#include <MR_Reactions.hh>

Inheritance diagram for ggl::chem::MR_Reactions:

Public Types
typedef std::set< Reaction >	Reaction_Container
	a container that stores Reaction objects More...

Public Member Functions
virtual void	add (const Molecule &graph)

virtual void	addMolecule (const Molecule &graph)

	MR_Reactions (const Smiles2GraphMap &smiles2graph, Smiles2GraphMap &newSmiles2graph, Reaction_Container &reactions, const bool addEachComponent=false, const ReactionRateCalculation *rateCalculation=NULL, const AromaticityPerception &aromaticity=AP_NSPDK("Marvin:general:2013"))

	MR_Reactions (const Smiles2GraphMap &smiles2graph, const Smiles2GraphMap &smiles2graph2, Smiles2GraphMap &newSmiles2graph, Reaction_Container &reactions, const bool addEachComponent=false, const ReactionRateCalculation *rateCalculation=NULL, const AromaticityPerception &aromaticity=AP_NSPDK("Marvin:general:2013"))

virtual void	reportHit (const sgm::Pattern_Interface &pattern, const sgm::Graph_Interface &target, const sgm::Match &match)

virtual	~MR_Reactions ()

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...

typedef SMILESwriter	Smiler
	the SMILESwriter to use for target-to-smiles conversion More...

typedef GS_SMILES_MOLp < Smiles2GraphMap >	SuperClass
	access to the superclass of this class More...

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

Protected Attributes
const bool	addEachComponent

Reaction	curReaction
	the current Reaction to fill and to store later More...

Graph2SmilesMap	graph2smiles
	A vice versa lookup table for smiles2graph. More...

GS_MolCheck	molchecker

const ReactionRateCalculation *	rateCalculation
	if != NULL, for each new reaction a rate is calculated More...

Reaction_Container &	reactions
	The container of Reaction objects to fill and extend. More...

ggl::MR_ApplyRule	Ruler

Smiles2GraphMap *	smiles2mol

const Smiles2GraphMap *	smiles2molCheckOnly1

const Smiles2GraphMap *	smiles2molCheckOnly2

Detailed Description

    A Match_Reporter that generates a Reaction object from a rule
    application.

    NOTE : this class currently only works for target graphs that are an
    object of Molecule_GraphV !!! Furthermore, it assumes that the
    elements (pointer) from the covered target graph are from the here
    maintained storage, to enable a fast lookup of their SMILES !!!
    Finaly, SMILES are generated using an instance of SMILESwriter !!!

Author: Martin Mann (c) 2009 http://www.bioinf.uni-freiburg.de/~mmann/

Definition at line 96 of file MR_Reactions.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.

typedef std::set< Reaction > ggl::chem::MR_Reactions::Reaction_Container

Definition at line 104 of file MR_Reactions.hh.

typedef SMILESwriter ggl::chem::MR_Reactions::Smiler

protected

Definition at line 109 of file MR_Reactions.hh.

typedef GS_SMILES_MOLp< Smiles2GraphMap > ggl::chem::MR_Reactions::SuperClass

protected

Definition at line 112 of file MR_Reactions.hh.

Constructor & Destructor Documentation

ggl::chem::MR_Reactions::MR_Reactions	(	const Smiles2GraphMap &	smiles2graph,
		Smiles2GraphMap &	newSmiles2graph,
		Reaction_Container &	reactions,
		const bool	addEachComponent = `false`,
		const ReactionRateCalculation *	rateCalculation = `NULL`,
		const AromaticityPerception &	aromaticity = `AP_NSPDK("Marvin:general:2013")`
	)

Construction

Parameters

smiles2graph	the initial container that contains all molecules known so far and is fixed
newSmiles2graph	the container where all new molecules will be stored in
reactions	the Reaction container to fill
addEachComponent	if set to true, than all components of the Rules LeftSidePattern are matched to an own target graph copy if two components map to the same target graph
rateCalculation	The object to use to calculate a reaction rate for each new reaction created. If not present (==NULL) no reaction rate will be calculated.
aromaticity	the aromaticity perception class to be used to correct rings in the product molecules after the rule application was done.

ggl::chem::MR_Reactions::MR_Reactions	(	const Smiles2GraphMap &	smiles2graph,
		const Smiles2GraphMap &	smiles2graph2,
		Smiles2GraphMap &	newSmiles2graph,
		Reaction_Container &	reactions,
		const bool	addEachComponent = `false`,
		const ReactionRateCalculation *	rateCalculation = `NULL`,
		const AromaticityPerception &	aromaticity = `AP_NSPDK("Marvin:general:2013")`
	)

Construction

Parameters

smiles2graph	the initial container that contains all molecules known so far and which is not changed
smiles2graph2	second container of the initial molecules known so far
newSmiles2graph	the container where all new molecules will be stored in
reactions	the Reaction container to fill
addEachComponent	if set to true, than all components of the Rules LeftSidePattern are matched to an own target graph copy if two components map to the same target graph,
rateCalculation	The object to use to calculate a reaction rate for each new reaction created. If not present (==NULL) no reaction rate will be calculated.
aromaticity	the aromaticity perception class to be used to correct rings in the product molecules after the rule application was done.

virtual ggl::chem::MR_Reactions::~MR_Reactions ( )

virtual

Destruction

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.

virtual void ggl::chem::GS_SMILES_MOLp< Smiles2GraphMap >::addMolecule ( const Molecule & graph )

virtualinherited

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.

virtual bool ggl::chem::MR_Reactions::insert2map	(	const std::string &	SMILES,
		const Molecule &	molGraph
	)

protectedvirtual

Writes a given SMILES and the corresponding molecule graph to the global storage. Furthermore, the given SMILES is added to the products of the currently processed ggl::chem::Reaction.

Parameters

SMILES	the SMILES string produced
molGraph	the molecule graph that corresponds to the given SMILES

Returns: true it the SMILES was not seen so far; false otherwise

Reimplemented from ggl::chem::GS_SMILES_MOLp< Smiles2GraphMap >.

virtual void ggl::chem::MR_Reactions::reportHit	(	const sgm::Pattern_Interface &	pattern,
		const sgm::Graph_Interface &	target,
		const sgm::Match &	match
	)

virtual

Reports a match. The match is encoded using a vector. The length of the vector corresponds to the number of vertices in the pattern and position i encodes the matched position of pattern node i in the target graph (an instance of sgm::Graph_boostV_p).

Parameters

pattern	the pattern graph that was searched for. NOTE: HAS TO BE AN INSTANCE OF ggl::chem::LeftSidePattern !!!
target	the graph the pattern was found within. NOTE: HAS TO BE AN INSTANCE OF sgm::Graph_boostV_p !!!
match	contains the indices of the matched pattern nodes in the target graph. match[i] corresponds to the mapping of the ith vertex in the pattern graph.

Implements sgm::Match_Reporter.

Field Documentation

const bool ggl::chem::MR_Reactions::addEachComponent

protected

if set to true, than all components of the Rules LeftSidePattern are matched to an own target graph copy if two components map to the same target graph

Definition at line 136 of file MR_Reactions.hh.

Reaction ggl::chem::MR_Reactions::curReaction

protected

Definition at line 131 of file MR_Reactions.hh.

Graph2SmilesMap ggl::chem::MR_Reactions::graph2smiles

protected

Definition at line 125 of file MR_Reactions.hh.

GS_MolCheck ggl::chem::MR_Reactions::molchecker

protected

the checker used to correct all molecules produced by the Ruler; it will apply an AP_NSPDK aromaticity perception instance.

Definition at line 140 of file MR_Reactions.hh.

const ReactionRateCalculation* ggl::chem::MR_Reactions::rateCalculation

protected

Definition at line 147 of file MR_Reactions.hh.

Reaction_Container& ggl::chem::MR_Reactions::reactions

protected

Definition at line 128 of file MR_Reactions.hh.

ggl::MR_ApplyRule ggl::chem::MR_Reactions::Ruler

protected

the Match_Reporter utilized to apply the rule and to produce the resulting molecules that will be stored in the reaction

Definition at line 144 of file MR_Reactions.hh.

Smiles2GraphMap * ggl::chem::GS_SMILES_MOLp< Smiles2GraphMap >::smiles2mol

protectedinherited

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

Definition at line 186 of file GS_SMILES.hh.

const Smiles2GraphMap * ggl::chem::GS_SMILES_MOLp< Smiles2GraphMap >::smiles2molCheckOnly1

protectedinherited

Definition at line 187 of file GS_SMILES.hh.

const Smiles2GraphMap * ggl::chem::GS_SMILES_MOLp< Smiles2GraphMap >::smiles2molCheckOnly2

protectedinherited

Definition at line 188 of file GS_SMILES.hh.

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

src/ggl/chem/MR_Reactions.hh

Public Types

Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Field Documentation