Handles specific relative arrangements of two atom stereopermutators joined by a bond. More...

#include <BondStereopermutator.h>

Data Structures
struct	FittingReferences

struct	Impl

Public Types
Public types
enum	Alignment { Alignment::Eclipsed, Alignment::Staggered, Alignment::EclipsedAndStaggered, Alignment::BetweenEclipsedAndStaggered }
	How dihedrals are aligned in the generation of stereopermutations. More...

enum	FittingMode { FittingMode::Thresholded, FittingMode::Nearest }
	Differentiates how viable assignments are chosen during fitting. More...

using	SitePositions = Eigen::Matrix< double, 3, Eigen::Dynamic >
	Spatial centroids of atom stereopermutator site atoms.

using	SitePositionsPair = std::pair< SitePositions, SitePositions >
	Spatial centroids of two atom stereopermutators' site atoms.

Public Member Functions
Special member functions
	BondStereopermutator (BondStereopermutator &&other) noexcept

BondStereopermutator &	operator= (BondStereopermutator &&other) noexcept

	BondStereopermutator (const BondStereopermutator &other)

BondStereopermutator &	operator= (const BondStereopermutator &other)

	~BondStereopermutator ()

Constructors
	BondStereopermutator ()=delete
	Constructs a bond stereopermutator on two atom stereopermutators without checking whether stereopermutations are feasible or not. More...

	BondStereopermutator (const AtomStereopermutator &stereopermutatorA, const AtomStereopermutator &stereopermutatorB, const BondIndex &edge, Alignment alignment=Alignment::Eclipsed)
	Constructs a bond stereopermutator on two atom stereopermutators without checking whether stereopermutations are feasible or not. More...

	BondStereopermutator (const PrivateGraph &graph, const StereopermutatorList &stereopermutators, const BondIndex &edge, Alignment alignment=Alignment::Eclipsed)
	Constructs a bond stereopermutator on two atom stereopermutators, removing obviously infeasible stereopermutations. More...

Modification
void	assign (boost::optional< unsigned > assignment)
	Changes the assignment of the stereopermutator. More...

void	assignRandom (Random::Engine &engine)
	Assign the Stereopermutator at random. More...

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

void	fit (const SitePositionsPair &sitePositions, std::pair< FittingReferences, FittingReferences > fittingReferences, FittingMode mode=FittingMode::Thresholded)
	Determines the assignment the permutator is in from positional information. More...

void	fit (const AngstromPositions &angstromWrapper, std::pair< FittingReferences, FittingReferences > fittingReferences, FittingMode mode=FittingMode::Thresholded)

void	propagateGraphChange (const AtomStereopermutator::PropagatedState &oldPermutator, const AtomStereopermutator &newPermutator, const PrivateGraph &inner, const StereopermutatorList &permutators)
	Propagates the bond stereocenter's state through a possible ranking change on one of its constituting atom stereopermutators. More...

void	propagateVertexRemoval (AtomIndex removedIndex)
	Propagates invalidated atom indices through the removal of an index.

Information
Alignment	alignment () const
	Returns alignment parameter this was constructed with. More...

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

const Stereopermutations::Composite &	composite () const
	Gives read-only access to the underlying Composite object. More...

std::pair< AtomIndex, AtomIndex >	compositeAlignment () const
	The atom identifier alignment of the permutational composite.

double	dihedral (const AtomStereopermutator &stereopermutatorA, SiteIndex siteIndexA, const AtomStereopermutator &stereopermutatorB, SiteIndex siteIndexB) const
	Angle between sites at stereopermutators in the current assignment. More...

bool	hasSameCompositeOrientation (const BondStereopermutator &other) const
	Returns whether this stereopermutator has the same relative orientation as another stereopermutator. More...

boost::optional< unsigned >	indexOfPermutation () const
	Returns the index of permutation. More...

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

unsigned	numStereopermutations () const
	Returns the number of possible stereopermutations. More...

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

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

BondIndex	placement () const
	Returns which bond this stereopermutator is placed on in the molecule. More...

Operators
bool	operator< (const BondStereopermutator &other) const
	Compares whether the underlying composite and the assignment are equivalent to those of another bond stereopermutator.

bool	operator== (const BondStereopermutator &other) const
	Compares whether the underlying composite and the assignment are equivalent to those of another bond stereopermutator.

bool	operator!= (const BondStereopermutator &other) const
	Inverts `operator==`.

Static Public Member Functions
Static functions
static std::vector< unsigned >	notObviouslyInfeasibleStereopermutations (const PrivateGraph &graph, const AtomStereopermutator &stereopermutatorA, const AtomStereopermutator &stereopermutatorB, const Stereopermutations::Composite &composite)
	Determine which stereopermutations aren't obviously infeasible. More...

Static Public Attributes
Static members
static constexpr double	assignmentAcceptanceParameter = 0.1
	Assignment acceptance is dependent on this parameter. More...

Private Attributes
std::unique_ptr< Impl >	pImpl_

Detailed Description

Handles specific relative arrangements of two atom stereopermutators joined by a bond.

This class exists to model rotational barriers along bonds joining an arbitrary pair of idealized shapes.

Member Enumeration Documentation

enum Scine::Molassembler::BondStereopermutator::Alignment

strong

How dihedrals are aligned in the generation of stereopermutations.

Enumerator
Eclipsed	At least two shape vertices 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.

enum Scine::Molassembler::BondStereopermutator::FittingMode

strong

Differentiates how viable assignments are chosen during fitting.

Enumerator
Thresholded	Positions must be close to the idealized assignment geometry.
Nearest	Choose whichever assignment best represents the geometry directly.

Constructor & Destructor Documentation

Scine::Molassembler::BondStereopermutator::BondStereopermutator ( )

delete

Constructs a bond stereopermutator on two atom stereopermutators without checking whether stereopermutations are feasible or not.

Complexity \(O(S!)\) where \(S\) is the size of the larger involved shape

Scine::Molassembler::BondStereopermutator::BondStereopermutator	(	const AtomStereopermutator &	stereopermutatorA,
		const AtomStereopermutator &	stereopermutatorB,
		const BondIndex &	edge,
		Alignment	alignment = `Alignment::Eclipsed`
	)

Constructs a bond stereopermutator on two atom stereopermutators without checking whether stereopermutations are feasible or not.

Complexity \(O(S!)\) where \(S\) is the size of the larger involved shape

Scine::Molassembler::BondStereopermutator::BondStereopermutator	(	const PrivateGraph &	graph,
		const StereopermutatorList &	stereopermutators,
		const BondIndex &	edge,
		Alignment	alignment = `Alignment::Eclipsed`
	)

Constructs a bond stereopermutator on two atom stereopermutators, removing obviously infeasible stereopermutations.

Complexity \(O(S!)\) where \(S\) is the size of the larger involved shape

Member Function Documentation

Alignment Scine::Molassembler::BondStereopermutator::alignment ( ) const

Returns alignment parameter this was constructed with.

Complexity \(\Theta(1)\)

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

Applies an atom index permutation.

Complexity \(\Theta(1)\)

Parameters

permutation The permutation to apply

void Scine::Molassembler::BondStereopermutator::assign ( boost::optional< unsigned > assignment )

Changes the assignment of the stereopermutator.

Parameters

assignment The new assignment of the stereopermutator. May be boost::none, which sets the chiral state as indeterminate. Must be less than the number of assignments if not None.

Complexity \(\Theta(1)\)

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

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

Complexity \(\Theta(1)\)

Returns: whether the stereopermutator is assigned or not, and if so, which assignment it is.

void Scine::Molassembler::BondStereopermutator::assignRandom ( Random::Engine & engine )

Assign the Stereopermutator at random.

Complexity \(\Theta(1)\)

Note: If the stereocenter is already assigned, it is reassigned.; The state of the passed PRNG is advanced.

const Stereopermutations::Composite& Scine::Molassembler::BondStereopermutator::composite ( ) const

Gives read-only access to the underlying Composite object.

Complexity \(\Theta(1)\)

double Scine::Molassembler::BondStereopermutator::dihedral	(	const AtomStereopermutator &	stereopermutatorA,
		SiteIndex	siteIndexA,
		const AtomStereopermutator &	stereopermutatorB,
		SiteIndex	siteIndexB
	)		const

Angle between sites at stereopermutators in the current assignment.

Complexity \(\Theta(1)\)

Parameters

stereopermutatorA	One constituting stereopermutator
siteIndexA	A site index of `stereopermutatorA`
stereopermutatorB	The other constituting stereopermutator
siteIndexB	A site index of `stereopermutatorB`

Exceptions

std::logic_error If the stereopermutator is unassigned or if no dihedral is found for the passed sites

void Scine::Molassembler::BondStereopermutator::fit	(	const SitePositionsPair &	sitePositions,
		std::pair< FittingReferences, FittingReferences >	fittingReferences,
		FittingMode	mode = `FittingMode::Thresholded`
	)

Determines the assignment the permutator is in from positional information.

The assignment of this permutator is determined from three-dimensional positions using penalties to modeled dihedral angles. An assignment is considered matched if each dihedral that is part of the permutation is within assignmentAcceptanceDihedralThreshold.

Complexity \(\Theta(P)\) where \(P\) is the number of permutations

Parameters

sitePositions	The site positions of each constuting atom stereopermutator, following the same ordering as compositeAlignment()
fittingReferences	Pair of FittingReferences to constituting atom stereopermutators (order is irrelevant)
mode	Mode altering the assignment of stereopermutations depending on geometric closeness to the idealized minimum

void Scine::Molassembler::BondStereopermutator::fit	(	const AngstromPositions &	angstromWrapper,
		std::pair< FittingReferences, FittingReferences >	fittingReferences,
		FittingMode	mode = `FittingMode::Thresholded`
	)

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

bool Scine::Molassembler::BondStereopermutator::hasSameCompositeOrientation ( const BondStereopermutator & other ) const

Returns whether this stereopermutator has the same relative orientation as another stereopermutator.

Complexity \(\Theta(1)\)

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

Returns the index of permutation.

Complexity \(\Theta(1)\)

std::string Scine::Molassembler::BondStereopermutator::info ( ) const

Returns an information string for diagnostic purposes.

Complexity \(\Theta(1)\)

static std::vector<unsigned> Scine::Molassembler::BondStereopermutator::notObviouslyInfeasibleStereopermutations	(	const PrivateGraph &	graph,
		const AtomStereopermutator &	stereopermutatorA,
		const AtomStereopermutator &	stereopermutatorB,
		const Stereopermutations::Composite &	composite
	)

static

Determine which stereopermutations aren't obviously infeasible.

Complexity \(\Theta(P)\), where \(P\) is the number of permutations in the underlying composite

unsigned Scine::Molassembler::BondStereopermutator::numAssignments ( ) const

Returns the number of possible assignments.

Complexity \(\Theta(1)\)

unsigned Scine::Molassembler::BondStereopermutator::numStereopermutations ( ) const

Returns the number of possible stereopermutations.

Complexity \(\Theta(1)\)

BondIndex Scine::Molassembler::BondStereopermutator::placement ( ) const

Returns which bond this stereopermutator is placed on in the molecule.

Complexity \(\Theta(1)\)

void Scine::Molassembler::BondStereopermutator::propagateGraphChange	(	const AtomStereopermutator::PropagatedState &	oldPermutator,
		const AtomStereopermutator &	newPermutator,
		const PrivateGraph &	inner,
		const StereopermutatorList &	permutators
	)

Propagates the bond stereocenter's state through a possible ranking change on one of its constituting atom stereopermutators.

Parameters

oldPermutator	The AtomStereopermutator that is changing at its state before a ranking change effects its current stereopermutation or substituent ranking
newPermutator	The AtomStereopermutator that is changing after its internal state has been propagated through a ranking change
inner	Inner graph for context
permutators	Stereopermutator list for context

Complexity \(O(S!)\) where \(S\) is the size of the larger involved shape

std::string Scine::Molassembler::BondStereopermutator::rankInfo ( ) const

Returns an information for ranking equality checking purposes.

Complexity \(\Theta(1)\)

Field Documentation

constexpr double Scine::Molassembler::BondStereopermutator::assignmentAcceptanceParameter = 0.1

static

Assignment acceptance is dependent on this parameter.

An assignment is accepted if the sum of absolute angular deviations of all dihedrals involved in a stereopermutation divided by the number of dihedrals is less than this factor times two pi divided by the larger number of involved substituents at the ends of the bond.

For the classic E/Z double bond case, there are two involved substituents at both sides. The tolerance per dihedral is then 0.1 * 360° / 2 = 18°.

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

Molassembler/BondStereopermutator.h

Data Structures

Public Types

Public Member Functions

Static Public Member Functions

Static Public Attributes

Private Attributes

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Field Documentation