Enumerates the tautomers of a molecular graph by iteratively applying a configurable set of Chem::TautomerizationRule instances and reporting each accepted tautomer to a user-supplied callback. More...

#include <TautomerGenerator.hpp>

Inheritance diagram for CDPL::Chem::TautomerGenerator:

Public Types
enum	Mode { TOPOLOGICALLY_UNIQUE , GEOMETRICALLY_UNIQUE , EXHAUSTIVE }
	Constants specifying the output tautomer filtering strategy. More...

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

typedef std::function< bool(MolecularGraph &)>	CallbackFunction
	Type of the callback invoked for every generated tautomer (returning `false` aborts the enumeration). More...

typedef std::function< void(MolecularGraph &)>	CustomSetupFunction
	Type of the optional setup function invoked on the input molecular graph before enumeration starts. More...

Public Member Functions
	TautomerGenerator ()
	Constructs the `TautomerGenerator` instance. More...

	TautomerGenerator (const TautomerGenerator &gen)
	Constructs a copy of the `TautomerGenerator` instance gen. More...

virtual	~TautomerGenerator ()
	Virtual destructor. More...

TautomerGenerator &	operator= (const TautomerGenerator &gen)
	Replaces the state of this generator by a copy of the state of gen. More...

void	addTautomerizationRule (const TautomerizationRule::SharedPointer &rule)
	Registers a new tautomerization rule. More...

const TautomerizationRule::SharedPointer &	getTautomerizationRule (std::size_t idx) const
	Returns the registered tautomerization rule at index idx. More...

void	removeTautomerizationRule (std::size_t idx)
	Removes the registered tautomerization rule at index idx. More...

std::size_t	getNumTautomerizationRules () const
	Returns the number of registered tautomerization rules. More...

void	setCallbackFunction (const CallbackFunction &func)
	Sets the callback invoked for every accepted output tautomer. More...

const CallbackFunction &	getCallbackFunction () const
	Returns the currently configured callback. More...

void	setMode (Mode mode)
	Sets the tautomer duplicate filtering mode. More...

Mode	getMode () const
	Returns the currently configured tautomer duplicate filtering mode. More...

void	regardStereochemistry (bool regard)
	Specifies whether atom/bond stereochemistry shall be regarded by the tautomer duplicate detection algorithm. More...

bool	stereochemistryRegarded () const
	Tells whether atom/bond stereochemistry is regarded by the tautomer duplicate detection algorithm. More...

void	regardIsotopes (bool regard)
	Specifies whether atom isotope information shall be regarded by the tautomer duplicate detection algorithm. More...

bool	isotopesRegarded () const
	Tells whether atom isotope information is regarded by the tautomer duplicate detection algorithm. More...

void	clearCoordinates2D (bool clear)
	Specifies whether 2D atom coordinates shall be cleared from the generated tautomers. More...

bool	coordinates2DCleared () const
	Tells whether 2D atom coordinates are cleared from the generated tautomers. More...

void	clearCoordinates3D (bool clear)
	Specifies whether 3D atom coordinates shall be cleared from the generated tautomers. More...

bool	coordinates3DCleared () const
	Tells whether 3D atom coordinates are cleared from the generated tautomers. More...

void	removeResonanceDuplicates (bool remove)
	Specifies whether tautomers that differ only by resonance (no atom-connectivity change) shall be filtered out. More...

bool	resonanceDuplicatesRemoved () const
	Tells whether resonance-only duplicates are filtered out. More...

void	setCustomSetupFunction (const CustomSetupFunction &func)
	Sets the optional setup function invoked on the generated tautomers. More...

void	generate (const MolecularGraph &molgraph)
	Enumerates the tautomers of molgraph and reports each accepted one to the registered callback. More...

Detailed Description

Enumerates the tautomers of a molecular graph by iteratively applying a configurable set of Chem::TautomerizationRule instances and reporting each accepted tautomer to a user-supplied callback.

After registering tautomerization rules (via addTautomerizationRule()) and a callback (via setCallbackFunction()), each call to generate() seeds the enumeration with the input molecular graph, applies every registered rule to every intermediate tautomer to derive the next generation, and reports each newly-generated tautomer to the callback. The Mode setting controls how various types of duplicates shall be handled.

Member Typedef Documentation

◆ SharedPointer

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

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

◆ CallbackFunction

typedef std::function<bool(MolecularGraph&)> CDPL::Chem::TautomerGenerator::CallbackFunction

Type of the callback invoked for every generated tautomer (returning false aborts the enumeration).

◆ CustomSetupFunction

typedef std::function<void(MolecularGraph&)> CDPL::Chem::TautomerGenerator::CustomSetupFunction

Type of the optional setup function invoked on the input molecular graph before enumeration starts.

Member Enumeration Documentation

◆ Mode

enum CDPL::Chem::TautomerGenerator::Mode

Constants specifying the output tautomer filtering strategy.

Enumerator
TOPOLOGICALLY_UNIQUE	Report a generated tautomer only if its molecular graph is not topologically equivalent to an already reported one.
GEOMETRICALLY_UNIQUE	Report a generated tautomer only if its ordinary H-deplete molecular graph connection table is different from already reported ones.
EXHAUSTIVE	Report a generated tautomer only if its molecular graph connection table is different from already reported ones.

Constructor & Destructor Documentation

◆ TautomerGenerator() [1/2]

CDPL::Chem::TautomerGenerator::TautomerGenerator ( )

Constructs the TautomerGenerator instance.

◆ TautomerGenerator() [2/2]

CDPL::Chem::TautomerGenerator::TautomerGenerator ( const TautomerGenerator & gen )

Constructs a copy of the TautomerGenerator instance gen.

Parameters

gen	The `TautomerGenerator` to copy.

◆ ~TautomerGenerator()

virtual CDPL::Chem::TautomerGenerator::~TautomerGenerator ( )

inlinevirtual

Virtual destructor.

Member Function Documentation

◆ operator=()

TautomerGenerator& CDPL::Chem::TautomerGenerator::operator= ( const TautomerGenerator & gen )

Replaces the state of this generator by a copy of the state of gen.

Parameters

gen	The source `TautomerGenerator`.

Returns: A reference to itself.

◆ addTautomerizationRule()

void CDPL::Chem::TautomerGenerator::addTautomerizationRule ( const TautomerizationRule::SharedPointer & rule )

Registers a new tautomerization rule.

Parameters

rule	The tautomerization rule to register.

◆ getTautomerizationRule()

const TautomerizationRule::SharedPointer& CDPL::Chem::TautomerGenerator::getTautomerizationRule ( std::size_t idx ) const

Returns the registered tautomerization rule at index idx.

Parameters

idx	The zero-based rule index.

Returns: A const reference to the rule smart pointer.

Exceptions

Base::IndexError if the number of rules is zero or idx is not in the range [0, getNumTautomerizationRules() - 1].

◆ removeTautomerizationRule()

void CDPL::Chem::TautomerGenerator::removeTautomerizationRule ( std::size_t idx )

Removes the registered tautomerization rule at index idx.

Parameters

idx	The zero-based rule index.

Exceptions

Base::IndexError if the number of rules is zero or idx is not in the range [0, getNumTautomerizationRules() - 1].

◆ getNumTautomerizationRules()

std::size_t CDPL::Chem::TautomerGenerator::getNumTautomerizationRules ( ) const

Returns the number of registered tautomerization rules.

Returns: The rule count.

◆ setCallbackFunction()

void CDPL::Chem::TautomerGenerator::setCallbackFunction ( const CallbackFunction & func )

Sets the callback invoked for every accepted output tautomer.

The callback receives the tautomer molecular graph as its argument and returns a boolean: returning false aborts the enumeration.

Parameters

func	The new callback function.

◆ getCallbackFunction()

const CallbackFunction& CDPL::Chem::TautomerGenerator::getCallbackFunction ( ) const

Returns the currently configured callback.

Returns: A const reference to the callback function.

◆ setMode()

void CDPL::Chem::TautomerGenerator::setMode ( Mode mode )

Sets the tautomer duplicate filtering mode.

Parameters

mode	The new duplicate filtering mode.

◆ getMode()

Mode CDPL::Chem::TautomerGenerator::getMode ( ) const

Returns the currently configured tautomer duplicate filtering mode.

Returns: The current duplicate filtering mode.

◆ regardStereochemistry()

void CDPL::Chem::TautomerGenerator::regardStereochemistry ( bool regard )

Specifies whether atom/bond stereochemistry shall be regarded by the tautomer duplicate detection algorithm.

Parameters

regard If true, atom/bond stereo configurations are taken into account.

◆ stereochemistryRegarded()

bool CDPL::Chem::TautomerGenerator::stereochemistryRegarded ( ) const

Tells whether atom/bond stereochemistry is regarded by the tautomer duplicate detection algorithm.

Returns: true if stereochemistry is regarded, and false otherwise.

◆ regardIsotopes()

void CDPL::Chem::TautomerGenerator::regardIsotopes ( bool regard )

Specifies whether atom isotope information shall be regarded by the tautomer duplicate detection algorithm.

Parameters

regard If true, atom isotope information is taken into account.

◆ isotopesRegarded()

bool CDPL::Chem::TautomerGenerator::isotopesRegarded ( ) const

Tells whether atom isotope information is regarded by the tautomer duplicate detection algorithm.

Returns: true if atom isotope information is regarded, and false otherwise.

◆ clearCoordinates2D()

void CDPL::Chem::TautomerGenerator::clearCoordinates2D ( bool clear )

Specifies whether 2D atom coordinates shall be cleared from the generated tautomers.

Parameters

clear If true, the output tautomers have no 2D coordinates.

Since: 1.3

◆ coordinates2DCleared()

bool CDPL::Chem::TautomerGenerator::coordinates2DCleared ( ) const

Tells whether 2D atom coordinates are cleared from the generated tautomers.

Returns: true if 2D coordinates are cleared, and false otherwise.

Since: 1.3

◆ clearCoordinates3D()

void CDPL::Chem::TautomerGenerator::clearCoordinates3D ( bool clear )

Specifies whether 3D atom coordinates shall be cleared from the generated tautomers.

Parameters

clear If true, the output tautomers have no 3D coordinates.

Since: 1.3

◆ coordinates3DCleared()

bool CDPL::Chem::TautomerGenerator::coordinates3DCleared ( ) const

Tells whether 3D atom coordinates are cleared from the generated tautomers.

Returns: true if 3D coordinates are cleared, and false otherwise.

Since: 1.3

◆ removeResonanceDuplicates()

void CDPL::Chem::TautomerGenerator::removeResonanceDuplicates ( bool remove )

Specifies whether tautomers that differ only by resonance (no atom-connectivity change) shall be filtered out.

Parameters

remove If true, resonance-only duplicates are not reported.

Since: 1.1

◆ resonanceDuplicatesRemoved()

bool CDPL::Chem::TautomerGenerator::resonanceDuplicatesRemoved ( ) const

Tells whether resonance-only duplicates are filtered out.

Returns: true if resonance duplicates are removed, and false otherwise.

Since: 1.1

◆ setCustomSetupFunction()

void CDPL::Chem::TautomerGenerator::setCustomSetupFunction ( const CustomSetupFunction & func )

Sets the optional setup function invoked on the generated tautomers.

Parameters

func	The new custom setup function.

◆ generate()

void CDPL::Chem::TautomerGenerator::generate ( const MolecularGraph & molgraph )

Enumerates the tautomers of molgraph and reports each accepted one to the registered callback.

Parameters

molgraph The molecular graph whose tautomers shall be generated.

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

TautomerGenerator.hpp

Public Types

Public Member Functions

Detailed Description

Member Typedef Documentation

◆ SharedPointer

◆ CallbackFunction

◆ CustomSetupFunction

Member Enumeration Documentation

◆ Mode

Constructor & Destructor Documentation

◆ TautomerGenerator() [1/2]

◆ TautomerGenerator() [2/2]

◆ ~TautomerGenerator()

Member Function Documentation

◆ operator=()

◆ addTautomerizationRule()

◆ getTautomerizationRule()

◆ removeTautomerizationRule()

◆ getNumTautomerizationRules()

◆ setCallbackFunction()

◆ getCallbackFunction()

◆ setMode()

◆ getMode()

◆ regardStereochemistry()

◆ stereochemistryRegarded()

◆ regardIsotopes()

◆ isotopesRegarded()

◆ clearCoordinates2D()

◆ coordinates2DCleared()

◆ clearCoordinates3D()

◆ coordinates3DCleared()

◆ removeResonanceDuplicates()

◆ resonanceDuplicatesRemoved()

◆ setCustomSetupFunction()

◆ generate()