Atom and Molecular Simulation in Java

This project provides a simulation of atoms and molecules using Java. The primary objective is to represent atoms, their bonds, and the construction of molecules using tree structures.

Components

1. Atom

The Atom class represents an individual atom. Each atom has:

• Element: Denotes the type of atom (e.g., H for Hydrogen, C for Carbon).
• List of bonds: Connections to other atoms.
• Valency: Represents the atom's combining power.

The class also provides a static map, VALENCY_MAP, which contains the valencies for various elements. The atom's valency is used to determine how many bonds it can form.

2. Bond

The Bond class represents a bond between two atoms. Each bond has:

• Child: The atom it's connected to.
• Weight: Represents the strength of the bond (single, double, or triple bond).

3. TreeMolecule

The TreeMolecule class represents a molecule using a tree structure. Each molecule has:

• First atom: The starting point of the molecule.

The class provides methods to:

• Add bonds between atoms
• Check if an atom is part of the molecule
• Generate the molecule's SMILES string and structural formula.

Usage

1. Create atoms using the Atom class.
2. Construct molecules using the TreeMolecule class.
3. Add bonds between atoms using the addBond method.
4. Check if an atom is part of a molecule using the contains method.
5. Generate the SMILES string and structural formula of the molecule using the smilesString and structuralFormula methods respectively.

Note

This is a basic simulation and might not cover all the intricacies of molecular chemistry. It's designed for educational purposes and to provide a foundation for further development. This work is inspired by the Algorithms and Data Structure coursework.