MaxCommonAtomSubstructureSearch. More...

Inheritance diagram for CDPL.Chem.MaxCommonAtomSubstructureSearch:

Public Member Functions
None	__init__ ()
	Constructs and initializes a `MaxCommonAtomSubstructureSearch` instance.

None	__init__ (MolecularGraph query)
	Constructs and initializes a `MaxCommonAtomSubstructureSearch` instance for the specified query structure. More...

int	getObjectID ()
	Returns the numeric identifier (ID) of the wrapped C++ class instance. More...

bool	mappingExists (MolecularGraph target)
	Searches for a common substructure between the query and the specified target molecular graph. More...

bool	findAllMappings (MolecularGraph target)
	Searches for all atom/bond mappings of query subgraphs to substructures of the specified target molecular graph with a maximum atom count. More...

bool	findMaxBondMappings (MolecularGraph target)
	Searches for all atom/bond mappings of query subgraphs to substructures of the specified target molecular graph with a maximum atom and bond count. More...

int	getNumMappings ()
	Returns the number of atom/bond mappings that were recorded in the last search for common substructures. More...

AtomBondMapping	getMapping (int idx)
	Returns a reference to the stored atom/bond mapping object at index idx. More...

None	uniqueMappingsOnly (bool unique)
	Allows to specify whether or not to store only unique atom/bond mappings. More...

bool	uniqueMappingsOnly ()
	Tells whether duplicate atom/bond mappings are discarded. More...

int	getMaxNumMappings ()
	Returns the specified limit on the number of stored atom/bond mappings. More...

None	setMaxNumMappings (int max_num_mappings)
	Allows to specify a limit on the number of stored atom/bond mappings. More...

int	getMinSubstructureSize ()
	Returns the minimum accepted common substructure size. More...

None	setMinSubstructureSize (int min_size)
	Allows to specify the minimum accepted common substructure size. More...

None	setQuery (MolecularGraph query)
	Allows to specify a new query structure. More...

AtomBondMapping	__getitem__ (int idx)

int	__len__ ()

bool	__nonzero__ (MolecularGraph self)

bool	__bool__ (MolecularGraph self)

Properties
	objectID = property(getObjectID)

	numMappings = property(getNumMappings)

	uniqueMappings = property(uniqueMappingsOnly, uniqueMappingsOnly)

	maxNumMappings = property(getMaxNumMappings, setMaxNumMappings)

	minSubstructureSize = property(getMinSubstructureSize, setMinSubstructureSize)

Detailed Description

MaxCommonAtomSubstructureSearch.

See also: [MCASA]

Constructor & Destructor Documentation

◆ init()

None CDPL.Chem.MaxCommonAtomSubstructureSearch.__init__ ( MolecularGraph query )

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

Parameters

query A molecular graph that represents the query structure.

Member Function Documentation

◆ getObjectID()

int CDPL.Chem.MaxCommonAtomSubstructureSearch.getObjectID ( )

Returns the numeric identifier (ID) of the wrapped C++ class instance.

Different Python MaxCommonAtomSubstructureSearch instances may reference the same underlying C++ class instance. The commonly used Python expression a is not b thus cannot tell reliably whether the two MaxCommonAtomSubstructureSearch instances a and b reference different C++ objects. The numeric identifier returned by this method allows to correctly implement such an identity test via the simple expression a.getObjectID() != b.getObjectID().

Returns: The numeric ID of the internally referenced C++ class instance.

◆ mappingExists()

bool CDPL.Chem.MaxCommonAtomSubstructureSearch.mappingExists ( 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() atoms could be found. If you need access to the atom/bond mappings, use findAllMappings() or findMaxBondMappings() 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 findAllMappings() or findMaxMappings() will be discarded.

◆ findAllMappings()

bool CDPL.Chem.MaxCommonAtomSubstructureSearch.findAllMappings ( MolecularGraph target )

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

The method will store all maximum-sized (in number of atoms) 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 findAllMappings() or findMaxBondMappings() will be discarded.

◆ findMaxBondMappings()

bool CDPL.Chem.MaxCommonAtomSubstructureSearch.findMaxBondMappings ( MolecularGraph target )

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

The method will store all maximum-sized (both in number of atoms and 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 findAllMappings() or findMaxBondMappings() will be discarded.

◆ getNumMappings()

int CDPL.Chem.MaxCommonAtomSubstructureSearch.getNumMappings ( )

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: findAllMappings(), findMaxBondMappings()

◆ getMapping()

AtomBondMapping CDPL.Chem.MaxCommonAtomSubstructureSearch.getMapping ( int idx )

Returns a 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 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].

◆ uniqueMappingsOnly() [1/2]

None CDPL.Chem.MaxCommonAtomSubstructureSearch.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.MaxCommonAtomSubstructureSearch.uniqueMappingsOnly ( )

Tells whether duplicate atom/bond mappings are discarded.

Returns: True if duplicate mappings are discarded, and False otherwise.

See also: uniqueMappingsOnly(bool unique)

◆ getMaxNumMappings()

int CDPL.Chem.MaxCommonAtomSubstructureSearch.getMaxNumMappings ( )

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()

◆ setMaxNumMappings()

None CDPL.Chem.MaxCommonAtomSubstructureSearch.setMaxNumMappings ( int max_num_mappings )

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

In a call to findAllMappings() or findMaxBondMappings() 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.

◆ getMinSubstructureSize()

int CDPL.Chem.MaxCommonAtomSubstructureSearch.getMinSubstructureSize ( )

Returns the minimum accepted common substructure size.

Returns: The minimum accepted common substructure size in number of atoms.

See also: setMinSubstructureSize()

◆ setMinSubstructureSize()

None CDPL.Chem.MaxCommonAtomSubstructureSearch.setMinSubstructureSize ( int min_size )

Allows to specify the minimum accepted common substructure size.

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

Parameters

min_size The minimum accepted common substructure size in number of atoms.

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

◆ setQuery()

None CDPL.Chem.MaxCommonAtomSubstructureSearch.setQuery ( MolecularGraph query )

Allows to specify a new query structure.

Parameters

query A molecular graph that represents the query structure.

◆ getitem()

AtomBondMapping CDPL.Chem.MaxCommonAtomSubstructureSearch.__getitem__ ( int idx )

Parameters

idx

Returns

◆ len()

int CDPL.Chem.MaxCommonAtomSubstructureSearch.__len__ ( )

Returns

◆ nonzero()

bool CDPL.Chem.MaxCommonAtomSubstructureSearch.__nonzero__ ( MolecularGraph self )

Parameters

arg1

Returns

◆ bool()

bool CDPL.Chem.MaxCommonAtomSubstructureSearch.__bool__ ( MolecularGraph self )

Parameters

arg1

Returns

Public Member Functions

Properties

Detailed Description

Constructor & Destructor Documentation

◆ __init__()

Member Function Documentation

◆ getObjectID()

◆ mappingExists()

◆ findAllMappings()

◆ findMaxBondMappings()

◆ getNumMappings()

◆ getMapping()

◆ uniqueMappingsOnly() [1/2]

◆ uniqueMappingsOnly() [2/2]

◆ getMaxNumMappings()

◆ setMaxNumMappings()

◆ getMinSubstructureSize()

◆ setMinSubstructureSize()

◆ setQuery()

◆ __getitem__()

◆ __len__()

◆ __nonzero__()

◆ __bool__()

◆ init()

◆ getitem()

◆ len()

◆ nonzero()

◆ bool()