Implements the perception of ring atoms and bonds in a molecular graph. More...

Inheritance diagram for CDPL.Chem.CyclicSubstructure:

Public Member Functions
None	__init__ ()
	Constructs an empty `CyclicSubstructure` instance.

None	__init__ (MolecularGraph molgraph)
	Construct a `CyclicSubstructure` instance that consists of the ring atoms and bonds of the molecular graph molgraph. More...

None	perceive (MolecularGraph molgraph)
	Replaces the currently stored atoms and bonds by the set of ring atoms and bonds of the molecular graph molgraph. More...

Public Member Functions inherited from CDPL.Chem.Fragment
None	__init__ (Fragment frag)
	Constructs a copy of the `Fragment` instance frag. More...

Fragment	assign (Fragment frag)
	Replaces the current set of atoms, bonds and properties by the atoms, bonds and properties of the fragment frag. More...

Fragment	assign (MolecularGraph molgraph)
	Replaces the current set of atoms, bonds and properties by the atoms, bonds and properties of the molecular graph molgraph. More...

bool	addAtom (Atom atom)
	Extends the fragment by the specified atom. More...

None	removeAtom (int idx)
	Removes the atom at the specified index. More...

bool	removeAtom (Atom atom)
	Removes the specified atom. More...

bool	addBond (Bond bond)
	Extends the fragment by the specified bond. More...

None	removeBond (int idx)
	Removes the bond at the specified index. More...

bool	removeBond (Bond bond)
	Removes the specified bond. More...

None	clear ()
	Removes all atoms and bonds.

None	swap (Fragment frag)
	Exchanges the atoms, bonds and properties of this fragment with the atoms, bonds and properties of the fragment frag. More...

AtomSequence	getAtoms ()

BondSequence	getBonds ()

None	reserveMemoryForAtoms (int num_atoms)

None	reserveMemoryForBonds (int num_bonds)

bool	__contains__ (Atom atom)
	Returns the result of the membership test operation `atom in self`. More...

bool	__contains__ (Bond bond)
	Returns the result of the membership test operation `bond in self`. More...

bool	__contains__ (Base.LookupKey key)
	Returns the result of the membership test operation `key in self`. More...

Base.Any	__getitem__ (Base.LookupKey key)

None	__setitem__ (Base.LookupKey key, Base.Any value)

bool	__delitem__ (Base.LookupKey key)

int	__len__ ()

Fragment	__iadd__ (MolecularGraph molgraph)
	Performs the in-place addition operation `self += molgraph`. More...

Fragment	__isub__ (MolecularGraph molgraph)
	Performs the in-place subtraction operation `self -= molgraph`. More...

Public Member Functions inherited from CDPL.Chem.MolecularGraph
MolecularGraph	clone ()
	Creates a copy of the molecular graph. More...

Atom	getAtom (int idx)

bool	containsAtom (Atom atom)

int	getAtomIndex (Atom atom)

int	getNumAtoms ()

None	orderAtoms (ForceField.InteractionFilterFunction2 func)

Entity3D	getEntity (int idx)

int	getNumEntities ()

Bond	getBond (int idx)

bool	containsBond (Bond bond)

None	orderBonds (BoolBond2Functor func)

int	getBondIndex (Bond bond)

int	getNumBonds ()

Public Member Functions inherited from CDPL.Chem.AtomContainer
Atom	__getitem__ (int idx)

Public Member Functions inherited from CDPL.Chem.Entity3DContainer
int	getObjectID ()
	Returns the numeric identifier (ID) of the wrapped C++ class instance. More...

Public Member Functions inherited from CDPL.Chem.BondContainer
int	getObjectID ()
	Returns the numeric identifier (ID) of the wrapped C++ class instance. More...

Bond	__getitem__ (int idx)

Public Member Functions inherited from CDPL.Base.PropertyContainer
int	getObjectID ()
	Returns the numeric identifier (ID) of the wrapped C++ class instance. More...

int	getNumProperties ()
	Returns the number of property entries. More...

Any	getPropertyOrDefault (LookupKey key, Any def_value)

list	getPropertyKeys ()

list	getPropertyValues ()

list	getProperties ()
	Returns a reference to itself. More...

None	setProperty (LookupKey key, Any value)

bool	removeProperty (LookupKey key)
	Clears the value of the property specified by key. More...

Any	getProperty (LookupKey key, bool throw_=False)
	Returns the value of the property specified by key. More...

bool	isPropertySet (LookupKey key)
	Tells whether or not a value has been assigned to the property specified by key. More...

None	clearProperties ()
	Clears all property values.

None	addProperties (PropertyContainer cntnr)
	Adds the property value entries in the `PropertyContainer` instance cntnr. More...

None	copyProperties (PropertyContainer cntnr)
	Replaces the current set of properties by a copy of the entries in cntnr. More...

None	swap (PropertyContainer cntnr)
	Exchanges the properties of this container with the properties of the container cntnr. More...

Any	__getitem__ (LookupKey key)

bool	__contains__ (LookupKey key)
	Returns the result of the membership test operation `key in self`. More...

None	__setitem__ (LookupKey key, Any value)

bool	__delitem__ (LookupKey key)

Additional Inherited Members
Properties inherited from CDPL.Chem.Fragment
	atoms = property(getAtoms)

	bonds = property(getBonds)

Properties inherited from CDPL.Chem.MolecularGraph
	atoms = property(getAtoms)

	bonds = property(getBonds)

Properties inherited from CDPL.Chem.AtomContainer
	numAtoms = property(getNumAtoms)

Properties inherited from CDPL.Chem.Entity3DContainer
	objectID = property(getObjectID)

	numEntities = property(getNumEntities)

Properties inherited from CDPL.Chem.BondContainer
	objectID = property(getObjectID)

	numBonds = property(getNumBonds)

Properties inherited from CDPL.Base.PropertyContainer
	objectID = property(getObjectID)

	propertyKeys = property(getPropertyKeys)

	propertyValues = property(getPropertyValues)

	properties = property(getProperties)

	numProperties = property(getNumProperties)

Detailed Description

Implements the perception of ring atoms and bonds in a molecular graph.

Constructor & Destructor Documentation

◆ init()

None CDPL.Chem.CyclicSubstructure.__init__ ( MolecularGraph molgraph )

Construct a CyclicSubstructure instance that consists of the ring atoms and bonds of the molecular graph molgraph.

Parameters

molgraph The molecular graph for which to perceive ring atoms and bonds.

Reimplemented from CDPL.Chem.Fragment.

Member Function Documentation

◆ perceive()

None CDPL.Chem.CyclicSubstructure.perceive ( MolecularGraph molgraph )

Replaces the currently stored atoms and bonds by the set of ring atoms and bonds of the molecular graph molgraph.