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));
}
public static void main(String[] args) {
try {
// instantiate the plugin object
ElementalAnalyserPlugin plugin = new ElementalAnalyserPlugin();
// set the parameters for the calculation (plugin specific))
plugin.setDoublePrecision(2);
// read the input molecules and perform the calculations
MolImporter importer = new MolImporter(args[0]);
Molecule mol;
while ((mol = importer.read()) != null) {
// set the input molecule
plugin.setMolecule(mol);
// run the calculation
plugin.run();
// get the results (plugin specific)
// mass and exact mass
double mass = plugin.getMass();
double exactMass = plugin.getExactMass();
// the number of all atoms in the molecule
int atomCount = plugin.getAllAtomCount();
// carbon atom count
int countOfC = plugin.getAtomCount(6);
// carbon-14 isotope count
int countOfC14 = plugin.getAtomCount(6, 14);
// formula
String formula = plugin.getFormula();
// composition
String composition = plugin.getComposition();
// display the results
System.out.println(
mol.toFormat("smiles")
+ "\n formula: "
+ formula
+ ", mass: "
+ mass
+ ", exact mass: "
+ exactMass
+ "\n number of atoms ("
+ atomCount
+ "): C ("
+ countOfC
+ "), C-14 ("
+ countOfC14
+ ")"
+ "\n composition: "
+ composition
+ "\n");
}
importer.close();
} catch (IOException e) {
System.err.println("I/O error has occurred.");
e.printStackTrace();
} catch (PluginException e) {
System.err.println("Plugin processing or calculation error.");
e.printStackTrace();
}
}