/**
* converts an MDL object to CML. returns cml:cml/cml:molecule
*
* @param xml
*/
public List<String> convertToText(Element xml) {
List<String> stringList = null;
CMLElement cml = CMLBuilder.ensureCML(xml);
CMLMolecule molecule = new CMLSelector(cml).getToplevelMoleculeDescendant(true);
if (molecule != null) {
setMolecule(molecule);
GaussianInputProcessor gaussianInputProcessor = new GaussianInputProcessor(this);
stringList = gaussianInputProcessor.makeInput();
}
return stringList;
}
/**
* This method is called when 'Finish' button is pressed in the wizard. We will create an
* operation and run it using wizard as execution context.
*/
public boolean performFinish() {
try {
Options opts = new Options(new String[0]);
opts.setDefaultURL(serverPage.getSelectedServer() + "/services/NMRShiftDB");
Service service = new Service();
Call call = (Call) service.createCall();
call.setOperationName("doSearch");
call.setTargetEndpointAddress(new URL(opts.getURL()));
DocumentBuilder builder;
builder = DocumentBuilderFactory.newInstance().newDocumentBuilder();
SOAPBodyElement[] input = new SOAPBodyElement[1];
Document doc = builder.newDocument();
Element cdataElem;
cdataElem = doc.createElementNS("http://www.nmrshiftdb.org/ws/NMRShiftDB/", "doSearch");
Element reqElem;
reqElem = doc.createElementNS("http://www.nmrshiftdb.org/ws/NMRShiftDB/", "searchstring");
/*DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
DocumentBuilder db = dbf.newDocumentBuilder();
Node node = db.parse(new ByteArrayInputStream(new Convertor(true,"").cdkAtomContainerToCMLMolecule(ac).toXML().getBytes()));*/
Node node =
DOMConverter.convert(
new nu.xom.Document(new Convertor(true, "").cdkAtomContainerToCMLMolecule(ac)),
builder.getDOMImplementation())
.getFirstChild();
reqElem.appendChild(doc.importNode(node, true));
Element reqElem2;
reqElem2 = doc.createElementNS("http://www.nmrshiftdb.org/ws/NMRShiftDB/", "searchtype");
Node node2;
node2 = doc.createTextNode("--");
reqElem2.appendChild(node2);
Element reqElem3;
reqElem3 = doc.createElementNS("http://www.nmrshiftdb.org/ws/NMRShiftDB/", "searchfield");
Node node3;
node3 = doc.createTextNode(NmrshiftdbUtils.replaceSpaces(serverPage.selectedOption()));
reqElem3.appendChild(node3);
cdataElem.appendChild(reqElem);
cdataElem.appendChild(reqElem2);
cdataElem.appendChild(reqElem3);
input[0] = new SOAPBodyElement(cdataElem);
Vector elems = (Vector) call.invoke(input);
SOAPBodyElement elem = (SOAPBodyElement) elems.get(0);
Element e = elem.getAsDOM();
CMLBuilder cmlbuilder = new CMLBuilder();
CMLElement cmlElement = (CMLElement) cmlbuilder.parseString(XMLUtils.ElementToString(e));
if (cmlElement.getChildCount() > 0) {
IFolder folder = NmrshiftdbUtils.createVirtualFolder();
for (int i = 0; i < cmlElement.getChildCount(); i++) {
net.bioclipse.specmol.Activator.getDefault()
.getJavaSpecmolManager()
.saveSpecmol(
new JumboSpecmol((CMLCml) cmlElement.getChildCMLElements().get(i)),
folder.getFile(
((CMLMolecule)
cmlElement
.getChildCMLElements()
.get(i)
.getChildCMLElement("molecule", 0))
.getId()
+ "."
+ SpectrumEditor.CML_TYPE));
}
} else {
MessageDialog.openInformation(
PlatformUI.getWorkbench().getActiveWorkbenchWindow().getShell(),
"No results",
"No spectra in NMRShiftDB for this structure!");
}
} catch (Exception ex) {
LogUtils.handleException(ex, logger);
}
return true;
}