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();
}
}
// initialize data hash table servers
// read server addresses from file and initialize the servers
private void initServers() {
try {
java.net.URL path = ClassLoader.getSystemResource(clientSettingFile);
FileReader fr = new FileReader(path.getFile());
BufferedReader br = new BufferedReader(fr);
try {
String[] portMap = br.readLine().split(",");
mServerCount = portMap.length;
mPortMap = new int[mServerCount];
for (int i = 0; i < mServerCount; i++) {
mPortMap[i] = Integer.parseInt(portMap[i]);
}
} catch (IOException e) {
e.printStackTrace();
System.exit(-1);
}
} catch (FileNotFoundException e2) {
e2.printStackTrace();
System.exit(-1);
}
mDhtServerArray = new IDistributedHashTable[mServerCount];
for (int i = 0; i < mServerCount; i++) {
try {
mDhtServerArray[i] =
(IDistributedHashTable)
Naming.lookup("rmi://localhost:" + mPortMap[i] + "/DistributedHashTable");
appendOutput("server: " + (i + 1) + " is connected");
} catch (Exception e) {
appendOutput("initServers: " + (i + 1) + " " + e.getMessage());
}
}
}
/** Shows JSort help in the jEdit help viewer */
private void showHelp() {
java.net.URL helpUrl = TextToolsSortDialog.class.getResource("TextTools.html");
if (helpUrl == null) {
Log.log(Log.NOTICE, this, "Help URL is null, cannot display help");
} else {
new org.gjt.sp.jedit.help.HelpViewer(helpUrl.toString());
}
} // }}}
// ===================================================
// ObjHtmlPanel.Listener
public void linkSelected(java.net.URL href, String target) {
String url = href.toExternalForm();
int slash = url.lastIndexOf('/');
if (slash > 0) url = url.substring(slash + 1);
Job t = actionMap.get(url);
fapp.guiRun().run(this, new Job(t.getPermissions(), t.getCBRunnable()));
}
// ===================================================
// ObjHtmlPanel.Listener
public void linkSelected(java.net.URL href, String target) {
String url = href.toExternalForm();
int slash = url.lastIndexOf('/');
if (slash > 0) url = url.substring(slash + 1);
Job job = actionMap.get(url);
if (job != null) app.guiRun().run(this, job);
}