BGL wrapper to help with distance bounds smoothing. More...

#include <ExplicitBoundsGraph.h>

Public Types
Member types
using	EdgeWeightProperty = boost::property< boost::edge_weight_t, double >

using	GraphType = boost::adjacency_list< boost::vecS, boost::vecS, boost::directedS, boost::no_property, EdgeWeightProperty >

using	VertexDescriptor = GraphType::vertex_descriptor

using	EdgeDescriptor = GraphType::edge_descriptor

using	BoundsMatrix = Eigen::MatrixXd

Public Member Functions
Special member functions
	ExplicitBoundsGraph (const PrivateGraph &inner, const DistanceBoundsMatrix &bounds)
	Construct from distance bounds matrix. More...

	ExplicitBoundsGraph (const PrivateGraph &inner, const BoundsMatrix &bounds)
	Construct from bounds matrix. More...

Modifiers
void	addBound (VertexDescriptor a, VertexDescriptor b, const ValueBounds &bound)
	Adds a bound between outer vertex indices to the graph. More...

double	lowerBound (VertexDescriptor a, VertexDescriptor b) const
	Fetches the lower bound between outer vertex indices from the graph. More...

double	upperBound (VertexDescriptor a, VertexDescriptor b) const
	Fetches the upper bound between outer vertex indices from the graph. More...

outcome::result< Eigen::MatrixXd >	makeDistanceMatrix (Random::Engine &engine) noexcept
	Generate a distance matrix. More...

outcome::result< Eigen::MatrixXd >	makeDistanceMatrix (Random::Engine &engine, Partiality partiality) noexcept

Information
double	maximalImplicitLowerBound (VertexDescriptor i) const
	Returns the length of the maximal implicit lower bound outgoing from a left vertex. More...

const GraphType &	graph () const
	Nonmodifiable access to underlying graph. More...

outcome::result< Eigen::MatrixXd >	makeDistanceBounds () const noexcept
	Make smooth distance bounds. More...

Static Public Member Functions
Static member functions
static void	explainContradictionPaths (VertexDescriptor a, VertexDescriptor b, const std::vector< VertexDescriptor > &predecessors, const std::vector< double > &distances)
	Explain contradictions between distance bounds on a path. More...

static bool	isLeft (const VertexDescriptor i) noexcept
	Check whether a vertex is part of the left subgraph. More...

static bool	sameSide (const VertexDescriptor i, const VertexDescriptor j) noexcept
	Explain contradictions between distance bounds on a path. More...

static VertexDescriptor	left (const VertexDescriptor a) noexcept
	Get the left subgraph vertex descriptor corresponding to an outer index. More...

static VertexDescriptor	right (const VertexDescriptor a) noexcept
	Get the right subgraph vertex descriptor corresponding to an outer index. More...

Private Member Functions
void	updateOrAddEdge_ (VertexDescriptor i, VertexDescriptor j, double edgeWeight)

void	updateGraphWithFixedDistance_ (VertexDescriptor a, VertexDescriptor b, double fixedDistance)

Private Attributes
GraphType	graph_

const PrivateGraph &	inner_

std::array< Utils::ElementType, 2 >	heaviestAtoms_
	Stores the two heaviest element types.

Detailed Description

BGL wrapper to help with distance bounds smoothing.

A class that helps with lower complexity determination of distance bounds compatible with the triangle inequality limits via reinterpretation as a graph shortest paths calculation.

The main idea is to transfer all ValueBounds collected by a SpatialModel to this class. The compatible triangle inequality bounds to this set of ValueBounds should then be extracted as a DistanceBoundsMatrix and kept for refinement. For every new conformation, the underlying graph containing the information from the ValueBounds needs to be copied and generateDistanceMatrix called upon it. This procedure modifies the underlying graph and hence cannot be called repeatedly.

The underlying data structure is a fully explicit BGL graph containing all edges and edge weights.

Constructor & Destructor Documentation

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

Construct from distance bounds matrix.

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

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

Construct from bounds matrix.

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

Member Function Documentation

void Scine::Molassembler::DistanceGeometry::ExplicitBoundsGraph::addBound	(	VertexDescriptor	a,
		VertexDescriptor	b,
		const ValueBounds &	bound
	)

Adds a bound between outer vertex indices to the graph.

This is represented by six edges:

Bidirectional within the left subgraph between a and b weighted with the upper bound
Bidirectional within the right subgraph between a and b weighted with the upper bound
Edges from the left vertices of a and b to the right opposite one with the negative lower bound

Complexity \(\Theta(1)\)

static void Scine::Molassembler::DistanceGeometry::ExplicitBoundsGraph::explainContradictionPaths	(	VertexDescriptor	a,
		VertexDescriptor	b,
		const std::vector< VertexDescriptor > &	predecessors,
		const std::vector< double > &	distances
	)

static

Explain contradictions between distance bounds on a path.

Complexity linear in the length of the path between a and b

const GraphType& Scine::Molassembler::DistanceGeometry::ExplicitBoundsGraph::graph ( ) const

Nonmodifiable access to underlying graph.

Complexity \(\Theta(1)\)

static bool Scine::Molassembler::DistanceGeometry::ExplicitBoundsGraph::isLeft ( const VertexDescriptor i )

inlinestaticnoexcept

Check whether a vertex is part of the left subgraph.

Complexity \(\Theta(1)\)

static VertexDescriptor Scine::Molassembler::DistanceGeometry::ExplicitBoundsGraph::left ( const VertexDescriptor a )

inlinestaticnoexcept

Get the left subgraph vertex descriptor corresponding to an outer index.

Complexity \(\Theta(1)\)

double Scine::Molassembler::DistanceGeometry::ExplicitBoundsGraph::lowerBound	(	VertexDescriptor	a,
		VertexDescriptor	b
	)		const

Fetches the lower bound between outer vertex indices from the graph.

Complexity \(\Theta(1)\)

outcome::result<Eigen::MatrixXd> Scine::Molassembler::DistanceGeometry::ExplicitBoundsGraph::makeDistanceBounds ( ) const

noexcept

Make smooth distance bounds.

Complexity \(\Theta(V \cdot E)\)

outcome::result<Eigen::MatrixXd> Scine::Molassembler::DistanceGeometry::ExplicitBoundsGraph::makeDistanceMatrix ( Random::Engine & engine )

noexcept

Generate a distance matrix.

Generates a distances matrix conforming to the triangle inequality bounds while modifying state information. Can only be called once!

Complexity \(O(V^2 \cdot E)\)

outcome::result<Eigen::MatrixXd> Scine::Molassembler::DistanceGeometry::ExplicitBoundsGraph::makeDistanceMatrix	(	Random::Engine &	engine,
		Partiality	partiality
	)

noexcept

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

double Scine::Molassembler::DistanceGeometry::ExplicitBoundsGraph::maximalImplicitLowerBound ( VertexDescriptor i ) const

Returns the length of the maximal implicit lower bound outgoing from a left vertex.

Complexity \(\Theta(1)\)

static VertexDescriptor Scine::Molassembler::DistanceGeometry::ExplicitBoundsGraph::right ( const VertexDescriptor a )

inlinestaticnoexcept

Get the right subgraph vertex descriptor corresponding to an outer index.

Complexity \(\Theta(1)\)

static bool Scine::Molassembler::DistanceGeometry::ExplicitBoundsGraph::sameSide	(	const VertexDescriptor	i,
		const VertexDescriptor	j
	)

inlinestaticnoexcept

Explain contradictions between distance bounds on a path.

Complexity linear in the length of the path between a and b

double Scine::Molassembler::DistanceGeometry::ExplicitBoundsGraph::upperBound	(	VertexDescriptor	a,
		VertexDescriptor	b
	)		const

Fetches the upper bound between outer vertex indices from the graph.

Complexity \(\Theta(1)\)

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

Molassembler/DistanceGeometry/ExplicitBoundsGraph.h

Public Types

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation