BALL  1.4.79
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)
 
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
 
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 More...
 
HashMap< Atom const *, floatatom_areas_
 mapping of atom to SAS area More...
 
float total_area_
 total solvent accessible area of the fragment More...
 
HashMap< Atom const *, floatatom_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 *, Surfaceatom_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

◆ NumericalSAS() [1/2]

BALL::NumericalSAS::NumericalSAS ( )

Default Constructor.

◆ NumericalSAS() [2/2]

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

Detailed Constructor.

◆ ~NumericalSAS()

virtual BALL::NumericalSAS::~NumericalSAS ( )
virtual

Destructor.

Member Function Documentation

◆ computeSphereTesselation_()

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

Precompute the sphere tesselation for the requested number of points.

◆ getAtomAreas() [1/2]

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.

◆ getAtomAreas() [2/2]

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.

◆ getAtomVolumes() [1/2]

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.

◆ getAtomVolumes() [2/2]

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.

◆ getSurface() [1/2]

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.

◆ getSurface() [2/2]

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.

◆ getSurfaceMap() [1/2]

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.

◆ getSurfaceMap() [2/2]

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.

◆ getSurfacePerAtom() [1/2]

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.

◆ getSurfacePerAtom() [2/2]

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.

◆ getTotalArea()

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.

◆ getTotalVolume()

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.

◆ operator()()

void BALL::NumericalSAS::operator() ( const AtomContainer fragment)

◆ setDefaultOptions_()

void BALL::NumericalSAS::setDefaultOptions_ ( )
protected

Set values from options.

Member Data Documentation

◆ atom_areas_

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

mapping of atom to SAS area

Definition at line 288 of file numericalSAS.h.

◆ atom_surface_map_

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.

◆ atom_surfaces_

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

mapping of atom to surface

Definition at line 303 of file numericalSAS.h.

◆ atom_volumes_

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

mapping of atom to SAS volume

Definition at line 294 of file numericalSAS.h.

◆ fragment_

AtomContainer const* BALL::NumericalSAS::fragment_
protected

the AtomContainer we are bound to

Definition at line 285 of file numericalSAS.h.

◆ options

Options BALL::NumericalSAS::options

Options.

Definition at line 273 of file numericalSAS.h.

◆ surface_

Surface BALL::NumericalSAS::surface_
protected

the SAS as a surface

Definition at line 300 of file numericalSAS.h.

◆ total_area_

float BALL::NumericalSAS::total_area_
protected

total solvent accessible area of the fragment

Definition at line 291 of file numericalSAS.h.

◆ total_volume_

float BALL::NumericalSAS::total_volume_
protected

total solvent accessible volume of the fragment

Definition at line 297 of file numericalSAS.h.