The definition of the SMILES grammar.

#include <SMILES_grammar.hh>

Data Structures
struct	atom1_parser

struct	atom2_parser

class	Atom_closure
	Utility helper class for parsing. More...

struct	AtomInfo

struct	bond_parser

struct	simpleSymbol_parser

Public Member Functions
	definition (SMILES_grammar const &self)
	Construction of the SMILES BNF grammar rules. More...

NS_BOOSTSPIRIT::rule< ScannerT > const &	start () const
	start parsing More...

Protected Types
typedef std::vector< AtomInfo >	atoms_t

typedef std::pair< int, int >	bond_t

typedef std::vector< std::pair < bond_t, std::string > >	bonds_t

typedef std::vector< std::pair < int, int > >	hcount_t

typedef std::map< int, std::string >	rcb_t

typedef std::map< int, int >	rcs_t

typedef NS_BOOSTSPIRIT::rule < ScannerT, typename Atom_closure::context_t >	rule_t
	type of rule context of this class More...

typedef std::vector< int >	stack_t

Protected Member Functions
void	add_explicit_hydrogens (void)

void	close_branch (void)

void	memorize_atom (int atom, std::string &alabel, std::string &blabel) throw (std::invalid_argument)

void	memorize_explicit_H (int atom, int hcount)

void	memorize_rc (int rc, int atom1, std::string blabel) throw (std::invalid_argument)

void	open_branch (int atom)

void	parser_warning (std::string msg)

void	reset_data_structures (void)

Protected Attributes
atom1_parser const	atom1_p

char	atom2_firstChar
	first character of a two letter atom label More...

char	atom2_tmp

int	atom_count

atoms_t	atoms

rule_t	bond

bond_parser const	bond_p

NS_BOOSTSPIRIT::rule< ScannerT >	bond_symbol

bonds_t	bonds

rule_t	branch

rule_t	chain

NS_BOOSTSPIRIT::rule< ScannerT >	charge

NS_BOOSTSPIRIT::rule< ScannerT >	chirality

rule_t	complex_atom

NS_BOOSTSPIRIT::rule< ScannerT >	complex_symbol

hcount_t	explicitH

NS_BOOSTSPIRIT::rule< ScannerT >	group_symbol

NS_BOOSTSPIRIT::rule< ScannerT >	hcount

NS_BOOSTSPIRIT::rule< ScannerT >	isotope

NS_BOOSTSPIRIT::rule< ScannerT >	name

rcs_t	rc_to_atom
	map of ring closure numbers to opening atom More...

rcb_t	rc_to_bond
	map of ring closure numbers to bond label of closing bond More...

rule_t	ringclosure

SMILES_grammar const &	self
	back reference to enclosing object for molecule creation More...

rule_t	simple_atom

NS_BOOSTSPIRIT::rule< ScannerT >	simple_symbol

simpleSymbol_parser const	simpleSymbol_p

NS_BOOSTSPIRIT::rule< ScannerT >	smiles

stack_t	stack

Detailed Description

template<typename ScannerT>
struct ggl::chem::SMILES_grammar::definition< ScannerT >

Definition at line 184 of file SMILES_grammar.hh.

Member Typedef Documentation

template<typename ScannerT >

typedef std::vector< AtomInfo > ggl::chem::SMILES_grammar::definition< ScannerT >::atoms_t

protected

Definition at line 362 of file SMILES_grammar.hh.

template<typename ScannerT >

typedef std::pair<int,int> ggl::chem::SMILES_grammar::definition< ScannerT >::bond_t

protected

Definition at line 352 of file SMILES_grammar.hh.

template<typename ScannerT >

typedef std::vector<std::pair<bond_t,std::string> > ggl::chem::SMILES_grammar::definition< ScannerT >::bonds_t

protected

Definition at line 353 of file SMILES_grammar.hh.

template<typename ScannerT >

typedef std::vector<std::pair<int,int> > ggl::chem::SMILES_grammar::definition< ScannerT >::hcount_t

protected

Definition at line 364 of file SMILES_grammar.hh.

template<typename ScannerT >

typedef std::map<int,std::string> ggl::chem::SMILES_grammar::definition< ScannerT >::rcb_t

protected

Definition at line 385 of file SMILES_grammar.hh.

template<typename ScannerT >

typedef std::map<int,int> ggl::chem::SMILES_grammar::definition< ScannerT >::rcs_t

protected

Definition at line 384 of file SMILES_grammar.hh.

template<typename ScannerT >

typedef NS_BOOSTSPIRIT::rule< ScannerT , typename Atom_closure::context_t > ggl::chem::SMILES_grammar::definition< ScannerT >::rule_t

protected

Definition at line 349 of file SMILES_grammar.hh.

template<typename ScannerT >

typedef std::vector<int> ggl::chem::SMILES_grammar::definition< ScannerT >::stack_t

protected

Definition at line 363 of file SMILES_grammar.hh.

Constructor & Destructor Documentation

template<typename ScannerT >

ggl::chem::SMILES_grammar::definition< ScannerT >::definition ( SMILES_grammar const & self )

Member Function Documentation

template<typename ScannerT >

void ggl::chem::SMILES_grammar::definition< ScannerT >::add_explicit_hydrogens ( void )

protected

Function called by the parser to add explicit hydrogens from complex atoms to constructed graph

template<typename ScannerT >

void ggl::chem::SMILES_grammar::definition< ScannerT >::close_branch ( void )

protected

Function called by the parser to report that the last molecule branching is ended

template<typename ScannerT >

void ggl::chem::SMILES_grammar::definition< ScannerT >::memorize_atom	(	int	atom,
		std::string &	alabel,
		std::string &	blabel
	)		throw (std::invalid_argument)

protected

Function called by the parser to report the next atom.

Parameters

atom	the atom to add
alabel	the label of the atom
blabel	the label of the bond to the last reported atom

Exceptions

std::invalid_argument in case a check fails

template<typename ScannerT >

void ggl::chem::SMILES_grammar::definition< ScannerT >::memorize_explicit_H	(	int	atom,
		int	hcount
	)

protected

Function called by the parser to report the explicit hydrogen count for complex atoms

Parameters

atom	the complex atom with explicit hydrogens
hcount	the number of explicit hydrogens

template<typename ScannerT >

void ggl::chem::SMILES_grammar::definition< ScannerT >::memorize_rc	(	int	rc,
		int	atom1,
		std::string	blabel
	)		throw (std::invalid_argument)

protected

Function called by the parser to report a ring closure.

Parameters

rc	the ring closure index that was closed
atom1	the first atom of the ring
blabel	the optional given label of the ring closing bond

Exceptions

std::invalid_argument in case a check fails

template<typename ScannerT >

void ggl::chem::SMILES_grammar::definition< ScannerT >::open_branch ( int atom )

protected

Function called by the parser to report the opening of a molecule branching

Parameters

atom	the atom id where the branching occured

template<typename ScannerT >

void ggl::chem::SMILES_grammar::definition< ScannerT >::parser_warning ( std::string msg )

protected

Function called by the parser that reports warnings to the standard error handle

template<typename ScannerT >

void ggl::chem::SMILES_grammar::definition< ScannerT >::reset_data_structures ( void )

protected

Resets the local data structures to allow for the parsing of the next SMILES string

template<typename ScannerT >

NS_BOOSTSPIRIT::rule<ScannerT> const& ggl::chem::SMILES_grammar::definition< ScannerT >::start ( ) const

Field Documentation

template<typename ScannerT >

atom1_parser const ggl::chem::SMILES_grammar::definition< ScannerT >::atom1_p

protected

Definition at line 252 of file SMILES_grammar.hh.

template<typename ScannerT >

char ggl::chem::SMILES_grammar::definition< ScannerT >::atom2_firstChar

protected

Definition at line 255 of file SMILES_grammar.hh.

template<typename ScannerT >

char ggl::chem::SMILES_grammar::definition< ScannerT >::atom2_tmp

protected

Definition at line 197 of file SMILES_grammar.hh.

template<typename ScannerT >

int ggl::chem::SMILES_grammar::definition< ScannerT >::atom_count

protected

Definition at line 403 of file SMILES_grammar.hh.

template<typename ScannerT >

atoms_t ggl::chem::SMILES_grammar::definition< ScannerT >::atoms

protected

Definition at line 408 of file SMILES_grammar.hh.

template<typename ScannerT >

rule_t ggl::chem::SMILES_grammar::definition< ScannerT >::bond

protected

Definition at line 395 of file SMILES_grammar.hh.

template<typename ScannerT >

bond_parser const ggl::chem::SMILES_grammar::definition< ScannerT >::bond_p

protected

Definition at line 311 of file SMILES_grammar.hh.

template<typename ScannerT >

NS_BOOSTSPIRIT::rule<ScannerT> ggl::chem::SMILES_grammar::definition< ScannerT >::bond_symbol

protected

Definition at line 398 of file SMILES_grammar.hh.

template<typename ScannerT >

bonds_t ggl::chem::SMILES_grammar::definition< ScannerT >::bonds

protected

Definition at line 409 of file SMILES_grammar.hh.

template<typename ScannerT >

rule_t ggl::chem::SMILES_grammar::definition< ScannerT >::branch

protected

Definition at line 395 of file SMILES_grammar.hh.

template<typename ScannerT >

rule_t ggl::chem::SMILES_grammar::definition< ScannerT >::chain

protected

Definition at line 395 of file SMILES_grammar.hh.

template<typename ScannerT >

NS_BOOSTSPIRIT::rule<ScannerT> ggl::chem::SMILES_grammar::definition< ScannerT >::charge

protected

Definition at line 399 of file SMILES_grammar.hh.

template<typename ScannerT >

NS_BOOSTSPIRIT::rule<ScannerT> ggl::chem::SMILES_grammar::definition< ScannerT >::chirality

protected

Definition at line 399 of file SMILES_grammar.hh.

template<typename ScannerT >

rule_t ggl::chem::SMILES_grammar::definition< ScannerT >::complex_atom

protected

Definition at line 395 of file SMILES_grammar.hh.

template<typename ScannerT >

NS_BOOSTSPIRIT::rule<ScannerT> ggl::chem::SMILES_grammar::definition< ScannerT >::complex_symbol

protected

Definition at line 398 of file SMILES_grammar.hh.

template<typename ScannerT >

hcount_t ggl::chem::SMILES_grammar::definition< ScannerT >::explicitH

protected

Definition at line 411 of file SMILES_grammar.hh.

template<typename ScannerT >

NS_BOOSTSPIRIT::rule<ScannerT> ggl::chem::SMILES_grammar::definition< ScannerT >::group_symbol

protected

Definition at line 398 of file SMILES_grammar.hh.

template<typename ScannerT >

NS_BOOSTSPIRIT::rule<ScannerT> ggl::chem::SMILES_grammar::definition< ScannerT >::hcount

protected

Definition at line 399 of file SMILES_grammar.hh.

template<typename ScannerT >

NS_BOOSTSPIRIT::rule<ScannerT> ggl::chem::SMILES_grammar::definition< ScannerT >::isotope

protected

Definition at line 399 of file SMILES_grammar.hh.

template<typename ScannerT >

NS_BOOSTSPIRIT::rule<ScannerT> ggl::chem::SMILES_grammar::definition< ScannerT >::name

protected

Definition at line 399 of file SMILES_grammar.hh.

template<typename ScannerT >

rcs_t ggl::chem::SMILES_grammar::definition< ScannerT >::rc_to_atom

protected

Definition at line 405 of file SMILES_grammar.hh.

template<typename ScannerT >

rcb_t ggl::chem::SMILES_grammar::definition< ScannerT >::rc_to_bond

protected

Definition at line 407 of file SMILES_grammar.hh.

template<typename ScannerT >

rule_t ggl::chem::SMILES_grammar::definition< ScannerT >::ringclosure

protected

Definition at line 395 of file SMILES_grammar.hh.

template<typename ScannerT >

SMILES_grammar const& ggl::chem::SMILES_grammar::definition< ScannerT >::self

protected

Definition at line 392 of file SMILES_grammar.hh.

template<typename ScannerT >

rule_t ggl::chem::SMILES_grammar::definition< ScannerT >::simple_atom

protected

Definition at line 395 of file SMILES_grammar.hh.

template<typename ScannerT >

NS_BOOSTSPIRIT::rule<ScannerT> ggl::chem::SMILES_grammar::definition< ScannerT >::simple_symbol

protected

Definition at line 398 of file SMILES_grammar.hh.

template<typename ScannerT >

simpleSymbol_parser const ggl::chem::SMILES_grammar::definition< ScannerT >::simpleSymbol_p

protected

Definition at line 227 of file SMILES_grammar.hh.

template<typename ScannerT >

NS_BOOSTSPIRIT::rule<ScannerT> ggl::chem::SMILES_grammar::definition< ScannerT >::smiles

protected

Definition at line 397 of file SMILES_grammar.hh.

template<typename ScannerT >

stack_t ggl::chem::SMILES_grammar::definition< ScannerT >::stack

protected

Definition at line 410 of file SMILES_grammar.hh.

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

src/ggl/chem/SMILES_grammar.hh

Data Structures

Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Detailed Description

template<typename ScannerT> struct ggl::chem::SMILES_grammar::definition< ScannerT >

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Field Documentation

template<typename ScannerT>
struct ggl::chem::SMILES_grammar::definition< ScannerT >