implemented mostSimilar function (c8fb4e63) · Commits · EC504 Spring 2024 Group Projects / Group4

src/Main.java

+9 −1

Original line number	Diff line number	Diff line
		@@ -53,11 +53,19 @@ 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");
		}
		break;
		// case "--similarMolecule":
		// Molecule molecule2= moleculeDb.similarMolecule(new Molecule(moleculePath));
		// printVerbose("FOUND! "+molecule2.moleculeName+" is the most similar molecule");
		default:
		printVerbose("unrecognized command: " + cmd);
		break;

src/MoleculeDatabase.java

+30 −0

Original line number	Diff line number	Diff line
		@@ -7,6 +7,7 @@ import java.io.ObjectInputStream;
		import java.io.ObjectOutputStream;
		import java.util.ArrayList;
		import java.util.HashMap;
		import java.util.Map;

		/**
		* A class represents the molecule database
		@@ -81,6 +82,35 @@ public class MoleculeDatabase {
		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;
		}

		/**
		* Save database to file system
		*/

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;

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

+88 −0

Original line number	Diff line number	Diff line
		@@ -123,6 +123,94 @@ public class Molecule implements Serializable {
		return this;
		}


		/**
		* Finds the Most Similar Molecule
		*/
		public int mostSimilar(Molecule otherMolecule) {

		int similarity=0; //counts similarity points

		// Points for an intersection of elements between this and otherMolecule
		for(int i=0;i<this.numElements.length;i++)
		{
		similarity+= Math.min( this.numElements[i], otherMolecule.numElements[i]);
		}

		//Points for same number of atoms
		if(this.numAtoms==otherMolecule.numAtoms)
		{
		similarity++;
		}

		//Points for same number of edges
		if(this.numEdges==otherMolecule.numEdges)
		{
		similarity++;
		}


		// Clean the otherMolecule atom list of any marked atoms
		for(Atom cleanAtom : otherMolecule.atomArrayList)
		{
		cleanAtom.marked = false;

		//clean the connected arraylist
		for(int i=0;i<cleanAtom.connectedMarked.size();i++)
		{
		cleanAtom.connectedMarked.set(i,false);
		}
		}
		// Clean the dbMolecule atom list of any marked atoms

		// Compare the atom lists
		for(Atom dbAtom : this.atomArrayList) {
		boolean matchingEdge=false;

		for (Atom newAtom : otherMolecule.atomArrayList) {

		if (newAtom.elementType == dbAtom.elementType) { //Check if elements are the same
		boolean [] edgeMarked = new boolean[newAtom.connected.size()];
		// Compare connected of each atom
		//for each connected atom in dbAtom
		for (Atom.ElemOrderPair dbValues : dbAtom.connected.values()) {
		int marker=0;

		for (Atom.ElemOrderPair newAtomValues : newAtom.connected.values()) {
		//if its a match
		//if first 2 yes, add points for min of bondOrder between the 2
		if (!newAtom.connectedMarked.get(marker) && !edgeMarked[marker] && dbValues.eType == newAtomValues.eType )
		{
		if( dbValues.bondOrder == newAtomValues.bondOrder)
		{
		//mark the newAtom edge as already found
		newAtom.connectedMarked.set(marker,true);
		matchingEdge=true;
		edgeMarked[marker]=true;
		similarity++; //add a point for each edge that is the same
		break;
		}

		}
		marker++;

		}
		}

		}

		if(matchingEdge)
		{
		break;
		}
		}

		}

		// If all comparisons passed, the molecules are equal
		return similarity;
		}

		/**
		* Return number of atoms of the molecule
		*/