Input and output. More...

Data Structures
struct	BinaryHandler
	Binary file IO. More...

struct	SmilesBondStereo
	Helper class to represent the stereo configuration of a double bond as indicated in a SMILES string. More...

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

class	MoleculeBuilder
	Semantic interpreter of the smiles grammar. More...

struct	ElementData

struct	ChiralData

struct	AtomData

struct	BondData

class	LineNotation
	Provides Molecule instances from line notations of molecules such as SMILES and InChI. More...

Enumerations
enum	SmilesBondType { Single, Double, Triple, Quadruple, Aromatic, Forward, Backward }

Functions
bool	isValenceFillElement (Utils::ElementType e)

int	vertexValence (PrivateGraph::Vertex i, const PrivateGraph &g)

unsigned	valenceFillElementImplicitHydrogenCount (int valence, Utils::ElementType e)

std::pair < Utils::AtomCollection, Utils::BondOrderCollection >	exchangeFormat (const Molecule &molecule, const AngstromPositions &angstromWrapper)
	Extract exchange format information from a molecule and positional data. More...

std::pair < Utils::AtomCollection, Utils::BondOrderCollection >	exchangeFormat (const Molecule &molecule, const Utils::PositionCollection &positions)

std::tuple < Utils::AtomCollection, Utils::BondOrderCollection, std::vector< AtomIndex > >	shuffle (const Utils::AtomCollection &ac, const Utils::BondOrderCollection &bos)
	Applies a random atom index permutation to exchange data. More...

Molecule	read (const std::string &filename)
	Read a single molecule from a file. More...

std::vector< Molecule >	split (const std::string &filename)
	Read multiple molecules from a file. More...

void	write (const std::string &filename, const Molecule &molecule, const AngstromPositions &angstromWrapper)
	Writer function for various chemical formats. More...

void	write (const std::string &filename, const Molecule &molecule, const Utils::PositionCollection &positions)

void	write (const std::string &filename, const Molecule &molecule)
	Writer function for Molecule serializations and graphviz representations. More...

Detailed Description

Input and output.

Function Documentation

std::pair<Utils::AtomCollection, Utils::BondOrderCollection> Scine::Molassembler::IO::exchangeFormat	(	const Molecule &	molecule,
		const AngstromPositions &	angstromWrapper
	)

Extract exchange format information from a molecule and positional data.

Complexity \(\Theta(N + B)\)

std::pair<Utils::AtomCollection, Utils::BondOrderCollection> Scine::Molassembler::IO::exchangeFormat	(	const Molecule &	molecule,
		const Utils::PositionCollection &	positions
	)

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Molecule Scine::Molassembler::IO::read ( const std::string & filename )

Read a single molecule from a file.

Complexity \(\Theta(N)\) typically

Exceptions

If	interpretation of coordinates and connectivity yields multiple molecules.

Note: Interprets file type from extension. mol is a MOLFile, xyz an XYZ file and cbor/bson/json are serializations of Molecule

std::tuple<Utils::AtomCollection, Utils::BondOrderCollection, std::vector<AtomIndex> > Scine::Molassembler::IO::shuffle	(	const Utils::AtomCollection &	ac,
		const Utils::BondOrderCollection &	bos
	)

Applies a random atom index permutation to exchange data.

Complexity \(\Theta(N + B)\)

std::vector<Molecule> Scine::Molassembler::IO::split ( const std::string & filename )

Read multiple molecules from a file.

Complexity \(\Theta(N)\) typically

Note: Interprets file format from its extension. See read(); Serializations of Molecules cannot be split, they always contain only a single molecule. Use read() instead.

void Scine::Molassembler::IO::write	(	const std::string &	filename,
		const Molecule &	molecule,
		const AngstromPositions &	angstromWrapper
	)

Writer function for various chemical formats.

For exceptions this might throw,

Complexity \(\Theta(N)\)

Note: Interprets which file type is to be written from filename extension.; Unless the file format is .json or .masm, canonicalization state of Molecule instances is lost.

void Scine::Molassembler::IO::write	(	const std::string &	filename,
		const Molecule &	molecule,
		const Utils::PositionCollection &	positions
	)

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

void Scine::Molassembler::IO::write	(	const std::string &	filename,
		const Molecule &	molecule
	)

Writer function for Molecule serializations and graphviz representations.

Complexity \(\Theta(V + E + A + B)\)

Exceptions

std::logic_error	If the file extension does not match .cbor, .bson, .json, .dot or .svg
std::runtime_error	If the file extension is .svg but the dot binary is not found in the path