CDPL::Chem::MaxCommonBondSubstructureSearch Class Reference

MaxCommonBondSubstructureSearch. More...

#include <MaxCommonBondSubstructureSearch.hpp>

Public Types
typedef std::shared_ptr< MaxCommonBondSubstructureSearch >	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...

Public Member Functions
	MaxCommonBondSubstructureSearch ()
	Constructs and initializes a MaxCommonBondSubstructureSearch instance. More...
	MaxCommonBondSubstructureSearch (const MolecularGraph &query)
	Constructs and initializes a MaxCommonBondSubstructureSearch instance for the specified query structure. More...
	~MaxCommonBondSubstructureSearch ()
	Destructor. More...
void	setQuery (const MolecularGraph &query)
	Allows to specify a new query structure. More...
bool	mappingExists (const MolecularGraph &target)
	Searches for a common substructure between the query and the specified target molecular graph. More...
bool	findMappings (const MolecularGraph &target)
	Searches for all atom/bond mappings of query subgraphs to substructures of the specified target molecular graph with a maximum bond count. More...
std::size_t	getNumMappings () const
	Returns the number of atom/bond mappings that were recorded in the last search for common substructures. 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	setMinSubstructureSize (std::size_t min_size)
	Allows to specify the minimum accepted common substructure size. More...
std::size_t	getMinSubstructureSize () const
	Returns the minimum accepted common substructure size. More...

Detailed Description

MaxCommonBondSubstructureSearch.

See also

[MCESA]

Member Typedef Documentation

SharedPointer

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

MappingIterator

typedef boost::indirect_iterator<ABMappingList::iterator, AtomBondMapping> CDPL::Chem::MaxCommonBondSubstructureSearch::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::MaxCommonBondSubstructureSearch::ConstMappingIterator

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

Constructor & Destructor Documentation

MaxCommonBondSubstructureSearch() [1/2]

CDPL::Chem::MaxCommonBondSubstructureSearch::MaxCommonBondSubstructureSearch

(

)

Constructs and initializes a MaxCommonBondSubstructureSearch instance.

MaxCommonBondSubstructureSearch() [2/2]

CDPL::Chem::MaxCommonBondSubstructureSearch::MaxCommonBondSubstructureSearch

(

const MolecularGraph &

query

)

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

Parameters

query

A molecular graph that represents the query structure.

~MaxCommonBondSubstructureSearch()

CDPL::Chem::MaxCommonBondSubstructureSearch::~MaxCommonBondSubstructureSearch

(

)

Destructor.

Destroys the MaxCommonBondSubstructureSearch instance and frees all allocated resources.

Member Function Documentation

setQuery()

void CDPL::Chem::MaxCommonBondSubstructureSearch::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::MaxCommonBondSubstructureSearch::mappingExists

(

const MolecularGraph &

target

)

Searches for a common substructure between the query and the specified target molecular graph.

The method does not store any atom/bond mappings between query and target substructures - it just tells if a valid common substructure mapping solution involving at least getMinSubstructureSize() bonds could be found. If you need access to the atom/bond mappings, use findMappings() instead.

Parameters

target

The molecular graph that has to be searched for a substructure in common with the query.

Returns

true if a common substructure of at least the minimum accepted size could be found, and false otherwise.

Note

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

findMappings()

bool CDPL::Chem::MaxCommonBondSubstructureSearch::findMappings

(

const MolecularGraph &

target

)

Searches for all atom/bond mappings of query subgraphs to substructures of the specified target molecular graph with a maximum bond count.

The method will store all maximum-sized (in number of bonds) common substructure mapping solutions involving at least getMinSubstructureSize() atoms 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 all maximum-sized substructures in common with the query.

Returns

true if common substructures of at least the minimum accepted size were found, and false otherwise.

Note

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

getNumMappings()

std::size_t CDPL::Chem::MaxCommonBondSubstructureSearch::getNumMappings

(

)

const

Returns the number of atom/bond mappings that were recorded in the last search for common substructures.

Returns

The number of atom/bond mappings that were recorded in the last search for common substructures.

See also

findMappings()

getMapping() [1/2]

AtomBondMapping& CDPL::Chem::MaxCommonBondSubstructureSearch::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::MaxCommonBondSubstructureSearch::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::MaxCommonBondSubstructureSearch::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::MaxCommonBondSubstructureSearch::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::MaxCommonBondSubstructureSearch::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::MaxCommonBondSubstructureSearch::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::MaxCommonBondSubstructureSearch::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::MaxCommonBondSubstructureSearch::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::MaxCommonBondSubstructureSearch::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::MaxCommonBondSubstructureSearch::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::MaxCommonBondSubstructureSearch::uniqueMappingsOnly

(

bool

unique

)

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

The mapping of a query pattern subgraph 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::MaxCommonBondSubstructureSearch::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::MaxCommonBondSubstructureSearch::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 common 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::MaxCommonBondSubstructureSearch::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()

setMinSubstructureSize()

void CDPL::Chem::MaxCommonBondSubstructureSearch::setMinSubstructureSize

(

std::size_t

min_size

)

Allows to specify the minimum accepted common substructure size.

Any found common substructures which cover less than min_size bonds are not accepted as a valid solution and will be discarded.

Parameters

min_size

The minimum accepted common substructure size in number of bonds.

Note

By default, the minimum common substructure size is set to zero.

getMinSubstructureSize()

std::size_t CDPL::Chem::MaxCommonBondSubstructureSearch::getMinSubstructureSize

(

)

const

Returns the minimum accepted common substructure size.

Returns

The minimum accepted common substructure size in number of bonds.

See also

setMinSubstructureSize()

---

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

• MaxCommonBondSubstructureSearch.hpp