Scine::Molassembler::ShapeInference Namespace Reference

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
double	bondWeight (BondType bond)
	Map bond type to a floating-point weight. More...
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...

Detailed Description

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

Function Documentation

bondWeight()

double Scine::Molassembler::ShapeInference::bondWeight

(

BondType

bond

)

Map bond type to a floating-point weight.

firstOfSize()

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

formalCharge()

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.

Warning

This will yield nonsense if the bond orders in your graph are not correct.

Warning

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

inferShape()

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

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 \(\Theta(1)\)