Transition state of a reaction. More...

#include <ReactionTransitionState.hh>

Inheritance diagram for ggl::chem::ReactionTransitionState:

Public Types
typedef ChemRule::TransitionState	SuperClass
	access to the superclass TransitionState type More...

Public Member Functions
const Molecule &	getGraph (void) const

const std::string &	getSMILES (void) const

	ReactionTransitionState (const LeftSidePattern &leftSide, const sgm::Graph_Interface &molecules, const sgm::Match &match, const bool addEachComponent=false)

virtual	~ReactionTransitionState ()

Protected Types
typedef std::map < CoreGraph::vertex_descriptor, size_t >	ValChangeMap

Protected Member Functions
void	initializeTransitionState (const CoreGraph &rule)

Static Protected Member Functions
static void	copyRuleToMol (const CoreGraph &rule, Molecule &mol)

static bool	mergeGraphs (ChemRule::CoreGraph &its, const LeftSidePattern &leftSide, const sgm::Graph_Interface &molecules, const sgm::Match &match, const bool addEachComponent=false)

static void	updateMap (const CoreGraph::vertex_descriptor &node, const size_t valChange, ValChangeMap &toUpdate)

Protected Attributes
Molecule	tState
	the graph encoding of the transition state More...

std::string	tStateSMILES
	SMILES representation of the transition state. More...

Detailed Description

  This class encodes an imaginary transition state (ITS) of a chemical
  reaction.

Author: Martin Mann - http://www.bioinf.uni-freiburg.de/~mmann/

Definition at line 22 of file ReactionTransitionState.hh.

Member Typedef Documentation

typedef ChemRule::TransitionState ggl::chem::ReactionTransitionState::SuperClass

Definition at line 27 of file ReactionTransitionState.hh.

typedef std::map< CoreGraph::vertex_descriptor, size_t > ggl::chem::ChemRule::TransitionState::ValChangeMap

protectedinherited

mapping of vertices to valence change internally used to sum over edge valence increases

Definition at line 318 of file ChemRule.hh.

Constructor & Destructor Documentation

ggl::chem::ReactionTransitionState::ReactionTransitionState	(	const LeftSidePattern &	leftSide,
		const sgm::Graph_Interface &	molecules,
		const sgm::Match &	match,
		const bool	addEachComponent = `false`
	)

Constructs an imaginary transition state based on the educts, products, and chemical GGL rule applied.

Parameters

leftSide	the left side pattern of the chemical rule applied
molecules	the molecules where leftSide was mapped on
match	the mapping of nodes of leftSide on the nodes of the molecules object
addEachComponent	if set to true, than all components of the Rules LeftSidePattern are matched to an own molecule graph copy if two components map to the same molecule graph.

virtual ggl::chem::ReactionTransitionState::~ReactionTransitionState ( )

virtual

Member Function Documentation

static void ggl::chem::ChemRule::TransitionState::copyRuleToMol	(	const CoreGraph &	rule,
		Molecule &	mol
	)

staticprotectedinherited

Copies a (modified) rule graph into a molecule object. Only the primary node and edge label is copied, all other rule information is ignored.

Parameters

rule	the rule to copy from
mol	the molecule to fill / copy to (NOTE: is assumed to be a new/empty graph)

const Molecule& ggl::chem::ChemRule::TransitionState::getGraph ( void ) const

inherited

Allows access to the graph encoding of the transition state.

Returns: the graph encoding of the transition state

const std::string& ggl::chem::ChemRule::TransitionState::getSMILES ( void ) const

inherited

Allows access to the SMILES encoding of the transition state.

Returns: the SMILES encoding of the transition state

void ggl::chem::ChemRule::TransitionState::initializeTransitionState ( const CoreGraph & rule )

protectedinherited

Initializes the transition state graph from a given graph grammar rule.

Parameters

rule	the graph grammar rule that encodes the transition state

static bool ggl::chem::ReactionTransitionState::mergeGraphs	(	ChemRule::CoreGraph &	its,
		const LeftSidePattern &	leftSide,
		const sgm::Graph_Interface &	molecules,
		const sgm::Match &	match,
		const bool	addEachComponent = `false`
	)

staticprotected

Merges the given molecules into a rule graph such that the left side pattern of the rule maps the matched subgraph of the molecules object. This is the first step to create the imaginary transition state.

Parameters

its	the intermediate transition state object to extend (NOTE : the object will be overwritten during the merge!)
leftSide	the left side pattern of the chemical rule applied
molecules	the molecule information to add to
match	the mapping of nodes of leftSide on the nodes of the molecules object
addEachComponent	if set to true, than all components of the Rules LeftSidePattern are matched to an own molecule graph copy if two components map to the same molecule graph.

static void ggl::chem::ChemRule::TransitionState::updateMap	(	const CoreGraph::vertex_descriptor &	node,
		const size_t	valChange,
		ValChangeMap &	toUpdate
	)

staticprotectedinherited

Updates a given ValChangeMap : the according entry is increased with the given valence change value.

Parameters

node	the entry key to update
valChange	the value to add to the current value
toUpdate	the mapping to update within

Field Documentation

Molecule ggl::chem::ChemRule::TransitionState::tState

protectedinherited

Definition at line 308 of file ChemRule.hh.

std::string ggl::chem::ChemRule::TransitionState::tStateSMILES

mutableprotectedinherited

Definition at line 311 of file ChemRule.hh.

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

src/ggl/chem/ReactionTransitionState.hh

Public Types

Public Member Functions

Protected Types

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Field Documentation