BALL
1.4.1
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#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 |
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 | |
HashMap< Atom const *, float > | atom_areas_ |
mapping of atom to SAS area | |
float | total_area_ |
total solvent accessible area of the fragment | |
HashMap< Atom const *, float > | atom_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 *, Surface > | atom_surfaces_ |
mapping of atom to surface | |
std::vector< std::pair < Vector3, Surface > > | atom_surface_map_ |
vector of (atom center, surface) |
Definition at line 44 of file numericalSAS.h.
Default Constructor.
BALL::NumericalSAS::NumericalSAS | ( | const Options & | options | ) |
Detailed Constructor.
Destructor.
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.
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.
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.