#include <AutomorphismGroupSearch.hpp>

Public Types
typedef std::shared_ptr< AutomorphismGroupSearch >	SharedPointer

typedef SubstructureSearch::MappingIterator	MappingIterator
	A mutable random access iterator used to iterate over the stored atom/bond mapping objects. More...

typedef SubstructureSearch::ConstMappingIterator	ConstMappingIterator
	A constant random access iterator used to iterate over the stored atom/bond mapping objects. More...

typedef std::function< bool(const MolecularGraph &, const AtomBondMapping &)>	MappingCallbackFunction

Public Member Functions
	AutomorphismGroupSearch (unsigned int atom_flags=DEF_ATOM_PROPERTY_FLAGS, unsigned int bond_flags=DEF_BOND_PROPERTY_FLAGS)
	Constructs and initializes a `AutomorphismGroupSearch` instance. More...

	AutomorphismGroupSearch (const AutomorphismGroupSearch &)=delete

AutomorphismGroupSearch &	operator= (const AutomorphismGroupSearch &)=delete

void	setAtomPropertyFlags (unsigned int flags)

unsigned int	getAtomPropertyFlags () const

void	setBondPropertyFlags (unsigned int flags)

unsigned int	getBondPropertyFlags () const

void	includeIdentityMapping (bool include)

bool	identityMappingIncluded () const

bool	findMappings (const MolecularGraph &molgraph)
	Searches for the possible atom/bond mappings in the automorphism group of the given molecular graph. More...

void	stopSearch ()

std::size_t	getNumMappings () const
	Returns the number of atom/bond mappings that were recorded in the last call to findMappings(). More...

AtomBondMapping &	getMapping (std::size_t idx)
	Returns a non-`const` reference to the stored atom/bond mapping object at index idx. More...

const AtomBondMapping &	getMapping (std::size_t idx) const
	Returns a `const` reference to the stored atom/bond mapping object at index idx. More...

MappingIterator	getMappingsBegin ()
	Returns a mutable iterator pointing to the beginning of the stored atom/bond mapping objects. More...

ConstMappingIterator	getMappingsBegin () const
	Returns a constant iterator pointing to the beginning of the stored atom/bond mapping objects. More...

MappingIterator	getMappingsEnd ()
	Returns a mutable iterator pointing to the end of the stored atom/bond mapping objects. More...

ConstMappingIterator	getMappingsEnd () const
	Returns a constant iterator pointing to the end of the stored atom/bond mapping objects. More...

MappingIterator	begin ()
	Returns a mutable iterator pointing to the beginning of the stored atom/bond mapping objects. More...

ConstMappingIterator	begin () const
	Returns a constant iterator pointing to the beginning of the stored atom/bond mapping objects. More...

MappingIterator	end ()
	Returns a mutable iterator pointing to the end of the stored atom/bond mapping objects. More...

ConstMappingIterator	end () const
	Returns a constant iterator pointing to the end of the stored atom/bond mapping objects. More...

void	setMaxNumMappings (std::size_t max_num_mappings)
	Allows to specify a limit on the number of stored atom/bond mappings. More...

std::size_t	getMaxNumMappings () const
	Returns the specified limit on the number of stored atom/bond mappings. More...

void	addAtomMappingConstraint (std::size_t atom1_idx, std::size_t atom2_idx)
	Adds a constraint on the allowed atom mappings. More...

void	clearAtomMappingConstraints ()
	Clears all previously defined atom mapping constraints. More...

void	addBondMappingConstraint (std::size_t bond1_idx, std::size_t bond2_idx)
	Adds a constraint on the allowed bond mappings. More...

void	clearBondMappingConstraints ()
	Clears all previously defined bond mapping constraints. More...

void	setFoundMappingCallback (const MappingCallbackFunction &func)

const MappingCallbackFunction &	getFoundMappingCallback () const

Static Public Attributes
static constexpr unsigned int	DEF_ATOM_PROPERTY_FLAGS
	Specifies the default set of atomic properties considered for atom matching. More...

static constexpr unsigned int	DEF_BOND_PROPERTY_FLAGS
	Specifies the default set of bond properties considered for bond matching. More...

Detailed Description

AutomorphismGroupSearch.

Member Typedef Documentation

◆ SharedPointer

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

◆ MappingIterator

typedef SubstructureSearch::MappingIterator CDPL::Chem::AutomorphismGroupSearch::MappingIterator

A mutable random access iterator used to iterate over the stored atom/bond mapping objects.

◆ ConstMappingIterator

typedef SubstructureSearch::ConstMappingIterator CDPL::Chem::AutomorphismGroupSearch::ConstMappingIterator

A constant random access iterator used to iterate over the stored atom/bond mapping objects.

◆ MappingCallbackFunction

typedef std::function<bool(const MolecularGraph&, const AtomBondMapping&)> CDPL::Chem::AutomorphismGroupSearch::MappingCallbackFunction

Constructor & Destructor Documentation

◆ AutomorphismGroupSearch() [1/2]

CDPL::Chem::AutomorphismGroupSearch::AutomorphismGroupSearch	(	unsigned int	atom_flags = `DEF_ATOM_PROPERTY_FLAGS`,
		unsigned int	bond_flags = `DEF_BOND_PROPERTY_FLAGS`
	)

Constructs and initializes a AutomorphismGroupSearch instance.

◆ AutomorphismGroupSearch() [2/2]

CDPL::Chem::AutomorphismGroupSearch::AutomorphismGroupSearch ( const AutomorphismGroupSearch & )

delete

Member Function Documentation

◆ operator=()

AutomorphismGroupSearch& CDPL::Chem::AutomorphismGroupSearch::operator= ( const AutomorphismGroupSearch & )

delete

◆ setAtomPropertyFlags()

void CDPL::Chem::AutomorphismGroupSearch::setAtomPropertyFlags ( unsigned int flags )

◆ getAtomPropertyFlags()

unsigned int CDPL::Chem::AutomorphismGroupSearch::getAtomPropertyFlags ( ) const

◆ setBondPropertyFlags()

void CDPL::Chem::AutomorphismGroupSearch::setBondPropertyFlags ( unsigned int flags )

◆ getBondPropertyFlags()

unsigned int CDPL::Chem::AutomorphismGroupSearch::getBondPropertyFlags ( ) const

◆ includeIdentityMapping()

void CDPL::Chem::AutomorphismGroupSearch::includeIdentityMapping ( bool include )

◆ identityMappingIncluded()

bool CDPL::Chem::AutomorphismGroupSearch::identityMappingIncluded ( ) const

◆ findMappings()

bool CDPL::Chem::AutomorphismGroupSearch::findMappings ( const MolecularGraph & molgraph )

Searches for the possible atom/bond mappings in the automorphism group of the given molecular graph.

The method will store all found mappings up to the maximum number of recorded mappings specified by setMaxNumMappings().

Parameters

molgraph The molecular graph that has to be searched for automorphisms.

Returns: true if any mappings of the specified molecular graph have been found, and false otherwise.

Note: Any atom/bond mappings that were recorded in a previous call to findMappings() will be discarded.

◆ stopSearch()

void CDPL::Chem::AutomorphismGroupSearch::stopSearch ( )

◆ getNumMappings()

std::size_t CDPL::Chem::AutomorphismGroupSearch::getNumMappings ( ) const

Returns the number of atom/bond mappings that were recorded in the last call to findMappings().

Returns: The number of atom/bond mappings that were recorded in the last call to findMappings().

◆ getMapping() [1/2]

AtomBondMapping& CDPL::Chem::AutomorphismGroupSearch::getMapping ( std::size_t idx )

Returns a non-const reference to the stored atom/bond mapping object at index idx.

Parameters

idx	The zero-based index of the atom/bond mapping object to return.

Returns: A non-const reference to the atom/bond mapping object at index idx.

Exceptions

Base::IndexError if no mappings are available or idx is not in the range [0, getNumMappings() - 1].

◆ getMapping() [2/2]

const AtomBondMapping& CDPL::Chem::AutomorphismGroupSearch::getMapping ( std::size_t idx ) const

Returns a const reference to the stored atom/bond mapping object at index idx.

Parameters

idx	The zero-based index of the atom/bond mapping object to return.

Returns: A const reference to the atom/bond mapping object at index idx.

Exceptions

Base::IndexError if no mappings are available or idx is not in the range [0, getNumMappings() - 1].

◆ getMappingsBegin() [1/2]

MappingIterator CDPL::Chem::AutomorphismGroupSearch::getMappingsBegin ( )

Returns a mutable iterator pointing to the beginning of the stored atom/bond mapping objects.

Returns: A mutable iterator pointing to the beginning of the stored atom/bond mapping objects.

◆ getMappingsBegin() [2/2]

ConstMappingIterator CDPL::Chem::AutomorphismGroupSearch::getMappingsBegin ( ) const

Returns a constant iterator pointing to the beginning of the stored atom/bond mapping objects.

Returns: A constant iterator pointing to the beginning of the stored atom/bond mapping objects.

◆ getMappingsEnd() [1/2]

MappingIterator CDPL::Chem::AutomorphismGroupSearch::getMappingsEnd ( )

Returns a mutable iterator pointing to the end of the stored atom/bond mapping objects.

Returns: A mutable iterator pointing to the end of the stored atom/bond mapping objects.

◆ getMappingsEnd() [2/2]

ConstMappingIterator CDPL::Chem::AutomorphismGroupSearch::getMappingsEnd ( ) const

Returns a constant iterator pointing to the end of the stored atom/bond mapping objects.

Returns: A constant iterator pointing to the end of the stored atom/bond mapping objects.

◆ begin() [1/2]

MappingIterator CDPL::Chem::AutomorphismGroupSearch::begin ( )

Returns a mutable iterator pointing to the beginning of the stored atom/bond mapping objects.

Returns: A mutable iterator pointing to the beginning of the stored atom/bond mapping objects.

◆ begin() [2/2]

ConstMappingIterator CDPL::Chem::AutomorphismGroupSearch::begin ( ) const

Returns a constant iterator pointing to the beginning of the stored atom/bond mapping objects.

Returns: A constant iterator pointing to the beginning of the stored atom/bond mapping objects.

◆ end() [1/2]

MappingIterator CDPL::Chem::AutomorphismGroupSearch::end ( )

Returns a mutable iterator pointing to the end of the stored atom/bond mapping objects.

Returns: A mutable iterator pointing to the end of the stored atom/bond mapping objects.

◆ end() [2/2]

ConstMappingIterator CDPL::Chem::AutomorphismGroupSearch::end ( ) const

Returns a constant iterator pointing to the end of the stored atom/bond mapping objects.

Returns: A constant iterator pointing to the end of the stored atom/bond mapping objects.

◆ setMaxNumMappings()

void CDPL::Chem::AutomorphismGroupSearch::setMaxNumMappings ( std::size_t max_num_mappings )

Allows to specify a limit on the number of stored atom/bond mappings.

In a call to findMappings() the automorphism search will terminate as soon as the specified maximum number of stored atom/bond mappings has been reached. A previously set limit on the number of mappings can be disabled by providing zero for the value of max_num_mappings.

Parameters

max_num_mappings The maximum number of atom/bond mappings to store.

Note: By default, no limit is imposed on the number of stored mappings.

◆ getMaxNumMappings()

std::size_t CDPL::Chem::AutomorphismGroupSearch::getMaxNumMappings ( ) const

Returns the specified limit on the number of stored atom/bond mappings.

Returns: The specified maximum number of stored atom/bond mappings.

See also: setMaxNumMappings(), findMappings()

◆ addAtomMappingConstraint()

void CDPL::Chem::AutomorphismGroupSearch::addAtomMappingConstraint	(	std::size_t	atom1_idx,
		std::size_t	atom2_idx
	)

Adds a constraint on the allowed atom mappings.

By default, an atom can be mapped to any valid other atom. When this method gets called for a particular atom pair (specified by atom1_idx and atom2_idx), a future search will report only those solutions which feature the specified mapping of the two atoms. Multiple calls to addAtomMappingConstraint() for a particular atom enlarges the set of valid mapping solutions.

Parameters

atom1_idx	The index of the first atom.
atom2_idx	The index of the second atom.

◆ clearAtomMappingConstraints()

void CDPL::Chem::AutomorphismGroupSearch::clearAtomMappingConstraints ( )

Clears all previously defined atom mapping constraints.

See also: addAtomMappingConstraint()

◆ addBondMappingConstraint()

void CDPL::Chem::AutomorphismGroupSearch::addBondMappingConstraint	(	std::size_t	bond1_idx,
		std::size_t	bond2_idx
	)

Adds a constraint on the allowed bond mappings.

By default, an bond can be mapped to any valid other bond. When this method gets called for a particular bond pair (specified by bond1_idx and bond2_idx), a future search will report only those solutions which feature the specified mapping of the two bonds. Multiple calls to addBondMappingConstraint() for a particular bond enlarges the set of valid mapping solutions.

Parameters

bond1_idx	The index of the first bond.
bond2_idx	The index of the second bond.

◆ clearBondMappingConstraints()

void CDPL::Chem::AutomorphismGroupSearch::clearBondMappingConstraints ( )

Clears all previously defined bond mapping constraints.

See also: addBondMappingConstraint()

◆ setFoundMappingCallback()

void CDPL::Chem::AutomorphismGroupSearch::setFoundMappingCallback ( const MappingCallbackFunction & func )

◆ getFoundMappingCallback()

const MappingCallbackFunction& CDPL::Chem::AutomorphismGroupSearch::getFoundMappingCallback ( ) const

Member Data Documentation

◆ DEF_ATOM_PROPERTY_FLAGS

constexpr unsigned int CDPL::Chem::AutomorphismGroupSearch::DEF_ATOM_PROPERTY_FLAGS

staticconstexpr

Initial value:

=
                AtomPropertyFlag::TYPE | AtomPropertyFlag::ISOTOPE |
                AtomPropertyFlag::H_COUNT | AtomPropertyFlag::FORMAL_CHARGE |
                AtomPropertyFlag::CONFIGURATION | AtomPropertyFlag::AROMATICITY |
                AtomPropertyFlag::EXPLICIT_BOND_COUNT | AtomPropertyFlag::HYBRIDIZATION_STATE

Specifies the default set of atomic properties considered for atom matching.

◆ DEF_BOND_PROPERTY_FLAGS

constexpr unsigned int CDPL::Chem::AutomorphismGroupSearch::DEF_BOND_PROPERTY_FLAGS

staticconstexpr

Initial value:

=
                BondPropertyFlag::ORDER | BondPropertyFlag::TOPOLOGY |
                BondPropertyFlag::AROMATICITY | BondPropertyFlag::CONFIGURATION

Specifies the default set of bond properties considered for bond matching.

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

AutomorphismGroupSearch.hpp

Public Types

Public Member Functions

Static Public Attributes

Detailed Description

Member Typedef Documentation

◆ SharedPointer

◆ MappingIterator

◆ ConstMappingIterator

◆ MappingCallbackFunction

Constructor & Destructor Documentation

◆ AutomorphismGroupSearch() [1/2]

◆ AutomorphismGroupSearch() [2/2]

Member Function Documentation

◆ operator=()

◆ setAtomPropertyFlags()

◆ getAtomPropertyFlags()

◆ setBondPropertyFlags()

◆ getBondPropertyFlags()

◆ includeIdentityMapping()

◆ identityMappingIncluded()

◆ findMappings()

◆ stopSearch()

◆ getNumMappings()

◆ getMapping() [1/2]

◆ getMapping() [2/2]

◆ getMappingsBegin() [1/2]

◆ getMappingsBegin() [2/2]

◆ getMappingsEnd() [1/2]

◆ getMappingsEnd() [2/2]

◆ begin() [1/2]

◆ begin() [2/2]

◆ end() [1/2]

◆ end() [2/2]

◆ setMaxNumMappings()

◆ getMaxNumMappings()

◆ addAtomMappingConstraint()

◆ clearAtomMappingConstraints()

◆ addBondMappingConstraint()

◆ clearBondMappingConstraints()

◆ setFoundMappingCallback()

◆ getFoundMappingCallback()

Member Data Documentation

◆ DEF_ATOM_PROPERTY_FLAGS

◆ DEF_BOND_PROPERTY_FLAGS