Class to help validate aromatic subgraphs in parsed smiles strings. More...

#include <SmilesMoleculeBuilder.h>

Data Structures
struct	EligibleOmissible
	Data struct for eligibleOmissible() More...

Public Types
Types
using	BaseGraph = boost::adjacency_list< boost::vecS, boost::vecS, boost::undirectedS, boost::no_property, boost::property< boost::edge_index_t, int > >

using	Graph = boost::subgraph< BaseGraph >

using	Vertex = typename BaseGraph::vertex_descriptor

using	Edge = typename BaseGraph::edge_descriptor

using	IndexMap = boost::bimap< Vertex, Vertex >

using	VertexSet = std::unordered_set< Vertex >

Public Member Functions
Modification
Vertex	findOrAdd (Vertex i)
	Find a precursor vertex's subgraph index, inserting it if not present.

boost::optional< VertexSet >	match ()
	Find a precursor vertex's subgraph index, inserting it if not present.

Static Public Member Functions
Static predicates
static bool	hasUnpairedElectrons (Vertex i, int charge, const PrivateGraph &g)
	Decide whether an element type is allowed to be in the pi subgraph. More...

static bool	permittedElementType (Utils::ElementType e)
	Decide whether an element type is allowed to be in the pi subgraph. More...

static EligibleOmissible	eligibleOmissible (Vertex i, const PrivateGraph &component, const AtomData &atomData)
	Determine viability and omissibility of a vertex in a pi subgraph. More...

static boost::optional < EligibleOmissible >	multipleOrderAdjacent (Vertex i, const PrivateGraph &component, const AtomData &atomData, const boost::optional< unsigned > &neighborCount)
	Decide whether an element type is allowed to be in the pi subgraph. More...

static boost::optional < EligibleOmissible >	threeNeighborChargedCarbon (Vertex i, const PrivateGraph &component, const AtomData &atomData, const boost::optional< unsigned > &neighborCount)
	Decide whether an element type is allowed to be in the pi subgraph. More...

static boost::optional < EligibleOmissible >	neutralTrivalents (Vertex i, const PrivateGraph &component, const AtomData &atomData, const boost::optional< unsigned > &neighborCount)
	Decide whether an element type is allowed to be in the pi subgraph. More...

static boost::optional < EligibleOmissible >	neutralDivalents (Vertex i, const PrivateGraph &component, const AtomData &atomData, const boost::optional< unsigned > &neighborCount)
	Decide whether an element type is allowed to be in the pi subgraph. More...

Data Fields
Data
Graph	graph
	Subgraph data structure.

IndexMap	index
	Index mapping from precursor to subgraph vertex index.

VertexSet	omissible
	Set of omissible subgraph vertices.

Detailed Description

Class to help validate aromatic subgraphs in parsed smiles strings.

Atoms marked aromatic in a SMILES string must form a valid pi subgraph. Also, a perfect matching of the pi subgraph must be found that indicates which vertices of the system receive incremented formal valences so that hydrogen filling can proceed correctly.

This class is here to help with both.

Member Function Documentation

static EligibleOmissible Scine::Molassembler::IO::PiSubgraph::eligibleOmissible	(	Vertex	i,
		const PrivateGraph &	component,
		const AtomData &	atomData
	)

static

Determine viability and omissibility of a vertex in a pi subgraph.

Vertices that are marked aromatic in a SMILES string may not be eligible for perfect matching, i.e. marking an adjacent edge as a double bond in finding an alternating sequence of single and double bonds. For instance, a neutral nitrogen atom with three neighbors is not viable for addition to the subgraph. If the nitrogen atom is neutral and has two neighbors, it is viable for addition but optionally omissible, since the missing valence can be filled by hydrogen filling. It can, but does need to have an adjacent edge marked as a double bond.

Parameters

i	Vertex index of the atom within the component graph
component	The graph of the smiles component
atomData	The parsed atom data from the SMILES string

static bool Scine::Molassembler::IO::PiSubgraph::hasUnpairedElectrons	(	Vertex	i,
		int	charge,
		const PrivateGraph &	g
	)

static