * >
::iterator 		SphericFaceIterator
typedef std::vector< SESFace * >
::const_iterator 		ConstSphericFaceIterator
typedef std::vector< SESFace * >
::iterator 		ToricFaceIterator
typedef std::vector< SESFace * >
::const_iterator 		ConstToricFaceIterator

Public Member Functions

Constructors and Destructors

 SolventExcludedSurface ()
 SolventExcludedSurface (const SolventExcludedSurface &ses, bool=false)
 SolventExcludedSurface (ReducedSurface *reduced_surface)
virtual ~SolventExcludedSurface ()
Accessors

void clear ()
void clean (const double &density)
void compute () throw (Exception::GeneralException)
void splitSphericFaces ()
bool check ()
External Iterators

VertexIterator beginVertex ()
ConstVertexIterator beginVertex () const
VertexIterator endVertex ()
ConstVertexIterator endVertex () const
EdgeIterator beginEdge ()
ConstEdgeIterator beginEdge () const
EdgeIterator endEdge ()
ConstEdgeIterator endEdge () const
SingularEdgeIterator beginSingularEdge ()
ConstSingularEdgeIterator beginSingularEdge () const
SingularEdgeIterator endSingularEdge ()
ConstSingularEdgeIterator endSingularEdge () const
ContactFaceIterator beginContactFace ()
ConstContactFaceIterator beginContactFace () const
ContactFaceIterator endContactFace ()
ConstContactFaceIterator endContactFace () const
SphericFaceIterator beginSphericFace ()
ConstSphericFaceIterator beginSphericFace () const
SphericFaceIterator endSphericFace ()
ConstSphericFaceIterator endSphericFace () const
ToricFaceIterator beginToricFace ()
ConstToricFaceIterator beginToricFace () const
ToricFaceIterator endToricFace ()
ConstToricFaceIterator endToricFace () const

Protected Attributes

Position number_of_vertices_
::std::vector< SESVertex * > vertices_
Position number_of_edges_
::std::vector< SESEdge * > edges_
Position number_of_singular_edges_
::std::list< SESEdge * > singular_edges_
Position number_of_contact_faces_
::std::vector< SESFace * > contact_faces_
Position number_of_toric_faces_
::std::vector< SESFace * > toric_faces_
Position number_of_spheric_faces_
::std::vector< SESFace * > spheric_faces_
ReducedSurface * reduced_surface_

Private Member Functions

void splitSphericFace (Position i)
void deleteSmallToricFace (SESFace *face)
void deleteSmallSingularToricFace (SESFace *face)
bool cleanToricFace (SESFace *face, const double &sqrt_density)
bool cleanSingularToricFace (SESFace *face, const double &sqrt_density)
void cleanVertices ()
void cleanEdges ()
void cleanContactFaces ()
void cleanToricFaces ()
void cleanSphericFaces ()

Friends

Class friends

- class SESComputer

class SESComputer
class SESSingularityCleaner
class TriangulatedSES
class SESTriangulator

Detailed Description

Generic SolventExcludedSurface Class.

Definition at line 66 of file solventExcludedSurface.h.

Member Typedef Documentation

typedef std::vector<SESFace*>::const_iterator BALL::SolventExcludedSurface::ConstContactFaceIterator

Definition at line 104 of file solventExcludedSurface.h.

typedef std::vector<SESEdge*>::const_iterator BALL::SolventExcludedSurface::ConstEdgeIterator

Definition at line 96 of file solventExcludedSurface.h.

typedef std::list<SESEdge*>::const_iterator BALL::SolventExcludedSurface::ConstSingularEdgeIterator

Definition at line 100 of file solventExcludedSurface.h.

typedef std::vector<SESFace*>::const_iterator BALL::SolventExcludedSurface::ConstSphericFaceIterator

Definition at line 108 of file solventExcludedSurface.h.

typedef std::vector<SESFace*>::const_iterator BALL::SolventExcludedSurface::ConstToricFaceIterator

Definition at line 112 of file solventExcludedSurface.h.

typedef std::vector<SESVertex*>::const_iterator BALL::SolventExcludedSurface::ConstVertexIterator

Definition at line 92 of file solventExcludedSurface.h.

typedef std::vector<SESFace*>::iterator BALL::SolventExcludedSurface::ContactFaceIterator

Definition at line 102 of file solventExcludedSurface.h.

typedef std::vector<SESEdge*>::iterator BALL::SolventExcludedSurface::EdgeIterator

Definition at line 94 of file solventExcludedSurface.h.

typedef std::list<SESEdge*>::iterator BALL::SolventExcludedSurface::SingularEdgeIterator

Definition at line 98 of file solventExcludedSurface.h.

typedef std::vector<SESFace*>::iterator BALL::SolventExcludedSurface::SphericFaceIterator

Definition at line 106 of file solventExcludedSurface.h.

typedef std::vector<SESFace*>::iterator BALL::SolventExcludedSurface::ToricFaceIterator

Definition at line 110 of file solventExcludedSurface.h.

typedef std::vector<SESVertex*>::iterator BALL::SolventExcludedSurface::VertexIterator

Definition at line 90 of file solventExcludedSurface.h.

Constructor & Destructor Documentation

BALL::SolventExcludedSurface::SolventExcludedSurface (  ) 

Default constructor. This method creates a new SolventExcludedSurface object.

BALL::SolventExcludedSurface::SolventExcludedSurface ( const SolventExcludedSurface &  ses,
bool  = false 
)

Copy constructor. Create a new SolventExcludedSurface object from another.

Parameters:
ses the SolventExcludedSurface object to be copied
bool ignored - just for interface consistency
BALL::SolventExcludedSurface::SolventExcludedSurface ( ReducedSurface *  reduced_surface  ) 

Detailed constructor

virtual BALL::SolventExcludedSurface::~SolventExcludedSurface (  )  [virtual]

Destructor. As there are no dynamic data structures, nothing happens.

Member Function Documentation

ConstContactFaceIterator BALL::SolventExcludedSurface::beginContactFace (  )  const
ContactFaceIterator BALL::SolventExcludedSurface::beginContactFace (  ) 
ConstEdgeIterator BALL::SolventExcludedSurface::beginEdge (  )  const
EdgeIterator BALL::SolventExcludedSurface::beginEdge (  ) 
ConstSingularEdgeIterator BALL::SolventExcludedSurface::beginSingularEdge (  )  const
SingularEdgeIterator BALL::SolventExcludedSurface::beginSingularEdge (  ) 
ConstSphericFaceIterator BALL::SolventExcludedSurface::beginSphericFace (  )  const
SphericFaceIterator BALL::SolventExcludedSurface::beginSphericFace (  ) 
ConstToricFaceIterator BALL::SolventExcludedSurface::beginToricFace (  )  const
ToricFaceIterator BALL::SolventExcludedSurface::beginToricFace (  ) 
ConstVertexIterator BALL::SolventExcludedSurface::beginVertex (  )  const
VertexIterator BALL::SolventExcludedSurface::beginVertex (  ) 
bool BALL::SolventExcludedSurface::check (  ) 
void BALL::SolventExcludedSurface::clean ( const double &  density  ) 
void BALL::SolventExcludedSurface::cleanContactFaces (  )  [private]
void BALL::SolventExcludedSurface::cleanEdges (  )  [private]
bool BALL::SolventExcludedSurface::cleanSingularToricFace ( SESFace *  face,
const double &  sqrt_density 
) [private]
void BALL::SolventExcludedSurface::cleanSphericFaces (  )  [private]
bool BALL::SolventExcludedSurface::cleanToricFace ( SESFace *  face,
const double &  sqrt_density 
) [private]
void BALL::SolventExcludedSurface::cleanToricFaces (  )  [private]
void BALL::SolventExcludedSurface::cleanVertices (  )  [private]
void BALL::SolventExcludedSurface::clear (  ) 
void BALL::SolventExcludedSurface::compute (  )  throw (Exception::GeneralException)

Computes the solvent excluded surface from a ReducedSurface object

void BALL::SolventExcludedSurface::deleteSmallSingularToricFace ( SESFace *  face  )  [private]
void BALL::SolventExcludedSurface::deleteSmallToricFace ( SESFace *  face  )  [private]
ConstContactFaceIterator BALL::SolventExcludedSurface::endContactFace (  )  const
ContactFaceIterator BALL::SolventExcludedSurface::endContactFace (  ) 
ConstEdgeIterator BALL::SolventExcludedSurface::endEdge (  )  const
EdgeIterator BALL::SolventExcludedSurface::endEdge (  ) 
ConstSingularEdgeIterator BALL::SolventExcludedSurface::endSingularEdge (  )  const
SingularEdgeIterator BALL::SolventExcludedSurface::endSingularEdge (  ) 
ConstSphericFaceIterator BALL::SolventExcludedSurface::endSphericFace (  )  const
SphericFaceIterator BALL::SolventExcludedSurface::endSphericFace (  ) 
ConstToricFaceIterator BALL::SolventExcludedSurface::endToricFace (  )  const
ToricFaceIterator BALL::SolventExcludedSurface::endToricFace (  ) 
ConstVertexIterator BALL::SolventExcludedSurface::endVertex (  )  const
VertexIterator BALL::SolventExcludedSurface::endVertex (  ) 
void BALL::SolventExcludedSurface::splitSphericFace ( Position  i  )  [private]
void BALL::SolventExcludedSurface::splitSphericFaces (  ) 

Friends And Related Function Documentation

friend class SESComputer [friend]

Definition at line 78 of file solventExcludedSurface.h.

friend class SESSingularityCleaner [friend]

Definition at line 79 of file solventExcludedSurface.h.

friend class SESTriangulator [friend]

Definition at line 81 of file solventExcludedSurface.h.

friend class TriangulatedSES [friend]

Definition at line 80 of file solventExcludedSurface.h.

Member Data Documentation

::std::vector<SESFace*> BALL::SolventExcludedSurface::contact_faces_ [protected]

Definition at line 281 of file solventExcludedSurface.h.

::std::vector<SESEdge*> BALL::SolventExcludedSurface::edges_ [protected]

Definition at line 269 of file solventExcludedSurface.h.

Position BALL::SolventExcludedSurface::number_of_contact_faces_ [protected]

Definition at line 278 of file solventExcludedSurface.h.

Position BALL::SolventExcludedSurface::number_of_edges_ [protected]

Definition at line 266 of file solventExcludedSurface.h.

Position BALL::SolventExcludedSurface::number_of_singular_edges_ [protected]

Definition at line 272 of file solventExcludedSurface.h.

Position BALL::SolventExcludedSurface::number_of_spheric_faces_ [protected]

Definition at line 290 of file solventExcludedSurface.h.

Position BALL::SolventExcludedSurface::number_of_toric_faces_ [protected]

Definition at line 284 of file solventExcludedSurface.h.

Position BALL::SolventExcludedSurface::number_of_vertices_ [protected]

Definition at line 260 of file solventExcludedSurface.h.

ReducedSurface* BALL::SolventExcludedSurface::reduced_surface_ [protected]

Definition at line 296 of file solventExcludedSurface.h.

::std::list<SESEdge*> BALL::SolventExcludedSurface::singular_edges_ [protected]

Definition at line 275 of file solventExcludedSurface.h.

::std::vector<SESFace*> BALL::SolventExcludedSurface::spheric_faces_ [protected]

Definition at line 293 of file solventExcludedSurface.h.

::std::vector<SESFace*> BALL::SolventExcludedSurface::toric_faces_ [protected]

Definition at line 287 of file solventExcludedSurface.h.

::std::vector<SESVertex*> BALL::SolventExcludedSurface::vertices_ [protected]

Definition at line 263 of file solventExcludedSurface.h.

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