ggl::chem::SMILESparser Class Reference

SMILES molecule parser. More...

#include <SMILESparser.hh>

Static Public Member Functions
static std::vector< Molecule * >	parseMultiSMILES (const std::string &SMILES_string) throw (std::invalid_argument)
static std::vector< Molecule * >	parseMultiSMILES (const std::string &SMILES_string, const GroupMap &groups) throw (std::invalid_argument)
static ChemRule::CoreGraph	parseReactionSMILES (const std::string &SMILES_string, const bool pruneClassID=true) throw (std::invalid_argument)
static std::pair< Molecule, int >	parseSMILES (const std::string &SMILES_string) throw (std::invalid_argument)
static std::pair< Molecule, int >	parseSMILES (const std::string &SMILES_string, const GroupMap &groups) throw (std::invalid_argument)

Static Protected Member Functions
static void	pruneAromaticNonRingBonds (Molecule &mol)

Detailed Description

     This class is a wrapper for the ggl::chem::SMILESparser that
     parses SMILES via their BNF grammar. See there for further details.

Author

Martin Mann (c) 2012 http://www.bioinf.uni-freiburg.de/~mmann/

Definition at line 23 of file SMILESparser.hh.

Member Function Documentation

static std::vector< Molecule * > ggl::chem::SMILESparser::parseMultiSMILES ( const std::string &  SMILES_string ) throw (std::invalid_argument)

static

Parses a SMILES string of multiple molecules separated by '.' and generates a graph representation of the molecules

Parameters

SMILES_string

the string to parse

Returns

vector of according molecule graphs

Exceptions

std::invalid_argument

in case a parsing fails

static std::vector< Molecule * > ggl::chem::SMILESparser::parseMultiSMILES ( const std::string &  SMILES_string, const GroupMap &  groups  ) throw (std::invalid_argument)

static

Parses a SMILES string of multiple molecules separated by '.' and generates a graph representation of the molecules

Parameters

SMILES_string	the string to parse
groups	a container that holds group IDs where each matching node has to be replaced by the according mapped subgraph

Returns

vector of according molecule graphs

Exceptions

std::invalid_argument

in case a parsing fails

static ChemRule::CoreGraph ggl::chem::SMILESparser::parseReactionSMILES ( const std::string &  SMILES_string, const bool  pruneClassID = true  ) throw (std::invalid_argument)

static

Parses a reaction SMILES string and uses the atom mapping encoded in the atom label class information to generate a graph grammar rule core graph, thus, each atom in the educts has to have a unique class ID and a corresponding atom (with same ID) in the products.

An example '[C:13][C-2:2].[O:3]>>[O:3]=[C:2][C:13]'

For protons part of complex labels like [CH3:1] are automatically given class IDs while it is expected that the adjacent atom (with given class ID) is present both in educt and product and features in both the same number of adjacent protons given without class ID within the complex atom label. Otherwise, an exception is raised.

NOTE: the reaction is not checked for sanity or chemical correctness. Furthermore, no constraints etc. are generated.

Parameters

SMILES_string	the string to parse
pruneClassID	whether or not the classID information is to be pruned from the atom labels

Returns

the parsed rule core graph

Exceptions

std::invalid_argument

with according description in case a check fails

static std::pair< Molecule, int > ggl::chem::SMILESparser::parseSMILES ( const std::string &  SMILES_string ) throw (std::invalid_argument)

static

Parses a SMILES string and generates a graph representation of the molecule

Parameters

SMILES_string

the string to parse

Returns

pair.first = the graph encoding of the molecule pair.second = -1 if parsing was successful, in error case it returns the string position that caused the parsing error

Exceptions

std::invalid_argument

in case a check fails

static std::pair< Molecule, int > ggl::chem::SMILESparser::parseSMILES ( const std::string &  SMILES_string, const GroupMap &  groups  ) throw (std::invalid_argument)

static

Parses a SMILES string and generates a graph representation of the molecule

Parameters

SMILES_string	the string to parse
groups	a container that holds group IDs where each matching node has to be replaced by the according mapped subgraph

Returns

pair.first = the graph encoding of the molecule pair.second = -1 if parsing was successfull, in error case it returns the string position that caused the parsing error

Exceptions

std::invalid_argument

in case a check fails

static void ggl::chem::SMILESparser::pruneAromaticNonRingBonds ( Molecule &  mol )

staticprotected

Prunes all aromatic bonds that are not part of a ring.

Parameters

mol	the molecule to correct

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

• src/ggl/chem/SMILESparser.hh