Merge branch 'master' into '8-implement-subgraph-search' (50deac6c) · Commits · EC504 Spring 2024 Group Projects / Group4

src/GUI.java

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		import edu.bu.ec504.project.Molecule;

		import javax.imageio.ImageIO;
		import javax.swing.*;
		import java.awt.*;
		import java.awt.event.*;
		import java.io.*;
		import java.net.*;
		import java.awt.image.BufferedImage;
		import java.util.ArrayList;
		import java.util.Arrays;

		public class GUI extends JFrame {
		private JTextArea outputTextArea;
		private JButton chooseFileButton;
		private JButton addMoleculeButton;
		private JButton findMoleculeButton;
		private JButton statisticsButton;
		private JButton displayMoleculeButton;
		private JButton findSubgraphButton;
		private JButton downloadPubChemButton;
		private JTextField filePathField;
		private static MDB moleculeDb;
		private Socket clientSocket;
		private PrintWriter writer;
		private BufferedReader reader;

		/**
		* GUI constructor
		*/
		public GUI() {
		// Set up the JFrame
		setTitle("Molecule Database");
		setDefaultCloseOperation(EXIT_ON_CLOSE);
		setLayout(new BorderLayout());
		getContentPane().setBackground(Color.BLACK);

		// Create components
		outputTextArea = new JTextArea(20, 50); // the text area for all outputs
		outputTextArea.setBackground(Color.BLACK); // Set the background color of the text area
		outputTextArea.setForeground(Color.WHITE); // Set the text color
		JScrollPane scrollPane = new JScrollPane(outputTextArea);
		chooseFileButton = new JButton("Choose File");
		downloadPubChemButton = new JButton("Download PubChem");
		addMoleculeButton = new JButton("Add Molecule");
		findMoleculeButton = new JButton("Find Molecule");
		findSubgraphButton = new JButton("Find Subgraph");
		statisticsButton = new JButton("Database Statistics");
		displayMoleculeButton = new JButton("Display Molecule");
		filePathField = new JTextField(20); // to show the file path
		JLabel filePathLabel = new JLabel("File Path:");
		filePathLabel.setForeground(Color.WHITE); // Set the text color
		filePathField.setBackground(Color.WHITE); // Set the background color of the text field
		filePathField.setForeground(Color.BLACK); // Set the text color

		// Add components to the JFrame
		JPanel controlPanel = new JPanel();
		controlPanel.setBackground(Color.BLACK);
		controlPanel.add(chooseFileButton);
		controlPanel.add(downloadPubChemButton);
		controlPanel.add(addMoleculeButton);
		controlPanel.add(findMoleculeButton);
		controlPanel.add(findSubgraphButton);
		controlPanel.add(displayMoleculeButton);
		controlPanel.add(statisticsButton);
		controlPanel.add(filePathLabel);
		controlPanel.add(filePathField);
		add(controlPanel, BorderLayout.NORTH); // to show the control panel (e.g., buttons)
		add(scrollPane, BorderLayout.CENTER); // to show the printed output text area

		// Initialize molecule database
		moleculeDb = new MDB(outputTextArea);

		// Action listener for Choose File button
		chooseFileButton.addActionListener(new ActionListener() {
		@Override
		public void actionPerformed(ActionEvent e) {
		// Create a file chooser
		JFileChooser fileChooser = new JFileChooser();
		fileChooser.setDialogTitle("Choose a file");
		int result = fileChooser.showOpenDialog(GUI.this);
		// If a file is selected, set its path in the molecule path field
		if (result == JFileChooser.APPROVE_OPTION) {
		File selectedFile = fileChooser.getSelectedFile();
		filePathField.setText(selectedFile.getAbsolutePath());
		}
		}
		});

		// Action listener for Download PubChem button
		downloadPubChemButton.addActionListener(new ActionListener() {
		@Override
		public void actionPerformed(ActionEvent e) {
		// Get the molecule path from the text field
		// Input format for the file path is "start,end" where 'start' and 'end' are the starting and ending CID indices of molecules in PubChem
		// For example, enter 12,24 to download molecules 12-24
		String twoIndices = filePathField.getText();

		// Repurposed moleculePath should be in format "start,end"
		String[] indexes = twoIndices.split(",");

		if (indexes.length == 2) {
		String start = indexes[0];
		String end = indexes[1];
		moleculeDb.downloadPubChem(start, end);
		} else {
		outputTextArea.append("Invalid Input" + "\n\n");
		}
		}
		});

		// Action listener for Add Molecule button
		addMoleculeButton.addActionListener(new ActionListener() {
		@Override
		public void actionPerformed(ActionEvent e) {
		// Get the molecule path from the text field
		String moleculePath = filePathField.getText();
		// Execute the addMolecule command
		moleculeDb.addMolecule(new Molecule(moleculePath));
		// Display output
		outputTextArea.append("Molecule added: " + moleculePath + "\n\n");
		}
		});

		// Action listener for Find Molecule button
		findMoleculeButton.addActionListener(new ActionListener() {
		@Override
		public void actionPerformed(ActionEvent e) {
		// Get the molecule path from the text field
		String moleculePath = filePathField.getText();
		// Execute the findMolecule command
		Molecule molecule = moleculeDb.findMolecule(new Molecule(moleculePath));
		if (molecule == null) {
		outputTextArea.append("NO EXACT MATCH FOUND" + "\n\n");
		molecule= moleculeDb.similarMolecule(new Molecule(moleculePath));
		if(molecule!=null)
		{
		// Perform most similar function
		outputTextArea.append(molecule.moleculeName + " is the most similar" + "\n\n");
		}
		} else {
		outputTextArea.append("FOUND\n\n");
		}
		}
		});

		// Action listener for Find Subgraph button
		findSubgraphButton.addActionListener(new ActionListener() {
		@Override
		public void actionPerformed(ActionEvent e) {
		String moleculePath = filePathField.getText();
		ArrayList<Molecule> mList = moleculeDb.findSubgraph(new Molecule(moleculePath));
		if (mList.isEmpty())
		outputTextArea.append("No subraphs found" + "\n\n");
		else
		for (Molecule m : mList)
		outputTextArea.append("Subgraph found: " + m.moleculeName + "\n\n");
		}
		});

		// Action listener for Display Molecule button
		displayMoleculeButton.addActionListener(new ActionListener() {
		@Override
		public void actionPerformed(ActionEvent e) {

		// Get the API for the molecule
		String moleculePath = filePathField.getText();
		String moleculeName = null;

		try (BufferedReader reader = new BufferedReader(new FileReader(moleculePath))) {
		moleculeName = reader.readLine(); // Read the first line to get the molecule name

		} catch (IOException ex) {
		System.err.println("Error reading the file: " + ex.getMessage());
		outputTextArea.append("Error reading the file:" + ex.getMessage() + "\n\n");
		return;
		}

		// https://cactus.nci.nih.gov/chemical/structure/isopropanol/image
		String imageURL = "https://cactus.nci.nih.gov/chemical/structure/" + moleculeName + "/image";

		try {
		// Download the image from the URL
		URL url = new URL(imageURL);
		BufferedImage image = ImageIO.read(url);

		// Create a JLabel to display the image
		JLabel imageLabel = new JLabel(new ImageIcon(image));

		// Create a new JFrame to display the image
		JFrame imageFrame = new JFrame("Molecule Display");
		imageFrame.getContentPane().add(imageLabel, BorderLayout.CENTER);
		imageFrame.setSize(400, 400);
		imageFrame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
		imageFrame.setLocationRelativeTo(null); // Center the frame
		imageFrame.setVisible(true); // Make the frame visible

		} catch (IOException ex) {
		ex.printStackTrace();
		outputTextArea.append("Molecule display failed. The provided molecule name may be incorrect or does not match any records in the PubChem database.\n\n");
		}
		}
		});

		// Action listener for Statistics button
		statisticsButton.addActionListener(new ActionListener() {
		@Override
		public void actionPerformed(ActionEvent e) {
		moleculeDb.printDb(); // print the content of database
		}
		});

		// Window listener to save the database before closing the GUI
		addWindowListener(new WindowAdapter() {
		@Override
		public void windowClosing(WindowEvent e) {
		try {
		moleculeDb.save("molecule.db"); // save the database
		} catch (IOException ex) {
		ex.printStackTrace();
		}
		}
		});

		// Connect to client or server
		connectToServerOrClient();

		// Display the JFrame
		pack();
		setLocationRelativeTo(null);
		setVisible(true);

		// Load database on startup
		try {
		initDb("molecule.db");
		} catch (IOException e) {
		e.printStackTrace();
		}

		}

		/**
		* Run as client or server
		*/
		private void connectToServerOrClient() {
		try {
		// Run the client side
		clientSocket = new Socket("localhost", 5000);
		writer = new PrintWriter(clientSocket.getOutputStream(), true);
		reader = new BufferedReader(new InputStreamReader(clientSocket.getInputStream()));
		} catch (ConnectException e) {
		// Run the server side
		try {
		ServerSocket serverSocket = new ServerSocket(5000);
		serverSocket.setSoTimeout(60 * 1000);

		// Close the server socket after accepting the connection
		serverSocket.close();

		} catch (IOException ex) {
		ex.printStackTrace();
		}
		} catch (IOException ex) {
		ex.printStackTrace();
		}
		}

		/**
		* Initialize a database
		*/
		public void initDb(String dbName) throws IOException {
		// Load the database
		moleculeDb = new MDB(outputTextArea);
		File dbFile = new File(dbName);
		if (dbFile.exists()) {
		moleculeDb.load(dbName);
		}
		}

		/**
		* Main function
		*/
		public static void main(String[] args) {
		SwingUtilities.invokeLater(new Runnable() {
		@Override
		public void run() {
		GUI gui = new GUI();
		}
		});
		}
		}

src/MDB.java

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		import edu.bu.ec504.project.Atom;
		import edu.bu.ec504.project.Molecule;

		import javax.swing.*;
		import java.io.*;
		import java.util.ArrayList;
		import java.util.HashMap;
		import java.util.Map;
		import java.util.List;

		/**
		* A class represents the molecule database that works with the GUI.
		*/
		public class MDB {

		public HashMap<Integer, ArrayList<Molecule>> db; // Molecule database
		public JTextArea outputTextArea; // Reference to the text area in the GUI

		/**
		* Constructs a database
		*/
		public MDB(JTextArea outputTextArea) {
		this.db = new HashMap<>();
		this.outputTextArea = outputTextArea;
		}

		/**
		* Print database statistics to GUI
		*/
		public void printDb() {
		// Print number of molecules
		int size = 0;
		for (ArrayList<Molecule> molecules : db.values()) {
		size += molecules.size();
		}
		outputTextArea.append("# of molecules: " + size + "\n\n");

		if (size == 0)
		return; // if database is empty, exit early

		// Print the list of molecules
		outputTextArea.append("List of molecules: " + "\n\n");
		for (Integer atomCount : this.db.keySet()) {
		ArrayList<Molecule> moleculesWithSameNumAtoms = this.db.get(atomCount);
		for (Molecule molecule : moleculesWithSameNumAtoms) {
		outputTextArea.append("Molecule name: " + molecule.moleculeName + "\n");
		outputTextArea.append("# of atoms: " + atomCount.toString() + "\n\n");
		}
		}

		// Print the largest and biggest molecules
		int maxAtoms = Integer.MIN_VALUE;
		int minAtoms = Integer.MAX_VALUE;
		Molecule largestMolecule = null;
		Molecule smallestMolecule = null;
		for (Map.Entry<Integer, ArrayList<Molecule>> entry : db.entrySet()) {
		int numAtoms = entry.getKey();
		if (numAtoms > maxAtoms) {
		maxAtoms = numAtoms;
		largestMolecule = entry.getValue().get(0); // only print 1 representative molecule
		}
		if (numAtoms < minAtoms) {
		minAtoms = numAtoms;
		smallestMolecule = entry.getValue().get(0); // only print 1 representative molecule
		}
		}
		outputTextArea.append("Smallest molecule: " + smallestMolecule.moleculeName + "\n");
		outputTextArea.append("Largest molecule: " + largestMolecule.moleculeName + "\n\n");

		}

		/**
		* Add a new molecule into the database
		*/
		public void addMolecule(Molecule molecule) {
		if (molecule == null) {
		outputTextArea.append("molecule == null" + "\n\n");
		return;
		}
		int numAtoms = molecule.getNumAtoms();
		//test if molecule has an unconnected atom
		for(Atom a: molecule.getAtomArrayList())
		if(a.connected.isEmpty()) {
		outputTextArea.append("Error: molecule file is incorrect (contains unconnected atom)" + "\n\n");
		return;
		}

		if (this.db.containsKey(numAtoms)) {
		this.db.get(numAtoms).add(molecule);
		} else {
		ArrayList<Molecule> moleculesWithSameNumAtoms = new ArrayList<>();
		moleculesWithSameNumAtoms.add(molecule);
		this.db.put(numAtoms, moleculesWithSameNumAtoms);
		}
		}

		/**
		* Find isomorphic molecule from the database
		*/
		public Molecule findMolecule(Molecule molecule) {
		// Retrieve the partitioned array list based on the number of atoms
		int numAtoms = molecule.getNumAtoms();
		if (!db.containsKey(numAtoms)) {
		outputTextArea.append("No ArrayList with correct # of atoms" + "\n\n");
		return null;
		}
		ArrayList<Molecule> moleculesWithSameNumAtoms = db.get(numAtoms);

		// Iterate through the array list of molecules with the same number of atoms
		for (Molecule dbMolecule : moleculesWithSameNumAtoms) {
		outputTextArea.append(dbMolecule.moleculeName + " vs " + molecule.moleculeName + "\n\n");
		Molecule result = dbMolecule.areMoleculesEqual(molecule);
		if (result != null) {
		return result; // Return the isomorphic molecule
		}
		}
		return null; // Return null if molecule not found
		}

		/**
		* Find the most similar Molecule from the database
		*/
		public Molecule similarMolecule(Molecule molecule) {

		// If an exact match is not found then find the most similar
		int maxResult=0;
		Molecule similar=null;
		for (Map.Entry<Integer, ArrayList<Molecule>> entry : db.entrySet()) {
		// Access the key and value of each entry
		Integer numberAtoms = entry.getKey();

		//only check for similarity if they have similar number of atoms within tolerance of 100
		if( (molecule.getNumAtoms()-100)<numberAtoms && numberAtoms<(molecule.getNumAtoms()+100) )
		{
		for (Molecule dbMolecule : db.get(numberAtoms)) {
		int res = dbMolecule.mostSimilar(molecule);
		if (res > maxResult) {
		similar = dbMolecule; // save the similar molecule
		maxResult = res;
		}
		}
		}
		}

		return similar;
		}

		/**
		* Find subgraph
		*/
		public ArrayList<Molecule> findSubgraph(Molecule molecule) {
		ArrayList<Molecule> returnList = new ArrayList<Molecule>();
		int startingNumber = molecule.getNumAtoms();
		for(int ii : db.keySet()) {
		if (ii >= startingNumber) {
		for(Molecule m: db.get(ii)) {
		if(m.isSubGraphPresent(molecule) != null) {
		returnList.add(m);
		outputTextArea.append(m.moleculeName + "\n\n");
		}
		}
		}
		}

		return returnList;
		}

		/**
		* Download Molecules from Pubchem in range [start, end]
		*/
		public void downloadPubChem(String start, String end) {
		String scriptPath = "testcases/downloadPubChem.py";
		List<String> filenames = new ArrayList<>();

		try {
		// build Python script call
		ProcessBuilder builder = new ProcessBuilder("python", scriptPath, start, end);
		Process process = builder.start();

		// get Python filename output
		InputStream stdout = process.getInputStream();
		BufferedReader reader = new BufferedReader(new InputStreamReader(stdout));

		String file;
		while ((file = reader.readLine()) != null) {
		outputTextArea.append("file created: " + file + "\n\n");
		filenames.add(file);
		}

		int exitCode = process.waitFor();
		outputTextArea.append("Exited with code: " + exitCode + "\n\n");

		// add created files to the database
		for (String filename : filenames) {
		this.addMolecule(new Molecule(filename));
		}

		} catch (Exception e) {
		outputTextArea.append("Error downloading from PubChem" + "\n\n");
		e.printStackTrace();
		}
		}

		/**
		* Save database to file system
		*/
		public void save(String filename) throws IOException {
		FileOutputStream fileOutStream = new FileOutputStream(filename);
		ObjectOutputStream objOutStream = new ObjectOutputStream(fileOutStream);
		objOutStream.writeObject(this.db);
		objOutStream.close();
		fileOutStream.close();
		}

		/**
		* Load database from file system
		*/
		public void load(String filename) throws IOException {
		FileInputStream fileInStream = new FileInputStream(filename);
		ObjectInputStream objInStream = new ObjectInputStream(fileInStream);
		try {
		this.db = (HashMap<Integer, ArrayList<Molecule>>) objInStream.readObject();
		outputTextArea.append("Database loaded successfully." + "\n\n");
		} catch (IOException \| ClassNotFoundException e) {
		outputTextArea.append("Error loading database: " + e.getMessage() + "\n\n");
		}
		objInStream.close();
		fileInStream.close();
		}

		}

src/Main.java

+19 −1

Original line number	Diff line number	Diff line
		@@ -54,7 +54,12 @@ public class Main {
		case "--findMolecule":
		Molecule molecule = moleculeDb.findMolecule(new Molecule(moleculePath));
		if (molecule == null) {
		System.out.println("NOT FOUND");
		System.out.println("NO EXACT MATCH FOUND");
		molecule= moleculeDb.similarMolecule(new Molecule(moleculePath));
		if(molecule!=null)
		{
		System.out.println(molecule.moleculeName + " is the most similar");
		}
		} else {
		printVerbose("FOUND");
		}
		@@ -67,6 +72,19 @@ public class Main {
		for(Molecule m: mList)
		System.out.println(m.moleculeName);
		break;
		case "--downloadPubChem":
		// Repurposed moleculePath should be in format "start,end"
		// Input format for the file path is "start,end" where 'start' and 'end' are the starting and ending CID indices of molecules in PubChem
		// For example, enter 12,24 to download molecules 12-24
		String[] indexes = moleculePath.split(",");
		if (indexes.length == 2) {
		String start = indexes[0];
		String end = indexes[1];
		moleculeDb.downloadPubChem(start, end);
		} else {
		printVerbose("invalid Input");
		}
		break;
		default:
		printVerbose("unrecognized command: " + cmd);
		break;

src/MoleculeDatabase.java

+141 −6

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src/edu/bu/ec504/project/Atom.java

+6 −2

Original line number	Diff line number	Diff line
		@@ -10,6 +10,7 @@ public class Atom implements Serializable {
		atomName = name;
		degree = 0;
		connected = new HashMap<>();
		connectedMarked= new ArrayList<>();
		elementType = elem;
		marked = false;
		}
		@@ -18,8 +19,10 @@ public class Atom implements Serializable {
		if(connected.containsKey(i.getName())) {
		connected.put(i.getName(),new ElemOrderPair(i.elementType,connected.get(i.getName()).bondOrder+1));
		}
		else
		else {
		connected.put(i.getName(), new ElemOrderPair(i.elementType, 1));
		connectedMarked.add(false);
		}
		}
		public String getName() {
		return this.atomName;
		@@ -28,6 +31,7 @@ public class Atom implements Serializable {
		public int elementType;
		public int degree;
		public Map<String,ElemOrderPair> connected;
		public ArrayList<Boolean> connectedMarked;
		public boolean marked;