Concrete Chem.Molecule implementation that owns Chem.BasicAtom and Chem.BasicBond instances. More...

Inheritance diagram for CDPL.Chem.BasicMolecule:

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

None	__init__ (BasicMolecule mol)
	Constructs a copy of the Chem.Molecule instance mol. More...

None	__init__ (Molecule mol)
	Constructs a copy of the Chem.Molecule instance mol. More...

None	__init__ (MolecularGraph molgraph)
	Constructs a `BasicMolecule` instance with copies of the atoms and bonds of the Chem.MolecularGraph instance molgraph. More...

None	copy (BasicMolecule mol)
	Replaces the current set of atoms, bonds and properties by a copy of mol. More...

None	copy (Molecule mol)
	Replaces the current set of atoms, bonds and properties by a copy of mol. More...

None	copy (MolecularGraph molgraph)
	Replaces the current set of atoms, bonds and properties by a copy of molgraph. More...

None	append (BasicMolecule mol)
	Extends the current set of atoms and bonds by a copy of those in mol. More...

None	append (Molecule mol)
	Extends the current set of atoms and bonds by a copy of those in mol. More...

None	append (MolecularGraph molgraph)
	Extends the current set of atoms and bonds by a copy of those in molgraph. More...

BasicMolecule	assign (BasicMolecule mol)
	Replaces the current set of atoms, bonds and properties by a copy of the atoms, bonds and properties of the molecule mol. More...

BasicMolecule	assign (Molecule mol)
	Replaces the current set of atoms, bonds and properties by a copy of the atoms, bonds and properties of the molecule mol. More...

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

BasicMolecule	__iadd__ (BasicMolecule mol)
	Performs the in-place addition operation `self += mol`. More...

BasicMolecule	__iadd__ (Molecule mol)
	Performs the in-place addition operation `self += mol`. More...

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

Public Member Functions inherited from CDPL.Chem.Molecule
None	reserveMemoryForAtoms (int num_atoms)
	Reserves memory for num_atoms atoms. More...

None	reserveMemoryForBonds (int num_bonds)
	Reserves memory for num_bonds bonds. More...

None	clear ()
	Removes all atoms and bonds and clears all properties of the molecule.

Atom	addAtom ()
	Creates a new atom and adds it to the molecule. More...

Bond	addBond (int atom1_idx, int atom2_idx)
	Creates a new or returns an already existing bond between the atoms specified by atom1_idx and atom2_idx. More...

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

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

None	remove (MolecularGraph molgraph)
	Removes atoms and bonds referenced by the molecular graph molgraph that are part of this `Molecule` instance. More...

AtomSequence	getAtoms ()

BondSequence	getBonds ()

None	invokeCopyPostprocessingFunctions (MolecularGraph src_molgraph)
	Invokes all registered copy-postprocessing functions on this molecule with src_molgraph as the source. More...

Atom	getAtom (int idx)
	Returns a reference to the atom at index idx. More...

bool	containsAtom (Atom atom)
	Tells whether the specified atom is part of this molecule. More...

int	getAtomIndex (Atom atom)
	Returns the index of the specified atom. More...

int	getNumAtoms ()
	Returns the number of explicit atoms. More...

None	orderAtoms (BoolAtom2Functor func)

Entity3D	getEntity (int idx)

int	getNumEntities ()

Bond	getBond (int idx)
	Returns a reference to the bond at index idx. More...

bool	containsBond (Bond bond)
	Tells whether the specified bond is part of this molecule. More...

None	orderBonds (BoolBond2Functor func)

int	getBondIndex (Bond bond)
	Returns the index of the specified bond. More...

int	getNumBonds ()
	Returns the number of explicit bonds. More...

tuple	__getstate__ ()

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

Base.Any	__getitem__ (Base.LookupKey key)

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

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

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

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

bool	__delitem__ (Base.LookupKey key)

int	__len__ ()

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

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
Static Public Member Functions inherited from CDPL.Chem.Molecule
None	registerCopyPostprocessingFunction (VoidMoleculeMolecularGraphFunctor func)
	Registers a new copy-postprocessing function in the global registry. More...

Properties inherited from CDPL.Chem.Molecule
	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

Concrete Chem.Molecule implementation that owns Chem.BasicAtom and Chem.BasicBond instances.

BasicMolecule provides the default in-memory representation of a molecular graph: atoms and bonds are allocated from internal object pools and accessed through random-access iterators. The class implements the full editing interface inherited from Chem.Molecule (addAtom, addBond, removeAtom, removeBond, copy, append, remove, reserveMemoryForAtoms, reserveMemoryForBonds) and is the standard concrete type used by readers and downstream algorithms throughout CDPKit.

Constructor & Destructor Documentation

◆ init() [1/3]

None CDPL.Chem.BasicMolecule.__init__ ( BasicMolecule mol )

Constructs a copy of the Chem.Molecule instance mol.

Parameters

mol	The other Chem.Molecule instance to copy.

◆ init() [2/3]

None CDPL.Chem.BasicMolecule.__init__ ( Molecule mol )

Constructs a copy of the Chem.Molecule instance mol.

Parameters

mol	The other Chem.Molecule instance to copy.

◆ init() [3/3]

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

Constructs a BasicMolecule instance with copies of the atoms and bonds of the Chem.MolecularGraph instance molgraph.

Parameters

molgraph The Chem.MolecularGraph instance providing the atoms and bonds to copy.

Member Function Documentation

◆ copy() [1/3]

None CDPL.Chem.BasicMolecule.copy ( BasicMolecule mol )

Replaces the current set of atoms, bonds and properties by a copy of mol.

Parameters

mol	The source molecule.

◆ copy() [2/3]

None CDPL.Chem.BasicMolecule.copy ( Molecule mol )

Replaces the current set of atoms, bonds and properties by a copy of mol.

Parameters

mol	The source molecule.

Reimplemented from CDPL.Chem.Molecule.

◆ copy() [3/3]

None CDPL.Chem.BasicMolecule.copy ( MolecularGraph molgraph )

Replaces the current set of atoms, bonds and properties by a copy of molgraph.

Parameters

molgraph The source molecular graph.

Reimplemented from CDPL.Chem.Molecule.

◆ append() [1/3]

None CDPL.Chem.BasicMolecule.append ( BasicMolecule mol )

Extends the current set of atoms and bonds by a copy of those in mol.

Parameters

mol	The source molecule.

Note: Does not affect any properties.

◆ append() [2/3]

None CDPL.Chem.BasicMolecule.append ( Molecule mol )

Extends the current set of atoms and bonds by a copy of those in mol.

Parameters

mol	The source molecule.

Note: Does not affect any properties.

Reimplemented from CDPL.Chem.Molecule.

◆ append() [3/3]

None CDPL.Chem.BasicMolecule.append ( MolecularGraph molgraph )

Extends the current set of atoms and bonds by a copy of those in molgraph.

Parameters

molgraph The source molecular graph.

Note: Does not affect any properties.

Reimplemented from CDPL.Chem.Molecule.

◆ assign() [1/3]

BasicMolecule CDPL.Chem.BasicMolecule.assign ( BasicMolecule mol )

Replaces the current set of atoms, bonds and properties by a copy of the atoms, bonds and properties of the molecule mol.

Internally calls copy() to perform the actual work.

Parameters

mol	The molecule to copy.

Returns: self

◆ assign() [2/3]

BasicMolecule CDPL.Chem.BasicMolecule.assign ( Molecule mol )

Replaces the current set of atoms, bonds and properties by a copy of the atoms, bonds and properties of the molecule mol.

Internally calls copy() to perform the actual work.

Parameters

mol	The molecule to copy.

Returns: self

Reimplemented from CDPL.Chem.Molecule.

◆ assign() [3/3]

BasicMolecule CDPL.Chem.BasicMolecule.assign ( MolecularGraph molgraph )

Replaces the current set of atoms, bonds and properties by a copy of the atoms, bonds and properties of the molecular graph molgraph.

Internally calls copy() to perform the actual work.

Parameters

molgraph The Chem.MolecularGraph instance providing the atoms and bonds to copy.

Returns: self

Reimplemented from CDPL.Chem.Molecule.

◆ iadd() [1/3]

BasicMolecule CDPL.Chem.BasicMolecule.__iadd__ ( BasicMolecule mol )

Performs the in-place addition operation self += mol.

Parameters

mol	Specifies the second addend.

Returns: The updated BasicMolecule instance self.

◆ iadd() [2/3]

BasicMolecule CDPL.Chem.BasicMolecule.__iadd__ ( Molecule mol )

Performs the in-place addition operation self += mol.

Parameters

mol	Specifies the second addend.

Returns: The updated BasicMolecule instance self.

Reimplemented from CDPL.Chem.Molecule.

◆ iadd() [3/3]

BasicMolecule CDPL.Chem.BasicMolecule.__iadd__ ( MolecularGraph molgraph )

Performs the in-place addition operation self += molgraph.

Parameters

molgraph Specifies the second addend.

Returns: The updated BasicMolecule instance self.

Reimplemented from CDPL.Chem.Molecule.

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ __init__() [1/3]

◆ __init__() [2/3]

◆ __init__() [3/3]

Member Function Documentation

◆ copy() [1/3]

◆ copy() [2/3]

◆ copy() [3/3]

◆ append() [1/3]

◆ append() [2/3]

◆ append() [3/3]

◆ assign() [1/3]

◆ assign() [2/3]

◆ assign() [3/3]

◆ __iadd__() [1/3]

◆ __iadd__() [2/3]

◆ __iadd__() [3/3]

◆ init() [1/3]

◆ init() [2/3]

◆ init() [3/3]

◆ iadd() [1/3]

◆ iadd() [2/3]

◆ iadd() [3/3]