Inheritance diagram for Scine::Molassembler::AtomStereopermutator::Impl:

Public Member Functions
	Impl (const Graph &graph, Shapes::Shape shape, AtomIndex centerAtom, RankingInformation ranking)
	Constructor. More...

	Impl (AtomIndex centerAtom, Shapes::Shape shape, RankingInformation ranking, const FeasiblesGenerator &feasibility, const ThermalizationPredicate &thermalization, const std::vector< std::vector< SiteIndex >> &siteGroups={})

void	assign (boost::optional< unsigned > assignment, const std::vector< std::vector< SiteIndex >> &siteGroups={})
	Changes the assignment of the stereopermutator.

void	assign (std::vector< Shapes::Vertex > vertexMapping)
	Assign with a vertex mapping. More...

void	assignRandom (Random::Engine &engine)
	Assigns the Stereopermutator randomly using relative stereopermutation weights.

void	applyPermutation (const std::vector< AtomIndex > &permutation)
	Applies an atom index permutation. More...

boost::optional< ShapeMap >	fit (const SiteCentroids &centroids, const FeasiblesGenerator &feasibility, const ThermalizationPredicate &thermalization)

boost::optional< PropagatedState >	propagate (RankingInformation newRanking, boost::optional< Shapes::Shape > shapeOption, const FeasiblesGenerator &feasibility, const ThermalizationPredicate &thermalization)

void	propagateVertexRemoval (AtomIndex removedIndex)

void	setShape (Shapes::Shape shape, const FeasiblesGenerator &feasibility, const ThermalizationPredicate &thermalization, const std::vector< std::vector< SiteIndex >> &siteGroups={})
	If the shape is changed, we must adapt.

void	thermalize (bool thermalization)
	Unconditionally alter the thermalization of stereopermutations.

double	angle (SiteIndex i, SiteIndex j) const
	Returns the angle between two site indices in the idealized shape.

boost::optional< unsigned >	assigned () const
	Returns the permutation index within the set of possible permutations, if set. More...

AtomIndex	placement () const
	Returns a single-element vector containing the central atom.

boost::optional< unsigned >	indexOfPermutation () const
	Returns IOP within the set of symbolic ligand permutations. More...

std::vector < MinimalChiralConstraint >	minimalChiralConstraints (bool enforce=false) const
	Returns a minimal representation of chiral constraints. More...

std::string	info () const
	Returns an information string for diagnostic purposes.

std::string	rankInfo () const
	Returns an information string for ranking equality checking purposes.

std::vector< std::vector < SiteIndex > >	siteGroups () const
	Returns site indices grouped by rotational interconversion. More...

SiteCentroids	sitePositions (const AngstromPositions &wrapper, const std::vector< std::pair< AtomIndex, AtomIndex >> &substitutions={}) const
	Generate site centroid positions from a whole-molecule set of positions.

bool	thermalized () const

const Stereopermutators::Abstract &	getAbstract () const
	Returns the underlying AbstractStereopermutation. More...

const std::vector< unsigned > &	getFeasible () const
	Returns the list of feasible abstract permutations.

const RankingInformation &	getRanking () const
	Returns the underlying ranking.

Shapes::Shape	getShape () const
	Returns the underlying shape.

const ShapeMap &	getShapePositionMap () const
	Yields the mapping from site indices to shape positions. More...

unsigned	numAssignments () const
	Returns the number of possible permutations. More...

unsigned	numStereopermutations () const
	Returns the number of symbolic ligand permutations. More...

auto	tie () const

Public Member Functions inherited from Scine::Molassembler::Temple::Crtp::LexicographicComparable< Impl >
constexpr bool	operator== (const LexicographicComparable &other) const

constexpr bool	operator!= (const LexicographicComparable &other) const

constexpr bool	operator< (const LexicographicComparable &other) const

constexpr bool	operator<= (const LexicographicComparable &other) const

constexpr bool	operator> (const LexicographicComparable &other) const

constexpr bool	operator>= (const LexicographicComparable &other) const

Static Public Member Functions
Static functions
static Shapes::Shape	up (Shapes::Shape shape)
	Picks a shape retaining as much chiral state as possible on a shape size increase. More...

static Shapes::Shape	down (Shapes::Shape shape, Shapes::Vertex removedVertex)
	Picks a shape retaining as much chiral state as possible on a shape size decrease. More...

static boost::optional < std::vector< Shapes::Vertex > >	selectTransitionMapping (const Shapes::Properties::ShapeTransitionGroup &mappingsGroup, const ChiralStatePreservation &preservationOption)
	Selects a shape vertex mapping from a shape transition group.

static bool	thermalized (AtomIndex centerAtom, Shapes::Shape shape, const RankingInformation &ranking, const Graph &graph)
	Whether the stereopermutations interconvert rapidly at selected temp.

Static Public Member Functions inherited from Scine::Molassembler::Temple::Crtp::LexicographicComparable< Impl >
static constexpr const Impl &	derived (const LexicographicComparable &base)

Private Attributes
AtomIndex	centerAtom_
	Central atom of the Stereopermutator.

Shapes::Shape	shape_
	The shape the stereopermutator represents.

RankingInformation	ranking_
	Ranking information of substituents.

Stereopermutators::Abstract	abstract_
	Abstract stereopermutations and intermediate state.

std::vector< unsigned >	feasibles_
	List of abstract permutation indices that are feasible in three dimensions.

boost::optional< unsigned >	assignmentOption_
	The current state of assignment (if or not, and if so, which)

ShapeMap	shapePositionMap_
	Derived property of `assignmentOption_`.

bool	thermalized_
	Whether all feasible assignments interconvert thermally.

Constructor & Destructor Documentation

Scine::Molassembler::AtomStereopermutator::Impl::Impl	(	const Graph &	graph,
		Shapes::Shape	shape,
		AtomIndex	centerAtom,
		RankingInformation	ranking
	)

Constructor.

Parameters

graph	Base graph
shape	Shape the stereopermutator represents
centerAtom	Placement
ranking	Ranking of its substituents

Member Function Documentation

void Scine::Molassembler::AtomStereopermutator::Impl::applyPermutation ( const std::vector< AtomIndex > & permutation )

Applies an atom index permutation.

Parameters

permutation The permutation to apply

void Scine::Molassembler::AtomStereopermutator::Impl::assign ( std::vector< Shapes::Vertex > vertexMapping )

Assign with a vertex mapping.

Precondition: Requires that this mapping was generated with centroid last!

boost::optional<unsigned> Scine::Molassembler::AtomStereopermutator::Impl::assigned ( ) const

Returns the permutation index within the set of possible permutations, if set.

Returns the (public) information of whether the stereopermutator is assigned or not, and if so, which assignment it is.

static Shapes::Shape Scine::Molassembler::AtomStereopermutator::Impl::down	(	Shapes::Shape	shape,
		Shapes::Vertex	removedVertex
	)

static

Picks a shape retaining as much chiral state as possible on a shape size decrease.

Exceptions

std::logic_error If there are no smaller shapes

Note: Behavior is dependent on ChiralStatePreservation option

boost::optional<ShapeMap> Scine::Molassembler::AtomStereopermutator::Impl::fit	(	const SiteCentroids &	centroids,
		const FeasiblesGenerator &	feasibility,
		const ThermalizationPredicate &	thermalization
	)

The shape and assignment are determined based on three-dimensional positions using angle and chiral distortions from the respective idealized shapes.

const Stereopermutators::Abstract& Scine::Molassembler::AtomStereopermutator::Impl::getAbstract ( ) const

Returns the underlying AbstractStereopermutation.

Note: This is library-internal and not part of the public API

const ShapeMap& Scine::Molassembler::AtomStereopermutator::Impl::getShapePositionMap ( ) const

Yields the mapping from site indices to shape positions.

Exceptions

std::logic_error if the stereopermutator is unassigned.

boost::optional<unsigned> Scine::Molassembler::AtomStereopermutator::Impl::indexOfPermutation ( ) const

Returns IOP within the set of symbolic ligand permutations.

This is different to the assignment. The assignment denotes the index within the set of possible (more specifically, not obviously infeasible) stereopermutations.

std::vector<MinimalChiralConstraint> Scine::Molassembler::AtomStereopermutator::Impl::minimalChiralConstraints ( bool enforce = false ) const

Returns a minimal representation of chiral constraints.

Every minimal representation consists only of ligand indices.

The minimal representation assumes that all shape tetrahedron definitions are defined to be Positive targets, which is checked in the shapes tests.

Parameters

enforce Emit minimal representations of chiral constraints even if the stereopermutator does not have any chiral state, i.e. numStereopermutators() <= 1, as long as it is assigned.

unsigned Scine::Molassembler::AtomStereopermutator::Impl::numAssignments ( ) const

Returns the number of possible permutations.

Fetches the number of different assignments possible with the current substituent ranking and connectivity information. This is also the upper exclusive bound on the assignment indices that can be used to change the arrangement of substituents.

unsigned Scine::Molassembler::AtomStereopermutator::Impl::numStereopermutations ( ) const

Returns the number of symbolic ligand permutations.

Fetches the number of permutations determined by symbolic ligand calculation, not considering linking or haptic ligand cones.

boost::optional<PropagatedState> Scine::Molassembler::AtomStereopermutator::Impl::propagate	(	RankingInformation	newRanking,
		boost::optional< Shapes::Shape >	shapeOption,
		const FeasiblesGenerator &	feasibility,
		const ThermalizationPredicate &	thermalization
	)

In case a graph modification changes the ranking of this stereopermutator's substituents, it must be redetermined whether the new configuration is a stereopermutator and if so, which assignment corresponds to the previous one.

void Scine::Molassembler::AtomStereopermutator::Impl::propagateVertexRemoval ( AtomIndex removedIndex )

Prepares for the removal of an atom on the graph level, which involves the generation of new atom indices.

std::vector<std::vector<SiteIndex> > Scine::Molassembler::AtomStereopermutator::Impl::siteGroups ( ) const

Returns site indices grouped by rotational interconversion.

Precondition: The stereopermutator must be assigned

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

Exceptions

std::runtime_error If the stereopermutator is unassigned

static Shapes::Shape Scine::Molassembler::AtomStereopermutator::Impl::up ( Shapes::Shape shape )

static

Picks a shape retaining as much chiral state as possible on a shape size increase.

Exceptions

std::logic_error If there are no larger shapes

Note: Behavior is dependent on ChiralStatePreservation option

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

Molassembler/Stereopermutators/AtomStereopermutatorImpl.h

Public Member Functions

Static Public Member Functions

Private Attributes

Constructor & Destructor Documentation

Member Function Documentation