#include <SubstructureSearch.hpp>

Public Types
typedef std::shared_ptr< SubstructureSearch >	SharedPointer

typedef boost::indirect_iterator< ABMappingList::iterator, AtomBondMapping >	MappingIterator
	A mutable random access iterator used to iterate over the stored atom/bond mapping objects. More...

typedef boost::indirect_iterator< ABMappingList::const_iterator, const AtomBondMapping >	ConstMappingIterator
	A constant random access iterator used to iterate over the stored atom/bond mapping objects. More...

typedef std::function< const AtomMatchExprPtr &(const Atom &)>	AtomMatchExpressionFunction

typedef std::function< const BondMatchExprPtr &(const Bond &)>	BondMatchExpressionFunction

typedef std::function< const MolGraphMatchExprPtr &(const MolecularGraph &)>	MolecularGraphMatchExpressionFunction

Public Member Functions
	SubstructureSearch ()
	Constructs and initializes a `SubstructureSearch` instance. More...

	SubstructureSearch (const MolecularGraph &query)
	Constructs and initializes a `SubstructureSearch` instance for the specified query structure. More...

	SubstructureSearch (const SubstructureSearch &)=delete

	~SubstructureSearch ()
	Destructor. More...

SubstructureSearch &	operator= (const SubstructureSearch &)=delete

void	setAtomMatchExpressionFunction (const AtomMatchExpressionFunction &func)

void	setBondMatchExpressionFunction (const BondMatchExpressionFunction &func)

void	setMolecularGraphMatchExpressionFunction (const MolecularGraphMatchExpressionFunction &func)

void	setQuery (const MolecularGraph &query)
	Allows to specify a new query structure. More...

bool	mappingExists (const MolecularGraph &target)
	Tells whether the query structure matches a substructure of the specified target molecular graph. More...

bool	findMappings (const MolecularGraph &target)
	Searches for all possible atom/bond mappings of the query structure to substructures of the specified target 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	uniqueMappingsOnly (bool unique)
	Allows to specify whether or not to store only unique atom/bond mappings. More...

bool	uniqueMappingsOnly () const
	Tells whether duplicate atom/bond mappings are discarded. 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 query_atom_idx, std::size_t target_atom_idx)
	Adds a constraint on the allowed mappings between query and target structure atoms. More...

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

void	addBondMappingConstraint (std::size_t query_bond_idx, std::size_t target_bond_idx)
	Adds a constraint on the allowed mappings between query and target structure bonds. More...

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

Detailed Description

SubstructureSearch.

See also: [VFLIB2]

Member Typedef Documentation

◆ SharedPointer

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

◆ MappingIterator

typedef boost::indirect_iterator<ABMappingList::iterator, AtomBondMapping> CDPL::Chem::SubstructureSearch::MappingIterator

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

◆ ConstMappingIterator

typedef boost::indirect_iterator<ABMappingList::const_iterator, const AtomBondMapping> CDPL::Chem::SubstructureSearch::ConstMappingIterator

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

◆ AtomMatchExpressionFunction

typedef std::function<const AtomMatchExprPtr&(const Atom&)> CDPL::Chem::SubstructureSearch::AtomMatchExpressionFunction

◆ BondMatchExpressionFunction

typedef std::function<const BondMatchExprPtr&(const Bond&)> CDPL::Chem::SubstructureSearch::BondMatchExpressionFunction

◆ MolecularGraphMatchExpressionFunction

typedef std::function<const MolGraphMatchExprPtr&(const MolecularGraph&)> CDPL::Chem::SubstructureSearch::MolecularGraphMatchExpressionFunction

Constructor & Destructor Documentation

◆ SubstructureSearch() [1/3]

CDPL::Chem::SubstructureSearch::SubstructureSearch ( )

Constructs and initializes a SubstructureSearch instance.

◆ SubstructureSearch() [2/3]

CDPL::Chem::SubstructureSearch::SubstructureSearch ( const MolecularGraph & query )

Constructs and initializes a SubstructureSearch instance for the specified query structure.

Parameters

query A molecular graph that represents the query structure.

◆ SubstructureSearch() [3/3]

CDPL::Chem::SubstructureSearch::SubstructureSearch ( const SubstructureSearch & )

delete

◆ ~SubstructureSearch()

CDPL::Chem::SubstructureSearch::~SubstructureSearch ( )

Destructor.

Destroys the SubstructureSearch instance and frees all allocated resources.

Member Function Documentation

◆ operator=()

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

delete

◆ setAtomMatchExpressionFunction()

void CDPL::Chem::SubstructureSearch::setAtomMatchExpressionFunction ( const AtomMatchExpressionFunction & func )

◆ setBondMatchExpressionFunction()

void CDPL::Chem::SubstructureSearch::setBondMatchExpressionFunction ( const BondMatchExpressionFunction & func )

◆ setMolecularGraphMatchExpressionFunction()

void CDPL::Chem::SubstructureSearch::setMolecularGraphMatchExpressionFunction ( const MolecularGraphMatchExpressionFunction & func )

◆ setQuery()

void CDPL::Chem::SubstructureSearch::setQuery ( const MolecularGraph & query )

Allows to specify a new query structure.

Parameters

query A molecular graph that represents the query structure.

◆ mappingExists()

bool CDPL::Chem::SubstructureSearch::mappingExists ( const MolecularGraph & target )

Tells whether the query structure matches a substructure of the specified target molecular graph.

The method does not store any atom/bond mappings between the query and target structure - it just tells if a complete mapping of the query is possible. If you need access to the atom/bond mappings, use findMappings() instead.

Parameters

target The molecular graph that has to be searched for a match of the query structure.

Returns: true if the query matches a substructure of the target molecular graph, and false otherwise.

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

◆ findMappings()

bool CDPL::Chem::SubstructureSearch::findMappings ( const MolecularGraph & target )

Searches for all possible atom/bond mappings of the query structure to substructures of the specified target molecular graph.

The method will store all found subgraph mapping solutions up to the maximum number of recorded mappings specified by setMaxNumMappings(). If only unique mappings have to be stored (see uniqueMappingsOnly(bool unique)), any duplicates of previously found mappings will be discarded.

Parameters

target The molecular graph that has to be searched for matches of the query structure.

Returns: true if the query matches at least one substructure of the specified target molecular graph, and false otherwise.

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

◆ stopSearch()

void CDPL::Chem::SubstructureSearch::stopSearch ( )

◆ getNumMappings()

std::size_t CDPL::Chem::SubstructureSearch::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::SubstructureSearch::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::SubstructureSearch::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::SubstructureSearch::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::SubstructureSearch::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::SubstructureSearch::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::SubstructureSearch::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::SubstructureSearch::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::SubstructureSearch::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::SubstructureSearch::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::SubstructureSearch::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.

◆ uniqueMappingsOnly() [1/2]

void CDPL::Chem::SubstructureSearch::uniqueMappingsOnly ( bool unique )

Allows to specify whether or not to store only unique atom/bond mappings.

A mapping of the query pattern to a substructure of the target molecular graph is considered to be unique if it differs from all previously found mappings by at least one atom or bond. If the unique argument is true, and a newly discovered mapping covers the same atoms and bonds of the target (including all permutations) as a mapping that was found earlier in the search process, it is considered as a duplicate and will be discarded.

Parameters

unique If true, only unique mappings will be stored, and all found mappings otherwise.

Note: By default, duplicate mappings are not discarded.

◆ uniqueMappingsOnly() [2/2]

bool CDPL::Chem::SubstructureSearch::uniqueMappingsOnly ( ) const

Tells whether duplicate atom/bond mappings are discarded.

Returns: true if duplicate mappings are discarded, and false otherwise.

See also: uniqueMappingsOnly(bool unique)

◆ setMaxNumMappings()

void CDPL::Chem::SubstructureSearch::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 substructure 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::SubstructureSearch::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::SubstructureSearch::addAtomMappingConstraint	(	std::size_t	query_atom_idx,
		std::size_t	target_atom_idx
	)

Adds a constraint on the allowed mappings between query and target structure atoms.

By default, an atom of the query structure is free to match any suitable target structure atom. When this method gets called for a particular query/target atom pair (specified by query_atom_idx and target_atom_idx), future substructure searches will find only those subgraph mapping solutions (if any) where the given query atom maps to the specified target structure atom. Multiple calls to addAtomMappingConstraint() for the same query atom have an additive effect and allow to restrict the valid query atom mappings not only to a single but also a larger set of target structure atoms.

Parameters

query_atom_idx	The index of the query structure atom.
target_atom_idx	The index of the target structure atom that has to be matched by the query atom.

◆ clearAtomMappingConstraints()

void CDPL::Chem::SubstructureSearch::clearAtomMappingConstraints ( )

Clears all previously defined query to target atom mapping constraints.

See also: addAtomMappingConstraint()

◆ addBondMappingConstraint()

void CDPL::Chem::SubstructureSearch::addBondMappingConstraint	(	std::size_t	query_bond_idx,
		std::size_t	target_bond_idx
	)

Adds a constraint on the allowed mappings between query and target structure bonds.

By default, a bond of the query structure is free to match any suitable target structure bond. When this method gets called for a particular query/target bond pair (specified by query_bond_idx and target_bond_idx), future substructure searches will find only those subgraph mapping solutions (if any) where the given query bond maps to the specified target structure bond. Multiple calls to addBondMappingConstraint() for the same query bond have an additive effect and allow to restrict the valid query bond mappings not only to a single but also a larger set of target structure bonds.

Parameters

query_bond_idx	The index of the query structure bond.
target_bond_idx	The index of the target structure bond that has to be matched by the query bond.

◆ clearBondMappingConstraints()

void CDPL::Chem::SubstructureSearch::clearBondMappingConstraints ( )

Clears all previously defined query to target bond mapping constraints.

See also: addBondMappingConstraint()

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

SubstructureSearch.hpp

Public Types

Public Member Functions

Detailed Description

Member Typedef Documentation

◆ SharedPointer

◆ MappingIterator

◆ ConstMappingIterator

◆ AtomMatchExpressionFunction

◆ BondMatchExpressionFunction

◆ MolecularGraphMatchExpressionFunction

Constructor & Destructor Documentation

◆ SubstructureSearch() [1/3]

◆ SubstructureSearch() [2/3]

◆ SubstructureSearch() [3/3]

◆ ~SubstructureSearch()

Member Function Documentation

◆ operator=()

◆ setAtomMatchExpressionFunction()

◆ setBondMatchExpressionFunction()

◆ setMolecularGraphMatchExpressionFunction()

◆ setQuery()

◆ mappingExists()

◆ 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]

◆ uniqueMappingsOnly() [1/2]

◆ uniqueMappingsOnly() [2/2]

◆ setMaxNumMappings()

◆ getMaxNumMappings()

◆ addAtomMappingConstraint()

◆ clearAtomMappingConstraints()

◆ addBondMappingConstraint()

◆ clearBondMappingConstraints()