Códigos de Java

public class ReactionTest {
   public static void main(String [] args) throws CDKException, IOException {
       //Crea una instancia sin crear nuevo elemento!

        IChemObjectBuilder iChemObjectBuilder = SilentChemObjectBuilder.getInstance();    

        //Convierte el texto a una molecula
       SmilesParser smilesParser = new SmilesParser(iChemObjectBuilder);

        //smilesParser crea la referencia;pareseSmiles es un método que devuelve    

        IAtomContainer
       IAtomContainer ethanol = smilesParser.parseSmiles("CCO");        

        IAtomContainer aceticAcid = smilesParser.parseSmiles("CC=OO");
       IAtomContainer bleach = smilesParser.parseSmiles("ClO");

       Reaction reaction = new Reaction();
       ethanol.setProperty(CDKConstants.TITLE,"Ethanol");//Crea un título a la imagen
       reaction.setProperty(CDKConstants.TITLE,"reaction1");//Crea tíyulo a la reacción
       reaction.addReactant(ethanol);
       reaction.addAgent(bleach);
       reaction.addProduct(aceticAcid);

       DepictionGenerator depictionGenerator = new DepictionGenerator();
       depictionGenerator = depictionGenerator.withFillToFit().withAtomColors()

        .withSize(500,500).withMolTitle().withRxnTitle(); //Usando ambos títulos
       //Al depict() se le asigna un elemento de IAtomContainer
       depictionGenerator.depict(reaction).writeTo("reaction.png");
       depictionGenerator.depict(ethanol).writeTo("ethanol.png");
   }
}

public class Test {
   public static void main(String [] args) throws CDKException, IOException {
       IAtom hydrogen = new Atom(Elements.HYDROGEN);
       IAtom hydrogen2 = new Atom("H");
       IBond bond1 = new Bond(hydrogen,hydrogen2,IBond.Order.SINGLE);
       IAtomContainer molecularHydrogen = new AtomContainer();
       molecularHydrogen.addAtom(hydrogen);
       molecularHydrogen.addAtom(hydrogen2);
       molecularHydrogen.addBond(bond1);
       for(IAtom atom:molecularHydrogen.atoms()){
           System.out.println(atom.getSymbol());
       }
       Ring cylohexane = new Ring(6,"CH");
       Ring benzene = cylohexane;
       int i=2;
       for(IBond bond:benzene.bonds()){
           bond.setIsAromatic(true);
           if(i%2==0){
               bond.setOrder(IBond.Order.DOUBLE);
           }
           i++;
       }
       DepictionGenerator depictionGenerator = new DepictionGenerator();
       depictionGenerator = depictionGenerator.withAtomColors().withFillToFit()

        .withSize(500,500);
       depictionGenerator.depict(benzene).writeTo("benzene.png");
       //depict returns a class from the same hierarchy as the class  

        depictionGenerator
       // depict generate the molecule you passed

       String lsdSmile = "CCN(CC)C(=O)[C@H]1CN([C@@H]2Cc3c[nH]c4c3c(ccc4)C2=C1)C";
       IChemObjectBuilder objectBuilder = SilentChemObjectBuilder.getInstance();
       SmilesParser smilesParser = new SmilesParser(objectBuilder);
       smilesParser.parseSmiles(lsdSmile);
       IAtomContainer lsd = smilesParser.parseSmiles(lsdSmile);
       depictionGenerator.depict(lsd).writeTo("lsd.png");
       //Parser takes a string and return another thing
   }
}

public class Atom {
   private int atomicNumber;
   private String symbol;
   private double weigth;
   private double radii;

   public Atom(int atomicNumber, String symbol, double weigth, double radii) {
       this.atomicNumber = atomicNumber;
       this.symbol = symbol;
       this.weigth = weigth;
       this.radii = radii;
   }
   public int getAtomicNumber() {
       return atomicNumber;
   }
   public void setAtomicNumber(int atomicNumber) {
       this.atomicNumber = atomicNumber;
   }
   public String getSymbol() {
       return symbol;
   }
   public void setSymbol(String symbol) {
       this.symbol = symbol;
   }
   public double getWeigth() {
       return weigth;
   }
   public void setWeigth(double weigth) {
       this.weigth = weigth;
   }
   public double getRadii() {
       return radii;
   }
   public void setRadii(double radii) {
       this.radii = radii;
   }
}

public class InorganicMolecule extends Molecule {
   private Atom[] atoms;
   public InorganicMolecule(Atom[] atoms){
       super(atoms);
       this.atoms=atoms;
   }

   public String moleculeContains(){
       return " lack of C-H carbons";
   }
}

public class OrganicMolecule extends Molecule{
   private Atom[] atoms;
   public OrganicMolecule(){}
   public OrganicMolecule(Atom[] atoms) {
       super(atoms);
       this.atoms = atoms;
   }
   public String moleculeContains(){
       return " contains C-H bonds";
   }
}

public abstract class Molecule{
   private Atom[]atoms;
   public Molecule(){}
   public Molecule(Atom[]atoms){
       this.atoms=atoms;
   }

   public String moleculeContains(){
       return "Molecule";
   }

   public String getStructure(){
       String s ="";
       for (Atom a: atoms){
           s+=a.getSymbol()+"-";
       }
       return s.substring(0,s.length()-1);
   }

   private double sum=0;
   public double calculateMolecularMass(){
       for(Atom a:atoms){
           sum+= a.getWeigth();
       }
       return sum;
   }
}

public class OrganicMolecule extends Molecule{
   private Atom[] atoms;
   public OrganicMolecule(){}
   public OrganicMolecule(Atom[] atoms) {
       super(atoms);
       this.atoms = atoms;
   }
   public String moleculeContains(){
       return " contains C-H bonds";
   }
}