derived class of SASABase which uses O(N^2) neighbour search More...

#include <sasa.h>

Inheritance diagram for Faunus::SASA::SASA:

Collaboration diagram for Faunus::SASA::SASA:

Public Member Functions
void	init (const Space &spc) override
	resizes areas buffer to size of ParticleVector and fill radii buffer with radii More...

std::vector< SASABase::Neighbours >	calcNeighbourData (const Space &spc, const std::vector< index_type > &target_indices) const override
	calculates neighbourData objects of particles specified by target indices in ParticleVector More...

SASA::Neighbours	calcNeighbourDataOfParticle (const Space &spc, index_type target_index) const override
	calculates neighbourData object of a target particle specified by target indiex in ParticleVector More...

void	update ([[maybe_unused]] const Space &spc, [[maybe_unused]] const Change &change) override
	updates radii vector in case of matter change More...

	SASA (const Space &spc, double probe_radius, int slices_per_atom)

	SASA (const json &j, const Space &spc)

Public Member Functions inherited from Faunus::SASA::SASABase
double	calcSASAOfParticle (const Space &spc, const Particle &particle) const

template<typename TBegin , typename TEnd >
double	calcSASA (const Space &spc, TBegin begin, TEnd end) const
	calculates total sasa of either particles or groups between given iterators More...

template<typename TSpecies >
double	calcSASAOf (const Space &spc, const TSpecies &species) const

void	updateSASA (const std::vector< SASABase::Neighbours > &neighbours_data, const std::vector< index_type > &target_indices)
	updates sasa of target particles More...

virtual void	update (const Space &spc, const Change &change)=0

const std::vector< double > &	getAreas () const

	SASABase (const Space &spc, double probe_radius, int slices_per_atom)

template<>
double	calcSASAOf (const Space &spc, const Group &group) const
	calculates total sasa of a group More...

template<>
double	calcSASAOf (const Space &spc, const Particle &particle) const
	calculates total sasa of a particle More...

Additional Inherited Members
Public Attributes inherited from Faunus::SASA::SASABase
bool	needs_syncing = false
	flag indicating if syncing of cell_lists is needed this is important in case there is a particle insertion which is rejected due to containerOverlap, because the sasa->update is not called

Protected Member Functions inherited from Faunus::SASA::SASABase
index_type	indexOf (const Particle &particle) const
	first particle in ParticleVector More...

double	calcSASAOfParticle (const Neighbours &neighbour) const
	Calcuates SASA of a single particle defined by NeighbourData object. More...

double	exposedArcLength (std::vector< std::pair< double, double >> &arcs) const
	Calcuates total arc length in radians of overlapping arcs defined by two angles. More...

Protected Attributes inherited from Faunus::SASA::SASABase
double	probe_radius = 1.4
	radius of the probe sphere

std::vector< double >	areas
	vector holding SASA area of each atom

std::vector< double >	sasa_radii
	Radii buffer for all particles.

int	slices_per_atom = 20
	number of slices of each sphere in SASA calculation

const double	two_pi = 2.0 * std::numbers::pi

const Particle *	first_particle

Detailed Description

derived class of SASABase which uses O(N^2) neighbour search

Constructor & Destructor Documentation

◆ SASA()

Faunus::SASA::SASA::SASA	(	const Space &	spc,
		double	probe_radius,
		int	slices_per_atom
	)

Parameters

spc
probe_radius	in angstrom
slices_per_atom	number of slices of each sphere in sasa calculations

Member Function Documentation

◆ calcNeighbourData()

std::vector< SASA::Neighbours > Faunus::SASA::SASA::calcNeighbourData	(	const Space &	spc,
		const std::vector< index_type > &	target_indices
	)		const

overridevirtual

calculates neighbourData objects of particles specified by target indices in ParticleVector

Parameters

space
target_indices	absolute indicies of target particles in ParticleVector

Implements Faunus::SASA::SASABase.

◆ calcNeighbourDataOfParticle()

SASA::Neighbours Faunus::SASA::SASA::calcNeighbourDataOfParticle	(	const Space &	spc,
		index_type	target_index
	)		const

overridevirtual

calculates neighbourData object of a target particle specified by target indiex in ParticleVector

using the naive O(N) neighbour search for a given target particle

Parameters

space
target_index	indicex of target particle in ParticleVector

Implements Faunus::SASA::SASABase.

◆ init()

void Faunus::SASA::SASA::init ( const Space & spc )

overridevirtual

resizes areas buffer to size of ParticleVector and fill radii buffer with radii

Parameters

space

Implements Faunus::SASA::SASABase.

◆ update()

void Faunus::SASA::SASA::update	(	[[maybe_unused] ] const Space &	spc,
		[[maybe_unused] ] const Change &	change
	)

override

updates radii vector in case of matter change

Parameters

space
change

The documentation for this class was generated from the following files:

src/sasa.h
src/sasa.cpp

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ SASA()

Member Function Documentation

◆ calcNeighbourData()

◆ calcNeighbourDataOfParticle()

◆ init()

◆ update()