RubyGems - toxtree - Versions diffs - 0.0.1 - Mend

toxtree 0.0.1

Files changed (1384) hide show

data/Toxtree-v2.6.13/src/toxtree/ui/molecule/NavigationPanel.java ADDED

@@ -0,0 +1,192 @@
+/*
+Copyright Ideaconsult Ltd. (C) 2005-2007
+Contact: nina@acad.bg
+This program is free software; you can redistribute it and/or
+modify it under the terms of the GNU General Public License
+as published by the Free Software Foundation; either version 2
+of the License, or (at your option) any later version.
+All we ask is that proper credit is given for our work, which includes
+- but is not limited to - adding the above copyright notice to the beginning
+of your source code files, and to any copyright notice that you may distribute
+with programs based on this work.
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+You should have received a copy of the GNU General Public License
+along with this program; if not, write to the Free Software
+Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
+*/
+package toxtree.ui.molecule;
+import java.awt.Color;
+import java.awt.Cursor;
+import java.awt.Dimension;
+import java.awt.EventQueue;
+import java.awt.FlowLayout;
+import java.awt.FontMetrics;
+import java.awt.LayoutManager;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.util.Observable;
+import java.util.Observer;
+import javax.swing.BorderFactory;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.SwingConstants;
+import toxtree.data.DataContainer;
+public class NavigationPanel extends JPanel implements Observer {
+	protected DataContainer dataContainer;
+	protected JLabel navStat = null;
+	protected Color bgColor = Color.BLACK;
+	protected Color fColor = Color.WHITE;
+	/**
+	 *
+	 */
+	private static final long serialVersionUID = -7523783333429225550L;
+	public NavigationPanel(DataContainer datacontainer, Color bgColor, Color fColor) {
+		super();
+		setDataContainer(datacontainer);
+		addWidgets(bgColor,fColor);
+	}
+	public NavigationPanel(DataContainer datacontainer,boolean arg0,Color bgColor, Color fColor) {
+		super(arg0);
+		setDataContainer(datacontainer);
+		addWidgets(bgColor,fColor);
+	}
+	public NavigationPanel(DataContainer datacontainer,LayoutManager arg0,Color bgColor, Color fColor) {
+		super(arg0);
+		setDataContainer(datacontainer);
+		addWidgets(bgColor,fColor);
+	}
+	public NavigationPanel(DataContainer datacontainer,LayoutManager arg0, boolean arg1,Color bgColor, Color fColor) {
+		super(arg0, arg1);
+		setDataContainer(datacontainer);
+		addWidgets(bgColor,fColor);
+	}
+	protected void addWidgets(Color bgColor, Color fColor) {
+		//navPanel.setBorder(BorderFactory.createTitledBorder("Title"));
+		this.bgColor = bgColor;
+		this.fColor = fColor;
+		setLayout(new FlowLayout());
+		setBackground(bgColor);
+		setForeground(fColor);
+		setPreferredSize(new Dimension(120,32));
+		setMinimumSize(new Dimension(64,32));
+		JLabel nav[] = new JLabel[4];
+        nav[0] = createLabel("<html><u><b> First</b></u></html>",
+                "Click here to go to the first molecule of the set"
+                );
+        nav[0].addMouseListener(new NavigatorMouseAdapter() {
+	   		@Override
+			public void mouseClicked(MouseEvent e) {
+	   			dataContainer.first();
+	   		}
+	    });
+        nav[1] = createLabel("<html><u><b> Prev</b></u></html>",
+                "Click here to go to the previous molecule of the set"
+                );
+        nav[1].addMouseListener(new NavigatorMouseAdapter() {
+	   		@Override
+			public void mouseClicked(MouseEvent e) {
+	   			dataContainer.prev();
+	   		}
+	    });
+        nav[2] = createLabel("<html><u><b> Next</b></u></html>",
+                "Click here to go to the next molecule of the set"
+                );
+        nav[2].addMouseListener(new NavigatorMouseAdapter() {
+	   		@Override
+			public void mouseClicked(MouseEvent e) {
+	   			dataContainer.next();
+	   		}
+	    });
+        nav[3] = createLabel("<html><u><b> Last</b></u></html>",
+                "Click here to go to the last molecule of the set"
+                );
+        nav[3].addMouseListener(new NavigatorMouseAdapter() {
+	   		@Override
+			public void mouseClicked(MouseEvent e) {
+	   			dataContainer.last();
+	   		}
+	    });
+	    navStat = createLabel("<html><font color=blue><b>1/1</b></font></html>","Number of molecules in the set loaded.");
+	    FontMetrics metric = getFontMetrics(getFont());
+	    Dimension d = new Dimension(metric.stringWidth("Next")*2,(int) (metric.getHeight()*1.66));
+	    for (int i = 0; i < nav.length; i++) {
+	    	nav[i].setHorizontalAlignment(SwingConstants.CENTER);
+	    	nav[i].setHorizontalTextPosition(SwingConstants.CENTER);
+	    	nav[i].setVerticalTextPosition(SwingConstants.CENTER);
+	    	nav[i].setPreferredSize(d);
+	    }
+        for (int i = 0; i < 2; i++) add(nav[i]);
+        add(navStat);
+        for (int i = 2; i < 4; i++) add(nav[i]);
+	}
+	public void update(Observable arg0, Object arg1) {
+		EventQueue.invokeLater(new Runnable() {
+			@Override
+			public void run() {
+				navStat.setToolTipText(dataContainer.toString());
+				navStat.setText("<html><font color=gray><b>" +
+						(dataContainer.getCurrentNo()+1) + " / " +
+						dataContainer.getMoleculesCount() +
+						"</b></font></html>");
+			}
+		});
+	}
+	public DataContainer getDataContainer() {
+		return dataContainer;
+	}
+	public void setDataContainer(DataContainer dataContainer) {
+		this.dataContainer = dataContainer;
+		dataContainer.addObserver(this);
+	}
+	public  JLabel createLabel(String title, String tooltip) {
+        JLabel label = new JLabel(title);
+        label.setAlignmentX(CENTER_ALIGNMENT);
+        label.setOpaque(true);
+        label.setBackground(bgColor);
+        label.setForeground(fColor);
+        label.setToolTipText(tooltip);
+        return label;
+	}
+}
+class NavigatorMouseAdapter extends MouseAdapter {
+	@Override
+	public void mouseEntered(MouseEvent e) {
+		super.mouseEntered(e);
+		e.getComponent().setCursor(Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
+		((JLabel)e.getComponent()).setBorder(BorderFactory.createLineBorder(Color.gray));
+	}
+	@Override
+	public void mouseExited(MouseEvent e) {
+		super.mouseExited(e);
+		//e.getComponent().setBackground(Color.black);
+		((JLabel)e.getComponent()).setBorder(null);
+		e.getComponent().setCursor(Cursor.getDefaultCursor());
+	}
+}

data/Toxtree-v2.6.13/src/toxtree/ui/molecule/PropertyPanel.java ADDED

@@ -0,0 +1,115 @@
+/*
+Copyright Ideaconsult Ltd. (C) 2005-2007
+Contact: nina@acad.bg
+This program is free software; you can redistribute it and/or
+modify it under the terms of the GNU General Public License
+as published by the Free Software Foundation; either version 2
+of the License, or (at your option) any later version.
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+You should have received a copy of the GNU General Public License
+along with this program; if not, write to the Free Software
+Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
+*/
+package toxtree.ui.molecule;
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Dimension;
+import javax.swing.BorderFactory;
+import javax.swing.JComponent;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTable;
+import javax.swing.ListSelectionModel;
+import org.openscience.cdk.interfaces.IAtomContainer;
+public class PropertyPanel extends JPanel {
+	protected AtomContainerPropertyTableModel tableModel;
+	/**
+	 *
+	 */
+	private static final long serialVersionUID = -712606150162538423L;
+	public PropertyPanel() {
+		this(Color.white,Color.BLACK);
+	}
+	public PropertyPanel(Color bgColor, Color fColor) {
+		super(new BorderLayout());
+		addWidgets(bgColor,fColor);
+	}
+	protected void addWidgets(Color bgColor, Color fColor) {
+        JLabel labelA = new JLabel("<html><b>Available structure attributes</b></html>");
+        labelA.setOpaque(true);
+        labelA.setBackground(bgColor);
+        labelA.setForeground(fColor);
+        labelA.setSize(120,32);
+        labelA.setAlignmentX(CENTER_ALIGNMENT);
+        labelA.setBorder(BorderFactory.createMatteBorder(5,0,0,0,bgColor));
+        add(labelA,BorderLayout.NORTH);
+        //molecule properties instead cas/name text boxes
+        tableModel = new AtomContainerPropertyTableModel();
+		JTable table = new JTable(tableModel) {
+			/**
+		     *
+		     */
+		    private static final long serialVersionUID = -7131465553536386479L;
+			public java.awt.Component prepareRenderer(javax.swing.table.TableCellRenderer renderer, int rowIndex, int vColIndex) {
+				Component c = super.prepareRenderer(renderer, rowIndex, vColIndex);
+	            if (c instanceof JComponent) {
+	                JComponent jc = (JComponent)c;
+	                jc.setToolTipText((String)getValueAt(rowIndex, vColIndex));
+	            }
+	            return c;
+			};
+		};
+		table.setTableHeader(null);
+		table.setShowHorizontalLines(true);
+		table.setShowVerticalLines(true);
+		table.setPreferredScrollableViewportSize(new Dimension(Integer.MAX_VALUE, Integer.MAX_VALUE));
+		table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+		table.setRowSelectionAllowed(true);
+		table.setOpaque(true);
+		JScrollPane p = new JScrollPane(table);
+     	p.setPreferredSize(new Dimension(256,3*24+2));
+     	p.setMinimumSize(new Dimension(256,3*24+2));
+     	p.setBackground(bgColor);
+     	p.setOpaque(true);
+		table.setBackground(Color.white);
+		add(p,BorderLayout.CENTER);
+	}
+	public AtomContainerPropertyTableModel getTableModel() {
+		return tableModel;
+	}
+	public void setTableModel(AtomContainerPropertyTableModel tableModel) {
+		this.tableModel = tableModel;
+	}
+	public void setAtomContainer(IAtomContainer ac) {
+		tableModel.setAtomContainer(ac);
+	}
+}

data/Toxtree-v2.6.13/src/toxtree/ui/molecule/ShowFilteredFileAction.java ADDED

@@ -0,0 +1,67 @@
+/*
+Copyright Ideaconsult Ltd. (C) 2005-2007
+Contact: nina@acad.bg
+This program is free software; you can redistribute it and/or
+modify it under the terms of the GNU General Public License
+as published by the Free Software Foundation; either version 2
+of the License, or (at your option) any later version.
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+You should have received a copy of the GNU General Public License
+along with this program; if not, write to the Free Software
+Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
+*/
+package toxtree.ui.molecule;
+import javax.swing.AbstractAction;
+import javax.swing.Icon;
+import javax.swing.JOptionPane;
+import toxTree.exceptions.FilterException;
+import toxTree.io.Tools;
+import toxtree.data.DecisionMethodsDataModule;
+import toxtree.ui.actions.DataModuleAction;
+public class ShowFilteredFileAction extends DataModuleAction {
+	/**
+	 *
+	 */
+	private static final long serialVersionUID = 3721636787386952400L;
+	public ShowFilteredFileAction(DecisionMethodsDataModule module) {
+		this(module,"Subsets");
+	}
+	public ShowFilteredFileAction(DecisionMethodsDataModule module, String name) {
+		this(module, name,Tools.getImage("application_cascade.png"));
+	}
+	public ShowFilteredFileAction(DecisionMethodsDataModule module, String name, Icon icon) {
+		super(module, name, icon);
+		putValue(AbstractAction.SHORT_DESCRIPTION,"Select which subset of chemical compounds to display");
+	}
+	@Override
+	public void runAction() throws Exception {
+		module.getActions().allActionsEnable(false);
+		try {
+			((DecisionMethodsDataModule)module).selectFilter(getFrame());
+		} catch (FilterException x) {
+			JOptionPane.showMessageDialog(getFrame(),x.getMessage());
+		}
+		module.getActions().allActionsEnable(true);
+	}
+}

data/Toxtree-v2.6.13/src/toxtree/ui/molecule/SmilesEntryPanel.java ADDED

@@ -0,0 +1,387 @@
+/*
+Copyright Ideaconsult Ltd. (C) 2005-2007
+Contact: nina@acad.bg
+This program is free software; you can redistribute it and/or
+modify it under the terms of the GNU General Public License
+as published by the Free Software Foundation; either version 2
+of the License, or (at your option) any later version.
+All we ask is that proper credit is given for our work, which includes
+- but is not limited to - adding the above copyright notice to the beginning
+of your source code files, and to any copyright notice that you may distribute
+with programs based on this work.
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+You should have received a copy of the GNU General Public License
+along with this program; if not, write to the Free Software
+Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
+*/
+package toxtree.ui.molecule;
+import java.awt.BorderLayout;
+import java.awt.Dimension;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.util.Locale;
+import java.util.ResourceBundle;
+import javax.swing.AbstractAction;
+import javax.swing.BoxLayout;
+import javax.swing.JButton;
+import javax.swing.JComboBox;
+import javax.swing.JLabel;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JPopupMenu;
+import javax.swing.SwingConstants;
+import javax.vecmath.Vector2d;
+import org.openscience.cdk.CDKConstants;
+import org.openscience.cdk.graph.ConnectivityChecker;
+import org.openscience.cdk.inchi.InChIGeneratorFactory;
+import org.openscience.cdk.inchi.InChIToStructure;
+import org.openscience.cdk.index.CASNumber;
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.interfaces.IMolecule;
+import org.openscience.cdk.interfaces.IMoleculeSet;
+import org.openscience.cdk.layout.StructureDiagramGenerator;
+import org.openscience.cdk.silent.SilentChemObjectBuilder;
+import org.openscience.cdk.smiles.SmilesGenerator;
+import toxTree.query.FunctionalGroups;
+import toxTree.query.remote.RemoteCompoundLookup;
+import ambit2.base.config.Preferences;
+import ambit2.base.data.Property;
+import ambit2.core.config.AmbitCONSTANTS;
+import ambit2.core.data.EINECS;
+import ambit2.namestructure.Name2StructureProcessor;
+/**
+ * A {@link javax.swing.JPanel} to enter a SMILES. Now it supports a history of entered SMILES that can be
+ * navigated back and forward and by a drop down list.
+ * @author Nina Jeliazkova
+ * <b>Modified</b> 2011-8-1
+ */
+public class SmilesEntryPanel extends StructureEntryPanel implements ItemListener, ActionListener {
+	JComboBox smilesBox = null;
+	protected JPopupMenu popup;
+	protected ResourceBundle labels;
+    protected StructureDiagramGenerator sdg = null;
+    enum _labels {
+    	go,
+    	title,
+    	hint,
+    	forwardButton,
+    	backButton,
+    	forwardButton_hint,
+    	backButton_hint,
+    	createdByOpsin,
+    	createdBySMILES,
+    	createdByInChI,
+    	error_cas,
+    	error_einecs,
+    	error_inchi,
+    	error_smiles,
+    	error_remote,
+    	error_unknown
+    }
+	/**
+	 * Comment for <code>serialVersionUID</code>
+	 */
+	private static final long serialVersionUID = -8184455436899528629L;
+	/**
+	 *
+	 */
+	public SmilesEntryPanel() {
+		super();
+		labels =  ResourceBundle.getBundle(getClass().getName(),
+					Locale.ENGLISH,
+					getClass().getClassLoader());
+		addWidgets();
+	}
+	private void initLayout() {
+		setLayout(new BorderLayout());
+	}
+	private void addWidgets() {
+		initLayout();
+        JPanel top = new JPanel();
+        top.setLayout(new BoxLayout(top,BoxLayout.LINE_AXIS));
+        Dimension d = new Dimension(48,24);
+        JButton backButton = new JButton(new AbstractAction(labels.getString(_labels.backButton.name())) {
+			private static final long serialVersionUID = 7046410922163328877L;
+			public void actionPerformed(ActionEvent arg0) {
+        		int index = smilesBox.getSelectedIndex();
+        		index = index -1;
+        		if (index < 0) index = 0;
+        		if (smilesBox.getItemAt(index) != null)
+        			smilesBox.setSelectedIndex(index);
+        	}
+        });
+        backButton.setDefaultCapable(false);
+        backButton.setPreferredSize(d);
+        backButton.setMinimumSize(d);
+        JButton forwardButton = new JButton(new AbstractAction(labels.getString(_labels.forwardButton.name())) {
+			private static final long serialVersionUID = 8892599118153155748L;
+			public void actionPerformed(ActionEvent arg0) {
+        		int index = smilesBox.getSelectedIndex();
+        		index = index +1 ;
+        		if (index >= smilesBox.getItemCount()) index = smilesBox.getItemCount()-1;
+        		if (smilesBox.getItemAt(index) != null)
+        			smilesBox.setSelectedIndex(index);
+        	}
+        });
+        forwardButton.setDefaultCapable(false);
+        forwardButton.setPreferredSize(d);
+        forwardButton.setMinimumSize(d);
+        forwardButton.setToolTipText(labels.getString(_labels.forwardButton_hint.name()));
+        backButton.setToolTipText(labels.getString(_labels.backButton_hint.name()));
+        top.add(backButton);top.add(forwardButton);
+        JLabel labelSmi = new JLabel(labels.getString(_labels.title.name()));
+        labelSmi.setOpaque(true);
+        //labelSmi.setBackground(Color.black);
+        //labelSmi.setForeground(Color.white);
+        labelSmi.setPreferredSize(new Dimension(80,24));
+        labelSmi.setAlignmentX(CENTER_ALIGNMENT);
+        top.add(labelSmi);
+        labelSmi.setHorizontalAlignment(SwingConstants.RIGHT);
+        smilesBox = new JComboBox();
+        smilesBox.setEditable(true);
+        smilesBox.setFocusable(true);
+        //smilesBox.setHorizontalAlignment(JTextField.LEFT);
+        smilesBox.setToolTipText(String.format("<html>%s</html>",labels.getString(_labels.hint.name())));
+        smilesBox.setPreferredSize(new Dimension(Integer.MAX_VALUE,24));
+        //smilesEdit.addActionListener(this);
+        //smilesBox.addPropertyChangeListener("value",this);
+        smilesBox.addItemListener(this);
+        popup = new JPopupMenu("Edit");
+        JMenuItem mi = new JMenuItem("Copy");
+        mi.addActionListener(this);
+        popup.add(mi);
+        mi = new JMenuItem("Paste");
+        mi.addActionListener(this);
+        popup.add(mi);
+        smilesBox.addMouseListener(new MouseAdapter() {
+        	//TODO towa ne raboti
+			@Override
+			public void mousePressed(MouseEvent e) {
+				super.mousePressed(e);
+				if (e.getButton()==MouseEvent.BUTTON3) {
+					popup.show(e.getComponent(),e.getX(),e.getY());
+				}
+			}
+        });
+        labelSmi.setLabelFor(smilesBox);
+        //add(labelSmi,BorderLayout.WEST);
+        add(top,BorderLayout.WEST);
+        add(smilesBox,BorderLayout.CENTER);
+        JButton go = new JButton(new AbstractAction(labels.getString(_labels.go.name())) {
+			private static final long serialVersionUID = 7605151410870720861L;
+			public void actionPerformed(ActionEvent e) {
+				if (smilesBox.getSelectedItem() != null) {
+					String s = smilesBox.getSelectedItem().toString();
+					createMoleculeFromSMILES(s);
+				}
+			}
+        }
+        		);
+        add(go,BorderLayout.EAST);
+        go.setDefaultCapable(true);
+	}
+	protected boolean createMoleculeFromSMILES(String input) {
+		String errormsg = null;
+		input = input.replace('\n',' ').trim();
+		boolean cas = CASNumber.isValid(input);
+		boolean einecs = EINECS.isValid(input);
+		IAtomContainer a = null;
+		if (cas || einecs) {
+			if (Preferences.getProperty(Preferences.REMOTELOOKUP).equals("true")) {
+				a =  retrieveRemote(input);
+				if (a!=null) {
+					a.setID(input);
+					if (cas) a.setProperty(Property.CAS, input);
+					else if (einecs) a.setProperty(Property.EC, input);
+				} else {
+					errormsg = String.format("%s entered, failed to retrieve from remote server",
+								cas?"CAS":einecs?"EINECS":"Unknown query");
+				}
+			} else {
+				errormsg = String.format("%s %s entered, but remote queries are disabled. Enable remote queries via 'Method/Decision Tree Options/Remote query' menu.",
+						cas?"CAS":einecs?"EINECS":"Unknown query",input);
+			}
+		} else {
+			try {
+				a = FunctionalGroups.createAtomContainer(input,false);
+			} catch (Exception x) {
+				errormsg = x.getMessage();
+			}
+	    	if (a != null) {
+		    	a.setProperty(CDKConstants.COMMENT,labels.getString(_labels.createdBySMILES.name()));
+		    	a.setProperty(AmbitCONSTANTS.SMILES,input);
+		    	//a.setProperty(AmbitCONSTANTS.FORMULA,mf.analyseAtomContainer(a));
+	    	} else try {
+	    		errormsg = String.format(labels.getString(_labels.error_smiles.name()),input);
+	    		a = isInChI(input);
+	    		if (a != null) {
+		    		a.setProperty(CDKConstants.COMMENT,labels.getString(_labels.createdByInChI.name()));
+			    	a.setProperty(AmbitCONSTANTS.INCHI,input);
+			    	a.setID(input);
+	    		} else {
+	    			errormsg = String.format(labels.getString(_labels.error_inchi.name()),input);
+	    			Name2StructureProcessor p = new Name2StructureProcessor();
+	    			try {
+	    				a = p.process(input);
+	    			} catch (Exception x) {
+	    	    		a = null;
+	    	    		errormsg = x.getMessage();
+	    			}
+	    			if (a != null) {
+	    	    		a.setProperty(CDKConstants.COMMENT,labels.getString(_labels.createdByOpsin.name()));
+	    		    	a.setProperty(AmbitCONSTANTS.NAMES,input);
+	    		    	a.setID(input);
+	    		    	if (a instanceof IMolecule)
+	    		    	try {
+	    		    		SmilesGenerator g = new SmilesGenerator();
+	    		    		a.setProperty(AmbitCONSTANTS.SMILES, g.createSMILES((IMolecule)a));
+	    		    	} catch (Exception x) {};
+	    			} else
+	    				if (Preferences.getProperty(Preferences.REMOTELOOKUP).equals("true")) {
+	    					a =  retrieveRemote(input);
+	    					if (a!=null) {
+	    						a.setID(input);
+	    						if (cas) a.setProperty(Property.CAS, input);
+	    						else if (einecs) a.setProperty(Property.EC, input);
+	    						else a.setProperty(Property.Names, input);
+	    					} else {
+	    						errormsg = String.format("%s entered, failed to retrieve from remote server",
+	    									cas?"CAS":einecs?"EINECS":"Unknown query");
+	    					}
+	    				} else {
+	    					errormsg = String.format("%s '%s' entered. Name to structure conversion failed. Please enable remote queries via 'Method/Decision Tree Options/Remote query' menu.",
+	    							"Name",input);
+	    				}
+	    		}
+	    	} catch (Exception x) {
+	    		a = null;
+	    		errormsg = x.getMessage();
+	    	}
+		}
+    	if (a != null) {
+    		if (a instanceof IMolecule)
+	            try {
+	            	if (sdg == null) sdg = new StructureDiagramGenerator();
+	            	if (ConnectivityChecker.isConnected(a)) {
+	                    sdg.setMolecule((IMolecule)a);
+	                    sdg.generateCoordinates(new Vector2d(0,1));
+	                    a = sdg.getMolecule();
+	            	} else {
+		            	IMoleculeSet molecules = ConnectivityChecker.partitionIntoMolecules(a);
+		                a.removeAllElements();
+		        		for (int i=0; i< molecules.getMoleculeCount();i++) {
+		       				sdg.setMolecule(molecules.getMolecule(i));
+		       				sdg.generateCoordinates(new Vector2d(0,1));
+		       				a.add(sdg.getMolecule());
+		        		}
+	            	}
+	            } catch (Exception x) {
+	                System.err.println(x);
+	            }
+	        setMolecule(a);
+	        smilesBox.addItem(input);
+	        return true;
+    	} else {
+			JOptionPane.showMessageDialog(getParent(),
+				    //"You have entered an invalid SMILES or InChI, please try again.",
+				    errormsg,
+				    "Please try again",
+				    JOptionPane.ERROR_MESSAGE);
+			return false;
+    	}
+	}
+	public IAtomContainer isInChI(String inchi) throws Exception {
+		if (inchi.startsWith(AmbitCONSTANTS.INCHI)) {
+			InChIGeneratorFactory f = InChIGeneratorFactory.getInstance();
+			InChIToStructure c =f.getInChIToStructure(inchi, SilentChemObjectBuilder.getInstance());
+			if ((c==null) || (c.getAtomContainer()==null) || (c.getAtomContainer().getAtomCount()==0))
+				throw new Exception("Invalid InChI");
+			return c.getAtomContainer();
+		} else return null;
+	}
+	/* (non-Javadoc)
+	 * @see java.awt.event.ItemListener#itemStateChanged(java.awt.event.ItemEvent)
+	 */
+	public void itemStateChanged(ItemEvent evt) {
+	    Object source = evt.getSource();
+	    try {
+	    	if ((source == smilesBox) && isVisible()) {
+	    		if (evt.getStateChange() == ItemEvent.SELECTED) {
+	    			String smiles = evt.getItem().toString();
+	    	    	if (createMoleculeFromSMILES(smiles))
+						smilesBox.repaint();
+	    	    }
+	    	    repaint();
+	    	}
+	    } catch (NullPointerException ex) {
+	    	ex.printStackTrace();
+	    }
+	}
+	/* (non-Javadoc)
+	 * @see java.awt.event.ActionListener#actionPerformed(java.awt.event.ActionEvent)
+	 */
+	public void actionPerformed(ActionEvent e) {
+	}
+	protected IAtomContainer retrieveRemote(String input)  {
+		try {
+			RemoteCompoundLookup lookup = new RemoteCompoundLookup();
+			return lookup.lookup(input);
+		} catch (Exception x) {
+			return null;
+		}
+	}
+}