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Inheritance#

Overview

Questions:

  • What is Inheritance?

  • Why should I use Inheritance in my code?

Objectives:

  • Understand the concepts behind Inheritance.

Inheritance#

Inheritance is the principle of extending a class to add capabilities without modifying the original class. We call the class that is being inherited the parent, and the class that is inheriting the child. The child class obtains the properties and behaviors of its parent unless it overrides them.

In coding terms, this means a class that inherits from a parent class will contain all of the data variables and methods of the parent class by default. The child class can either utilize the methods as is or they can override the methods to modify their behavior without affecting the parent class or any objects that have instantiated that class.

Using inheritance in code development creates a hierarchy of objects, which often improves the readability of your code. It also saves time end effort by avoiding duplicate code production, i.e., inheriting from classes that have similar behavior and modifying them instead of writting a new class from scratch.

We can utilize our Molecule class to create an example. Of note, we are using the version prior to applying name mangling. Since name mangling is applied based on the class it is defined in and not where it is called from, it will cause issues with inheritance.

class Molecule:
    def __init__(self, name, charge, symbols, coordinates):
        self.name = name
        self.charge = charge
        self.symbols = symbols
        self.coordinates = coordinates

    @property
    def symbols(self):
        return self._symbols
        
    @symbols.setter
    def symbols(self, symbols):
        self._symbols = symbols
        self._update_num_atoms()

    def _update_num_atoms(self):
        self.num_atoms = len(self.symbols)

    def __str__(self):
        return f'name: {self.name}\ncharge: {self.charge}\nsymbols: {self.symbols}\ncoordinates: {self.coordinates}\nnumber of atoms: {self.num_atoms}'

Currently the Molecule class takes in lists for both symbols and coordinates, relying on the indexes of each list to tie the appropriate atom symbol to it’s coordinates. Depending on your software’s needs, it may be more appropriate to store each atom as an object, allowing the Molecule class to store a list of atoms.

A simple Atom class may look like the following:

class Atom:
    def __init__(self, name, symbol, number, mass, coordinates):
        self.name = name
        self.symbol = symbol
        self.number = number
        self.mass = mass
        self.coordinates = coordinates

Given this Atom class, we have a few possibilities for incorporating it into the Molecule class. We could try and make the symbols, coordinates, and atoms variables optional and rely on keyword arguments to properly assign them in the constructor. Alternatively we could utilize inheritance to extend the behavior of the Molecule class while preserving its behavior.

To do so, we can create a new class called AtomMolecule. First, let us look at just the class definition and the constructor.

class AtomMolecule(Molecule):
    def __init__(self, name, charge, atoms):
        self.atoms = atoms
        super().__init__(name, charge, self.symbols, self.coordinates)

Notice that after the class name, we have now included (Molecule). Python uses the above syntax to specify inheritance. The class definition specifies that AtomMolecule should inherit the data and methods from its parent class Molecule.

As far as the constructor is concerned, we are not passing in a set of symbols or coordinates, as those are both derived from the set of atoms. We set the given list of atoms to the instance variable self.atoms. Finally, we are utilizing the __init__() method from the parent class. The syntax super(). is telling python where to look to find __init__(), so that it searches in the parent class.

If you try and run just this code and create an AtomMolecule, you will run into some errors. Even though we are inheriting from Molecule, AtomMolecule has no understanding of symbols, so we cannot use the constructor. A solution to this is to add a setter and property for atoms so we can control how atoms is updated. When atoms is updated, we need to update both symbols and coordinates. Here is one option for how to generate the values for symbols:

def _update_symbols(self):
        list_symbols = []
        for atom in self.atoms:
            list_symbols.append(atom.symbol)
        self._symbols = list_symbols

which iterates through each atom and appends the symbol to the list. Adding a similar function for coordinates creates the complete class.

class AtomMolecule(Molecule):
    def __init__(self, name, charge, atoms):
        self.atoms = atoms
        super().__init__(name, charge, self.symbols, self.coordinates)

    @property
    def atoms(self):
        return self._atoms

    @atoms.setter
    def atoms(self, atoms):
        self._atoms = atoms
        self._update_symbols()
        self._update_coordinates()

    def _update_symbols(self):
        list_symbols = []
        for atom in self.atoms:
            list_symbols.append(atom.symbol)
        self._symbols = list_symbols

    def _update_coordinates(self):
        list_coordinates = []
        for atom in self.atoms:
            list_coordinates.append(atom.coordinates)
        self.coordinates = list_coordinates

To test it we can create a set of atoms to pass into an AtomMolecule:

oxygen = Atom("oxygen", "O", 8, 15.999, [0,0,0])
hydrogen1 = Atom("hydrogen", "H", 1, 1.00784, [0,1,0])
hydrogen2 = Atom("hydrogen", "H", 1, 1.00784, [0,0,1])

mol1 = AtomMolecule(name='water molecule', charge=0.0, atoms=[oxygen, hydrogen1, hydrogen2])
print(mol1)

name: water molecule
charge: 0.0
symbols: ['O', 'H', 'H']
coordinates: [[0, 0, 0], [0, 1, 0], [0, 0, 1]]
number of atoms: 3

We can see in the output that AtomMolecule is correctly printing out the contents of the molecule, but we have not defined a __str__() method. Since AtomMolecule is inheriting from Molecule, it is inheriting all of the methods defined in Molecule. As a dictionary based language, when you call a method, python will first look in the object you are calling the method from. If it is unable to find the method, it will attempt to look in the parent class of the object. It will continue looking up through the inheritance tree until it either finds the method or runs out of parents to look in.

Similarly, we did not add a setter for symbols in AtomMolecule, yet the number of atoms was correctly set, since we inherited the property and setter methods from Molecule.

By creating AtomMolecule, we have extended the behavior of Molecule. Instead of only working with a set of symbols and coordinates, we are now capable of working with a set of Atom objects. Note that the external behavior/functionality of AtomMolecule is still identical to Molecule, but the internal operations are different to adjust to different input.

Composition and Aggregation#

When creating AtomMolecule, we used a type of object inside another object. We grouped a set of related data together through encapsulation, then utilized the created object in another class. There are two different forms that this can take, Composition and Aggregation. The main difference is the ownership of the object.

With the current example of AtomMolecule, we are creating Atoms and passing them into the object. If the AtomMolecule object was deleted, the defined Atoms would persist. This is an example of aggregation. The AtomMolecule object is using the Atoms, but it does not have ownership of them.

If, instead, we had the Molecule class create atoms from the set of symbols and coordinates, the Molecule class would own the Atoms, which would be an example of composition.

Key Points

  • Parent vs Child classes

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