Molecular Surface Computation

Classes
singleton	BALL::GraphEdge< Vertex, Edge, Face >
singleton	BALL::GraphFace< Vertex, Edge, Face >
singleton	BALL::GraphTriangle< Vertex, Edge, Face >
class	BALL::GraphVertex< Vertex, Edge, Face >
class	BALL::ReducedSurface
class	BALL::RSComputer
struct	BALL::RSComputer::ProbePosition
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
class	BALL::SESSingularityCleaner
struct	BALL::SESSingularityCleaner::ProbeIntersection
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
class	BALL::TriangulatedSphere
struct	BALL::TriangulatedSphere::Face

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

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 502 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 490 of file reducedSurface.h.

enum BALL::SurfaceProcessor::SurfaceType

Enumerator
SOLVENT_EXCLUDED_SURFACE
SOLVENT_ACCESSIBLE_SURFACE

Definition at line 57 of file surfaceProcessor.h.

enum BALL::SESEdge::Type

type of SESEdge: 0 concave 1 convex 2 singular

Enumerator
TYPE_CONCAVE
TYPE_CONVEX
TYPE_SINGULAR

Definition at line 67 of file SESEdge.h.

enum BALL::SESFace::Type

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

fragment	the kernel object containing the atoms
probe_radius	the probe radius used for the SAS

Returns

the SES area in

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

fragment	the kernel object containing the atoms
probe_radius	the probe radius used for the SAS
atom_areas

Returns

the SES area in

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

fragment	the kernel object containing the atoms
probe_radius	the probe radius used for the SAS

Returns

the volume in