Abstract base class representing a chemical atom and its bonded neighborhood. More...

Inheritance diagram for CDPL.Chem.Atom:

Classes
class	AtomSequence

class	BondSequence

Public Member Functions
None	__init__ ()
	Initializes the `Atom` instance.

Molecule	getMolecule ()
	Returns a reference to the parent molecule. More...

Bond	getBondToAtom (Atom atom)
	Returns a reference to the bond that connects this atom to the argument atom. More...

Bond	findBondToAtom (Atom atom)
	Returns a reference to the bond that connects this atom to the argument atom. More...

int	getIndex ()
	Returns the index of the atom in its parent molecule. More...

Atom	assign (Atom atom)
	Assignment operator that replaces the current set of properties with the properties of atom. More...

AtomSequence	getAtoms ()

BondSequence	getBonds ()

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

bool	containsAtom (Atom atom)
	Tells whether this atom and the specified atom are connected by a bond. More...

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

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

None	orderAtoms (BoolAtom2Functor func)
	Orders the atoms according to criteria implemented by the provided atom comparison function. More...

Entity3D	getEntity (int idx)
	Returns a reference to the entity at index idx. More...

int	getNumEntities ()
	Returns the number of stored Chem.Entity3D objects. More...

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

bool	containsBond (Bond bond)
	Tells whether the specified bond is incident to this atom. More...

None	orderBonds (BoolBond2Functor func)
	Orders the bonds according to criteria implemented by the provided bond comparison function. More...

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

int	getNumBonds ()
	Returns the number of incident bonds. 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.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)
	Returns the value of the property specified by key. More...

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)

Properties
	molecule = property(getMolecule)

	index = property(getIndex)

	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

Abstract base class representing a chemical atom and its bonded neighborhood.

Atom combines the per-atom property storage inherited from Chem.Entity3D (and via it Base.PropertyContainer) with two adjacency views: a Chem.AtomContainer over the connected neighbor atoms and a Chem.BondContainer over the incident bonds, in matching order. Concrete implementation (Chem.BasicAtom) instances are created, owned and managed by a parent Chem.Molecule instance.

Member Function Documentation

◆ getMolecule()

Molecule CDPL.Chem.Atom.getMolecule ( )

Returns a reference to the parent molecule.

Returns: A reference to the parent molecule.

◆ getBondToAtom()

Bond CDPL.Chem.Atom.getBondToAtom ( Atom atom )

Returns a reference to the bond that connects this atom to the argument atom.

Parameters

atom	The adjacent atom for which to return the connecting bond.

Returns: A reference to the bond connecting this atom and the argument atom.

Exceptions

Base.ItemNotFound if the argument atom is not connected to this atom.

◆ findBondToAtom()

Bond CDPL.Chem.Atom.findBondToAtom ( Atom atom )

Returns a reference to the bond that connects this atom to the argument atom.

Parameters

atom	The adjacent atom for which to return a reference to the connecting bond.

Returns: A reference to the bond that connects this atom to the argument atom, or None if the argument atom is not connected.

◆ getIndex()

int CDPL.Chem.Atom.getIndex ( )

Returns the index of the atom in its parent molecule.

Returns: The zero-based index of the atom.

◆ assign()

Atom CDPL.Chem.Atom.assign ( Atom atom )

Assignment operator that replaces the current set of properties with the properties of atom.

Parameters

atom	The atom whose properties get copied.

Returns: self

Reimplemented in CDPL.Chem.BasicAtom.

◆ getAtom()

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

Returns a reference to the connected atom at index idx.

Parameters

idx	The index of the atom to return.

Returns: A reference to the connected atom at index idx.

Exceptions

Base.IndexError if idx is not in the range [0, getNumAtoms()).

Note: The order of connected atoms corresponds to the order of connecting bonds.

Reimplemented from CDPL.Chem.AtomContainer.

◆ containsAtom()

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

Tells whether this atom and the specified atom are connected by a bond.

Parameters

atom	The atom to test for adjacency.

Returns: True if the argument atom is connected to this atom, and False otherwise.

Reimplemented from CDPL.Chem.AtomContainer.

◆ getAtomIndex()

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

Returns the index of the specified connected atom.

Parameters

atom	The connected 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 connected to this atom.

Reimplemented from CDPL.Chem.AtomContainer.

◆ getNumAtoms()

int CDPL.Chem.Atom.getNumAtoms ( )

Returns the number of connected atoms.

Equivalent to getNumBonds().

Returns: The number of connected atoms.

Reimplemented from CDPL.Chem.AtomContainer.

◆ orderAtoms()

None CDPL.Chem.Atom.orderAtoms ( BoolAtom2Functor func )

Orders the atoms according to criteria implemented by the provided atom comparison function.

Parameters

func	The atom comparison function implementing the applied ordering criteria.

Reimplemented from CDPL.Chem.AtomContainer.

◆ getEntity()

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

Returns a reference to the entity at index idx.

Forwards to getAtom() and exists to satisfy the Chem.Entity3DContainer interface.

Parameters

idx	The zero-based entity index.

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

Exceptions

Base.IndexError if idx is not in the range [0, getNumAtoms()).

Reimplemented from CDPL.Chem.AtomContainer.

◆ getNumEntities()

int CDPL.Chem.Atom.getNumEntities ( )

Returns the number of stored Chem.Entity3D objects.

Forwards to getNumAtoms() and exists to satisfy the Chem.Entity3DContainer interface.

Returns: The number of contained atoms.

Reimplemented from CDPL.Chem.AtomContainer.

◆ getBond()

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

Returns a reference to the incident bond at index idx.

Parameters

idx	The index of the incident bond to return.

Returns: A reference to the incident bond at index idx.

Exceptions

Base.IndexError if idx is not in the range [0, getNumBonds()).

Note: The order of incident bonds corresponds to the order of connected atoms.

Reimplemented from CDPL.Chem.BondContainer.

◆ containsBond()

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

Tells whether the specified bond is incident to this atom.

Parameters

bond	The bond to test for incidence.

Returns: True if the argument bond is incident to this atom, and False otherwise.

Reimplemented from CDPL.Chem.BondContainer.

◆ orderBonds()

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

Orders the bonds according to criteria implemented by the provided bond comparison function.

Parameters

func	The bond comparison function implementing the applied ordering criteria.

Reimplemented from CDPL.Chem.BondContainer.

◆ getBondIndex()

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

Returns the index of the specified incident 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 incident to this atom.

Reimplemented from CDPL.Chem.BondContainer.

◆ getNumBonds()

int CDPL.Chem.Atom.getNumBonds ( )

Returns the number of incident bonds.

Equivalent to getNumAtoms().

Returns: The number of incident bonds.

Reimplemented from CDPL.Chem.BondContainer.

◆ contains() [1/3]

bool CDPL.Chem.Atom.__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.Entity3D.

◆ contains() [2/3]

bool CDPL.Chem.Atom.__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.BondContainer.

◆ contains() [3/3]

bool CDPL.Chem.Atom.__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.AtomContainer.

Classes

Public Member Functions

Properties

Detailed Description

Member Function Documentation

◆ getMolecule()

◆ getBondToAtom()

◆ findBondToAtom()

◆ getIndex()

◆ assign()

◆ getAtom()

◆ containsAtom()

◆ getAtomIndex()

◆ getNumAtoms()

◆ orderAtoms()

◆ getEntity()

◆ getNumEntities()

◆ getBond()

◆ containsBond()

◆ orderBonds()

◆ getBondIndex()

◆ getNumBonds()

◆ __contains__() [1/3]

◆ __contains__() [2/3]

◆ __contains__() [3/3]

◆ contains() [1/3]

◆ contains() [2/3]

◆ contains() [3/3]