Runtime-computed properties of shapes. More...

Data Structures
struct	DistortionInfo
	Data type grouping distortions between shapes. More...

struct	ShapeTransitionGroup
	A grouping of index mappings of equal angular and chiral distortion. More...

Functions
Permutation	applyPermutation (const Permutation &occupation, const Permutation &permutation)
	Rotates a passed list of indices with a specified rotation vector. More...

std::vector< Vertex >	applyRotation (const Permutation &occupation, Shape shape, unsigned rotationFunctionIndex)
	Rotates a passed list of indices of a specific shape. More...

unsigned	rotationPeriodicity (Shape shape, const Permutation &rotation)
	Calculate the periodicty of a shape's index rotation. More...

PURITY_WEAK std::vector < std::vector< Vertex > >	positionGroups (Shape shape)
	Group shape vertices according to whether they can be interconverted by rotation. More...

std::vector< char >	positionGroupCharacters (Shape shape)
	Generate a character representation of a shape's position groups. More...

Permutation	inverseRotation (const Permutation &rotation)
	Generate the inverse rotation to a shape's rotation. More...

Eigen::Vector3d	getCoordinates (Shape shape, const boost::optional< Vertex > &vertexOption)
	Gets the coordinates of an indexOptional for a specific shape. More...

double	getTetrahedronVolume (const Eigen::Vector3d &i, const Eigen::Vector3d &j, const Eigen::Vector3d &k, const Eigen::Vector3d &l)
	Tetrahedron volume spanned by four positions. More...

double	calculateAngleDistortion (Shape from, Shape to, const std::vector< Vertex > &indexMapping)
	Calculates angular distorition for an index mapping between shapes. More...

boost::optional< Vertex >	propagateIndexOptionalThroughMapping (const boost::optional< Vertex > &indexOptional, const std::vector< Vertex > &indexMapping)
	Propagates an index optional through an index mapping. More...

double	calculateChiralDistortion (Shape from, Shape to, const std::vector< Vertex > &indexMapping)
	Calculates chiral distortion for a transition between shapes. More...

std::set< std::vector< Vertex >>	generateAllRotations (Shape shape, const std::vector< Vertex > &indices)
	Generates all rotations of a sequence of indices within a shape. More...

std::vector< Vertex >	applyIndexMapping (Shape to, const std::vector< Vertex > &mapping)
	Transform shape positions through a mapping. More...

std::vector< DistortionInfo >	shapeTransitionMappings (Shape from, Shape to)
	Calculates ideal index mappings for +1, 0 size transitions. More...

std::vector< DistortionInfo >	ligandLossTransitionMappings (Shape from, Shape to, Vertex positionInSourceShape)
	Calculates ideal index mappings for ligand loss transitions. More...

ShapeTransitionGroup	selectBestTransitionMappings (const std::vector< DistortionInfo > &distortions)
	Selects the best transition mapping from many DistortionInfos. More...

PURITY_WEAK unsigned	numUnlinkedStereopermutations (Shape shape, unsigned nIdenticalLigands)
	Calculates the number of stereopermutations in a specific shape and a number of identical ligands. More...

PURITY_WEAK bool	hasMultipleUnlinkedStereopermutations (Shape shape, unsigned nIdenticalLigands)
	Calculates if there are multiple unlinked stereopermutations in a specific shape for a number of identical ligands. More...

PURITY_WEAK Shape	mostSymmetric (std::vector< Shape > selection)
	Yields the shape with the most rotations from a selection. More...

PURITY_WEAK Shape	mostSymmetric (unsigned shapeSize)
	Yields the shape with the most rotations of a particular size. More...

Variables
constexpr double	floatingPointEqualityThreshold [[gnu::unused]] = 1e-4

Detailed Description

Runtime-computed properties of shapes.

Function Documentation

std::vector<Vertex> Scine::Molassembler::Shapes::Properties::applyIndexMapping	(	Shape	to,
		const std::vector< Vertex > &	mapping
	)

Transform shape positions through a mapping.

Writes the indices of the original shape in the mapping into the target shape's indexing scheme.

Complexity \(\Theta(S)\)

Parameters

to	The shape whose index mapping is to be applied
mapping	An index mapping that specifies how indices are mapped from a source shape to a target shape

Permutation Scine::Molassembler::Shapes::Properties::applyPermutation	(	const Permutation &	occupation,
		const Permutation &	permutation
	)

Rotates a passed list of indices with a specified rotation vector.

Complexity \(\Theta(S)\)

std::vector<Vertex> Scine::Molassembler::Shapes::Properties::applyRotation	(	const Permutation &	occupation,
		Shape	shape,
		unsigned	rotationFunctionIndex
	)

Rotates a passed list of indices of a specific shape.

Complexity \(\Theta(S)\)

double Scine::Molassembler::Shapes::Properties::calculateAngleDistortion	(	Shape	from,
		Shape	to,
		const std::vector< Vertex > &	indexMapping
	)

Calculates angular distorition for an index mapping between shapes.

Calculates the angular distortion for a transition between two shapes and a specific index mapping that connects indices from the source shape to the target shape

Complexity \(\Theta(S^2)\)

double Scine::Molassembler::Shapes::Properties::calculateChiralDistortion	(	Shape	from,
		Shape	to,
		const std::vector< Vertex > &	indexMapping
	)

Calculates chiral distortion for a transition between shapes.

Calculates the chiral distortion for a transition between two shapes and a specific index mapping that connects indices from the source shape to the target shape

Complexity \(\Theta(T)\) where \(T\) is the number of tetrahedra for the shape, typically small

std::set< std::vector<Vertex>> Scine::Molassembler::Shapes::Properties::generateAllRotations	(	Shape	shape,
		const std::vector< Vertex > &	indices
	)

Generates all rotations of a sequence of indices within a shape.

Complexity At most maxRotation iterations

Eigen::Vector3d Scine::Molassembler::Shapes::Properties::getCoordinates	(	Shape	shape,
		const boost::optional< Vertex > &	vertexOption
	)

Gets the coordinates of an indexOptional for a specific shape.

As was defined previously, boost::none is a placeholder for the central atom, which is not explicitly held in memory as it is always placed at {0, 0, 0}.

Complexity \(\Theta(1)\)

double Scine::Molassembler::Shapes::Properties::getTetrahedronVolume	(	const Eigen::Vector3d &	i,
		const Eigen::Vector3d &	j,
		const Eigen::Vector3d &	k,
		const Eigen::Vector3d &	l
	)

Tetrahedron volume spanned by four positions.

Returns the Eigen calculation of a signed tetrahedron volume from four tetrahedron edge point vectos

Complexity \(\Theta(1)\)

PURITY_WEAK bool Scine::Molassembler::Shapes::Properties::hasMultipleUnlinkedStereopermutations	(	Shape	shape,
		unsigned	nIdenticalLigands
	)

Calculates if there are multiple unlinked stereopermutations in a specific shape for a number of identical ligands.

Complexity \(\Theta(S!)\)

Permutation Scine::Molassembler::Shapes::Properties::inverseRotation ( const Permutation & rotation )

Generate the inverse rotation to a shape's rotation.

Inverts the permutation provided by rotation. UB if rotation is not an index permutation.

Complexity \(\Theta(N)\)

std::vector<DistortionInfo> Scine::Molassembler::Shapes::Properties::ligandLossTransitionMappings	(	Shape	from,
		Shape	to,
		Vertex	positionInSourceShape
	)

Calculates ideal index mappings for ligand loss transitions.

Generates shape transition index mappings for the special case of ligand loss, in which a ligand is removed from a particular position in the shape

Complexity \(\Theta(S!)\)

Parameters

from	Transition source shape
to	Transition target shape
positionInSourceShape	position lost in source shape

Precondition: Shapes::size(from) == Shapes::size(to) + 1

PURITY_WEAK Shape Scine::Molassembler::Shapes::Properties::mostSymmetric ( std::vector< Shape > selection )

Yields the shape with the most rotations from a selection.

Complexity \(\Theta(1)\)

PURITY_WEAK Shape Scine::Molassembler::Shapes::Properties::mostSymmetric ( unsigned shapeSize )

Yields the shape with the most rotations of a particular size.

Complexity \(\Theta(1)\)

PURITY_WEAK unsigned Scine::Molassembler::Shapes::Properties::numUnlinkedStereopermutations	(	Shape	shape,
		unsigned	nIdenticalLigands
	)

Calculates the number of stereopermutations in a specific shape and a number of identical ligands.

Complexity \(\Theta(S!)\)

std::vector<char> Scine::Molassembler::Shapes::Properties::positionGroupCharacters ( Shape shape )

Generate a character representation of a shape's position groups.

Groups shape vertices according to whether they can be interconverted. Then transforms the shape positions themselves to character representations of the groups they belong to.

Complexity \(\Theta(S^2)\)

Parameters

shape Shape for which to generate the character representation

PURITY_WEAK std::vector<std::vector<Vertex> > Scine::Molassembler::Shapes::Properties::positionGroups ( Shape shape )

Group shape vertices according to whether they can be interconverted by rotation.

Complexity \(\Theta(S^2)\)

boost::optional<Vertex> Scine::Molassembler::Shapes::Properties::propagateIndexOptionalThroughMapping	(	const boost::optional< Vertex > &	indexOptional,
		const std::vector< Vertex > &	indexMapping
	)

Propagates an index optional through an index mapping.

Index optionals as used in tetrahedron definitions in shapes need to be propagated through index mappings generated in the process of finding the optimal shape transitions. Shorthand function that performs a propagation if a the passed indexOptional is not boost::none, returns none otherwise.

Complexity \(\Theta(1)\)

unsigned Scine::Molassembler::Shapes::Properties::rotationPeriodicity	(	Shape	shape,
		const Permutation &	rotation
	)

Calculate the periodicty of a shape's index rotation.

Complexity \(\Theta(M S)\) where \(M\) is the multiplicity of the rotation and \(S\) is the shape size

ShapeTransitionGroup Scine::Molassembler::Shapes::Properties::selectBestTransitionMappings ( const std::vector< DistortionInfo > & distortions )

Selects the best transition mapping from many DistortionInfos.

Selects index mappings from a DistortionInfo list, choosing those with lowest angular distortion first, and lowest chiral distortion afterwards. Groups them into a ShapeTransitionGroup.

Complexity \(\Theta(N)\)

std::vector<DistortionInfo> Scine::Molassembler::Shapes::Properties::shapeTransitionMappings	(	Shape	from,
		Shape	to
	)

Calculates ideal index mappings for +1, 0 size transitions.

Generates shape transition index mappings with the lowest angular distortion and then subsets that group to those with the lowest chiral distortion. Transitions are limited to shapes with size differences of 0 and ±1.

Complexity \(\Theta(S!)\)

Parameters

from	Transition source shape
to	Transition target shape

Precondition: Shapes::size(from) + {0, 1} == Shapes::size(to)

Data Structures

Functions

Variables

Detailed Description

Function Documentation