CDPL.Chem.AutomorphismGroupSearch Class Reference

AutomorphismGroupSearch. More...

Inheritance diagram for CDPL.Chem.AutomorphismGroupSearch:

Public Member Functions
None	__init__ (int atom_flags=12702, int bond_flags=30)
	Constructs and initializes a AutomorphismGroupSearch instance.
int	getObjectID ()
	Returns the numeric identifier (ID) of the wrapped C++ class instance. More...
None	setAtomPropertyFlags (int flags)
int	getAtomPropertyFlags ()
None	setBondPropertyFlags (int flags)
int	getBondPropertyFlags ()
None	includeIdentityMapping (bool include)
bool	identityMappingIncluded ()
bool	findMappings (MolecularGraph molgraph)
	Searches for the possible atom/bond mappings in the automorphism group of the given molecular graph. More...
None	stopSearch ()
int	getNumMappings ()
	Returns the number of atom/bond mappings that were recorded in the last call to findMappings(). More...
AtomBondMapping	getMapping (int idx)
	Returns a reference to the stored atom/bond mapping object at index idx. 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...
None	clearAtomMappingConstraints ()
	Clears all previously defined atom mapping constraints. More...
None	addAtomMappingConstraint (int atom1_idx, int atom2_idx)
	Adds a constraint on the allowed atom mappings. More...
None	clearBondMappingConstraints ()
	Clears all previously defined bond mapping constraints. More...
None	addBondMappingConstraint (int bond1_idx, int bond2_idx)
	Adds a constraint on the allowed bond mappings. More...
None	setFoundMappingCallback (BoolMolecularGraphAtomBondMappingFunctor func)
BoolMolecularGraphAtomBondMappingFunctor	getFoundMappingCallback ()
AtomBondMapping	__getitem__ (int idx)
int	__len__ ()

Properties
	objectID = property(getObjectID)
	atomPropertyFlags = property(getAtomPropertyFlags, setAtomPropertyFlags)
	bondPropertyFlags = property(getBondPropertyFlags, setBondPropertyFlags)
	incIdentityMapping = property(identityMappingIncluded, includeIdentityMapping)
	numMappings = property(getNumMappings)
	maxNumMappings = property(getMaxNumMappings, setMaxNumMappings)
	foundMappingCallback = property(getFoundMappingCallback, setFoundMappingCallback)

Detailed Description

AutomorphismGroupSearch.

Member Function Documentation

getObjectID()

int CDPL.Chem.AutomorphismGroupSearch.getObjectID

(

)

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

Different Python AutomorphismGroupSearch 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 AutomorphismGroupSearch 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.

setAtomPropertyFlags()

None CDPL.Chem.AutomorphismGroupSearch.setAtomPropertyFlags

(

int

flags

)

Parameters

flags

getAtomPropertyFlags()

int CDPL.Chem.AutomorphismGroupSearch.getAtomPropertyFlags

(

)

Returns

setBondPropertyFlags()

None CDPL.Chem.AutomorphismGroupSearch.setBondPropertyFlags

(

int

flags

)

Parameters

flags

getBondPropertyFlags()

int CDPL.Chem.AutomorphismGroupSearch.getBondPropertyFlags

(

)

Returns

includeIdentityMapping()

None CDPL.Chem.AutomorphismGroupSearch.includeIdentityMapping

(

bool

include

)

Parameters

include

identityMappingIncluded()

bool CDPL.Chem.AutomorphismGroupSearch.identityMappingIncluded

(

)

Returns

findMappings()

bool CDPL.Chem.AutomorphismGroupSearch.findMappings

(

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.

getNumMappings()

int CDPL.Chem.AutomorphismGroupSearch.getNumMappings

(

)

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()

AtomBondMapping CDPL.Chem.AutomorphismGroupSearch.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].

getMaxNumMappings()

int CDPL.Chem.AutomorphismGroupSearch.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.AutomorphismGroupSearch.setMaxNumMappings

(

int

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.

clearAtomMappingConstraints()

None CDPL.Chem.AutomorphismGroupSearch.clearAtomMappingConstraints

(

)

Clears all previously defined atom mapping constraints.

See also

addAtomMappingConstraint()

addAtomMappingConstraint()

None CDPL.Chem.AutomorphismGroupSearch.addAtomMappingConstraint	(	int	atom1_idx,
		int	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.

clearBondMappingConstraints()

None CDPL.Chem.AutomorphismGroupSearch.clearBondMappingConstraints

(

)

Clears all previously defined bond mapping constraints.

See also

addBondMappingConstraint()

addBondMappingConstraint()

None CDPL.Chem.AutomorphismGroupSearch.addBondMappingConstraint	(	int	bond1_idx,
		int	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.

setFoundMappingCallback()

None CDPL.Chem.AutomorphismGroupSearch.setFoundMappingCallback

(

BoolMolecularGraphAtomBondMappingFunctor

func

)

Parameters

func

getFoundMappingCallback()

BoolMolecularGraphAtomBondMappingFunctor CDPL.Chem.AutomorphismGroupSearch.getFoundMappingCallback

(

)

Returns

__getitem__()

AtomBondMapping CDPL.Chem.AutomorphismGroupSearch.__getitem__

(

int

idx

)

Parameters

idx

Returns

__len__()

int CDPL.Chem.AutomorphismGroupSearch.__len__

(

)

Returns