ggl::chem::ChemRule::TransitionState Class Reference

#include <ChemRule.hh>

Inheritance diagram for ggl::chem::ChemRule::TransitionState:

Public Member Functions
const Molecule &	getGraph (void) const
const std::string &	getSMILES (void) const
	TransitionState (const ChemRule &rule)
	TransitionState (const TransitionState &toCopy)
virtual	~TransitionState ()
	destruction More...

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

Protected Member Functions
void	initializeTransitionState (const CoreGraph &rule)
	TransitionState ()

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

Encodes the minimal transition state of a chemical reaction that is encoded by a (chemical) graph grammar rule.

Therein, valence changes (!=0) for each atom are identified and appended to the class information. All such values show a leading "000" to make them distinguishable from previously present class information (which will be the leading number in front of the "000" separator.

Definition at line 261 of file ChemRule.hh.

Member Typedef Documentation

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

protected

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::ChemRule::TransitionState::TransitionState ( )

protected

Default construction which is only accessible for subclasses

ggl::chem::ChemRule::TransitionState::TransitionState

(

const ChemRule &

rule

)

Derives a transition state graph from a given graph grammar rule.

Parameters

rule	the graph grammar rule that encodes the transition state

ggl::chem::ChemRule::TransitionState::TransitionState

(

const TransitionState &

toCopy

)

Copy construction

Parameters

toCopy

the object to make this a copy of

virtual ggl::chem::ChemRule::TransitionState::~TransitionState ( )

virtual

Member Function Documentation

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

staticprotected

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

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

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 )

protected

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

Parameters

rule	the graph grammar rule that encodes the transition state

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

staticprotected

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

protected

Definition at line 308 of file ChemRule.hh.

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

mutableprotected

Definition at line 311 of file ChemRule.hh.

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

• src/ggl/chem/ChemRule.hh