CDPL::Chem::AutomorphismGroupSearch Class Reference

AutomorphismGroupSearch. More...

#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...
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	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()

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.

Member Function Documentation

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()

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