Semantic interpreter of the smiles grammar. More...

Public Member Functions
std::vector< Molecule >	interpret (const std::string &smiles)
	Interpret the collected graph as (possibly multiple molecules)

Parsing triggers
void	addAtom (AtomData atom)
	Parsing trigger on encountering a ring closure marker.

void	addRingClosure (const BondData &bond)
	Parsing trigger on encountering a ring closure marker.

void	branchOpen ()
	Parsing trigger on branch open.

void	branchClose ()
	Parsing trigger on branch close.

void	setNextAtomUnbonded ()
	Parsing trigger on finding a dot (molecule separator) in place of a bond.

void	setNextAtomBondInformation (const BondData &bond)
	Parsing trigger on encountering non-default bond information.

Private Member Functions
Private member functions
std::unordered_set < PrivateGraph::Vertex >	matchAromatics (std::vector< PrivateGraph > &precursors, const std::vector< unsigned > &componentMap, const std::vector< PrivateGraph::Vertex > &indexInComponentMap) const
	Determine valence-incremented atoms by aromatics in each component.

void	setShapes (std::vector< Molecule > &molecules, const std::vector< unsigned > &componentMap, const std::vector< PrivateGraph::Vertex > &indexInComponentMap)
	Set shapes according to specified charges and stereo markers.

void	setAtomStereo (std::vector< Molecule > &molecules, const std::vector< unsigned > &componentMap, const std::vector< PrivateGraph::Vertex > &indexInComponentMap, const std::string &smiles)
	Set atom stereo post-parse and conversion to molecules.

void	setBondStereo (std::vector< Molecule > &molecules, const std::vector< unsigned > &componentMap, const std::vector< PrivateGraph::Vertex > &indexInComponentMap, const std::string &smiles)
	Set bond stereo post-parse and conversion to molecules.

void	addAromaticBondStereo (std::vector< Molecule > &molecules, const std::vector< unsigned > &componentMap, const std::vector< PrivateGraph::Vertex > &indexInComponentMap)
	Add bond stereopermutators in aromatic cycles.

Static Private Member Functions
Static private members
static BondType	mutualBondType (const boost::optional< BondType > &a, const boost::optional< BondType > &b)

static std::vector < Shapes::Vertex >	shapeMap (const ChiralData &chiralData)

Private member data
using	StereoMarkedBondTuple = std::tuple< PrivateGraph::Vertex, PrivateGraph::Vertex, SmilesBondType >
	Storage for bonds marked with stereo indicators ("/" and "\")

boost::optional< BondData >	lastBondData
	State for last stored bond data.

PrivateGraph	graph
	Possibly disconnected tracking graph.

std::stack< PrivateGraph::Vertex >	vertexStack
	State to track the vertex a new vertex is bound to.

std::vector < StereoMarkedBondTuple >	stereoMarkedBonds
	Storage for bonds marked with stereo indicators ("/" and "\")

std::vector< PrivateGraph::Edge >	piSubgraphEdges
	Storage for pi-subgraph edges.

std::unordered_map< unsigned, std::pair < PrivateGraph::Vertex, boost::optional< BondType > > >	ringClosures
	Storage for ring closure bond indicators.

std::vector< AtomData >	vertexData
	AtomData for each created vertex.

Detailed Description

Semantic interpreter of the smiles grammar.

Constructs possibly disconnected graph during parsing, then constructs molecules from accrued data and inference where necessary.

Member Function Documentation

static BondType Scine::Molassembler::IO::MoleculeBuilder::mutualBondType	(	const boost::optional< BondType > &	a,
		const boost::optional< BondType > &	b
	)

staticprivate

Determines the mutual bond type of two bond type optionals

For simplification of ring closure double-checking, where the ring-closure bond type may or may not be specified at either or both markers.

Exceptions

std::runtime_error If the bond types are mismatched

static std::vector<Shapes::Vertex> Scine::Molassembler::IO::MoleculeBuilder::shapeMap ( const ChiralData & chiralData )

staticprivate

Fetches a map to help with the atom chiral markers

Maps the order in which substituents were specified in the SMILES onto shape vertices. Note that there is rotational freedom to these.

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