ggl::chem::GS_SMILES_MOLp< SMILES_MOL_MAP > Class Template Reference

SMILES graph storage using STL SMILES-GraphPointer map. More...

#include <GS_SMILES.hh>

Inheritance diagram for ggl::chem::GS_SMILES_MOLp< SMILES_MOL_MAP >:

Public Member Functions
virtual void	add (const Molecule &graph)
virtual void	addMolecule (const Molecule &graph)
	GS_SMILES_MOLp (SMILES_MOL_MAP &smiles2mol)
	GS_SMILES_MOLp (SMILES_MOL_MAP &smiles2mol, const SMILES_MOL_MAP &smiles2molCheckOnly)
	GS_SMILES_MOLp (SMILES_MOL_MAP &smiles2mol, const SMILES_MOL_MAP &smiles2molCheckOnly1, const SMILES_MOL_MAP &smiles2molCheckOnly2)
virtual	~GS_SMILES_MOLp ()

Protected Types
typedef boost::filtered_graph < Molecule, edge_is_in_component, node_is_in_component >	ComponentGraph
typedef std::vector< int >	ComponentIdVec
typedef boost::property_map < Molecule, PropNodeIndex > ::const_type	IndexMap
	the type of a constant index map of a Molecule boost graph More...

Protected Member Functions
virtual bool	insert2map (const std::string &SMILES, const Molecule &graph)

Protected Attributes
SMILES_MOL_MAP *	smiles2mol
const SMILES_MOL_MAP *	smiles2molCheckOnly1
const SMILES_MOL_MAP *	smiles2molCheckOnly2

Detailed Description

template<class SMILES_MOL_MAP>
class ggl::chem::GS_SMILES_MOLp< SMILES_MOL_MAP >

   A Graph_Storage implementation that converts each added Molecule graph
   into a SMILES string representation and adds it, if not already
   existing, to the specified STL map container using the SMILES as key
   and the pointer to the newly allocated Molecule object as value.

Author

Martin Mann (c) 2008 http://www.bioinf.uni-freiburg.de/~mmann/

Template Parameters

STL_INSERTER

an STL insert iterator (e.g. std::insert_iterator) to add all SMILES to store to

Definition at line 180 of file GS_SMILES.hh.

Member Typedef Documentation

typedef boost::filtered_graph< Molecule , edge_is_in_component , node_is_in_component > ggl::chem::GS_chem::ComponentGraph

protectedinherited

a component graph definition if more than one connected component present is present and it is needed to split the graph to report into its components

Definition at line 128 of file GS_chem.hh.

typedef std::vector<int> ggl::chem::GS_chem::ComponentIdVec

protectedinherited

the container type used to represent the connected component id for each node

Definition at line 32 of file GS_chem.hh.

typedef boost::property_map<Molecule, PropNodeIndex>::const_type ggl::chem::GS_chem::IndexMap

protectedinherited

Definition at line 35 of file GS_chem.hh.

Constructor & Destructor Documentation

template<class SMILES_MOL_MAP>

ggl::chem::GS_SMILES_MOLp< SMILES_MOL_MAP >::GS_SMILES_MOLp

(

SMILES_MOL_MAP &

smiles2mol

)

Construction

Parameters

smiles2mol

the map (SMILES->molecule) to that each generated SMILES and its molecule is added to if not already present

template<class SMILES_MOL_MAP>

ggl::chem::GS_SMILES_MOLp< SMILES_MOL_MAP >::GS_SMILES_MOLp	(	SMILES_MOL_MAP &	smiles2mol,
		const SMILES_MOL_MAP &	smiles2molCheckOnly
	)

Construction

Parameters

smiles2mol	the map (SMILES->molecule) to that each generated SMILES and its molecule is added to if not already present
smiles2molCheckOnly	an additional map to check for existence of a new molecule to store

template<class SMILES_MOL_MAP>

ggl::chem::GS_SMILES_MOLp< SMILES_MOL_MAP >::GS_SMILES_MOLp	(	SMILES_MOL_MAP &	smiles2mol,
		const SMILES_MOL_MAP &	smiles2molCheckOnly1,
		const SMILES_MOL_MAP &	smiles2molCheckOnly2
	)

Construction

Parameters

smiles2mol	the map (SMILES->molecule) to that each generated SMILES and its molecule is added to if not already present
smiles2molCheckOnly1	an additional map to check for existence of a new molecule to store
smiles2molCheckOnly2	an additional map to check for existence of a new molecule to store

template<class SMILES_MOL_MAP>

virtual ggl::chem::GS_SMILES_MOLp< SMILES_MOL_MAP >::~GS_SMILES_MOLp ( )

virtual

Member Function Documentation

virtual void ggl::chem::GS_chem::add ( const Molecule &  graph )

virtualinherited

The reported graphs is split into its individual independent components. Each component is forwarded to addMolecule to be implemented by any sub class.

Parameters

graph

the graph object to add that encodes one or more molecules

Implements ggl::Graph_Storage.

template<class SMILES_MOL_MAP>

virtual void ggl::chem::GS_SMILES_MOLp< SMILES_MOL_MAP >::addMolecule ( const Molecule &  graph )

virtual

Converts a given molecule graph to SMILES and adds it to the storage container.

Parameters

graph

the Graph object to add.

Implements ggl::chem::GS_chem.

template<class SMILES_MOL_MAP>

virtual bool ggl::chem::GS_SMILES_MOLp< SMILES_MOL_MAP >::insert2map ( const std::string &  SMILES, const Molecule &  graph  )

protectedvirtual

Reimplemented in ggl::chem::MR_Reactions.

Field Documentation

template<class SMILES_MOL_MAP>

SMILES_MOL_MAP* ggl::chem::GS_SMILES_MOLp< SMILES_MOL_MAP >::smiles2mol

protected

the map where each SMILES string is mapped to the represented molecule

Definition at line 186 of file GS_SMILES.hh.

template<class SMILES_MOL_MAP>

const SMILES_MOL_MAP* ggl::chem::GS_SMILES_MOLp< SMILES_MOL_MAP >::smiles2molCheckOnly1

protected

Definition at line 187 of file GS_SMILES.hh.

template<class SMILES_MOL_MAP>

const SMILES_MOL_MAP* ggl::chem::GS_SMILES_MOLp< SMILES_MOL_MAP >::smiles2molCheckOnly2

protected

Definition at line 188 of file GS_SMILES.hh.

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

• src/ggl/chem/GS_SMILES.hh