base class for calculating solvent accessible surface areas of target particles derived classes implement specific neighbour search algorithms More...

#include <sasa.h>

Inheritance diagram for Faunus::SASA::SASABase:

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Collaboration diagram for Faunus::SASA::SASABase:

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Classes
struct	Neighbours

Public Member Functions
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	init (const Space &spc)=0

virtual std::vector< SASABase::Neighbours >	calcNeighbourData (const Space &spc, const std::vector< index_type > &target_indices) const =0

virtual SASABase::Neighbours	calcNeighbourDataOfParticle (const Space &spc, index_type target_index) const =0

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...

Public Attributes
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
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
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

base class for calculating solvent accessible surface areas of target particles derived classes implement specific neighbour search algorithms

Constructor & Destructor Documentation

◆ SASABase()

Faunus::SASA::SASABase::SASABase	(	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

◆ calcSASA()

template<typename TBegin , typename TEnd >

double Faunus::SASA::SASABase::calcSASA	(	const Space &	spc,
		TBegin	begin,
		TEnd	end
	)		const

inline

calculates total sasa of either particles or groups between given iterators

Parameters

spc
begin	iterator to either a first particle or group in a range
end	iterator to either end of particle or group in a range

Template Parameters

TBegin
TEnd

◆ calcSASAOf() [1/2]

template<>

double Faunus::SASA::SASABase::calcSASAOf	(	const Space &	spc,
		const Group &	group
	)		const

calculates total sasa of a group

Parameters

spc
Group

Returns: total sasa of a given group

◆ calcSASAOf() [2/2]

template<>

double Faunus::SASA::SASABase::calcSASAOf	(	const Space &	spc,
		const Particle &	particle
	)		const

calculates total sasa of a particle

Parameters

spc
Particle

Returns: total sasa of a given particle

◆ calcSASAOfParticle()

double Faunus::SASA::SASABase::calcSASAOfParticle ( const Neighbours & neighbour ) const

protected

Calcuates SASA of a single particle defined by NeighbourData object.

cuts a sphere in z-direction, for each slice, radius of circle_i in the corresponding z-plane is calculated then for each neighbour, calculate the overlaping part of circle_i with neighbouring circle_j and add these arcs into vector, finally from this vector, calculate the exposed part of circle_i

Parameters

neighbour NeighbourData object of given particle

◆ exposedArcLength()

double Faunus::SASA::SASABase::exposedArcLength ( std::vector< std::pair< double, double >> & arcs ) const

protected

Calcuates total arc length in radians of overlapping arcs defined by two angles.

Parameters

vector of arcs, defined by a pair (first angle, second angle)

◆ indexOf()

index_type Faunus::SASA::SASABase::indexOf ( const Particle & particle ) const

inlineprotected

first particle in ParticleVector

returns absolute index of particle in ParticleVector

Parameters

particle

◆ updateSASA()

void Faunus::SASA::SASABase::updateSASA	(	const std::vector< SASABase::Neighbours > &	neighbours_data,
		const std::vector< index_type > &	target_indices
	)

updates sasa of target particles

Parameters

neighbours	array of NeighbourData objects
target_indices	absolute indicies of target particles in ParticleVector

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

src/sasa.h
src/sasa.cpp

Classes

Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ SASABase()

Member Function Documentation

◆ calcSASA()

◆ calcSASAOf() [1/2]

◆ calcSASAOf() [2/2]

◆ calcSASAOfParticle()

◆ exposedArcLength()

◆ indexOf()

◆ updateSASA()