Update Molecule.java

package edu.bu.ec504.project;

import java.io.BufferedReader;

import java.io.FileReader;

import java.io.IOException;

import java.util.ArrayList;

import java.util.Arrays;

/**

 * Represents a molecule containing atoms and edges.

 */

public class Molecule {

    //FIELDS

    String moleculeName; // name of the molecule

    int numAtoms; // number of atoms in the molecule

    int numEdges; // number of edges in the molecule

    ArrayList<Atom> atomArrayList;  // list of atoms in the molecule

    int[] numElements; // array to store quantity of each element

    /**

     * Constructs a molecule by reading data from a file.

     * @param moleculeFile the file containing the molecule.

     */

    public Molecule(String MoleculeFile){

        //Init values

        numElements= new int [119];

        }

    }

    /**

     * Compare two molecules and check if they are isomorphic.

     * @param otherMolecule The molecule to compare with.

     * @return The first molecule if they are equal, otherwise null.

     */

    public Molecule areMoleculesEqual(Molecule otherMolecule) {

        // Compare the name of the molecule

        if (!this.moleculeName.equals(otherMolecule.moleculeName)) {

            return null; // Names are different, molecules are not equal

        }

    //FIELDS

    String moleculeName;

    int numAtoms;

    int numEdges;

    ArrayList<Atom> atomArrayList;

    int[] numElements; //stores quantity of each element

        // Compare the number of atoms

        if (this.numAtoms != otherMolecule.numAtoms) {

            return null; // Number of atoms is different, molecules are not equal

        }

        // Compare the number of edges

        if (this.numEdges != otherMolecule.numEdges) {

            return null; // Number of edges is different, molecules are not equal

        }

        // Compare the atom lists

        if (!this.atomArrayList.equals(otherMolecule.atomArrayList)) {

            return null; // Atom lists are different, molecules are not equal

        }

        // Compare the number of elements

        if (!Arrays.equals(this.numElements, otherMolecule.numElements)) {

            return null; // Number of elements is different, molecules are not equal

        }

        // If all comparisons passed, the molecules are equal

        return this;

    }

}