コード例 #1
0
 public static void main(String[] args) {
   Example4 ef = new Example4();
   try {
     final String molS = "C1C2=CC=CC=C2C3=C4CC5=CC=CC=C5C4=C6CC7=CC=CC=C7C6=C13";
     Molecule mol = MolImporter.importMol(molS);
     PolarizabilityPlugin plugin = new PolarizabilityPlugin();
     plugin.setMolecule(mol);
     plugin.run();
     ArrayList values = new ArrayList();
     java.text.NumberFormat nf = java.text.NumberFormat.getInstance();
     nf.setMaximumFractionDigits(3);
     for (int i = 0; i < mol.getAtomCount(); i++) {
       values.add(Float.valueOf(nf.format(((Double) plugin.getResult(i)).floatValue())));
     }
     mol.hydrogenize(true);
     for (int i = 0; i < mol.getExplicitHcount(); i++) {
       values.add(new Double(0));
     }
     ef.setPlugin(plugin);
     JFrame frame = ef.createSpaceFrame(mol, values);
     frame.setTitle("Polarizability");
     java.net.URL u = ef.getClass().getResource("/chemaxon/marvin/space/gui/mspace16.gif");
     frame.setIconImage(
         Toolkit.getDefaultToolkit().createImage((java.awt.image.ImageProducer) u.getContent()));
     frame.setVisible(true);
   } catch (Exception e) {
     e.printStackTrace();
   }
 }
コード例 #2
0
 private static void saveImage(String notation, String imageFilePath)
     throws NotationException, MonomerException, StructureException, JDOMException, IOException {
   String complexNotation = SimpleNotationParser.getComplextNotationForRNA(notation);
   String smiles = ComplexNotationParser.getComplexPolymerSMILES(complexNotation);
   Molecule mol = MolImporter.importMol(smiles);
   Image image = (Image) mol.toObject("image");
   new SaveAsPNG(image, imageFilePath);
 }
コード例 #3
0
  public static void main(String[] args) throws IOException {

    // Import a molecule from smiles
    Molecule mol = MolImporter.importMol("O=C1NC=CC=C1");
    mol.setDim(0);

    // Call basic aromatization method
    mol.aromatize(MoleculeGraph.AROM_BASIC);
    System.out.println("Aromatic: " + isAromatic(mol));

    // Call general aromatization method
    mol.aromatize(MoleculeGraph.AROM_GENERAL);
    System.out.println("Aromatic: " + isAromatic(mol));
  }