BALL::NumericalSAS Class Reference

#include <BALL/STRUCTURE/numericalSAS.h>

Classes
struct	Default
struct	Option

Public Member Functions
Constructors and Destructors.
	NumericalSAS ()
	NumericalSAS (const Options &options)
virtual	~NumericalSAS ()
Accessors.
void	operator() (const AtomContainer &fragment)
float	getTotalArea () const
HashMap< const Atom *, float > &	getAtomAreas ()
const HashMap< const Atom *, float > &	getAtomAreas () const
float	getTotalVolume () const
HashMap< const Atom *, float > &	getAtomVolumes ()
const HashMap< const Atom *, float > &	getAtomVolumes () const
Surface &	getSurface ()
const Surface &	getSurface () 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 More...
HashMap< Atom const *, float >	atom_areas_
	mapping of atom to SAS area More...
float	total_area_
	total solvent accessible area of the fragment More...
HashMap< Atom const *, float >	atom_volumes_
	mapping of atom to SAS volume More...
float	total_volume_
	total solvent accessible volume of the fragment More...
Surface	surface_
	the SAS as a surface More...
HashMap< Atom const *, Surface >	atom_surfaces_
	mapping of atom to surface More...
std::vector< std::pair < Vector3, Surface > >	atom_surface_map_
	vector of (atom center, surface) More...

Detailed Description

Definition at line 44 of file numericalSAS.h.

Constructor & Destructor Documentation

BALL::NumericalSAS::NumericalSAS

(

)

Default Constructor.

BALL::NumericalSAS::NumericalSAS

(

const Options &

options

)

Detailed Constructor.

virtual BALL::NumericalSAS::~NumericalSAS ( )

virtual

Destructor.

Member Function Documentation

Size BALL::NumericalSAS::computeSphereTesselation_ ( TriangulatedSphere &  result, int  num_points  )

protected

Precompute the sphere tesselation for the requested number of points.

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.

Definition at line 187 of file numericalSAS.h.

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.

Definition at line 195 of file numericalSAS.h.

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.

Definition at line 211 of file numericalSAS.h.

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.

Definition at line 219 of file numericalSAS.h.

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.

Definition at line 227 of file numericalSAS.h.

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.

Definition at line 235 of file numericalSAS.h.

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.

Definition at line 259 of file numericalSAS.h.

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.

Definition at line 267 of file numericalSAS.h.

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.

Definition at line 243 of file numericalSAS.h.

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.

Definition at line 251 of file numericalSAS.h.

float BALL::NumericalSAS::getTotalArea ( ) const

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.

Definition at line 179 of file numericalSAS.h.

float BALL::NumericalSAS::getTotalVolume ( ) const

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.

Definition at line 203 of file numericalSAS.h.

void BALL::NumericalSAS::operator()

(

const AtomContainer &

fragment

)

void BALL::NumericalSAS::setDefaultOptions_ ( )

protected

Set values from options.

Member Data Documentation

HashMap<Atom const*, float> BALL::NumericalSAS::atom_areas_

protected

mapping of atom to SAS area

Definition at line 288 of file numericalSAS.h.

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

protected

vector of (atom center, surface)

Definition at line 306 of file numericalSAS.h.

HashMap<Atom const*, Surface> BALL::NumericalSAS::atom_surfaces_

protected

mapping of atom to surface

Definition at line 303 of file numericalSAS.h.

HashMap<Atom const*, float> BALL::NumericalSAS::atom_volumes_

protected

mapping of atom to SAS volume

Definition at line 294 of file numericalSAS.h.

AtomContainer const* BALL::NumericalSAS::fragment_

protected

the AtomContainer we are bound to

Definition at line 285 of file numericalSAS.h.

Options BALL::NumericalSAS::options

Options.

Definition at line 273 of file numericalSAS.h.

Surface BALL::NumericalSAS::surface_

protected

the SAS as a surface

Definition at line 300 of file numericalSAS.h.

float BALL::NumericalSAS::total_area_

protected

total solvent accessible area of the fragment

Definition at line 291 of file numericalSAS.h.

float BALL::NumericalSAS::total_volume_

protected

total solvent accessible volume of the fragment

Definition at line 297 of file numericalSAS.h.