BALL  1.4.1
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Classes | Public Attributes | Protected Member Functions | Protected Attributes | List of all members
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)
 ~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
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)

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.

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.

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.