BALL  1.4.79
Classes | Functions
Molecular Surface Computation

Classes

class  BALL::GraphEdge< Vertex, Edge, Face >
 
class  BALL::GraphFace< Vertex, Edge, Face >
 
class  BALL::GraphTriangle< Vertex, Edge, Face >
 
class  BALL::GraphVertex< Vertex, Edge, Face >
 
class  BALL::ReducedSurface
 
struct  BALL::RSComputer::ProbePosition
 
class  BALL::RSComputer
 
class  BALL::RSEdge
 
class  BALL::RSFace
 
class  BALL::RSVertex
 
class  BALL::SASEdge
 
class  BALL::SASFace
 
class  BALL::SASVertex
 
class  BALL::SESEdge
 
class  BALL::SESFace
 
class  BALL::SESVertex
 
class  BALL::SolventAccessibleSurface
 
class  BALL::SolventExcludedSurface
 
class  BALL::SESComputer
 
struct  BALL::SESSingularityCleaner::ProbeIntersection
 
class  BALL::SESSingularityCleaner
 
class  BALL::SurfaceProcessor
 
class  BALL::Triangle
 
class  BALL::TriangleEdge
 
class  BALL::TrianglePoint
 
class  BALL::TriangulatedSAS
 
class  BALL::SASTriangulator
 
class  BALL::TriangulatedSES
 
class  BALL::SESTriangulator
 
class  BALL::TriangulatedSurface
 
struct  BALL::TriangulatedSphere::Face
 
class  BALL::TriangulatedSphere
 

Functions

BALL_EXPORT float BALL::calculateSESAtomAreas (const AtomContainer &fragment, HashMap< const Atom *, float > &atom_areas, float probe_radius=1.5)
 
BALL_EXPORT float BALL::calculateSESArea (const AtomContainer &fragment, float probe_radius=1.5)
 
BALL_EXPORT float BALL::calculateSESVolume (const AtomContainer &fragment, float probe_radius=1.5)
 

Enums

enum  BALL::RSComputer::ProbeStatus { BALL::RSComputer::STATUS_OK = 0, BALL::RSComputer::STATUS_NOT_OK, BALL::RSComputer::STATUS_NOT_TESTED }
 
enum  BALL::RSComputer::AtomStatus { BALL::RSComputer::STATUS_ON_SURFACE = 0, BALL::RSComputer::STATUS_INSIDE, BALL::RSComputer::STATUS_UNKNOWN }
 

Enums

enum  BALL::SESEdge::Type { BALL::SESEdge::TYPE_CONCAVE = 0, BALL::SESEdge::TYPE_CONVEX = 1, BALL::SESEdge::TYPE_SINGULAR = 2 }
 

Enums

enum  BALL::SESFace::Type { BALL::SESFace::TYPE_SPHERIC = 0, BALL::SESFace::TYPE_TORIC = 1, BALL::SESFace::TYPE_CONTACT = 2, BALL::SESFace::TYPE_TORIC_SINGULAR = 3 }
 

Enums

enum  BALL::SurfaceProcessor::SurfaceType { BALL::SurfaceProcessor::SOLVENT_EXCLUDED_SURFACE, BALL::SurfaceProcessor::SOLVENT_ACCESSIBLE_SURFACE }
 

Detailed Description

Enumeration Type Documentation

status of an atom 0 on surface 1 inside 2 outside

Enumerator
STATUS_ON_SURFACE 
STATUS_INSIDE 
STATUS_UNKNOWN 

Definition at line 502 of file reducedSurface.h.

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 490 of file reducedSurface.h.

Enumerator
SOLVENT_EXCLUDED_SURFACE 
SOLVENT_ACCESSIBLE_SURFACE 

Definition at line 57 of file surfaceProcessor.h.

type of SESEdge: 0 concave 1 convex 2 singular

Enumerator
TYPE_CONCAVE 
TYPE_CONVEX 
TYPE_SINGULAR 

Definition at line 67 of file SESEdge.h.

type of SESFace: 0 spheric reentrant face 1 toric reentrant face 2 contact face 3 singular toric reentrant face

Enumerator
TYPE_SPHERIC 
TYPE_TORIC 
TYPE_CONTACT 
TYPE_TORIC_SINGULAR 

Definition at line 72 of file SESFace.h.

Function Documentation

BALL_EXPORT float BALL::calculateSESArea ( const AtomContainer fragment,
float  probe_radius = 1.5 
)

Calculate the solvent excluded surface area analytically. This method uses the algorithm by Michael L. Connolly. ?????

Parameters
fragmentthe kernel object containing the atoms
probe_radiusthe probe radius used for the SAS
Returns
the SES area in $\AA^2$
BALL_EXPORT float BALL::calculateSESAtomAreas ( const AtomContainer fragment,
HashMap< const Atom *, float > &  atom_areas,
float  probe_radius = 1.5 
)

Calculate the solvent excluded surface area analytically. This method uses the algorithm by Michael L. Connolly. ?????

Parameters
fragmentthe kernel object containing the atoms
probe_radiusthe probe radius used for the SAS
atom_areas
Returns
the SES area in $\AA^2$
BALL_EXPORT float BALL::calculateSESVolume ( const AtomContainer fragment,
float  probe_radius = 1.5 
)

Calculate the solvent excluded volume analytically. This method uses the algorithm by Michael L. Connolly. ?????

Parameters
fragmentthe kernel object containing the atoms
probe_radiusthe probe radius used for the SAS
Returns
the volume in $\AA^3$