Scine::Molassembler::Stereopermutations Namespace Reference

Data classes for permutational spatial arrangement modeling. More...

Data Structures
class	Composite
	Represents the composite of two shapes joined by a bond at arbitrary shape vertices. More...
struct	Uniques
class	RotationEnumerator
	Enumerate rotations of stereopermutations in shapes. More...
class	Stereopermutation
	Represent abstract stereopermutation around atom center. More...

Typedefs
using	UnorderedStereopermutations = std::unordered_set< Stereopermutation, boost::hash< Stereopermutation >>

Functions
std::vector< Stereopermutation >	generateAllRotations (Stereopermutation s, Shapes::Shape shape)
	Generate all superimposable rotations of a stereopermutation. More...
bool	rotationallySuperimposable (Stereopermutation a, const Stereopermutation &b, Shapes::Shape shape)
	whether this Stereopermutation is rotationally superimposable with another. More...
boost::optional< bool >	enantiomer (const Stereopermutation &a, const Stereopermutation &b, Shapes::Shape shape)
	Checks whether a stereopermutation is a mirror image of another within a particular shape. More...
bool	hasTransArrangedLinks (const Stereopermutation &s, Shapes::Shape shape)
	Whether a stereopermutation has trans arranged linked substituents. More...
Uniques	uniques (const Stereopermutation &base, Shapes::Shape shape, bool removeTransSpanningGroups=false)
	Generate the set of rotationally unique stereopermutations for a given stereopermutation. More...
PURITY_WEAK std::size_t	hash_value (const Stereopermutation &assignment)

Detailed Description

Data classes for permutational spatial arrangement modeling.

Function Documentation

boost::optional<bool> Scine::Molassembler::Stereopermutations::enantiomer	(	const Stereopermutation &	a,
		const Stereopermutation &	b,
		Shapes::Shape	shape
	)

Checks whether a stereopermutation is a mirror image of another within a particular shape.

Complexity As generateAllRotations

Returns

boost::none If the shape does not generate enantiomers

true If the shape has enantiomers, and this is the enantiomeric stereopermutation to other

false If the shape has enantiomers, and this is not the enantiomeric to other

std::vector<Stereopermutation> Scine::Molassembler::Stereopermutations::generateAllRotations	(	Stereopermutation	s,
		Shapes::Shape	shape
	)

Generate all superimposable rotations of a stereopermutation.

Generates a set of all rotational equivalents of this Stereopermutation as defined by its shape template parameter.

Complexity \(O(\prod_i^Rm_i)\) where \(R\) is the set of rotations and \(m_i\) is the multiplicity of rotation \(i\)

bool Scine::Molassembler::Stereopermutations::hasTransArrangedLinks	(	const Stereopermutation &	s,
		Shapes::Shape	shape
	)

Whether a stereopermutation has trans arranged linked substituents.

Complexity \(O(L)\)

bool Scine::Molassembler::Stereopermutations::rotationallySuperimposable	(	Stereopermutation	a,
		const Stereopermutation &	b,
		Shapes::Shape	shape
	)

whether this Stereopermutation is rotationally superimposable with another.

Complexity As generateAllRotations

Uniques Scine::Molassembler::Stereopermutations::uniques	(	const Stereopermutation &	base,
		Shapes::Shape	shape,
		bool	removeTransSpanningGroups = false
	)

Generate the set of rotationally unique stereopermutations for a given stereopermutation.

By default does not remove trans-spanning groups (where a linked group's directly bonded atoms span an angle of 180°).

Note

Gives NO guarantees as to satisfiability (if stereopermutation can be fulfilled with real ligands)

E.g. M (A-A)_3 generates a trans-trans-trans stereopermutation, which is extremely hard to find actual ligands for that work.

The satisfiability of stereopermutation must be checked before trying to embed structures with completely nonsensical constraints. Perhaps restrict A-A ligands with bridge length 4 (chelating atoms included), maybe even up to 6 to cis arrangements. Xantphos (with bridge length 7) is the smallest trans-spanning ligand mentioned in Wikipedia.

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