Represents the composite of two shapes joined by a bond at arbitrary shape vertices. More...

#include <Composites.h>

Data Structures
struct	AngleGroup
	A group of shape vertices at an angle from the fused position. More...

struct	OrientationState
	Encompasses the orientation of a shape along a fused bond. More...

struct	Permutation
	Class representing a single rotational permutation. More...

struct	PermutationGenerator

Public Types
Member types
enum	Alignment { Alignment::Eclipsed, Alignment::Staggered, Alignment::EclipsedAndStaggered, Alignment::BetweenEclipsedAndStaggered }
	Relative orientation of substituent groups along the dihedral. More...

using	PermutationsList = std::vector< Permutation >
	Relative orientation of substituent groups along the dihedral.

Public Member Functions
Constructors
	Composite (OrientationState first, OrientationState second, Alignment alignment=Alignment::Eclipsed)
	Constructor calculating all permutations. More...

Modification
void	applyIdentifierPermutation (const std::vector< std::size_t > &permutation)

template<typename F >
void	updateIdentifiers (F f)

Information
const PermutationsList &	allPermutations () const
	Returns all permutations, including ranking-duplicates.

bool	isIsotropic () const
	Returns whether the Composite is isotropic overall. More...

std::pair< unsigned, unsigned >	orders () const
	Returns the number of relevant substituent shape vertices for each side.

unsigned	order () const
	Returns the higher number of relevant substituent shape vertices of both sides. More...

unsigned	rotationalAxisSymmetryOrder () const
	Rotational axis symmetry element order.

const Temple::OrderedPair < OrientationState > &	orientations () const
	Returns the orientation state of the composite. More...

unsigned	rankingEquivalentBase (unsigned permutation) const
	Index of the ranking equivalent base to a permutation.

std::vector< unsigned >	nonEquivalentPermutationIndices () const
	List of all base permutation indices (without ranking-equivalents)

unsigned	countNonEquivalentPermutations () const
	Returns the number of non-ranking-equivalent permutations for this Composite. More...

Alignment	alignment () const
	Returns the alignment with which the Composite was generated with. More...

Iterators
PermutationsList::const_iterator	begin () const
	Through-iteration of all generated dihedral permutations.

PermutationsList::const_iterator	end () const
	Through-iteration of all generated dihedral permutations.

Operators
bool	operator< (const Composite &other) const
	Less-than comparison by orientations()

bool	operator== (const Composite &other) const
	Equality comparison by orientations()

bool	operator!= (const Composite &other) const
	Inequality comparison by orientations()

Static Private Member Functions
static double	perpendicularSubstituentAngle (double angleFromBoundShapeVertex, double angleBetweenSubstituents)
	Calculates the angle between two substituents that have the same angle from the bound shape vertices in a plane perpendicular to their shared axis. More...

Private Attributes
Private state
Temple::OrderedPair < OrientationState >	orientations_
	Stores the relative orientation with which the permutations were generated.

PermutationsList	stereopermutations_
	List of dihedral sets that comprise all spatial arrangements.

Alignment	alignment_
	Stores with which Alignment the stereopermutations were generated.

Static members
static constexpr Temple::Floating::ExpandedAbsoluteEqualityComparator < double >	fpComparator
	1° absolute tolerance floating point comparison helper for angle groups More...

static std::vector < Shapes::Vertex >	generateRotation (Shapes::Shape shape, Shapes::Vertex fixedVertex, const std::vector< Shapes::Vertex > &changedVertices)
	Generates a shape rotation subject to constraints. More...

static std::vector < Shapes::Vertex >	rotation (Shapes::Shape shape, Shapes::Vertex fixedVertex, const std::vector< Shapes::Vertex > &perpendicularPlaneVertices)
	1° absolute tolerance floating point comparison helper for angle groups

Detailed Description

Represents the composite of two shapes joined by a bond at arbitrary shape vertices.

Acts as a container-like type for the generated stereopermutations after construction.

Member Enumeration Documentation

enum Scine::Molassembler::Stereopermutations::Composite::Alignment

strong

Relative orientation of substituent groups along the dihedral.

Enumerator
Eclipsed	At least two substituents eclipse one another along the axis.
Staggered	At least one pair of substituents are staggered along the axis.
EclipsedAndStaggered	Both eclipsed and staggered alignments.
BetweenEclipsedAndStaggered	Offset exactly halfway between eclipsed and staggered alignments.

Constructor & Destructor Documentation

Scine::Molassembler::Stereopermutations::Composite::Composite	(	OrientationState	first,
		OrientationState	second,
		Alignment	alignment = `Alignment::Eclipsed`
	)

Constructor calculating all permutations.

Complexity \(O(S!)\) where S is the size of the larger shape of the two OrientationState instances

Postcondition: Each permutations' dihedrals are sorted (lexicographically)

Member Function Documentation

Alignment Scine::Molassembler::Stereopermutations::Composite::alignment ( ) const

Returns the alignment with which the Composite was generated with.

Complexity \(\Theta(1)\)

unsigned Scine::Molassembler::Stereopermutations::Composite::countNonEquivalentPermutations ( ) const

Returns the number of non-ranking-equivalent permutations for this Composite.

Complexity \(\Theta(1)\)

static std::vector<Shapes::Vertex> Scine::Molassembler::Stereopermutations::Composite::generateRotation	(	Shapes::Shape	shape,
		Shapes::Vertex	fixedVertex,
		const std::vector< Shapes::Vertex > &	changedVertices
	)

static

Generates a shape rotation subject to constraints.

Parameters

shape	The shape in which the rotation is sought
fixedVertex	The shape vertex in `shape` that is kept constant
changedVertices	The shape vertices which must change in the sought rotation

bool Scine::Molassembler::Stereopermutations::Composite::isIsotropic ( ) const

Returns whether the Composite is isotropic overall.

Complexity \(\Theta(1)\)

unsigned Scine::Molassembler::Stereopermutations::Composite::order ( ) const

Returns the higher number of relevant substituent shape vertices of both sides.

E.g. In a combination of EquilateralTriangle and Tetrahedron, the order is three.

const Temple::OrderedPair<OrientationState>& Scine::Molassembler::Stereopermutations::Composite::orientations ( ) const

Returns the orientation state of the composite.

Complexity \(\Theta(1)\)

static double Scine::Molassembler::Stereopermutations::Composite::perpendicularSubstituentAngle	(	double	angleFromBoundShapeVertex,
		double	angleBetweenSubstituents
	)

staticprivate

Calculates the angle between two substituents that have the same angle from the bound shape vertices in a plane perpendicular to their shared axis.

The axis is defined by the bound shape position and the central point of the shape. shape positions with identical angles from the bound shape position are situated together in a plane perpendicular to the axis. The angle between these shape positions via the intersection with the axis in that plane is calculated by this function.

Warning: Do not call this with angleFromBoundShapeVertex == M_PI as the geometrical idea collapses.

Field Documentation

constexpr Temple::Floating::ExpandedAbsoluteEqualityComparator<double> Scine::Molassembler::Stereopermutations::Composite::fpComparator

static

Initial value:

{
    Temple::Math::toRadians(1.0)
  }

1° absolute tolerance floating point comparison helper for angle groups

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

Molassembler/Stereopermutation/Composites.h

Data Structures

Public Types

Public Member Functions

Static Private Member Functions

Private Attributes

Static members

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Field Documentation