Public Types
Member types
using	BoundsMatrix = Eigen::MatrixXd

Public Member Functions
Special member functions
	DistanceBoundsMatrix ()
	Initializes nothing.

	DistanceBoundsMatrix (long unsigned N)
	Initializes the matrix with defaultLower and defaultUpper.

	DistanceBoundsMatrix (Eigen::MatrixXd matrix)
	Sets the underlying matrix as the argument.

template<typename PrivateGraph >
	DistanceBoundsMatrix (const PrivateGraph &inner, BoundsMatrix bounds)
	Constructs a bounds matrix from a graph and a bounds matrix. More...

Modifiers
bool	setUpperBound (AtomIndex i, AtomIndex j, double newUpperBound)
	Smoothes the underlying matrix using smooth(Eigen::Ref<Eigen::MatrixXd>)

bool	setLowerBound (AtomIndex i, AtomIndex j, double newLowerBound)
	Smoothes the underlying matrix using smooth(Eigen::Ref<Eigen::MatrixXd>)

void	smooth ()
	Smoothes the underlying matrix using smooth(Eigen::Ref<Eigen::MatrixXd>)

Information
double	upperBound (AtomIndex i, AtomIndex j) const
	Access to upper bound of unordered indices. More...

double	lowerBound (AtomIndex i, AtomIndex j) const
	Access to lower bound of unordered indices. More...

unsigned	boundInconsistencies () const
	Checks for cases in which the lower bound is greater than the upper bound. More...

const Eigen::MatrixXd &	access () const
	Nonmodifiable access to bounds matrix. More...

Result< Eigen::MatrixXd >	makeDistanceMatrix (Random::Engine &engine, Partiality partiality=Partiality::All) const noexcept
	Generate a distance matrix. More...

Eigen::MatrixXd	makeSquaredBoundsMatrix () const
	Squares all bounds and returns a new matrix. More...

unsigned	N () const
	Yields the number of particles. More...

Static Public Member Functions
Static member functions
static double &	lowerBound (Eigen::Ref< Eigen::MatrixXd > matrix, const AtomIndex i, const AtomIndex j)
	Uses Floyd's algorithm to smooth the matrix. More...

static double &	upperBound (Eigen::Ref< Eigen::MatrixXd > matrix, const AtomIndex i, const AtomIndex j)
	Uses Floyd's algorithm to smooth the matrix. More...

static void	smooth (Eigen::Ref< Eigen::MatrixXd > matrix)
	Uses Floyd's algorithm to smooth the matrix. More...

Static Public Attributes
static constexpr double	defaultLower = 0.0

static constexpr double	defaultUpper = 100.0

Private Member Functions
double &	lowerBound_ (const AtomIndex i, const AtomIndex j)

double &	upperBound_ (const AtomIndex i, const AtomIndex j)

Private Attributes
Eigen::MatrixXd	matrix_

Constructor & Destructor Documentation

template<typename PrivateGraph >

Scine::Molassembler::DistanceGeometry::DistanceBoundsMatrix::DistanceBoundsMatrix	(	const PrivateGraph &	inner,
		BoundsMatrix	bounds
	)

inline

Constructs a bounds matrix from a graph and a bounds matrix.

Replaces default lower bounds with the sum of the elements' vdw radii.

Member Function Documentation

const Eigen::MatrixXd& Scine::Molassembler::DistanceGeometry::DistanceBoundsMatrix::access ( ) const

Nonmodifiable access to bounds matrix.

Complexity \(\Theta(1)\)

unsigned Scine::Molassembler::DistanceGeometry::DistanceBoundsMatrix::boundInconsistencies ( ) const

Checks for cases in which the lower bound is greater than the upper bound.

Complexity \(\Theta(N^2)\)

static double& Scine::Molassembler::DistanceGeometry::DistanceBoundsMatrix::lowerBound	(	Eigen::Ref< Eigen::MatrixXd >	matrix,
		const AtomIndex	i,
		const AtomIndex	j
	)

inlinestatic

Uses Floyd's algorithm to smooth the matrix.

Complexity \(\Theta(N^3)\)

double Scine::Molassembler::DistanceGeometry::DistanceBoundsMatrix::lowerBound	(	AtomIndex	i,
		AtomIndex	j
	)		const

inline

Access to lower bound of unordered indices.

Complexity \(\Theta(1)\)

Result<Eigen::MatrixXd> Scine::Molassembler::DistanceGeometry::DistanceBoundsMatrix::makeDistanceMatrix	(	Random::Engine &	engine,
		Partiality	partiality = `Partiality::All`
	)		const

noexcept

Generate a distance matrix.

Generates a distance matrix from the contained bounds without altering underlying state.

Complexity \(O(N^5)\)

Eigen::MatrixXd Scine::Molassembler::DistanceGeometry::DistanceBoundsMatrix::makeSquaredBoundsMatrix ( ) const

Squares all bounds and returns a new matrix.

Complexity \(\Theta(N^2)\)

unsigned Scine::Molassembler::DistanceGeometry::DistanceBoundsMatrix::N ( ) const

Yields the number of particles.

Complexity \(\Theta(1)\)

static void Scine::Molassembler::DistanceGeometry::DistanceBoundsMatrix::smooth ( Eigen::Ref< Eigen::MatrixXd > matrix )

static

Uses Floyd's algorithm to smooth the matrix.

Complexity \(\Theta(N^3)\)

static double& Scine::Molassembler::DistanceGeometry::DistanceBoundsMatrix::upperBound	(	Eigen::Ref< Eigen::MatrixXd >	matrix,
		const AtomIndex	i,
		const AtomIndex	j
	)

inlinestatic

Uses Floyd's algorithm to smooth the matrix.

Complexity \(\Theta(N^3)\)

double Scine::Molassembler::DistanceGeometry::DistanceBoundsMatrix::upperBound	(	AtomIndex	i,
		AtomIndex	j
	)		const

inline

Access to upper bound of unordered indices.

Complexity \(\Theta(1)\)

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

Molassembler/DistanceGeometry/DistanceBoundsMatrix.h

Public Types

Public Member Functions

Static Public Member Functions

Static Public Attributes

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

Member Function Documentation