Inheritance diagram for CDPL.Chem.Molecule:

Classes
class	AtomSequence

class	BondSequence

Public Member Functions
None	__init__ ()
	Initializes the Molecule instance.

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	copy (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...

None	copy (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...

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

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

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

Molecule	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...

Molecule	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...

AtomSequence	getAtoms ()

BondSequence	getBonds ()

None	invokeCopyPostprocessingFunctions (MolecularGraph src_molgraph)

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 (ForceField.InteractionFilterFunction2 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	__iadd__ (Molecule mol)
	Performs the in-place addition operation `self += mol`. More...

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

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

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__ ()

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)

Static Public Member Functions
None	registerCopyPostprocessingFunction (VoidMoleculeMolecularGraphFunctor func)

Properties
	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

Molecule.

Member Function Documentation

◆ reserveMemoryForAtoms()

None CDPL.Chem.Molecule.reserveMemoryForAtoms ( int num_atoms )

Reserves memory for num_atoms atoms.

Allows implementors to speed up the creation of molecules with a known large number of atoms.

Parameters

num_atoms The expected number of atoms for which memory shall be allocated in advance.

◆ reserveMemoryForBonds()

None CDPL.Chem.Molecule.reserveMemoryForBonds ( int num_bonds )

Reserves memory for num_bonds bonds.

Allows implementors to speed up the creation of molecules with a known large number of bonds.

Parameters

num_bonds The expected number of bonds for which memory shall be allocated in advance.

◆ addAtom()

Atom CDPL.Chem.Molecule.addAtom ( )

Creates a new atom and adds it to the molecule.

Note that this method does not create any bonds - the returned atom is always unconnected.

Returns: A reference to the newly created atom.

◆ addBond()

Bond CDPL.Chem.Molecule.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.

If a bond between the specified atoms already exists, then the existing bond will be returned. If a bond does not yet exist, a new bond will be created. The atom specified by atom1_idx becomes the start atom and the atom specified by atom2_idx the end atom of the newly created bond.

Parameters

atom1_idx	The zero-based index of the first atom of the bond.
atom2_idx	The zero-based index of the second atom of the bond.

Returns: A reference to the newly created or already existing bond between the specified atoms.

Exceptions

Base.IndexError if the number of atoms is zero or atom1_idx and/or atom2_idx is not in the range [0, getNumAtoms() - 1].

◆ removeAtom()

None CDPL.Chem.Molecule.removeAtom ( int idx )

Removes the atom at the specified index.

If the specified atom is connected to any other atoms of the molecule, the connecting bonds will also be removed.

Parameters

idx	The index of the atom to remove.

Exceptions

Base.IndexError if the number of atoms is zero or idx is not in the range [0, getNumAtoms() - 1].

◆ removeBond()

None CDPL.Chem.Molecule.removeBond ( int idx )

Removes the bond at the specified index.

Parameters

idx	The zero-based index of the bond to remove.

Exceptions

Base.IndexError if the number of bonds is zero or idx is not in the range [0, getNumBonds() - 1].

◆ copy() [1/2]

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

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

Parameters

mol	The molecule to copy.

Reimplemented in CDPL.Chem.BasicMolecule.

◆ copy() [2/2]

None CDPL.Chem.Molecule.copy ( 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.

Parameters

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

Reimplemented in CDPL.Chem.BasicMolecule.

◆ append() [1/2]

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

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

Parameters

mol	The molecule providing the atoms and bonds to append.

Note: Does not affect any properties.

Reimplemented in CDPL.Chem.BasicMolecule.

◆ append() [2/2]

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

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

Parameters

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

Note: Does not affect any properties.

Reimplemented in CDPL.Chem.BasicMolecule.

◆ remove()

None CDPL.Chem.Molecule.remove ( MolecularGraph molgraph )

Removes atoms and bonds referenced by the molecular graph molgraph that are part of this Molecule instance.

Parameters

molgraph The Chem.MolecularGraph instance specifying the atoms and bonds to remove.

Note: Does not affect any properties if this != &molgraph.

◆ assign() [1/2]

Molecule CDPL.Chem.Molecule.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 in CDPL.Chem.BasicMolecule.

◆ assign() [2/2]

Molecule CDPL.Chem.Molecule.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 in CDPL.Chem.BasicMolecule.

◆ getAtoms()

AtomSequence CDPL.Chem.Molecule.getAtoms ( )

Returns

Reimplemented from CDPL.Chem.MolecularGraph.

◆ getBonds()

BondSequence CDPL.Chem.Molecule.getBonds ( )

Returns

Reimplemented from CDPL.Chem.MolecularGraph.

◆ registerCopyPostprocessingFunction()

None CDPL.Chem.Molecule.registerCopyPostprocessingFunction ( VoidMoleculeMolecularGraphFunctor func )

static

Parameters

func

◆ invokeCopyPostprocessingFunctions()

None CDPL.Chem.Molecule.invokeCopyPostprocessingFunctions ( MolecularGraph src_molgraph )

Parameters

src_molgraph

◆ getAtom()

Atom CDPL.Chem.Molecule.getAtom ( int idx )

Returns a reference to the atom at index idx.

Parameters

idx	The zero-based index of the atom to return.

Returns: A reference to the atom at the specified index.

Exceptions

Base.IndexError if the number of atoms is zero or idx is not in the range [0, getNumAtoms() - 1].

Reimplemented from CDPL.Chem.MolecularGraph.

◆ containsAtom()

bool CDPL.Chem.Molecule.containsAtom ( Atom atom )

Tells whether the specified atom is part of this molecule.

Parameters

atom	The atom to look for.

Returns: True if atom is part of the molecule, and False otherwise.

Reimplemented from CDPL.Chem.MolecularGraph.

◆ getAtomIndex()

int CDPL.Chem.Molecule.getAtomIndex ( Atom atom )

Returns the index of the specified atom.

Parameters

atom	The atom for which to return the index.

Returns: The zero-based index of the specified atom.

Exceptions

Base.ItemNotFound if the specified atom is not part of the molecule.

Reimplemented from CDPL.Chem.MolecularGraph.

◆ getNumAtoms()

int CDPL.Chem.Molecule.getNumAtoms ( )

Returns the number of explicit atoms.

Returns: The number of explicit atoms.

Reimplemented from CDPL.Chem.MolecularGraph.

◆ orderAtoms()

None CDPL.Chem.Molecule.orderAtoms ( ForceField.InteractionFilterFunction2 func )

Parameters

func

Reimplemented from CDPL.Chem.MolecularGraph.

◆ getEntity()

Entity3D CDPL.Chem.Molecule.getEntity ( int idx )

Parameters

idx

Returns

Reimplemented from CDPL.Chem.MolecularGraph.

◆ getNumEntities()

int CDPL.Chem.Molecule.getNumEntities ( )

Returns

Reimplemented from CDPL.Chem.MolecularGraph.

◆ getBond()

Bond CDPL.Chem.Molecule.getBond ( int idx )

Returns a reference to the bond at index idx.

Parameters

idx	The zero-based index of the bond to return.

Returns: A reference to the bond at the specified index.

Exceptions

Base.IndexError if the number of bonds is zero or idx is not in the range [0, getNumBonds() - 1].

Reimplemented from CDPL.Chem.MolecularGraph.

◆ containsBond()

bool CDPL.Chem.Molecule.containsBond ( Bond bond )

Tells whether the specified bond is part of this molecule.

Parameters

bond	The bond to look for.

Returns: True if bond is part of the molecule, and False otherwise.

Reimplemented from CDPL.Chem.MolecularGraph.

◆ orderBonds()

None CDPL.Chem.Molecule.orderBonds ( BoolBond2Functor func )

Parameters

func

Reimplemented from CDPL.Chem.MolecularGraph.

◆ getBondIndex()

int CDPL.Chem.Molecule.getBondIndex ( Bond bond )

Returns the index of the specified bond.

Parameters

bond	The bond for which to return the index.

Returns: The zero-based index of the specified bond.

Exceptions

Base.ItemNotFound if the specified bond is not part of the molecule.

Reimplemented from CDPL.Chem.MolecularGraph.

◆ getNumBonds()

int CDPL.Chem.Molecule.getNumBonds ( )

Returns the number of explicit bonds.

Returns: The number of explicit bonds.

Reimplemented from CDPL.Chem.MolecularGraph.

◆ getstate()

tuple CDPL.Chem.Molecule.__getstate__ ( )

Parameters

arg1

Returns

◆ iadd() [1/2]

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

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

Parameters

mol	Specifies the second addend.

Returns: The updated Molecule instance self.

Reimplemented in CDPL.Chem.BasicMolecule.

◆ iadd() [2/2]

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

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

Parameters

molgraph Specifies the second addend.

Returns: The updated Molecule instance self.

Reimplemented in CDPL.Chem.BasicMolecule.

◆ isub()

Molecule CDPL.Chem.Molecule.__isub__ ( MolecularGraph molgraph )

Performs the in-place subtraction operation self -= molgraph.

Parameters

molgraph Specifies the subtrahend.

Returns: The updated Molecule instance self.

◆ contains() [1/3]

bool CDPL.Chem.Molecule.__contains__ ( Atom atom )

Returns the result of the membership test operation atom in self.

Parameters

atom	The value to test for membership.

Returns: The result of the membership test operation.

Reimplemented from CDPL.Chem.MolecularGraph.

◆ contains() [2/3]

bool CDPL.Chem.Molecule.__contains__ ( Bond bond )

Returns the result of the membership test operation bond in self.

Parameters

bond	The value to test for membership.

Returns: The result of the membership test operation.

Reimplemented from CDPL.Chem.MolecularGraph.

◆ contains() [3/3]

bool CDPL.Chem.Molecule.__contains__ ( Base.LookupKey key )

Returns the result of the membership test operation key in self.

Parameters

key	The value to test for membership.

Returns: The result of the membership test operation.

Reimplemented from CDPL.Chem.MolecularGraph.

◆ getitem()

Base.Any CDPL.Chem.Molecule.__getitem__ ( Base.LookupKey key )

Parameters

key

Returns

Reimplemented from CDPL.Chem.MolecularGraph.

◆ setitem()

None CDPL.Chem.Molecule.__setitem__	(	Base.LookupKey	key,
		Base.Any	value
	)

Parameters

key
value

Reimplemented from CDPL.Chem.MolecularGraph.

◆ delitem()

bool CDPL.Chem.Molecule.__delitem__ ( Base.LookupKey key )

Parameters

key

Returns

Reimplemented from CDPL.Chem.MolecularGraph.

◆ len()

int CDPL.Chem.Molecule.__len__ ( )

Returns

Reimplemented from CDPL.Chem.MolecularGraph.

Classes

Public Member Functions

Static Public Member Functions

Properties

Detailed Description

Member Function Documentation

◆ reserveMemoryForAtoms()

◆ reserveMemoryForBonds()

◆ addAtom()

◆ addBond()

◆ removeAtom()

◆ removeBond()

◆ copy() [1/2]

◆ copy() [2/2]

◆ append() [1/2]

◆ append() [2/2]

◆ remove()

◆ assign() [1/2]

◆ assign() [2/2]

◆ getAtoms()

◆ getBonds()

◆ registerCopyPostprocessingFunction()

◆ invokeCopyPostprocessingFunctions()

◆ getAtom()

◆ containsAtom()

◆ getAtomIndex()

◆ getNumAtoms()

◆ orderAtoms()

◆ getEntity()

◆ getNumEntities()

◆ getBond()

◆ containsBond()

◆ orderBonds()

◆ getBondIndex()

◆ getNumBonds()

◆ __getstate__()

◆ __iadd__() [1/2]

◆ __iadd__() [2/2]

◆ __isub__()

◆ __contains__() [1/3]

◆ __contains__() [2/3]

◆ __contains__() [3/3]

◆ __getitem__()

◆ __setitem__()

◆ __delitem__()

◆ __len__()

◆ getstate()

◆ iadd() [1/2]

◆ iadd() [2/2]

◆ isub()

◆ contains() [1/3]

◆ contains() [2/3]

◆ contains() [3/3]

◆ getitem()

◆ setitem()

◆ delitem()

◆ len()