GUIVertexInspector.java

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/*
 *   DENOPTIM
 *   Copyright (C) 2020 Marco Foscato <marco.foscato@uib.no>
 *
 *   This program is free software: you can redistribute it and/or modify
 *   it under the terms of the GNU Affero General Public License as published
 *   by the Free Software Foundation, either version 3 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 Affero General Public License for more details.
 *
 *   You should have received a copy of the GNU Affero General Public License
 *   along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */
 
package denoptim.gui;
 
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Component;
import java.awt.Cursor;
import java.awt.Dimension;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
import java.io.BufferedReader;
import java.io.File;
import java.io.InputStreamReader;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.concurrent.atomic.AtomicInteger;
 
import javax.swing.BoxLayout;
import javax.swing.DefaultListModel;
import javax.swing.GroupLayout;
import javax.swing.JButton;
import javax.swing.JComponent;
import javax.swing.JLabel;
import javax.swing.JList;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.JSeparator;
import javax.swing.JSpinner;
import javax.swing.JSpinner.DefaultEditor;
import javax.swing.ListSelectionModel;
import javax.swing.SpinnerNumberModel;
import javax.swing.SwingConstants;
import javax.swing.UIManager;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
import javax.swing.table.DefaultTableModel;
import javax.vecmath.Point3d;
 
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBond;
 
import denoptim.constants.DENOPTIMConstants;
import denoptim.exception.DENOPTIMException;
import denoptim.files.FileAndFormat;
import denoptim.files.FileUtils;
import denoptim.fragmenter.FragmenterTools;
import denoptim.graph.APClass;
import denoptim.graph.AttachmentPoint;
import denoptim.graph.DGraph;
import denoptim.graph.Edge.BondType;
import denoptim.graph.EmptyVertex;
import denoptim.graph.Fragment;
import denoptim.graph.Vertex;
import denoptim.graph.Vertex.BBType;
import denoptim.io.DenoptimIO;
import denoptim.programs.fragmenter.CuttingRule;
import denoptim.programs.fragmenter.FragmenterParameters;
import denoptim.utils.DummyAtomHandler;
import denoptim.utils.MoleculeUtils;
 
 
public class GUIVertexInspector extends GUICardPanel
{
    private static final long serialVersionUID = 912850110991449553L;
    
    public static AtomicInteger prepVrtxTabUID = new AtomicInteger(1);
    
    private ArrayList<Vertex> verticesLibrary = new ArrayList<Vertex>();
    
    private Vertex vertex;
    
    private int currVrtxIdx = 0;
    
    private boolean unsavedChanges = false;
    
    private VertexViewPanel vertexViewer;
    private JPanel ctrlPane;
    private JPanel navigPanel;
    private JPanel navigPanel2;
    private JPanel navigPanel3;
    
    private JButton btnAddVrtx;
    private JButton btnDelVrtx;
    
    private JButton btnOpenVrtxs;
    
    private JSpinner navigSpinner;
    private JLabel totalVrtxsLabel;
    private final VrtxSpinnerChangeEvent vrtxSpinnerListener = 
            new VrtxSpinnerChangeEvent();
    
    private JPanel pnlImportStruct;
    private JButton btnOpenMol;
    private JButton btnOpenSMILES;
    
    private JPanel pnlEmptFrag;
    private JButton btnEmptFrag;
    
    private JPanel pnlAtmToAP;
    private JButton btnAtmToAP;
 
    private JPanel pnlBondToAPPair;
    private JButton btnBondToAPPair;
 
    private JPanel pnlTmplBasedChop;
    private JButton btnTmplBldChop;
 
    private JPanel pnlChop;
    private JButton btnChop;
    
    private JPanel pnlDelSel;
    private JButton btnDelSel;
    
    private JPanel pnlSaveEdits;
    private JButton btnSaveEdits;
 
    
//-----------------------------------------------------------------------------
    
    public GUIVertexInspector(GUIMainPanel mainPanel)
    {
        super(mainPanel, "Vertex Inspector #" + prepVrtxTabUID.getAndIncrement());
        super.setLayout(new BorderLayout());
        initialize();
    }
    
//-----------------------------------------------------------------------------
 
    private void initialize() {
        
        // BorderLayout is needed to allow dynamic resizing!
        this.setLayout(new BorderLayout()); 
        
        // This card structure includes center, east and south panels:
        // - (Center) molecular/graph viewer and APs
        // - (East) vertex controls
        // - (South) general controls (load, save, close)
        
        // The viewer with Jmol and APtable
        vertexViewer = new VertexViewPanel(true);
        vertexViewer.addPropertyChangeListener(
                IVertexAPSelection.APDATACHANGEEVENT, 
                new PropertyChangeListener() {
            @Override
            public void propertyChange(PropertyChangeEvent evt) {
                protectEditedSystem();              
            }
        });
        this.add(vertexViewer,BorderLayout.CENTER);
        
        // General panel on the right: it containing all controls
        ctrlPane = new JPanel();
        ctrlPane.setVisible(true);
        ctrlPane.setLayout(new BoxLayout(ctrlPane, SwingConstants.VERTICAL));
        ctrlPane.add(new JSeparator());
        
        // NB: avoid GroupLayout because it interferes with Jmol viewer and causes exception
        
        // Controls to navigate the list of vertices
        navigPanel = new JPanel();
        navigPanel2 = new JPanel();
        navigPanel3 = new JPanel();
        JLabel navigationLabel1 = new JLabel("Vertex # ");
        JLabel navigationLabel2 = new JLabel("Current library size: ");
        totalVrtxsLabel = new JLabel("0");
        
        navigSpinner = new JSpinner(new SpinnerNumberModel(0, 0, 0, 1));
        navigSpinner.setToolTipText("Move to vertex number # in the currently loaded library.");
        navigSpinner.setPreferredSize(new Dimension(75,20));
        navigSpinner.addChangeListener(vrtxSpinnerListener);
        navigPanel.add(navigationLabel1);
        navigPanel.add(navigSpinner);
        ctrlPane.add(navigPanel);
        
        navigPanel2.add(navigationLabel2);
        navigPanel2.add(totalVrtxsLabel);
        ctrlPane.add(navigPanel2);
        
        btnAddVrtx = new JButton("Add");
        btnAddVrtx.setToolTipText("Append vertices taken from a file.");
        btnAddVrtx.addActionListener(new ActionListener() {
            public void actionPerformed(ActionEvent e) {
                File inFile = GUIFileOpener.pickFile(btnAddVrtx);
                if (inFile == null || inFile.getAbsolutePath().equals(""))
                {
                    return;
                }
                
                ArrayList<Vertex> vrtxLib = new ArrayList<>();
                try {
                    vrtxLib = DenoptimIO.readVertexes(inFile, BBType.FRAGMENT);
                } catch (Exception e1) {
                    e1.printStackTrace();
                    JOptionPane.showMessageDialog(btnAddVrtx,
                            "<html>Could not read building blocks from file"
                            + "<br>'" + inFile + "'"
                            + "<br>Hint on cause: " + e1.getMessage() 
                            +"</html>",
                            "Error",
                            JOptionPane.ERROR_MESSAGE,
                            UIManager.getIcon("OptionPane.errorIcon"));
                    return;
                }
 
                if (vrtxLib.size() == 0)
                {
                    JOptionPane.showMessageDialog(btnAddVrtx,
                            "<html>No building blocks in file"
                            + "<br>'" + inFile + "'</html>",
                            "Error",
                            JOptionPane.ERROR_MESSAGE,
                            UIManager.getIcon("OptionPane.errorIcon"));
                    return;
                }
                
                if (vrtxLib.size() == 1)
                {
                    importVertices(vrtxLib);
                    return;
                }
                
                String[] options = new String[]{"All", 
                        "Selected",
                        "Cancel"};
                String txt = "<html><body width='%1s'>Do you want to "
                        + "append all building blocks or only selected ones?"
                        + "</html>";
                int res = JOptionPane.showOptionDialog(btnAddVrtx,
                        String.format(txt,200),
                        "Append Building Blocks",
                        JOptionPane.DEFAULT_OPTION,
                        JOptionPane.QUESTION_MESSAGE,
                        UIManager.getIcon("OptionPane.warningIcon"),
                        options,
                        options[0]);
                
                if (res == 2)
                {
                    return;
                }
                
                switch (res)
                {
                    case 0:
                        importVertices(vrtxLib);
                        break;
                        
                    case 1:
                        ArrayList<Vertex> selectedVrtxs = 
                                new ArrayList<Vertex>();
                        GUIVertexSelector vrtxSelector = new GUIVertexSelector(
                                btnAddVrtx,true);
                        vrtxSelector.setRequireApSelection(false);
                        vrtxSelector.load(vrtxLib, 0);
                        Object selected = vrtxSelector.showDialog();
 
                        if (selected != null)
                        {
                            @SuppressWarnings("unchecked")
                            ArrayList<ArrayList<Integer>> selList = 
                                    (ArrayList<ArrayList<Integer>>) selected;
                            for (ArrayList<Integer> pair : selList)
                            {
                                selectedVrtxs.add(vrtxLib.get(pair.get(0)));
                            }
                        }
                        importVertices(selectedVrtxs);
                        break;
                    
                    default:
                        return;
                }
            }
        });
        btnDelVrtx = new JButton("Remove");
        btnDelVrtx.setToolTipText("Remove the present building block from the "
                + "library.");
        btnDelVrtx.addActionListener(new ActionListener() {
            public void actionPerformed(ActionEvent e) {
                try {
                    removeCurrentVrtx();
                } catch (DENOPTIMException e1) {
                    System.out.println("Exception while removing the current "
                            + "building block:");
                    e1.printStackTrace();
                }
            }
        });
        navigPanel3.add(btnAddVrtx);
        navigPanel3.add(btnDelVrtx);
        ctrlPane.add(navigPanel3);
        
        ctrlPane.add(new JSeparator());
        
        pnlImportStruct = new JPanel();
        GroupLayout lyoImportStructure = new GroupLayout(pnlImportStruct);
        JLabel lblImportStruct = new JLabel("Import a structure from");
        btnOpenMol = new JButton("File");
        btnOpenMol.setToolTipText("Imports a chemical system"
                + " from file.");
        btnOpenMol.addActionListener(new ActionListener() {
            public void actionPerformed(ActionEvent e) {
                File inFile = GUIFileOpener.pickFile(btnOpenMol);
                if (inFile == null || inFile.getAbsolutePath().equals(""))
                {
                    return;
                }
                importStructureFromFile(inFile);
            }
        });
        
        // the '+' is to prevent search/replace of the string
        btnOpenSMILES = new JButton("SMI"+"LES"); 
        btnOpenSMILES.setToolTipText("<html>Imports chemical system"
                        + " from SMILES string.<br>The conversion of SMILES "
                        + "to 3D structure requires"
                        + "<br> an internet connection.</html>");
        btnOpenSMILES.addActionListener(new ActionListener() {
                public void actionPerformed(ActionEvent e) {
                    String smiles = JOptionPane.showInputDialog(btnOpenSMILES,
                            "Please input SMILES: ");
                    if (smiles != null && !smiles.trim().equals(""))
                    {
                        importStructureFromSMILES(smiles);
                    }
                }
        });
 
        pnlImportStruct.setLayout(lyoImportStructure);
        lyoImportStructure.setAutoCreateGaps(true);
        lyoImportStructure.setAutoCreateContainerGaps(true);
        lyoImportStructure.setHorizontalGroup(lyoImportStructure.createParallelGroup(
                                        GroupLayout.Alignment.CENTER)
                        .addComponent(lblImportStruct)
                        .addGroup(lyoImportStructure.createSequentialGroup()
                                        .addComponent(btnOpenMol)
                                        .addComponent(btnOpenSMILES)));
        lyoImportStructure.setVerticalGroup(lyoImportStructure.createSequentialGroup()
                        .addComponent(lblImportStruct)
                        .addGroup(lyoImportStructure.createParallelGroup()
                                    .addComponent(btnOpenMol)
                                    .addComponent(btnOpenSMILES)));       
        ctrlPane.add(pnlImportStruct);
 
        ctrlPane.add(new JSeparator());
        
        pnlEmptFrag = new JPanel();
        btnEmptFrag = new JButton("Create Empty Vertex");
        btnEmptFrag.setToolTipText("<html>Creates an empty vertex:<br>a vertex "
                + "that contains no molecular structure.<html>");
        btnEmptFrag.addActionListener(new ActionListener() {
            public void actionPerformed(ActionEvent e) {
                GUIEmptyVertexMaker makeEmptyVertexDialog = 
                        new GUIEmptyVertexMaker(btnEmptFrag, BBType.FRAGMENT);
                makeEmptyVertexDialog.pack();
                Object ev = makeEmptyVertexDialog.showDialog();
                if (ev == null)
                {
                    return;
                }
                ArrayList<Vertex> lst = new ArrayList<Vertex>(1);
                lst.add((EmptyVertex) ev);
                GUIVertexSelector fragSelector = new GUIVertexSelector(
                        btnEmptFrag,false);
                fragSelector.load(lst, 0);
                fragSelector.btnDone.setText("Confirm");
                fragSelector.ctrlPane.setVisible(false);
                fragSelector.setRequireApSelection(false);
                Object selected = fragSelector.showDialog();
                if (selected == null)
                {
                    return;
                }
                importVertices(lst);
            }
        });
        pnlEmptFrag.add(btnEmptFrag);
        ctrlPane.add(pnlEmptFrag);
        
        ctrlPane.add(new JSeparator());
        
        pnlAtmToAP = new JPanel();
        btnAtmToAP = new JButton("Atom to AP");
        btnAtmToAP.setToolTipText("<html>Replaces the selected atoms with "
                + "attachment points.<br>Click on atoms to select"
                + " them. Click again to unselect.<br>"
                + "<br><b>WARNING:</b> this action cannot be undone!<html>");
        btnAtmToAP.addActionListener(new ActionListener() {
            public void actionPerformed(ActionEvent e) {
                vertex = vertexViewer.getLoadedStructure();
                
                ArrayList<IAtom> selectedAtms = 
                        vertexViewer.getAtomsSelectedFromJMol();
                
                if (selectedAtms.size() == 0)
                {
                    JOptionPane.showMessageDialog(btnAtmToAP,
                            "<html>No atom selected! Click on atoms to select"
                            + " them.<br>Click again to unselect.</html>",
                            "Error",
                            JOptionPane.ERROR_MESSAGE,
                            UIManager.getIcon("OptionPane.errorIcon"));
                    return;
                }
                else
                {   
                    List<APClass> selectedAPCs = choseOrCreateNewAPClass(
                            btnAtmToAP, true);
                    
                    //The size of the list is either 0 or 1
                    if (selectedAPCs.size() == 0)
                    {
                        // We have pressed cancel or closed the dialog, so abandon
                        return;
                    }
                    String apClass = selectedAPCs.get(0).toString();
                    
                    ArrayList<IAtom> failed = new ArrayList<IAtom>();
                    for (IAtom atm : selectedAtms)
                    {
                        if (!convertAtomToAP(atm, apClass))
                        {
                            failed.add(atm);
                        }
                    }
                    for (IAtom atm : failed)
                    {
                        selectedAtms.remove(atm);
                    }
                    if (selectedAtms.size() == 0)
                    {
                        return;
                    }
                    
                    removeAtoms(selectedAtms);
 
                    vertexViewer.loadVertexToViewer(vertex);
                    
                    unsavedChanges = true;
                    protectEditedSystem();
                }
            }
        });
        pnlAtmToAP.add(btnAtmToAP);
        ctrlPane.add(pnlAtmToAP);
 
        pnlBondToAPPair = new JPanel();
        String bndToApLabel = "Bond to AP Pair";
        btnBondToAPPair = new JButton(bndToApLabel);
        btnBondToAPPair.setToolTipText("<html>Replaces bonds with "
                + "pairs of attachment points. "
                + "</br>Click on this button to start the selection of atoms that define the bonds to break."
                + "<br><b>WARNING:</b> this action cannot be undone!<html>");
        btnBondToAPPair.addActionListener(new ActionListener() {
            public void actionPerformed(ActionEvent e) {
                vertex = vertexViewer.getLoadedStructure();
 
                GUIAtomSelectionDialog firstAtomSelectionDialog = new GUIAtomSelectionDialog(
                    btnAtmToAP, vertex, null, 2, 1);
                Object firstSelected = firstAtomSelectionDialog.showDialog();
                if (firstSelected == null)
                {
                    return;
                }
                List<IAtom> firstSelAtoms = (List<IAtom>) firstSelected;
 
                GUIAtomSelectionDialog secondAtomSelectionDialog = new GUIAtomSelectionDialog(
                    btnAtmToAP, vertex, firstSelAtoms, 2, 2);
                Object secondSelected = secondAtomSelectionDialog.showDialog();
                if (secondSelected == null)
                {
                    return;
                }
                List<IAtom> secondSelAtoms = (List<IAtom>) secondSelected;
 
                List<List<List<IAtom>>> atomPairs = new ArrayList<>();
                if (firstSelAtoms.size() == secondSelAtoms.size())
                {
                    // Assume 2-center bonds
                    for (int i = 0; i < firstSelAtoms.size(); i++)
                    {
                        if (firstSelAtoms.get(i).getBond(secondSelAtoms.get(i)) == null)
                        {
                            String[] options = new String[]{"Ignore bonds", "Cancel"};
                            String txt =  "<html>Atom " 
                                + MoleculeUtils.getAtomRef(firstSelAtoms.get(i), vertex.getIAtomContainer()) 
                                + " is not bound to "
                                + MoleculeUtils.getAtomRef(secondSelAtoms.get(i), vertex.getIAtomContainer()) 
                                + ". Proceed the creation of AP pairs irrespective of the bonds?</html>";
                            int answer = JOptionPane.showOptionDialog(btnBondToAPPair,
                                    String.format(txt,200),
                                    "Ignore bonds?",
                                    JOptionPane.DEFAULT_OPTION,
                                    JOptionPane.QUESTION_MESSAGE,
                                    UIManager.getIcon("OptionPane.warningIcon"),
                                    options,
                                    options[1]);
                            if (answer == 1) 
                            {
                                return;
                            }
                        }
                        atomPairs.add(Arrays.asList(Arrays.asList(firstSelAtoms.get(i)), 
                        Arrays.asList(secondSelAtoms.get(i))));
                    }
                } else {
                    String[] options = new String[]{"Multihaptic bond", 
                        "Multidentate bonds",
                        "Cancel"};
                    String txt = "<html>Unequal number of atoms in the two sets. Bonds may "
                        + "be treated as:<ul>"
                        + "<li> multihapto bond (create a single AP pair)</li>"
                        + "<li> multiple multidentate bonds (create multiple AP pairs)</li>"
                        + "</ul>"
                        + "<br>How to threat the selected atoms?</html>";
                    int answer = JOptionPane.showOptionDialog(btnBondToAPPair,
                            String.format(txt,200),
                            "Multihaptic or Multidentate?",
                            JOptionPane.DEFAULT_OPTION,
                            JOptionPane.QUESTION_MESSAGE,
                            UIManager.getIcon("OptionPane.warningIcon"),
                            options,
                            options[2]);
                    
                    if (answer == 0) 
                    {
                        // Assume multihapto bonds
                        if (firstSelAtoms.size() < secondSelAtoms.size())
                        {
                            Set<IAtom> assignedSecondAtoms = new HashSet<>();
                            for (int i = 0; i < firstSelAtoms.size(); i++)
                            {
                                IAtom firstAtom = firstSelAtoms.get(i);
                                List<IAtom> secondAtomsConnectedToFirstAtom = new ArrayList<>();
                                for (int j = 0; j < secondSelAtoms.size(); j++)
                                {
                                    IAtom secondAtom = secondSelAtoms.get(j);
                                    if (firstAtom.getBond(secondAtom) != null)
                                    {
                                        if (i>0 && assignedSecondAtoms.contains(secondSelAtoms.get(j)))
                                        {
                                            JOptionPane.showMessageDialog(btnBondToAPPair,
                                                "<html>Atom " 
                                                + MoleculeUtils.getAtomRef(secondAtom, vertex.getIAtomContainer()) 
                                                + " is bound to "
                                                + MoleculeUtils.getAtomRef(firstAtom, vertex.getIAtomContainer()) 
                                                + " but is already assigned to another atom. "
                                                + "<br>Aborting: you'll have to break bonds involving "
                                                + MoleculeUtils.getAtomRef(secondAtom, vertex.getIAtomContainer()) 
                                                + " one at the time.</html>",
                                                "Error",
                                                JOptionPane.ERROR_MESSAGE,
                                                UIManager.getIcon("OptionPane.errorIcon"));
                                            return;
                                        }
                                        assignedSecondAtoms.add(secondAtom);
                                        secondAtomsConnectedToFirstAtom.add(secondAtom);
                                    }
                                }
                                if (secondAtomsConnectedToFirstAtom.size() == 0)
                                {
                                    JOptionPane.showMessageDialog(btnBondToAPPair,
                                        "<html>No atoms in the second set is connected to atom " 
                                        + MoleculeUtils.getAtomRef(firstAtom, vertex.getIAtomContainer()) 
                                        + ". Aborting.</html>",
                                        "Error",
                                        JOptionPane.ERROR_MESSAGE,
                                        UIManager.getIcon("OptionPane.errorIcon"));
                                    return;
                                }
                                atomPairs.add(Arrays.asList(Arrays.asList(firstAtom), secondAtomsConnectedToFirstAtom));
                            }
                        } else {
                        Set<IAtom> assignedFirstAtoms = new HashSet<>();
                        for (int i = 0; i < secondSelAtoms.size(); i++)
                        {
                            IAtom secondAtom = secondSelAtoms.get(i);
                            List<IAtom> firstAtomsConnectedToSecondAtom = new ArrayList<>();
                            for (int j = 0; j < firstSelAtoms.size(); j++)
                            {
                                IAtom firstAtom = firstSelAtoms.get(j);
                                if (firstAtom.getBond(secondAtom) != null)
                                {
                                    if (i>0 && assignedFirstAtoms.contains(firstSelAtoms.get(j)))
                                    {
                                        JOptionPane.showMessageDialog(btnBondToAPPair,
                                            "<html>Atom " 
                                            + MoleculeUtils.getAtomRef(firstAtom, vertex.getIAtomContainer()) 
                                            + " is bound to "
                                            + MoleculeUtils.getAtomRef(secondAtom, vertex.getIAtomContainer()) 
                                            + " but is already assigned to another atom. "
                                            + "<br>Aborting: you'll have to break bonds involving "
                                            + MoleculeUtils.getAtomRef(firstAtom, vertex.getIAtomContainer()) 
                                            + " one at the time.</html>",
                                            "Error",
                                            JOptionPane.ERROR_MESSAGE,
                                            UIManager.getIcon("OptionPane.errorIcon"));
                                        return;
                                    }
                                    assignedFirstAtoms.add(firstAtom);
                                    firstAtomsConnectedToSecondAtom.add(firstAtom);
                                }
                            }
                            if (firstAtomsConnectedToSecondAtom.size() == 0)
                            {
                                JOptionPane.showMessageDialog(btnBondToAPPair,
                                    "<html>No atoms in the second set is connected to atom " 
                                    + MoleculeUtils.getAtomRef(secondAtom, vertex.getIAtomContainer()) 
                                    + ". Aborting.</html>",
                                    "Error",
                                    JOptionPane.ERROR_MESSAGE,
                                    UIManager.getIcon("OptionPane.errorIcon"));
                                return;
                            }
                            atomPairs.add(Arrays.asList(firstAtomsConnectedToSecondAtom, Arrays.asList(secondAtom)));
                        }
                    }
                    } else if (answer == 1) {
                        // Assume multiple multidentate bonds
                        for (IAtom firstAtom : firstSelAtoms)
                        {
                            for (IAtom secondAtom : secondSelAtoms)
                            {
                                if (firstAtom.getBond(secondAtom) != null)
                                {
                                    atomPairs.add(Arrays.asList(Arrays.asList(firstAtom), Arrays.asList(secondAtom)));
                                }
                            }
                        }
                    } else {
                        return;
                    }
                }
 
                List<List<APClass>> apClasses = new ArrayList<>();
                List<APClass> selectedAPCs = choseOrCreateNewAPClass(
                    btnBondToAPPair, true, "APClass on 1st set of atoms");
                if (selectedAPCs.size() == 0)
                {
                    return;
                }
                APClass apc0 = selectedAPCs.get(0);
 
                selectedAPCs = choseOrCreateNewAPClass(
                    btnBondToAPPair, true, "APClass on 2nd set of atoms");
                if (selectedAPCs.size() == 0)
                {
                    return;
                }
                APClass apc1 = selectedAPCs.get(0);
                for (int i = 0; i < atomPairs.size(); i++)
                {
                    apClasses.add(Arrays.asList(apc0, apc1));
                }
 
                // Get default parameters
                FragmenterParameters settings = new FragmenterParameters();
 
                // Now chop the structure to produce fragments
                List<Vertex> fragments;
                try
                {
                    fragments = FragmenterTools.fragmentation(
                            vertex.getIAtomContainer(), 
                            atomPairs, 
                            apClasses);
                } catch (Throwable t)
                {
                    JOptionPane.showMessageDialog(btnChop,String.format(
                            "<html><body width='%1s'"
                            + "Could not complete fragmentation. Hint: "
                            + t.getMessage() + "</html>", 400),
                            "Error",
                            JOptionPane.ERROR_MESSAGE,
                            UIManager.getIcon("OptionPane.errorIcon"));
                    return;
                }
                
                // Add linearity-breaking dummy atoms
                for (Vertex frag : fragments)
                {
                    DummyAtomHandler.addDummiesOnLinearities((Fragment) frag,
                            settings.getLinearAngleLimit());
                }
                
                // Signal no result obtained
                if (fragments.size() < 1 || (fragments.size() == 1 &&
                        ((Fragment)fragments.get(0)).isIsomorphicTo(vertex)))
                {
                    JOptionPane.showMessageDialog(btnAddVrtx,
                            "<html>Fragmentation produced no fragments!</html>",
                            "Error",
                            JOptionPane.WARNING_MESSAGE,
                            UIManager.getIcon("OptionPane.warningIcon"));
                    return;
                }
                
                // The resulting fragments are loaded into the viewer, without
                // removing the original structure.
                
                String[] options = new String[]{"All", 
                        "Select",
                        "Cancel"};
                String txt = "<html><body width='%1s'>Fragmentation produced "
                        + fragments.size() + " fragments. Do you want to "
                        + "append all or select some?"
                        + "</html>";
                int answer = JOptionPane.showOptionDialog(btnAddVrtx,
                        String.format(txt,200),
                        "Append Building Blocks",
                        JOptionPane.DEFAULT_OPTION,
                        JOptionPane.QUESTION_MESSAGE,
                        UIManager.getIcon("OptionPane.warningIcon"),
                        options,
                        options[0]);
                
                if (answer == 2)
                {
                    return;
                }
                
                switch (answer)
                {
                    case 0:
                        importVertices(fragments);
                        break;
                        
                    case 1:
                        List<Vertex> selectedVrtxs = 
                                new ArrayList<Vertex>();
                        GUIVertexSelector vrtxSelector = new GUIVertexSelector(
                                btnAddVrtx,true);
                        vrtxSelector.setRequireApSelection(false);
                        vrtxSelector.load(fragments, 0);
                        Object selected = vrtxSelector.showDialog();
 
                        if (selected != null)
                        {
                            @SuppressWarnings("unchecked")
                            List<ArrayList<Integer>> selList = 
                                    (ArrayList<ArrayList<Integer>>) selected;
                            for (ArrayList<Integer> pair : selList)
                            {
                                selectedVrtxs.add(fragments.get(pair.get(0)));
                            }
                        }
                        importVertices(selectedVrtxs);
                        break;
                    
                    default:
                        return;
                }
            }
        });
        pnlBondToAPPair.add(btnBondToAPPair);
        ctrlPane.add(pnlBondToAPPair);
        
        pnlChop = new JPanel();
        btnChop = new JButton("Chop Structure");
        btnChop.setToolTipText(String.format("<html><body width='%1s'>"
                + "Applies cutting rules on "
                + "the current structure to generate fragments.</html>", 400));
        btnChop.addActionListener(new ActionListener() {
            public void actionPerformed(ActionEvent event) {
                vertex = vertexViewer.getLoadedStructure();
                if (vertex==null 
                        || vertex.getIAtomContainer().getBondCount() == 0)
                {
                    JOptionPane.showMessageDialog(btnChop,
                            "<html>System contains 0 bonds. "
                            + "Nothing to chop.</html>",
                            "Error",
                            JOptionPane.ERROR_MESSAGE,
                            UIManager.getIcon("OptionPane.errorIcon"));
                    return;
                }
                
                FragmenterParameters settings = new FragmenterParameters();
                boolean result = dialogToDefineCuttingRules(
                        settings, 
                        this.getClass().getClassLoader(), 
                        btnChop, 
                        false);
                if (!result)
                    return;
                
                String pathnameLastUsedCutRules = 
                        settings.getCuttingRulesFilePathname();
                if (pathnameLastUsedCutRules != null 
                        && !pathnameLastUsedCutRules.isBlank())
                {
                    GUIPreferences.lastCutRulesFile = 
                            new File(pathnameLastUsedCutRules);
                }
                
                // Now chop the structure to produce fragments
                List<Vertex> fragments;
                try
                {
                    fragments = FragmenterTools.fragmentation(
                            vertex.getIAtomContainer(), 
                            settings.getCuttingRules(), 
                            settings.getLogger());
                } catch (DENOPTIMException e)
                {
                    JOptionPane.showMessageDialog(btnChop,String.format(
                            "<html><body width='%1s'"
                            + "Could not complete fragmentation. Hint: "
                            + e.getMessage() + "</html>", 400),
                            "Error",
                            JOptionPane.ERROR_MESSAGE,
                            UIManager.getIcon("OptionPane.errorIcon"));
                    return;
                }
                
                // Add linearity-breaking dummy atoms
                for (Vertex frag : fragments)
                {
                    DummyAtomHandler.addDummiesOnLinearities((Fragment) frag,
                            settings.getLinearAngleLimit());
                }
                
                // Signal no result obtained
                if (fragments.size() < 1 || (fragments.size() == 1 &&
                        ((Fragment)fragments.get(0)).isIsomorphicTo(vertex)))
                {
                    JOptionPane.showMessageDialog(btnAddVrtx,
                            "<html>Fragmentation produced no fragments!</html>",
                            "Error",
                            JOptionPane.WARNING_MESSAGE,
                            UIManager.getIcon("OptionPane.warningIcon"));
                    return;
                }
                
                // The resulting fragments are loaded into the viewer, without
                // removing the original structure.
                
                String[] options = new String[]{"All", 
                        "Select",
                        "Cancel"};
                String txt = "<html><body width='%1s'>Fragmentation produced "
                        + fragments.size() + " fragments. Do you want to "
                        + "append all or select some?"
                        + "</html>";
                int answer = JOptionPane.showOptionDialog(btnAddVrtx,
                        String.format(txt,200),
                        "Append Building Blocks",
                        JOptionPane.DEFAULT_OPTION,
                        JOptionPane.QUESTION_MESSAGE,
                        UIManager.getIcon("OptionPane.warningIcon"),
                        options,
                        options[0]);
                
                if (answer == 2)
                {
                    return;
                }
                
                switch (answer)
                {
                    case 0:
                        importVertices(fragments);
                        break;
                        
                    case 1:
                        List<Vertex> selectedVrtxs = 
                                new ArrayList<Vertex>();
                        GUIVertexSelector vrtxSelector = new GUIVertexSelector(
                                btnAddVrtx,true);
                        vrtxSelector.setRequireApSelection(false);
                        vrtxSelector.load(fragments, 0);
                        Object selected = vrtxSelector.showDialog();
 
                        if (selected != null)
                        {
                            @SuppressWarnings("unchecked")
                            List<ArrayList<Integer>> selList = 
                                    (ArrayList<ArrayList<Integer>>) selected;
                            for (ArrayList<Integer> pair : selList)
                            {
                                selectedVrtxs.add(fragments.get(pair.get(0)));
                            }
                        }
                        importVertices(selectedVrtxs);
                        break;
                    
                    default:
                        return;
                }
            }
        });
        pnlChop.add(btnChop);
        ctrlPane.add(pnlChop);
 
        pnlTmplBasedChop = new JPanel();
        btnTmplBldChop = new JButton("Chop by Template");
        btnTmplBldChop.setToolTipText(String.format("<html><body width='%1s'>"
                + "Chops the current structure according to a given graph template expected to be a substructure of the current structure.</html>", 400));
        btnTmplBldChop.addActionListener(new ActionListener() {
            public void actionPerformed(ActionEvent event) {
                // NB: we call it vertex because we are in the vertex viewer, but it is a structure that may not be a vertex.
                vertex = vertexViewer.getLoadedStructure();
                if (vertex==null)
                {
                    return;
                }
 
                File inFile = GUIFileOpener.pickFile(btnTmplBldChop);
                if (inFile == null || inFile.getAbsolutePath().equals(""))
                {
                    return;
                }
                
                List<DGraph> fragmentationTmpls = new ArrayList<>();
                try
                {
                    fragmentationTmpls = DenoptimIO.readDENOPTIMGraphsFromFile(inFile);
                } catch (Throwable e)
                {
                    JOptionPane.showMessageDialog(btnTmplBldChop,String.format(
                            "<html><body width='%1s'"
                            + "Could not read template file. Hint: "
                            + e.getMessage() + "</html>", 400),
                            "Error",
                            JOptionPane.ERROR_MESSAGE,
                            UIManager.getIcon("OptionPane.errorIcon"));
                    return;
                }
 
                if (fragmentationTmpls.size() == 0)
                {
                    JOptionPane.showMessageDialog(btnTmplBldChop,
                            "<html>No graphs found in file '"
                            + inFile + "'.</html>",
                            "Error",
                            JOptionPane.ERROR_MESSAGE,
                            UIManager.getIcon("OptionPane.errorIcon"));
                    return;
                }
 
                FragmenterParameters settings = new FragmenterParameters();
                settings.setFragmentationTmpls(fragmentationTmpls);
                
                // Now chop the structure to produce fragments
                List<Vertex> fragments;
                try
                {
                    fragments = FragmenterTools.fragmentation(vertex.getIAtomContainer(),
                        settings.getFragmentationTmpls(), 
                        settings.getMaxBufferShellSize(),
                        settings.getRandomizer(), 
                        settings.getLogger());
                } catch (DENOPTIMException e)
                {
                    JOptionPane.showMessageDialog(btnChop,String.format(
                            "<html><body width='%1s'"
                            + "Could not complete fragmentation. Hint: "
                            + e.getMessage() + "</html>", 400),
                            "Error",
                            JOptionPane.ERROR_MESSAGE,
                            UIManager.getIcon("OptionPane.errorIcon"));
                    return;
                }
                
                // Add linearity-breaking dummy atoms
                for (Vertex frag : fragments)
                {
                    DummyAtomHandler.addDummiesOnLinearities((Fragment) frag,
                            settings.getLinearAngleLimit());
                }
                
                // Signal no result obtained
                if (fragments.size() < 1 || (fragments.size() == 1 &&
                        ((Fragment)fragments.get(0)).isIsomorphicTo(vertex)))
                {
                    JOptionPane.showMessageDialog(btnAddVrtx,
                            "<html>Fragmentation produced no fragments!</html>",
                            "Error",
                            JOptionPane.WARNING_MESSAGE,
                            UIManager.getIcon("OptionPane.warningIcon"));
                    return;
                }
                
                // The resulting fragments are loaded into the viewer, without
                // removing the original structure.
                
                String[] options = new String[]{"All", 
                        "Select",
                        "Cancel"};
                String txt = "<html><body width='%1s'>Fragmentation produced "
                        + fragments.size() + " fragments. Do you want to "
                        + "append all or select some?"
                        + "</html>";
                int answer = JOptionPane.showOptionDialog(btnAddVrtx,
                        String.format(txt,200),
                        "Append Building Blocks",
                        JOptionPane.DEFAULT_OPTION,
                        JOptionPane.QUESTION_MESSAGE,
                        UIManager.getIcon("OptionPane.warningIcon"),
                        options,
                        options[0]);
                
                if (answer == 2)
                {
                    return;
                }
                
                switch (answer)
                {
                    case 0:
                        importVertices(fragments);
                        break;
                        
                    case 1:
                        List<Vertex> selectedVrtxs = 
                                new ArrayList<Vertex>();
                        GUIVertexSelector vrtxSelector = new GUIVertexSelector(
                                btnAddVrtx,true);
                        vrtxSelector.setRequireApSelection(false);
                        vrtxSelector.load(fragments, 0);
                        Object selected = vrtxSelector.showDialog();
 
                        if (selected != null)
                        {
                            @SuppressWarnings("unchecked")
                            List<ArrayList<Integer>> selList = 
                                    (ArrayList<ArrayList<Integer>>) selected;
                            for (ArrayList<Integer> pair : selList)
                            {
                                selectedVrtxs.add(fragments.get(pair.get(0)));
                            }
                        }
                        importVertices(selectedVrtxs);
                        break;
                    
                    default:
                        return;
                }
            }
        });
        pnlTmplBasedChop.add(btnTmplBldChop);
        ctrlPane.add(pnlTmplBasedChop);
        
        pnlDelSel = new JPanel();
        btnDelSel = new JButton("Remove Atoms");
        btnDelSel.setToolTipText("<html>Removes all selected atoms from the "
                + "system.<br><br><b>WARNING:</b> this action cannot be "
                + "undone!");
        btnDelSel.addActionListener(new ActionListener() {
            public void actionPerformed(ActionEvent e) {
                ArrayList<IAtom> selectedAtms = 
                        vertexViewer.getAtomsSelectedFromJMol();
                
                if (selectedAtms.size() == 0)
                {
                    JOptionPane.showMessageDialog(btnDelSel,
                            "<html>No atom selected! Click on atoms to select"
                            + " them.<br>Click again to unselect.</html>",
                            "Error",
                            JOptionPane.ERROR_MESSAGE,
                            UIManager.getIcon("OptionPane.errorIcon"));
                    return;
                }
                else
                {                   
                    removeAtoms(selectedAtms);
                    
                    vertexViewer.loadVertexToViewer(vertex);
                    
                    unsavedChanges = true;
                    protectEditedSystem();
                }
            }
        });
        pnlDelSel.add(btnDelSel);
        ctrlPane.add(pnlDelSel);
        
        ctrlPane.add(new JSeparator());
        
        pnlSaveEdits = new JPanel();
        btnSaveEdits = new JButton("Save Changes");
        //btnSaveEdits.setForeground(Color.RED);
        btnSaveEdits.setEnabled(true);
        btnSaveEdits.setToolTipText("<html>Save the current system replacing"
                + " <br>the original one in the loaded library.</html>");
        btnSaveEdits.addActionListener(new ActionListener() {
                public void actionPerformed(ActionEvent e) {
                    saveUnsavedChanges();
                }
        });
        pnlSaveEdits.add(btnSaveEdits);
        ctrlPane.add(pnlSaveEdits);
        this.add(ctrlPane, BorderLayout.EAST);
        
        
        // Panel with buttons to the bottom of the frame
        ButtonsBar commandsPane = new ButtonsBar();
        super.add(commandsPane, BorderLayout.SOUTH);
        
        btnOpenVrtxs = new JButton("Load Library of Building Blocks");
        btnOpenVrtxs.setToolTipText("Reads building blocks or structures from "
                + "file.");
        btnOpenVrtxs.addActionListener(new ActionListener() {
            public void actionPerformed(ActionEvent e) {
                File inFile = GUIFileOpener.pickFile(btnOpenVrtxs);
                if (inFile == null || inFile.getAbsolutePath().equals(""))
                {
                    return;
                }
                ArrayList<Vertex> vrtxLib = new ArrayList<>();
                try {
                    vrtxLib = DenoptimIO.readVertexes(inFile, BBType.FRAGMENT);
                } catch (Exception e1) {
                    e1.printStackTrace();
                    JOptionPane.showMessageDialog(btnAddVrtx,
                            "<html>Could not read building blocks from file"
                            + "<br>'" + inFile + "'"
                            + "<br>Hint on cause: " + e1.getMessage() 
                            +"</html>",
                            "Error",
                            JOptionPane.ERROR_MESSAGE,
                            UIManager.getIcon("OptionPane.errorIcon"));
                    return;
                }
 
                if (vrtxLib.size() == 0)
                {
                    JOptionPane.showMessageDialog(btnAddVrtx,
                            "<html>No building blocks in file"
                            + "<br>'" + inFile + "'</html>",
                            "Error",
                            JOptionPane.ERROR_MESSAGE,
                            UIManager.getIcon("OptionPane.errorIcon"));
                    return;
                }
                importVertices(vrtxLib);
            }
        });
        commandsPane.add(btnOpenVrtxs);
        
        JButton btnSaveVrtxs = new JButton("Save Library of Building Blocks");
        btnSaveVrtxs.setToolTipText("Write all building blocks to a file.");
        btnSaveVrtxs.addActionListener(new ActionListener() {
            public void actionPerformed(ActionEvent e) {
                FileAndFormat fileAndFormat = 
                        GUIFileSaver.pickFileForSavingVertexes(btnSaveVrtxs);
                if (fileAndFormat == null)
                {
                    return;
                }
                File outFile = fileAndFormat.file;
                try
                {
                    // The writing method may change the extension. So we need
                    // to get the return value.
                    outFile = DenoptimIO.writeVertexesToFile(outFile,
                            fileAndFormat.format,
                            verticesLibrary);
                }
                catch (Exception ex)
                {
                    ex.printStackTrace();
                    JOptionPane.showMessageDialog(btnSaveVrtxs,
                            "Could not write to '" + outFile + "'! "
                            + "Hint: "+ex.getMessage(),
                            "Error",
                            JOptionPane.PLAIN_MESSAGE,
                            UIManager.getIcon("OptionPane.errorIcon"));
                    return;
                }
                navigSpinner.setModel(new SpinnerNumberModel(currVrtxIdx+1, 1, 
                        verticesLibrary.size(), 1));
                deprotectEditedSystem();
                unsavedChanges = false;
                FileUtils.addToRecentFiles(outFile, fileAndFormat.format);
            }
        });
        commandsPane.add(btnSaveVrtxs);
 
        JButton btnCanc = new JButton("Close Tab");
        btnCanc.setToolTipText("Closes this tab.");
        btnCanc.addActionListener(new removeCardActionListener(this));
        commandsPane.add(btnCanc);
        
        JButton btnHelp = new JButton("?");
        btnHelp.setToolTipText("<html>Hover over the buttons and fields "
                    + "to get a tip.</html>");
        btnHelp.addActionListener(new ActionListener() {
            public void actionPerformed(ActionEvent e) {
                String txt = "<html><body width='%1s'>"
                        + "<p>This tab allows to create, inspect, and edit "
                        + "building blocks and "
                        + "three-dimensional molecular fragments.</p>"
                        + "<p>New fragments can be created starting from any "
                        + "chemical structure that can be loaded from file or "
                        + "generated from SMILES (SMILES-to-3D conversion "
                        + "requires an Internet connection).</p>"
                        + "<p>Any terminal atom (i.e., atoms that have only "
                        + "one connected neighbor) can be transformed into "
                        + "on attachment point (AP). Click on the atom to "
                        + "select it, and press <code><b>Atom to AP</b></code>."
                        + "</p>"
                        + "<p>Attachment points are depicted in the molecular "
                        + "viewer as yellow arrows in the 3D space, and their "
                        + "attachment point class (APClass) is specified in "
                        + "the table below the viewer. Double-click on a "
                        + "specific APClass field to change its value.</p>"
                        + "<br>"
                        + "<p>Hover over buttons get a tip.</p>"
                        + "<br>"
                        + "<p>Right-click on the Jmol viewer will open the "
                        + "Jmol menu. However, since Jmol cannot handle the "
                        + "attachment points data. Therefore, Jmol "
                        + "functionality should only be used on systems "
                        + "that have no attachment points, or for alterations "
                        + "of the molecular structure that do not change the "
                        + "list of atoms au to the last atom decorated with an "
                        + "attachment point.</p></html>";
                JOptionPane.showMessageDialog(btnHelp, 
                        String.format(txt, 400),
                        "Tips",
                        JOptionPane.PLAIN_MESSAGE);
            }
        });
        commandsPane.add(btnHelp);
    }
    
//-----------------------------------------------------------------------------
    
    public static boolean dialogToDefineCuttingRules(
            FragmenterParameters settings, ClassLoader classLoader,
            Component parent,
            boolean setMolToGraphSettings)
    {
        settings.startConsoleLogger("GUI-controlledFragmenterLogger");
        
        List<CuttingRule> defaultCuttingRules = new ArrayList<CuttingRule>();
        try
        {
            defaultCuttingRules = settings.getDefaultCuttingRules(classLoader);
        } catch (Exception e )
        {
            e.printStackTrace();
            JOptionPane.showMessageDialog(parent,String.format(
                    "<html><body width='%1s'>"
                    + "Could not read default cutting rules from "
                    + "bundled jar. "
                    + "Hint: "
                    + e.getMessage() + "</html>", 400),
                    "Error",
                    JOptionPane.ERROR_MESSAGE,
                    UIManager.getIcon("OptionPane.errorIcon"));
            return false;
        }
     
        // Read last used cutting rules
        List<CuttingRule> customCuttingRules = new ArrayList<CuttingRule>();
        boolean useDefaultCuttingRules = true;
        try
        {
            if (GUIPreferences.lastCutRulesFile!=null)
            {
                DenoptimIO.readCuttingRules(
                        GUIPreferences.lastCutRulesFile, 
                        customCuttingRules);
                useDefaultCuttingRules = false;
            }
        } catch (DENOPTIMException e)
        {
            JOptionPane.showMessageDialog(parent,String.format(
                    "<html><body width='%1s'"
                    + "Could not read last-used cutting rules from '"
                    + GUIPreferences.lastCutRulesFile + "'. "
                    + "Hint: "
                    + e.getMessage() + "</html>", 400),
                    "Error",
                    JOptionPane.ERROR_MESSAGE,
                    UIManager.getIcon("OptionPane.errorIcon"));
            return false;
        }
        
        // Build a dialog that offers the possibility to see and edit 
        // default cutting rules, and to define custom ones from scratch
        CuttingRulesSelectionDialog crs = null;
        if (setMolToGraphSettings)
        {
            crs = new MolToGraphParametersDialog(
                defaultCuttingRules, customCuttingRules, 
                useDefaultCuttingRules, parent, settings);
        } else {
            crs = new CuttingRulesSelectionDialog(
                defaultCuttingRules, customCuttingRules, 
                useDefaultCuttingRules, parent, settings);
        }
        crs.pack();
        crs.setVisible(true);
        
        if (crs.result==null)
            return false;
        
        String pathnameLastUsedCutRules = settings.getCuttingRulesFilePathname();
        if (pathnameLastUsedCutRules != null 
                && !pathnameLastUsedCutRules.isBlank())
        {
            GUIPreferences.lastCutRulesFile = new File(pathnameLastUsedCutRules);
        }
        
        return true;
    }
 
//-----------------------------------------------------------------------------
    
    public void importStructureFromFile(File file)
    {
        this.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR));
        
        // Cleanup
        clearCurrentSystem();
        
        try {
            for (IAtomContainer mol : DenoptimIO.readAllAtomContainers(file))
            {   
                // We mean to import only the structure: get rid of AP
                mol.setProperty(DENOPTIMConstants.APSTAG,null);
                
                // NB: here we let the vertexViewer create a fragment object that we
                // then put into the local library. This to make sure that the 
                // references to atoms selected in the viewer are referring to
                // members of the "vertex" object
                vertexViewer.loadPlainStructure(mol);
                vertex = vertexViewer.getLoadedStructure();
 
                // the system is not a fragment but, this is done for consistency:
                // when we have a molecule loaded the list is not empty
                // The currently viewed fragment (if any) is always part of the lib
                verticesLibrary.add(vertex);
                currVrtxIdx = verticesLibrary.size()-1;
            }
            updateVrtxListSpinner();
            unsavedChanges = true;
            btnDelSel.setEnabled(true);
            btnAtmToAP.setEnabled(true);
            btnBondToAPPair.setEnabled(true);
        } catch (Exception e) {
            this.setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
            e.printStackTrace();
            JOptionPane.showMessageDialog(this,
                    "<html>Could not read file '" + file.getAbsolutePath() 
                    + "'!<br>Hint about reason: " + e.getCause() + "</html>",
                    "Error",
                    JOptionPane.PLAIN_MESSAGE,
                    UIManager.getIcon("OptionPane.errorIcon"));
        }
        
        this.setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
    }
 
//-----------------------------------------------------------------------------
 
    public void importStructureFromSMILES(String smiles)
    {   
        this.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR));
 
        // Cleanup
        clearCurrentSystem();
        
        // Load the structure using CACTUS service or CDK builder
        try {
            vertexViewer.loadSMILES(smiles);
        } catch (Exception e) {
            this.setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
            return;
        }
        
        vertex = vertexViewer.getLoadedStructure();
        
        // The system is not a fragment but, this is done for consistency:
        // when we have a molecule loaded the list is not empty:
        // The currently viewed fragment (if any) is always part of the library
        verticesLibrary.add(vertex);
        currVrtxIdx = verticesLibrary.size()-1;
        
        // finalize GUI status
        updateVrtxListSpinner();
        unsavedChanges = true;
        btnDelSel.setEnabled(true);
        btnAtmToAP.setEnabled(true);
        btnBondToAPPair.setEnabled(true);
        btnSaveEdits.setEnabled(true);
        
        this.setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
    }
    
//-----------------------------------------------------------------------------
    
    public void importVerticesFromFile(File file)
    {   
        this.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR));
        
        ArrayList<Vertex> vrtxLib = new ArrayList<>();
        try {
            vrtxLib = DenoptimIO.readVertexes(file, BBType.FRAGMENT);
        } catch (Exception e1) {
            e1.printStackTrace();
            JOptionPane.showMessageDialog(btnAddVrtx,
                    "<html>Could not read building blocks from file"
                    + "<br>'" + file + "'"
                    + "<br>Hint on cause: " + e1.getMessage() 
                    +"</html>",
                    "Error",
                    JOptionPane.ERROR_MESSAGE,
                    UIManager.getIcon("OptionPane.errorIcon"));
            return;
        }
 
        if (vrtxLib.size() == 0)
        {
            JOptionPane.showMessageDialog(btnAddVrtx,
                    "<html>No building blocks in file"
                    + "<br>'" + file + "'</html>",
                    "Error",
                    JOptionPane.ERROR_MESSAGE,
                    UIManager.getIcon("OptionPane.errorIcon"));
            return;
        }
        importVertices(vrtxLib);
        this.setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
    }
    
//-----------------------------------------------------------------------------
    
    public void importVertices(List<Vertex> fragments)
    {   
        this.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR));
        
        int firstOfNew = 0;
        boolean libFromScrtch = false;
        if (verticesLibrary == null)
        {
            libFromScrtch = true;
            verticesLibrary = new ArrayList<Vertex>();
        }
        else
        {
            firstOfNew = verticesLibrary.size();
        }
        
        boolean addedOne = false;
        if (fragments.size() > 0)
        {
            verticesLibrary.addAll(fragments);
            addedOne = true;
            
            // Display the first
            if (libFromScrtch)
            {
                currVrtxIdx = 0;
            }
            else if (addedOne)
            {
                currVrtxIdx = firstOfNew;
            }
            loadCurrentVrtxIdxToViewer();
            
            // Update the fragment spinner
            updateVrtxListSpinner();
        } else {
            this.setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
            JOptionPane.showMessageDialog(this,
                    "<html>No vertices to import from the given list.</html>",
                    "Error",
                    JOptionPane.PLAIN_MESSAGE,
                    UIManager.getIcon("OptionPane.errorIcon"));
        }
        this.setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
    }
    
    
//-----------------------------------------------------------------------------
    
    private void loadCurrentVrtxIdxToViewer()
    {
        if (verticesLibrary == null)
        {
            JOptionPane.showMessageDialog(this,
                    "No list of building blocks loaded.",
                    "Error",
                    JOptionPane.PLAIN_MESSAGE,
                    UIManager.getIcon("OptionPane.errorIcon"));
            return;
        }
        
        clearCurrentSystem();
 
        vertex = verticesLibrary.get(currVrtxIdx);
        vertexViewer.loadVertexToViewer(vertex);
        if (vertex == null || vertex instanceof Fragment == false)
        {
            btnDelSel.setEnabled(false);
            btnAtmToAP.setEnabled(false);
            btnBondToAPPair.setEnabled(false);
        } else {
            btnDelSel.setEnabled(true);
            btnAtmToAP.setEnabled(true);
            btnBondToAPPair.setEnabled(true);
        }
    }
    
//-----------------------------------------------------------------------------
    
    private void clearCurrentSystem()
    {
        // Get rid of currently loaded mol
        vertex = null;
        vertexViewer.clearCurrentSystem();
    }
 
//-----------------------------------------------------------------------------
 
    private void updateVrtxListSpinner()
    {       
        navigSpinner.setModel(new SpinnerNumberModel(currVrtxIdx+1, 1, 
                verticesLibrary.size(), 1));
        totalVrtxsLabel.setText(Integer.toString(verticesLibrary.size()));
    }
    
//-----------------------------------------------------------------------------
    
    private boolean convertAtomToAP(IAtom trgAtm, String ruleAndSubClass)
    {
        if (!(vertex instanceof Fragment))
        {
            return false;
        }
        Fragment frag = (Fragment) vertex;
        // Accept ONLY if the atom has one and only one connected neighbour
        if (frag.getConnectedAtomsCount(trgAtm) != 1)
        {
            String str = "";
            for (IAtom atm : frag.getConnectedAtomsList(trgAtm))
            {
                str = str + " " + atm.getSymbol() 
                        + (frag.indexOf(atm));
            }
            System.out.println("Connected atoms: "+str);
            
            JOptionPane.showMessageDialog(this,
                    "<html>Atom "+ trgAtm.getSymbol() 
                    + (frag.indexOf(trgAtm)) 
                    + " has zero or more than one neighbour.<br>I can only "
                    + "transform atoms"
                    + " that have one and only one neighbour.</html>",
                    "Error",
                    JOptionPane.ERROR_MESSAGE,
                    UIManager.getIcon("OptionPane.errorIcon"));
            return false;
        }
        
        IAtom srcAtm = frag.getConnectedAtomsList(trgAtm).get(0);
        BondType bt = BondType.valueOf(
                srcAtm.getBond(trgAtm).getOrder().toString());
        
        Point3d srcP3d = MoleculeUtils.getPoint3d(srcAtm);
        Point3d trgP3d = MoleculeUtils.getPoint3d(trgAtm);
        Point3d vector = new Point3d();
        vector.x = srcP3d.x + (trgP3d.x - srcP3d.x);
        vector.y = srcP3d.y + (trgP3d.y - srcP3d.y);
        vector.z = srcP3d.z + (trgP3d.z - srcP3d.z);
        
        //NB: assumption of validity!
        String[] parts = ruleAndSubClass.split(
                DENOPTIMConstants.SEPARATORAPPROPSCL);
        try {
            // NB: here we change the bond type to make it fit with the one we
            // have in the molecular model.
            frag.addAPOnAtom(srcAtm, APClass.make(parts[0],
                    Integer.parseInt(parts[1]), bt), vector);
        } catch (DENOPTIMException e) {
            e.printStackTrace();
            JOptionPane.showMessageDialog(this,
                    "<html>Could not make AP.<br>Possible cause: " 
                    + e.getMessage() +"</html>",
                    "Error",
                    JOptionPane.ERROR_MESSAGE,
                    UIManager.getIcon("OptionPane.errorIcon"));
            return false;
        }       
        return true;
    }
    
//----------------------------------------------------------------------------
 
    private void removeAtoms(ArrayList<IAtom> atmsToDels)
    {
        if (!(vertex instanceof Fragment))
        {
            return;
        }
        Fragment frag = (Fragment) vertex;
        ArrayList<IBond> bnsToDel = new ArrayList<IBond>();
        for (IAtom atm : atmsToDels)
        {
            for (IBond bnd : frag.bonds())
            {
                if (bnd.contains(atm))
                {
                    bnsToDel.add(bnd);
                }
            }
        }
        for (IBond bnd : bnsToDel)
        {
            frag.removeBond(bnd);
        }
        for (IAtom atm : atmsToDels)
        {
            if (atm.getProperty(DENOPTIMConstants.ATMPROPAPS)!=null)
            {
                ArrayList<AttachmentPoint> apsOnAtm = frag.getAPsFromAtom(atm);
                frag.getAttachmentPoints().removeAll(apsOnAtm);
            }
            frag.removeAtom(atm);
        }
        frag.updateAPs();
    }
    
//-----------------------------------------------------------------------------
    
    private class VrtxSpinnerChangeEvent implements ChangeListener
    {
        private boolean inEnabled = true;
        
        public VrtxSpinnerChangeEvent()
        {}
        
        public void setEnabled(boolean var)
        {
            this.inEnabled = var;
        }
        
        @Override
        public void stateChanged(ChangeEvent event)
        {
            if (!inEnabled)
            {
                return;
            }
      
            activateTabEditsListener(false);
            
            //NB here we convert from 1-based index in GUI to 0-based index
            currVrtxIdx = ((Integer) navigSpinner.getValue()).intValue() - 1;
            loadCurrentVrtxIdxToViewer();
            
            activateTabEditsListener(true);
        }
    }
    
//-----------------------------------------------------------------------------
 
    private void deprotectEditedSystem()
    {
        //btnSaveEdits.setEnabled(false);
        btnAddVrtx.setEnabled(true);
        btnOpenVrtxs.setEnabled(true);
        btnOpenSMILES.setEnabled(true); 
        btnOpenMol.setEnabled(true);
        btnEmptFrag.setEnabled(true);
        if (vertex == null || vertex instanceof Fragment == false)
        {
            btnDelSel.setEnabled(false);
            btnAtmToAP.setEnabled(false);
            btnBondToAPPair.setEnabled(false);
        } else {
            btnDelSel.setEnabled(true);
            btnAtmToAP.setEnabled(true);
            btnBondToAPPair.setEnabled(true);
        }
        
        ((DefaultEditor) navigSpinner.getEditor())
            .getTextField().setEditable(true); 
        ((DefaultEditor) navigSpinner.getEditor())
            .getTextField().setForeground(Color.BLACK);
        vertexViewer.deprotectEdits();
        vertexViewer.setSwitchable(true);
        
        vrtxSpinnerListener.setEnabled(true);
    }
    
//-----------------------------------------------------------------------------
    
    private void protectEditedSystem()
    {
        btnSaveEdits.setEnabled(true);
        btnAddVrtx.setEnabled(false);
        btnOpenVrtxs.setEnabled(false);
        btnOpenSMILES.setEnabled(false); 
        btnOpenMol.setEnabled(false);
        btnEmptFrag.setEnabled(false);
        //btnDelSel.setEnabled(false);
        //btnAtmToAP.setEnabled(false);
        
        navigSpinner.setModel(new SpinnerNumberModel(currVrtxIdx+1, 
                currVrtxIdx+1, currVrtxIdx+1, 1));
        ((DefaultEditor) navigSpinner.getEditor())
            .getTextField().setEditable(false); 
        ((DefaultEditor) navigSpinner.getEditor())
            .getTextField().setForeground(Color.GRAY);
        
        vertexViewer.setSwitchable(false);
        
        vrtxSpinnerListener.setEnabled(false);
    }
    
//-----------------------------------------------------------------------------
 
    private void activateTabEditsListener(boolean var)
    {
        vertexViewer.activateTabEditsListener(var);
    }
    
//-----------------------------------------------------------------------------
    
    private void removeCurrentVrtx() throws DENOPTIMException
    {
        if (vertexViewer.hasUnsavedAPEdits())
        {
            String[] options = new String[]{"Yes","No"};
            int res = JOptionPane.showOptionDialog(this,
                    "<html>Removing unsaved vertex?",
                    "Warning",
                    JOptionPane.DEFAULT_OPTION,
                    JOptionPane.QUESTION_MESSAGE,
                    UIManager.getIcon("OptionPane.warningIcon"),
                    options,
                    options[1]);
            if (res == 1)
            {
                return;
            }
        }
 
        clearCurrentSystem();
        
        // Actual removal from the library
        if (verticesLibrary.size()>0)
        {
            verticesLibrary.remove(currVrtxIdx);
            int libSize = verticesLibrary.size();
            
            if (currVrtxIdx>=0 && currVrtxIdx<libSize)
            {
                //we keep currFrgIdx as it will correspond to the next item
            }
            else
            {
                currVrtxIdx = currVrtxIdx-1;
            }
            
            if (currVrtxIdx==-1 || verticesLibrary.size()==0)
            {
                // The viewer gets hidden so we do not need to clear it
                // with 'zap' (which is a very slow operation)
                vertexViewer.clearMolecularViewer(true);
                currVrtxIdx = 0;
                navigSpinner.setModel(new SpinnerNumberModel(0,0,0,1));
                totalVrtxsLabel.setText(Integer.toString(0));
                deprotectEditedSystem();
            }
            else
            {
                loadCurrentVrtxIdxToViewer();
                updateVrtxListSpinner();
                navigSpinner.setModel(new SpinnerNumberModel(currVrtxIdx+1, 1, 
                        verticesLibrary.size(), 1));
                deprotectEditedSystem();
            }
        }
    }
 
//-----------------------------------------------------------------------------
 
    private void saveUnsavedChanges() 
    {
        this.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR));
        
        if (vertexViewer.hasUnsavedAPEdits())
        {
            DefaultTableModel tabModel = vertexViewer.getAPTableModel();
            // Import changes from AP table into molecular representation
            for (int i=0; i<tabModel.getRowCount(); i++) 
            {               
                int apId = ((Integer) tabModel.getValueAt(i, 0)).intValue();
                String currApClass = tabModel.getValueAt(i, 1).toString();
                
                // Make sure the new class has a proper syntax
                GUIAPClassDefinitionDialog apcDefiner = 
                        new GUIAPClassDefinitionDialog(btnSaveEdits, false);
                apcDefiner.setTitle("Confirm APClass on AP #"+i);
                apcDefiner.setPreDefinedAPClass(currApClass);
                Object chosen = apcDefiner.showDialog();
                if (chosen != null)
                {
                    Object[] pair = (Object[]) chosen;
                    currApClass = pair[0].toString();
                } else {
                    currApClass = "dafaultAPClass:0";
                }
                
                Map<Integer, AttachmentPoint> mapAPs = 
                        vertexViewer.getActiveMapAPs();
                
                if (mapAPs.containsKey(apId))
                {
                    String origApClass = mapAPs.get(apId).getAPClass().toString();
                    if (!origApClass.equals(currApClass))
                    {
                        try {
                            mapAPs.get(apId).setAPClass(currApClass);
                        } catch (DENOPTIMException e) {
                            // We made sure the class is valid, so this
                            // should never happen, though one never knows
                            e.printStackTrace();
                            JOptionPane.showMessageDialog(btnSaveEdits,
                                    "<html>Could not save due to errors setting a "
                                    + "new APClass.<br>Please report this to the "
                                    + "DENOPTIM team.</html>",
                                    "Error",
                                    JOptionPane.PLAIN_MESSAGE,
                                    UIManager.getIcon("OptionPane.errorIcon"));
                            return; 
                        }
                    }
                }
                else
                {
                    JOptionPane.showMessageDialog(btnSaveEdits,
                            "<html>Could not save due to mistmatch between AP "
                            + "table and map.<br>Please report this to the "
                            + "DENOPTIM team.</html>",
                            "Error",
                            JOptionPane.PLAIN_MESSAGE,
                            UIManager.getIcon("OptionPane.errorIcon"));
                    return; 
                }
            }
        }
        
        // Retrieve chemical object from the viewer, if edited, otherwise
        // we get what is already in 'vertex'
        vertex = vertexViewer.getLoadedStructure();
        if (verticesLibrary.size()==0
                && (vertex==null || vertex.getNumberOfAPs()==0))
        {
            //Nothing to same
            this.setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
            return;
        }
        verticesLibrary.set(currVrtxIdx,vertex);
        
        // Reload fragment from library to refresh table and viewer
        activateTabEditsListener(false);
        try {
            loadCurrentVrtxIdxToViewer();
        } catch (Throwable t) {
            //This can happen if the viewer has been started but is empty
            // E.G:, if the cactvs server is down).
            // We just keep going, and make sure we get the default cursor back.
        }
        // Release constraints
        activateTabEditsListener(true);
        navigSpinner.setModel(new SpinnerNumberModel(currVrtxIdx+1, 1, 
                verticesLibrary.size(), 1));
        deprotectEditedSystem();
        
        this.setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
    }
    
//----------------------------------------------------------------------------
 
    public static List<APClass> choseOrCreateNewAPClass(JComponent parent,
            boolean singleSelection)
    {
        return choseOrCreateNewAPClass(parent, singleSelection, "Choose APClasses to Add");
    }
    
//----------------------------------------------------------------------------
 
    public static List<APClass> choseOrCreateNewAPClass(JComponent parent,
            boolean singleSelection, String title)
    {
        // To facilitate selection of existing APCs we offer a list...
        DefaultListModel<String> apClassLstModel =
              new DefaultListModel<String>();
        JList<String> apClassList = new JList<String>(apClassLstModel);
        for (String apc : APClass.getAllAPClassesAsString())
        {
            apClassLstModel.addElement(apc);
        }
        //...and to the list we add the option to create a new APClass.
        apClassLstModel.addElement(
              "<html><b><i>Define a new APClass...<i></b></html>");
        if (singleSelection)
        {
            apClassList.setSelectionMode(
                    ListSelectionModel.SINGLE_SELECTION);
        } else {
            apClassList.setSelectionMode(
                    ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
        }
        if (apClassList.getModel().getSize() == 1)
        {
            apClassList.setSelectedIndex(0);
        } else {
            apClassList.setSelectedIndex(apClassLstModel.getSize()-1);
        }
      
        //Make and launch dialog for the user to make the selection
        JPanel chooseApPanel = new JPanel();
        JLabel header = new JLabel("Choose APClass:");
        JScrollPane apClassScroll = new JScrollPane(apClassList);
        chooseApPanel.add(header);
        chooseApPanel.add(apClassScroll);
      
        int res = JOptionPane.showConfirmDialog(parent,
              chooseApPanel, 
              title, 
              JOptionPane.OK_CANCEL_OPTION,
              JOptionPane.PLAIN_MESSAGE, 
              null);
        if (res != JOptionPane.OK_OPTION)
        {
          return new ArrayList<APClass>();
        }
      
        // Interpret the selection made by the user
        ArrayList<APClass> selectedSPCs = new ArrayList<APClass>();
        int[] selectedIds = apClassList.getSelectedIndices();
        if (selectedIds.length > 0)
        {
            for (int ii=0; ii<selectedIds.length; ii++)
            {
                APClass apc = null;
                Integer idAPC = selectedIds[ii];
                
                try {
                    if (idAPC.intValue() == (apClassLstModel.size()-1))
                    {
                        // We chose to create a new class
                        GUIAPClassDefinitionDialog apcDefiner = 
                                new GUIAPClassDefinitionDialog(parent, false);
                        Object chosen = apcDefiner.showDialog();
                        if (chosen != null)
                        {
                            Object[] pair = (Object[]) chosen;
                            apc = APClass.make(pair[0].toString(),
                                    (BondType) pair[1]);
                        }
                    } else {
                        apc = APClass.make(apClassLstModel.getElementAt(idAPC));
                    }
                } catch (Exception e1) {
                    // We have pressed cancel or closed the dialog: abandon
                    continue;
                }
                selectedSPCs.add(apc);
            }
        }
        return selectedSPCs;
    }
    
//-----------------------------------------------------------------------------
    
    public static String ensureGoodAPRuleString(String currApRule, 
            String title, boolean mustReply, JComponent parent) 
                    throws DENOPTIMException 
    {       
        String preStr = "";
        while (!APClass.isValidAPRuleString(currApRule))
        {
            if (currApRule != "")
            {
                preStr = "APRule '" + currApRule + "' is not valid!<br>"
                        + "The valid syntax for APClass is:<br><br><code>APRule" 
                        + DENOPTIMConstants.SEPARATORAPPROPSCL 
                        + "subClass</code><br><br> where "
                        + "<ul><li><code>APRule</code>"
                        + " is the string you should provide now, and is "
                        + "typically any string with no spaces,</li>"
                        + "<li><code>subClass</code> is an integer.</ul>";
            }
            
            currApRule = JOptionPane.showInputDialog(parent,String.format( 
                    "<html><body width='%1s'>" + preStr 
                    + " Please, provide a valid APClass rule string: </html>",
                    300),
                    title,
                    JOptionPane.PLAIN_MESSAGE);
            
            if (currApRule == null)
            {
                currApRule = "";
                if (!mustReply)
                {
                    throw new DENOPTIMException();
                }
            }
        }
        
        return currApRule;
    }
    
//-----------------------------------------------------------------------------
 
    public boolean hasUnsavedChanges()
    {
        return unsavedChanges;
    }
    
//-----------------------------------------------------------------------------
 
    /*
     * This is needed to stop Jmol threads upon closure of this gui card.
     */
    public void dispose() 
    {
        vertexViewer.dispose();
    }
        
//-----------------------------------------------------------------------------
    
}