Describes an electron system of a molecule in terms of involved atoms and their electron contributions. More...

Inheritance diagram for CDPL.Chem.ElectronSystem:

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

None	__init__ (ElectronSystem elec_sys)
	Initializes a copy of the ElectronSystem instance elec_sys. More...

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

ElectronSystem	assign (ElectronSystem elec_sys)
	Replaces the current state of self with a copy of the state of the ElectronSystem instance elec_sys. More...

bool	addAtom (Atom atom, int elec_contrib)
	Extends the electron system by the specified atom and its electron contributions. More...

bool	addAtoms (ElectronSystem elec_sys)
	Adds the atoms and associated electron contributions in the electron system elec_sys to this system. More...

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

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

None	clear ()
	Removes all atoms.

None	swap (ElectronSystem elec_sys)
	Exchanges the state of this electron system with the state of the system elec_sys. More...

int	getNumElectrons ()
	Returns the total number of electrons contributed by the involved atoms. More...

int	getElectronContrib (Atom atom)
	Returns the number of electrons contributed by the specified atom. More...

int	getElectronContrib (int atom)
	Returns the number of electrons contributed by the specified atom. More...

None	setElectronContrib (Atom atom, int elec_contrib)
	Changes the number of electrons that are contributed by the specified atom. More...

None	setElectronContrib (int atom, int elec_contrib)
	Changes the number of electrons that are contributed by the specified atom. More...

None	merge (ElectronSystem elec_sys)
	Merges the atoms and associated electron contributions in the electron system elec_sys with this system. More...

bool	overlaps (ElectronSystem elec_sys)
	Checks if the electron system shares at least one atom with the system elec_sys. More...

bool	contains (ElectronSystem elec_sys)
	Checks if all atoms in the electron system elec_sys are also part of this electron system. More...

bool	connected (ElectronSystem elec_sys, BondContainer bonds)
	Checks if the atom sets of the electron systems do not intersect but are linked by at least one bond. More...

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

Atom	__getitem__ (int idx)

int	__len__ ()

Public Member Functions inherited from CDPL.Chem.AtomContainer
Atom	getAtom (int idx)
	Returns a reference to the atom at index idx. More...

bool	containsAtom (Atom atom)
	Tells whether the specified Chem.Atom instance is stored in this container. More...

int	getAtomIndex (Atom atom)
	Returns the index of the specified Chem.Atom instance in this container. More...

int	getNumAtoms ()
	Returns the number of stored Chem.Atom objects. More...

None	orderAtoms (ForceField.InteractionFilterFunction2 func)
	Orders the stored 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...

Properties
	objectID = property(getObjectID)

	numElectrons = property(getNumElectrons)

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

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

	numEntities = property(getNumEntities)

Detailed Description

Describes an electron system of a molecule in terms of involved atoms and their electron contributions.

Constructor & Destructor Documentation

◆ init()

None CDPL.Chem.ElectronSystem.__init__ ( ElectronSystem elec_sys )

Initializes a copy of the ElectronSystem instance elec_sys.

Parameters

elec_sys The ElectronSystem instance to copy.

Member Function Documentation

◆ getObjectID()

int CDPL.Chem.ElectronSystem.getObjectID ( )

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

Different Python ElectronSystem 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 ElectronSystem 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.

Reimplemented from CDPL.Chem.Entity3DContainer.

◆ assign()

ElectronSystem CDPL.Chem.ElectronSystem.assign ( ElectronSystem elec_sys )

Replaces the current state of self with a copy of the state of the ElectronSystem instance elec_sys.

Parameters

elec_sys The ElectronSystem instance to copy.

Returns: self

◆ addAtom()

bool CDPL.Chem.ElectronSystem.addAtom	(	Atom	atom,
		int	elec_contrib
	)

Extends the electron system by the specified atom and its electron contributions.

Parameters

atom	The atom to add.
elec_contrib	The number of electrons contributed by the added atom.

Returns: True if the atom was not already involved in this electron system and False, otherwise.

Note: If the atom is already part of the system no changes will be made.

◆ addAtoms()

bool CDPL.Chem.ElectronSystem.addAtoms ( ElectronSystem elec_sys )

Adds the atoms and associated electron contributions in the electron system elec_sys to this system.

The method is equivalent to repeatedly calling addAtom() for each atom in elec_sys.

Parameters

elec_sys The electron system to add.

Returns: True if the electron system was extended by atoms from elec_sys and False, otherwise.

◆ removeAtom() [1/2]

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

Removes the atom at the specified index.

Parameters

idx	The zero-based 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].

◆ removeAtom() [2/2]

bool CDPL.Chem.ElectronSystem.removeAtom ( Atom atom )

Removes the specified atom.

Parameters

atom	The atom to remove.

Returns: True if the atom was part of the electron system and has been removed, and False otherwise.

◆ swap()

None CDPL.Chem.ElectronSystem.swap ( ElectronSystem elec_sys )

Exchanges the state of this electron system with the state of the system elec_sys.

Parameters

elec_sys The other ElectronSystem instance.

◆ getNumElectrons()

int CDPL.Chem.ElectronSystem.getNumElectrons ( )

Returns the total number of electrons contributed by the involved atoms.

Returns: The total electron count of this system.

◆ getElectronContrib() [1/2]

int CDPL.Chem.ElectronSystem.getElectronContrib ( Atom atom )

Returns the number of electrons contributed by the specified atom.

Parameters

atom	The atom for which to return the contributed electron count.

Returns: The number of electrons contributed by the specified atom.

Exceptions

Base.ItemNotFound if the specified atom is not part of the electron system.

◆ getElectronContrib() [2/2]

int CDPL.Chem.ElectronSystem.getElectronContrib ( int atom )

Returns the number of electrons contributed by the specified atom.

Parameters

atom	The atom for which to return the contributed electron count.

Returns: The number of electrons contributed by the specified atom.

Exceptions

Base.ItemNotFound if the specified atom is not part of the electron system.

◆ setElectronContrib() [1/2]

None CDPL.Chem.ElectronSystem.setElectronContrib	(	Atom	atom,
		int	elec_contrib
	)

Changes the number of electrons that are contributed by the specified atom.

Parameters

atom	The atom for which to update the electron contribution.
elec_contrib	The number of electrons contributed by the specified atom.

Exceptions

Base.ItemNotFound if the specified atom is not part of the electron system.

◆ setElectronContrib() [2/2]

None CDPL.Chem.ElectronSystem.setElectronContrib	(	int	atom,
		int	elec_contrib
	)

Changes the number of electrons that are contributed by the specified atom.

Parameters

atom	The atom for which to update the electron contribution.
elec_contrib	The number of electrons contributed by the specified atom.

Exceptions

Base.ItemNotFound if the specified atom is not part of the electron system.

◆ merge()

None CDPL.Chem.ElectronSystem.merge ( ElectronSystem elec_sys )

Merges the atoms and associated electron contributions in the electron system elec_sys with this system.

For atoms that are present in both electron systems, the resulting electron contribution will be the sum of their contributions to the respective systems!

Parameters

elec_sys The electron system to merge.

◆ overlaps()

bool CDPL.Chem.ElectronSystem.overlaps ( ElectronSystem elec_sys )

Checks if the electron system shares at least one atom with the system elec_sys.

Parameters

elec_sys The electron system to check for atom set intersection.

Returns: True if at least one atom in elec_sys is also part of this electron system and False, otherwise.

◆ contains()

bool CDPL.Chem.ElectronSystem.contains ( ElectronSystem elec_sys )

Checks if all atoms in the electron system elec_sys are also part of this electron system.

Parameters

elec_sys The electron system to check for atom set containment.

Returns: True if all atoms in elec_sys are also part of this electron system and False, otherwise.

◆ connected()

bool CDPL.Chem.ElectronSystem.connected	(	ElectronSystem	elec_sys,
		BondContainer	bonds
	)

Checks if the atom sets of the electron systems do not intersect but are linked by at least one bond.

Parameters

elec_sys	The electron system to check.
bonds	The set of available bonds.

Returns: True if the electron systems do not share any atoms but are linked by at least one bond and False, otherwise.

◆ contains()

bool CDPL.Chem.ElectronSystem.__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.

◆ getitem()

Atom CDPL.Chem.ElectronSystem.__getitem__ ( int idx )

Parameters

idx

Returns

Reimplemented from CDPL.Chem.AtomContainer.

◆ len()

int CDPL.Chem.ElectronSystem.__len__ ( )

Returns

Reimplemented from CDPL.Chem.AtomContainer.

Public Member Functions

Properties

Detailed Description

Constructor & Destructor Documentation

◆ __init__()

Member Function Documentation

◆ getObjectID()

◆ assign()

◆ addAtom()

◆ addAtoms()

◆ removeAtom() [1/2]

◆ removeAtom() [2/2]

◆ swap()

◆ getNumElectrons()

◆ getElectronContrib() [1/2]

◆ getElectronContrib() [2/2]

◆ setElectronContrib() [1/2]

◆ setElectronContrib() [2/2]

◆ merge()

◆ overlaps()

◆ contains()

◆ connected()

◆ __contains__()

◆ __getitem__()

◆ __len__()

◆ init()

◆ contains()

◆ getitem()

◆ len()