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();
}
}
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);
}
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));
}