/**
* Gets the mol file from a specified KEGG ID.
*
* @param accessionID the accession id (e.g. C00509)
* @return the string
* @throws CDKException
*/
public static IAtomContainer getMol(String accessionID, String keggPath, boolean getAll)
throws CDKException {
String ret = "";
try {
KEGGLocator locator = new KEGGLocator();
KEGGPortType serv = locator.getKEGGPort();
// get molecule by accession ID
String str = "-f m cpd:" + accessionID;
boolean webservice = false;
String mol = "";
try {
// Open the file that is the first
// command line parameter
FileInputStream fstream = new FileInputStream(keggPath + accessionID + ".mol");
// Get the object of DataInputStream
DataInputStream in = new DataInputStream(fstream);
BufferedReader br = new BufferedReader(new InputStreamReader(in));
// Read File Line By Line
String line;
while ((line = br.readLine()) != null) {
// Print the content on the console
mol += line + "\n";
}
// Close the input stream
in.close();
} catch (FileNotFoundException e) {
webservice = true;
}
// if this file is not found use webservice...otherwise use local molfile
if (webservice) ret = serv.bget(str);
else ret = mol;
} catch (Exception e) {
System.err.println(e.toString());
}
MDLReader reader;
List<IAtomContainer> containersList;
reader = new MDLReader(new StringReader(ret));
ChemFile chemFile = (ChemFile) reader.read((ChemObject) new ChemFile());
containersList = ChemFileManipulator.getAllAtomContainers(chemFile);
IAtomContainer molecule = containersList.get(0);
if (getAll) return molecule;
if (!MolecularFormulaTools.isBiologicalCompound(molecule)) molecule = null;
return molecule;
}
@Test
public void testBug70() throws FileNotFoundException, CDKException {
JPanelFixture jcppanel = applet.panel("appletframe");
JChemPaintPanel panel = (JChemPaintPanel) jcppanel.target;
applet.button("hexagon").click();
applet.click();
Point2d point = getAtomPoint(panel, 0);
applet
.panel("renderpanel")
.robot
.click(
applet.panel("renderpanel").component(),
new Point((int) point.x, (int) point.y),
MouseButton.RIGHT_BUTTON,
1);
applet
.panel("renderpanel")
.robot
.click(
applet.panel("renderpanel").component(),
new Point((int) point.x, (int) point.y),
MouseButton.RIGHT_BUTTON,
1);
applet.menuItem("showACProperties").click();
DialogFixture dialog = applet.dialog();
JTextComponent textfield = dialog.robot.finder().find(JTextComponentMatcher.withName("Title"));
textfield.setText("aaa");
JButtonFixture okbutton =
new JButtonFixture(
dialog.robot, dialog.robot.finder().find(new ButtonTextComponentMatcher("OK")));
okbutton.click();
applet.menuItem("save").click();
dialog = applet.dialog();
File file = new File(System.getProperty("java.io.tmpdir") + File.separator + "test.mol");
if (file.exists()) file.delete();
JComboBox combobox =
dialog
.robot
.finder()
.find(new ComboBoxTextComponentMatcher("org.openscience.jchempaint.io.JCPFileFilter"));
combobox.setSelectedItem(combobox.getItemAt(SAVE_AS_MOL_COMBOBOX_POS));
JTextComponentFixture text = dialog.textBox();
text.setText(file.toString());
JButtonFixture savebutton =
new JButtonFixture(
dialog.robot, dialog.robot.finder().find(new ButtonTextComponentMatcher("Save")));
savebutton.click();
MDLReader reader = new MDLReader(new FileInputStream(file));
IAtomContainer mol =
(IAtomContainer)
reader.read(DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainer.class));
Assert.assertEquals("aaa", (String) mol.getProperty(CDKConstants.TITLE));
}
/** Test some sugars */
@Test
public void testSugarSMILES() {
try {
String filename = "data/mdl/D-mannose.mol";
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
MDLReader reader = new MDLReader(ins, Mode.STRICT);
IAtomContainer mol1 = reader.read(new AtomContainer());
addExplicitHydrogens(mol1);
new HydrogenPlacer().placeHydrogens2D(mol1, 1.0);
filename = "data/mdl/D+-glucose.mol";
ins = this.getClass().getClassLoader().getResourceAsStream(filename);
reader = new MDLReader(ins, Mode.STRICT);
IAtomContainer mol2 = reader.read(new AtomContainer());
addExplicitHydrogens(mol2);
new HydrogenPlacer().placeHydrogens2D(mol2, 1.0);
SmilesGenerator sg = new SmilesGenerator();
String smiles1 = sg.createChiralSMILES(mol1, new boolean[20]);
String smiles2 = sg.createChiralSMILES(mol2, new boolean[20]);
Assert.assertNotSame(smiles2, smiles1);
} catch (Exception exc) {
System.out.println(exc);
}
}