BALL::NumericalSAS Class Reference

#include <BALL/STRUCTURE/numericalSAS.h>

List of all members.

Classes

struct  Default
struct  Option

Public Member Functions

Constructors and Destructors.
 NumericalSAS ()
 NumericalSAS (const Options &options)
 ~NumericalSAS ()
Accessors.
void operator() (const AtomContainer &fragment)
float getTotalArea ()
HashMap< const Atom *, float > & getAtomAreas ()
const HashMap< const Atom
*, float > & 
getAtomAreas () const
float getTotalVolume ()
HashMap< const Atom *, float > & getAtomVolumes ()
const HashMap< const Atom
*, float > & 
getAtomVolumes () const
SurfacegetSurface ()
const SurfacegetSurface () const
HashMap< const Atom *, Surface > & getSurfacePerAtom ()
const HashMap< const Atom
*, Surface > & 
getSurfacePerAtom () const
std::vector< std::pair
< Vector3, Surface > > & 
getSurfaceMap ()
const std::vector< std::pair
< Vector3, Surface > > & 
getSurfaceMap () const

Public Attributes

Options options

Protected Member Functions

void setDefaultOptions_ ()
Size computeSphereTesselation_ (TriangulatedSphere &result, int num_points)

Protected Attributes

AtomContainer const * fragment_
 the AtomContainer we are bound to
HashMap< Atom const *, floatatom_areas_
 mapping of atom to SAS area
float total_area_
 total solvent accessible area of the fragment
HashMap< Atom const *, floatatom_volumes_
 mapping of atom to SAS volume
float total_volume_
 total solvent accessible volume of the fragment
Surface surface_
 the SAS as a surface
HashMap< Atom const *, Surfaceatom_surfaces_
 mapping of atom to surface
std::vector< std::pair
< Vector3, Surface > > 
atom_surface_map_
 vector of (atom center, surface)

Constructor & Destructor Documentation

BALL::NumericalSAS::NumericalSAS ( )

Default Constructor.

BALL::NumericalSAS::NumericalSAS ( const Options options)

Detailed Constructor.

BALL::NumericalSAS::~NumericalSAS ( )

Destructor.


Member Function Documentation

Size BALL::NumericalSAS::computeSphereTesselation_ ( TriangulatedSphere result,
int  num_points 
) [protected]

Precompute the sphere tesselation for the requested number of points.

const HashMap<const Atom*, float>& BALL::NumericalSAS::getAtomAreas ( ) const [inline]

Returns the area per atom of the fragment, const version.

This function only returns sensible values after a call to operator() and only if area computation has not been disabled through the options.

HashMap<const Atom*, float>& BALL::NumericalSAS::getAtomAreas ( ) [inline]

Returns the area per atom of the fragment.

This function only returns sensible values after a call to operator() and only if area computation has not been disabled through the options.

const HashMap<const Atom*, float>& BALL::NumericalSAS::getAtomVolumes ( ) const [inline]

Returns the volume per atom of the fragment, const version.

This function only returns sensible values after a call to operator() and only if volume computation has not been disabled through the options.

HashMap<const Atom*, float>& BALL::NumericalSAS::getAtomVolumes ( ) [inline]

Returns the volume per atom of the fragment.

This function only returns sensible values after a call to operator() and only if volume computation has not been disabled through the options.

Surface& BALL::NumericalSAS::getSurface ( ) [inline]

Returns the solvent accessible surface as a collection of points and normals.

This function only returns sensible values after a call to operator() and only if surface computation has not been disabled through the options.

const Surface& BALL::NumericalSAS::getSurface ( ) const [inline]

Returns the solvent accessible surface as a collection of points and normals, const version.

This function only returns sensible values after a call to operator() and only if surface computation has not been disabled through the options.

const std::vector< std::pair<Vector3, Surface> >& BALL::NumericalSAS::getSurfaceMap ( ) const [inline]

Returns the solvent accessible surface as a collection of points and normals per atom center, const version.

This function only returns sensible values after a call to operator() and only if surface computation per atom center has not been disabled through the options.

std::vector< std::pair<Vector3, Surface> >& BALL::NumericalSAS::getSurfaceMap ( ) [inline]

Returns the solvent accessible surface as a collection of points and normals per atom center.

This function only returns sensible values after a call to operator() and only if surface computation per atom center has not been disabled through the options.

const HashMap<const Atom*, Surface>& BALL::NumericalSAS::getSurfacePerAtom ( ) const [inline]

Returns the solvent accessible surface as a collection of points and normals per atom, const version.

This function only returns sensible values after a call to operator() and only if surface computation per atom has not been disabled through the options.

HashMap<const Atom*, Surface>& BALL::NumericalSAS::getSurfacePerAtom ( ) [inline]

Returns the solvent accessible surface as a collection of points and normals per atom.

This function only returns sensible values after a call to operator() and only if surface computation per atom has not been disabled through the options.

float BALL::NumericalSAS::getTotalArea ( ) [inline]

Returns the total area of the fragment.

This function only returns sensible values after a call to operator() and only if area computation has not been disabled through the options.

float BALL::NumericalSAS::getTotalVolume ( ) [inline]

Returns the total volume of the fragment.

This function only returns sensible values after a call to operator() and only if volume computation has not been disabled through the options.

void BALL::NumericalSAS::operator() ( const AtomContainer fragment)
void BALL::NumericalSAS::setDefaultOptions_ ( ) [protected]

Set values from options.


Member Data Documentation

mapping of atom to SAS area

std::vector< std::pair<Vector3, Surface> > BALL::NumericalSAS::atom_surface_map_ [protected]

vector of (atom center, surface)

mapping of atom to surface

mapping of atom to SAS volume

the AtomContainer we are bound to

the SAS as a surface

total solvent accessible area of the fragment

total solvent accessible volume of the fragment