SMARTS-pattern-based implementation of a Chem::TautomerizationRule. More...

#include <PatternBasedTautomerizationRule.hpp>

Inheritance diagram for CDPL::Chem::PatternBasedTautomerizationRule:

Classes
struct	BondOrderChange
	Encodes a single bond-order change between two pattern atoms applied when the parent transformation pattern matches. More...

Public Types
typedef std::shared_ptr< PatternBasedTautomerizationRule >	SharedPointer
	A reference-counted smart pointer [SHPTR] for dynamically allocated `PatternBasedTautomerizationRule` instances. More...

Public Types inherited from CDPL::Chem::TautomerizationRule
typedef std::shared_ptr< TautomerizationRule >	SharedPointer
	A reference-counted smart pointer [SHPTR] for dynamically allocated `TautomerizationRule` instances. More...

Public Member Functions
	PatternBasedTautomerizationRule (unsigned int rule_id)
	Constructs the `PatternBasedTautomerizationRule` instance with the given rule identifier. More...

	PatternBasedTautomerizationRule (const PatternBasedTautomerizationRule &rule)
	Constructs a copy of the `PatternBasedTautomerizationRule` instance rule. More...

PatternBasedTautomerizationRule &	operator= (const PatternBasedTautomerizationRule &rule)
	Replaces the state of this rule by a copy of the state of rule. More...

template<typename Iter >
void	addTransformationPattern (const MolecularGraph::SharedPointer &molgraph, Iter bond_chgs_beg, Iter bond_chgs_end)
	Registers a new transformation pattern together with the associated bond-order changes. More...

void	addExcludePattern (const MolecularGraph::SharedPointer &molgraph)
	Registers an exclude pattern: when this substructure is present in the parent molecular graph, the matching transformation will not be applied. More...

void	addExcludePatterns (const PatternBasedTautomerizationRule &rule)
	Copies all exclude patterns of rule into this rule. More...

void	clearExcludePatterns ()
	Removes all registered exclude patterns. More...

bool	setup (MolecularGraph &parent_molgraph)
	Prepares the rule for tautomer enumeration on parent_molgraph. More...

unsigned int	getID () const
	Returns the rule identifier supplied at construction. More...

bool	generate (Molecule &tautomer)
	Writes the next tautomer reachable from the parent molecular graph into tautomer. More...

TautomerizationRule::SharedPointer	clone () const
	Creates and returns a deep copy of this rule. More...

Public Member Functions inherited from CDPL::Chem::TautomerizationRule
virtual	~TautomerizationRule ()
	Virtual destructor. More...

Detailed Description

SMARTS-pattern-based implementation of a Chem::TautomerizationRule.

The rule is configured with a set of transformation patterns (SMARTS queries describing the source substructure together with per-atom-pair bond-order changes that apply when the pattern matches) plus optional exclude patterns (substructures that, when present, suppress the application of the rule). The setup() / generate() pair from the base class then enumerates the tautomers reachable from the parent molecular graph by applying the configured transformations.

Member Typedef Documentation

◆ SharedPointer

typedef std::shared_ptr<PatternBasedTautomerizationRule> CDPL::Chem::PatternBasedTautomerizationRule::SharedPointer

A reference-counted smart pointer [SHPTR] for dynamically allocated PatternBasedTautomerizationRule instances.

Constructor & Destructor Documentation

◆ PatternBasedTautomerizationRule() [1/2]

CDPL::Chem::PatternBasedTautomerizationRule::PatternBasedTautomerizationRule ( unsigned int rule_id )

Constructs the PatternBasedTautomerizationRule instance with the given rule identifier.

Parameters

rule_id The numeric rule identifier (returned by getID() and forwarded to the generated tautomers).

◆ PatternBasedTautomerizationRule() [2/2]

CDPL::Chem::PatternBasedTautomerizationRule::PatternBasedTautomerizationRule ( const PatternBasedTautomerizationRule & rule )

Constructs a copy of the PatternBasedTautomerizationRule instance rule.

Parameters

rule	The `PatternBasedTautomerizationRule` to copy.

Member Function Documentation

◆ operator=()

PatternBasedTautomerizationRule& CDPL::Chem::PatternBasedTautomerizationRule::operator= ( const PatternBasedTautomerizationRule & rule )

Replaces the state of this rule by a copy of the state of rule.

Parameters

rule	The source `PatternBasedTautomerizationRule`.

Returns: A reference to itself.

◆ addTransformationPattern()

template<typename Iter >

void CDPL::Chem::PatternBasedTautomerizationRule::addTransformationPattern	(	const MolecularGraph::SharedPointer &	molgraph,
		Iter	bond_chgs_beg,
		Iter	bond_chgs_end
	)

inline

Registers a new transformation pattern together with the associated bond-order changes.

Bond-order changes are read from the iterator range [bond_chgs_beg, bond_chgs_end); each element must be a BondOrderChange value referring to atom IDs of molgraph.

Template Parameters

Iter	Input iterator type yielding BondOrderChange values.

Parameters

molgraph	The SMARTS transformation pattern.
bond_chgs_beg	Iterator pointing to the first bond-order change.
bond_chgs_end	Iterator pointing one past the last bond-order change.

◆ addExcludePattern()

void CDPL::Chem::PatternBasedTautomerizationRule::addExcludePattern ( const MolecularGraph::SharedPointer & molgraph )

Registers an exclude pattern: when this substructure is present in the parent molecular graph, the matching transformation will not be applied.

Parameters

molgraph The exclude SMARTS pattern.

◆ addExcludePatterns()

void CDPL::Chem::PatternBasedTautomerizationRule::addExcludePatterns ( const PatternBasedTautomerizationRule & rule )

Copies all exclude patterns of rule into this rule.

Parameters

rule	The source rule whose exclude patterns are copied.

◆ clearExcludePatterns()

void CDPL::Chem::PatternBasedTautomerizationRule::clearExcludePatterns ( )

Removes all registered exclude patterns.

◆ setup()

bool CDPL::Chem::PatternBasedTautomerizationRule::setup ( MolecularGraph & parent_molgraph )

virtual

Prepares the rule for tautomer enumeration on parent_molgraph.

Parameters

parent_molgraph The parent molecular graph from which tautomers are generated.

Returns: true if the rule could be set up (at least one transformation pattern matched), and false otherwise.

Implements CDPL::Chem::TautomerizationRule.

◆ getID()

unsigned int CDPL::Chem::PatternBasedTautomerizationRule::getID ( ) const

virtual

Returns the rule identifier supplied at construction.

Returns: The numeric rule ID.

Implements CDPL::Chem::TautomerizationRule.

◆ generate()

bool CDPL::Chem::PatternBasedTautomerizationRule::generate ( Molecule & tautomer )

virtual

Writes the next tautomer reachable from the parent molecular graph into tautomer.

Parameters

tautomer The output molecule receiving the next tautomer.

Returns: true if a new tautomer was generated, and false when the enumeration is exhausted.

Implements CDPL::Chem::TautomerizationRule.

◆ clone()

TautomerizationRule::SharedPointer CDPL::Chem::PatternBasedTautomerizationRule::clone ( ) const

virtual

Creates and returns a deep copy of this rule.

Returns: A smart pointer to the cloned Chem::TautomerizationRule.

Implements CDPL::Chem::TautomerizationRule.

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

PatternBasedTautomerizationRule.hpp

Classes

Public Types

Public Member Functions

Detailed Description

Member Typedef Documentation

◆ SharedPointer

Constructor & Destructor Documentation

◆ PatternBasedTautomerizationRule() [1/2]

◆ PatternBasedTautomerizationRule() [2/2]

Member Function Documentation

◆ operator=()

◆ addTransformationPattern()

◆ addExcludePattern()

◆ addExcludePatterns()

◆ clearExcludePatterns()

◆ setup()

◆ getID()

◆ generate()

◆ clone()