Semantic interpreter of the smiles grammar, constructs molecules from the data accrued by the parser. More...

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

Parsing triggers
void	addAtom (const 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
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)
	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)
	Set bond stereo post-parse and conversion to molecules.

Static Private Member Functions
Static private members
static bool	isValenceFillElement (Utils::ElementType e)
	Checks whether an element type is valence filled.

static unsigned	valenceFillElementImplicitHydrogenCount (int valence, Utils::ElementType e)
	Determines the implicit hydrogen count of a valence fill element.

static BondType	mutualBondType (const boost::optional< BondType > &a, const boost::optional< BondType > &b)

static std::vector < Shapes::Vertex >	shapeMap (const ChiralData &chiralData)
	Fetches a map to help with the atom chiral markers.

Private member data
enum	SimpleLastBondData { Unbonded, Unspecified }
	Storage for bonds marked with stereo indicators ("/" and "\")

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

boost::variant < SimpleLastBondData, BondData >	lastBondData = SimpleLastBondData::Unbonded
	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::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 molecules from the data accrued by the parser.

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

Exceptions

std::runtime_error If the bond types are mismatched

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