Added the atom class, which contains a hashmap(adj list) of connected atoms...

package edu.bu.ec504.project;

import java.util.ArrayList;

import java.util.HashMap;

import java.util.Map;

public class Atom {

    public Atom(String name,int elem){

        atomName = name;

        degree = 0;

        connected = new HashMap<>();

        elementType = elem;

    }

    public void addEdge(Atom i) {

        degree++;

        if(connected.containsKey(i.getName())) {

            connected.put(i.getName(),connected.get(i.getName())+1);

        }

        else

            connected.put(i.getName(),1);

    }

    public String getName() {

        return this.atomName;

    }

    private String atomName;

    private int elementType;

    private int degree;

    private Map<String,Integer> connected;

}

import java.io.BufferedReader;

import java.io.FileReader;

import java.io.IOException;

import java.util.ArrayList;

import java.util.HashMap;

import java.util.Map;

public class Molecule {

    //Current implementation is in the constructor

    public Molecule(String MoleculeFile){

        //Init values

        numElements= new int [119];

        pt.put("C",6);

        pt.put("H",1);

        //Creates dictionary of elements, want to add more to this & relocate this variable outside of molecule class to save space.

        int f,l;

        // Read and process input

        try (BufferedReader reader = new BufferedReader(new FileReader(MoleculeFile))) {

        try (BufferedReader reader = new BufferedReader(new FileReader(MoleculeFile))) { //Might want to move reader outside molecule class in the future to save space

            String line;

            moleculeName = reader.readLine(); //Reads name

            numAtoms = Integer.parseInt(reader.readLine()); //Reads # of atoms

            atomArrayList = new ArrayList<Atom>(numAtoms); //Creates arraylist of atoms

            for(int ii = 0; ii <numAtoms;ii++) {

                line = reader.readLine();

                int num = pt.get(line); //Looks up element in Periodic Table

                atomArrayList.add(new Atom(line+numElements[num],num)); //Adds atom to list (with index)

                numElements[num]++; //Increases count for specific atom

            }

            while ((line = reader.readLine()) != null) {

                numEdges++; //Counts # of edges

                f = Integer.parseInt(line.substring(0,1)); //Reads first atom in edge

                l = Integer.parseInt(line.substring(2)); //Reads second atom in edge

                atomArrayList.get(f).addEdge(atomArrayList.get(l)); //Marks edge for first atom

                atomArrayList.get(l).addEdge(atomArrayList.get(f)); //Marks edge for second atom

                System.out.println(line); // TODO: we can change this to parse the file rather than print it

            }

        } catch (IOException e) {

    //FIELDS

    String moleculeName;

    Map <String, Integer> pt = new HashMap<String,Integer>();

    int numAtoms;

    int numEdges;

    // numDegrees for each atom;

    ArrayList<Atom> atomArrayList;

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