Methods to determine local shapes of atoms based on graph information. More...

Data Structures
struct	BindingSite
	Type used to represent minimal binding site information. More...

Functions
int	formalCharge (const Graph &graph, AtomIndex index)
	Calculates the formal charge on a main group-element atom. More...

boost::optional< Shapes::Shape >	vsepr (Utils::ElementType centerAtomType, const std::vector< BindingSite > &sites, int formalCharge)
	Applies very basic VSEPR theory to derive a shape based on graph information. More...

Shapes::Shape	firstOfSize (unsigned size)
	Yields the first shape of required size. More...

std::vector< BindingSite >	reduceToSiteInformation (const Graph &molGraph, AtomIndex index, const RankingInformation &ranking)
	Reduces a ranking to binding site information.

boost::optional< Shapes::Shape >	inferShape (const Graph &graph, AtomIndex index, const RankingInformation &ranking)
	Forwards inference to appropriate model depending on environment. More...

Variables
const std::map< BondType, double >	bondWeights
	Mapping of bond type to a floating-point weight. More...

Detailed Description

Methods to determine local shapes of atoms based on graph information.

Function Documentation

Shapes::Shape Scine::Molassembler::ShapeInference::firstOfSize ( unsigned size )

Yields the first shape of required size.

Complexity \(\Theta(1)\)

Exceptions

std::runtime_error If no shapes of size exist

int Scine::Molassembler::ShapeInference::formalCharge	(	const Graph &	graph,
		AtomIndex	index
	)

Calculates the formal charge on a main group-element atom.

Complexity \(\Theta(1)\)

Parameters

graph	The graph to which the atom index belongs
index	The atom index for which to calculate the formal charge

Warning: This is an awful concept and should be avoided in any sort of important calculation.; This will yield nonsense if the bond orders in your graph are not correct.; This function may work sometimes for organic neighborhoods. That's how confident we are in this function.

Returns: 0 for non-main group elements, possibly the formal charge otherwise

boost::optional<Shapes::Shape> Scine::Molassembler::ShapeInference::inferShape	(	const Graph &	graph,
		AtomIndex	index,
		const RankingInformation &	ranking
	)

Forwards inference to appropriate model depending on environment.

Currently just a stub forwarding to VSEPR

boost::optional<Shapes::Shape> Scine::Molassembler::ShapeInference::vsepr	(	Utils::ElementType	centerAtomType,
		const std::vector< BindingSite > &	sites,
		int	formalCharge
	)

Applies very basic VSEPR theory to derive a shape based on graph information.

Complexity \(\Theta(1)\)

const std::map<BondType, double> Scine::Molassembler::ShapeInference::bondWeights

Mapping of bond type to a floating-point weight.