Examples with Bond org.vcell.model.rbm.SpeciesPattern.Bond used on opensource projects

Example 1 with Bond

use of org.vcell.model.rbm.SpeciesPattern.Bond in project vcell by virtualcell.

the class XmlReader method getRbmMolecularComponentPattern.

private MolecularComponentPattern getRbmMolecularComponentPattern(Element e, MolecularTypePattern mtp, MolecularType mt, Model newModel) {
    RbmModelContainer mc = newModel.getRbmModelContainer();
    String s = e.getAttributeValue(XMLTags.RbmMolecularComponentTag);
    if (s == null || s.isEmpty()) {
        System.out.println("XMLReader: getRbmMolecularComponentPattern: MolecularComponent name is missing.");
        return null;
    }
    MolecularComponent c = mt.getMolecularComponent(s);
    if (c == null) {
        System.out.println("XMLReader: getRbmMolecularComponentPattern: encountered reference " + s + " to non-existing MolecularComponent.");
        return null;
    }
    ComponentStatePattern csp = new ComponentStatePattern();
    MolecularComponentPattern mcp = new MolecularComponentPattern(c);
    s = e.getAttributeValue(XMLTags.RbmMolecularComponentStatePatternTag);
    if (s != null && !s.isEmpty()) {
        // state may be missing, we set it only if is present
        ComponentStateDefinition cs = c.getComponentStateDefinition(s);
        if (cs == null) {
            System.out.println("XMLReader: getRbmMolecularComponentPattern: encountered reference " + s + " to non-existing MolecularComponentState.");
            return null;
        }
        csp = new ComponentStatePattern(cs);
        mcp.setComponentStatePattern(csp);
    }
    // s = e.getAttributeValue(XMLTags.RbmMolecularTypeAnyTag);
    // if(s!=null && !s.isEmpty()) {
    // boolean any = Boolean.parseBoolean(s);
    // csp.setAny(any);
    // }
    s = e.getAttributeValue(XMLTags.RbmBondTypeAttrTag);
    BondType bondType = BondType.fromSymbol(s);
    if (bondType == BondType.Specified) {
        int bondId = Integer.parseInt(s);
        mcp.setBondId(bondId);
    }
    mcp.setBondType(bondType);
    // sanity check, we only read the names here and make sure they make sense
    Element bondElement = e.getChild(XMLTags.RbmBondTag, vcNamespace);
    if (bondElement != null) {
        // it's actually the name of the MolecularType inside this pattern
        String molecularTypeName = bondElement.getAttributeValue(XMLTags.RbmMolecularTypePatternTag);
        String molecularComponentName = bondElement.getAttributeValue(XMLTags.RbmMolecularComponentPatternTag);
        if (molecularTypeName == null || molecularTypeName.isEmpty()) {
            System.out.println("XMLReader: getRbmMolecularComponentPattern: Bond Attribute molecularTypeName missing.");
            return mcp;
        }
        if (molecularComponentName == null || molecularComponentName.isEmpty()) {
            System.out.println("XMLReader: getRbmMolecularComponentPattern: Bond Attribute molecularComponentName missing.");
            return mcp;
        }
        // we'll have a bond here, it will be properly initialized during RbmObservable.resolveBonds() call  !!!
        Bond bond = new Bond();
        mcp.setBond(bond);
    }
    return mcp;
}

Example 2 with Bond

use of org.vcell.model.rbm.SpeciesPattern.Bond in project vcell by virtualcell.

the class ModelRuleFactory method createRuleEntry.

public ModelRuleEntry createRuleEntry(ReactionRule reactionRule, int reactionRuleIndex, ReactionRuleDirection direction) {
    ModelRuleEntry rule = new ModelRuleEntry(reactionRule, reactionRuleIndex);
    // 
    // for each molecular type in reactant, find all possible matches in products (without regard for consistency).
    // 
    int participantIndex = 0;
    for (ReactantPattern rp : reactionRule.getReactantPatterns()) {
        ModelParticipantEntry reactantEntry = new ModelParticipantEntry(rule, participantIndex, rp);
        rule.reactantEntries.add(reactantEntry);
        int moleculeIndex = 0;
        for (MolecularTypePattern mtp : rp.getSpeciesPattern().getMolecularTypePatterns()) {
            ModelMolecularTypeEntry molecularTypeEntry = new ModelMolecularTypeEntry(reactantEntry, moleculeIndex, mtp);
            rule.reactantMolecularTypeEntries.add(molecularTypeEntry);
            int componentIndex = 0;
            for (MolecularComponentPattern mcp : mtp.getComponentPatternList()) {
                // TODO: divergence point vs. MathRuleFactory
                // we need to look at all components when we compare reactants to products looking for changes
                // if(mcp.getBondType() == BondType.Possible && (mcp.getComponentStatePattern() == null || mcp.getComponentStatePattern().isAny())) {
                // continue;
                // }
                ModelMolecularComponentEntry mce = new ModelMolecularComponentEntry(molecularTypeEntry, componentIndex, mcp);
                rule.reactantMolecularComponentEntries.add(mce);
                // 
                // if this reactant component has a bond, find partner already in list (will always find second binding site where first one is in the list already).
                // 
                Bond bond = mcp.getBond();
                if (bond != null) {
                    ReactantBondEntry bondEntry = null;
                    for (MolecularComponentEntry otherMCE : rule.reactantMolecularComponentEntries) {
                        if (((ModelMolecularComponentEntry) otherMCE).molecularComponentPattern == bond.molecularComponentPattern) {
                            bondEntry = new ReactantBondEntry(otherMCE, mce);
                            break;
                        }
                    }
                    if (bondEntry != null) {
                        rule.reactantBondEntries.add(bondEntry);
                    }
                }
                componentIndex++;
            }
            moleculeIndex++;
        }
        participantIndex++;
    }
    participantIndex = 0;
    for (ProductPattern pp : reactionRule.getProductPatterns()) {
        ModelParticipantEntry productEntry = new ModelParticipantEntry(rule, participantIndex, pp);
        rule.productEntries.add(productEntry);
        int moleculeIndex = 0;
        for (MolecularTypePattern mtp : pp.getSpeciesPattern().getMolecularTypePatterns()) {
            ModelMolecularTypeEntry molecularTypeEntry = new ModelMolecularTypeEntry(productEntry, moleculeIndex, mtp);
            rule.productMolecularTypeEntries.add(molecularTypeEntry);
            int componentIndex = 0;
            for (MolecularComponentPattern mcp : mtp.getComponentPatternList()) {
                // TODO: divergence point vs. MathRuleFactory
                // we need to look at all components when we compare reactants to products looking for changes
                // if(mcp.getBondType() == BondType.Possible && (mcp.getComponentStatePattern() == null || mcp.getComponentStatePattern().isAny())) {
                // continue;
                // }
                ModelMolecularComponentEntry mce = new ModelMolecularComponentEntry(molecularTypeEntry, componentIndex, mcp);
                rule.productMolecularComponentEntries.add(mce);
                // 
                // if this product component has a bond, find partner already in list (will always find second binding site where first one is in the list already).
                // 
                Bond bond = mcp.getBond();
                if (bond != null) {
                    ProductBondEntry bondEntry = null;
                    for (MolecularComponentEntry otherMCE : rule.productMolecularComponentEntries) {
                        if (((ModelMolecularComponentEntry) otherMCE).molecularComponentPattern == bond.molecularComponentPattern) {
                            bondEntry = new ProductBondEntry(otherMCE, mce);
                            break;
                        }
                    }
                    if (bondEntry != null) {
                        rule.productBondEntries.add(bondEntry);
                    }
                }
                componentIndex++;
            }
            moleculeIndex++;
        }
        participantIndex++;
    }
    return rule;
}

Example 3 with Bond

use of org.vcell.model.rbm.SpeciesPattern.Bond in project vcell by virtualcell.

the class ObservablePropertiesPanel method manageComponentPatternFromShape.

public void manageComponentPatternFromShape(final RbmElementAbstract selectedObject, PointLocationInShapeContext locationContext, ShowWhat showWhat) {
    final MolecularComponentPattern mcp = (MolecularComponentPattern) selectedObject;
    final MolecularComponent mc = mcp.getMolecularComponent();
    popupFromShapeMenu.removeAll();
    // ------------------------------------------------------------------- State
    if (showWhat == ShowWhat.ShowState && mc.getComponentStateDefinitions().size() != 0) {
        String prefix = "State:  ";
        String csdCurrentName = "";
        final Map<String, String> itemMap = new LinkedHashMap<String, String>();
        if (mcp.getComponentStatePattern() == null || mcp.getComponentStatePattern().isAny()) {
            csdCurrentName = "<html>" + prefix + "<b>" + ComponentStatePattern.strAny + "</b></html>";
        } else {
            csdCurrentName = "<html>" + prefix + ComponentStatePattern.strAny + "</html>";
        }
        itemMap.put(csdCurrentName, ComponentStatePattern.strAny);
        for (final ComponentStateDefinition csd : mc.getComponentStateDefinitions()) {
            csdCurrentName = "";
            if (mcp.getComponentStatePattern() != null && !mcp.getComponentStatePattern().isAny()) {
                ComponentStateDefinition csdCurrent = mcp.getComponentStatePattern().getComponentStateDefinition();
                csdCurrentName = csdCurrent.getName();
            }
            String name = csd.getName();
            if (name.equals(csdCurrentName)) {
                // currently selected menu item is shown in bold
                name = "<html>" + prefix + "<b>" + name + "</b></html>";
            } else {
                name = "<html>" + prefix + name + "</html>";
            }
            itemMap.put(name, csd.getName());
        }
        for (String name : itemMap.keySet()) {
            JMenuItem menuItem = new JMenuItem(name);
            popupFromShapeMenu.add(menuItem);
            menuItem.setIcon(VCellIcons.rbmComponentStateIcon);
            menuItem.addActionListener(new ActionListener() {

                public void actionPerformed(ActionEvent e) {
                    String key = e.getActionCommand();
                    String name = itemMap.get(key);
                    if (name.equals(ComponentStatePattern.strAny)) {
                        ComponentStatePattern csp = new ComponentStatePattern();
                        mcp.setComponentStatePattern(csp);
                    } else {
                        ComponentStateDefinition csd = mcp.getMolecularComponent().getComponentStateDefinition(name);
                        if (csd == null) {
                            throw new RuntimeException("Missing ComponentStateDefinition " + name + " for Component " + mcp.getMolecularComponent().getName());
                        }
                        ComponentStatePattern csp = new ComponentStatePattern(csd);
                        mcp.setComponentStatePattern(csp);
                    }
                }
            });
        }
    }
    if (showWhat == ShowWhat.ShowState) {
        return;
    }
    // ------------------------------------------------------------------------------------------- Bonds
    final MolecularTypePattern mtp = locationContext.getMolecularTypePattern();
    final SpeciesPattern sp = locationContext.getSpeciesPattern();
    JMenu editBondMenu = new JMenu();
    final String specifiedString = mcp.getBondType() == BondType.Specified ? "<html><b>" + "Site bond specified" + "</b></html>" : "<html>" + "Site bond specified" + "</html>";
    editBondMenu.setText(specifiedString);
    editBondMenu.setToolTipText("Specified");
    editBondMenu.removeAll();
    final Map<String, Bond> itemMap = new LinkedHashMap<String, Bond>();
    // String noneString = "<html>Bond:&nbsp;&nbsp;<b>" + BondType.None.symbol + "</b> " + BondType.None.name() + "</html>";
    // String existsString = "<html>Bond:&nbsp;&nbsp;<b>" + BondType.Exists.symbol + "</b> " + BondType.Exists.name() + "</html>";
    // String possibleString = "<html>Bond:&nbsp;&nbsp;<b>" + BondType.Possible.symbol + "</b> " + BondType.Possible.name() + "</html>";
    String noneString = mcp.getBondType() == BondType.None ? "<html><b>" + "Site is unbound" + "</b></html>" : "<html>" + "Site is unbound" + "</html>";
    // Site is bound
    String existsString = mcp.getBondType() == BondType.Exists ? "<html><b>" + "Site has external bond" + "</b></html>" : "<html>" + "Site has external bond" + "</html>";
    String possibleString = mcp.getBondType() == BondType.Possible ? "<html><b>" + "Site may be bound" + "</b></html>" : "<html>" + "Site may be bound" + "</html>";
    itemMap.put(noneString, null);
    itemMap.put(existsString, null);
    itemMap.put(possibleString, null);
    if (mtp != null && sp != null) {
        List<Bond> bondPartnerChoices = sp.getAllBondPartnerChoices(mtp, mc);
        for (Bond b : bondPartnerChoices) {
            // if(b.equals(mcp.getBond())) {
            // continue;	// if the mcp has a bond already we don't offer it
            // }
            int index = 0;
            if (mcp.getBondType() == BondType.Specified) {
                index = mcp.getBondId();
            } else {
                index = sp.nextBondId();
            }
            // itemMap.put(b.toHtmlStringLong(mtp, mc, sp, index), b);
            itemMap.put(b.toHtmlStringLong(sp, mtp, mc, index), b);
        // itemMap.put(b.toHtmlStringLong(sp, index), b);
        }
    }
    int index = 0;
    Graphics gc = splitPaneHorizontal.getGraphics();
    for (String name : itemMap.keySet()) {
        JMenuItem menuItem = new JMenuItem(name);
        if (index == 0) {
            menuItem.setIcon(VCellIcons.rbmBondNoneIcon);
            menuItem.setToolTipText("None");
            popupFromShapeMenu.add(menuItem);
        } else if (index == 1) {
            menuItem.setIcon(VCellIcons.rbmBondExistsIcon);
            menuItem.setToolTipText("Exists");
            popupFromShapeMenu.add(menuItem);
        } else if (index == 2) {
            menuItem.setIcon(VCellIcons.rbmBondPossibleIcon);
            menuItem.setToolTipText("Possible");
            popupFromShapeMenu.add(menuItem);
        } else if (index > 2) {
            Bond b = itemMap.get(name);
            // clone of the sp, with only the bond of interest
            SpeciesPattern spBond = new SpeciesPattern(bioModel.getModel(), sp);
            spBond.resetBonds();
            spBond.resetStates();
            MolecularTypePattern mtpFrom = spBond.getMolecularTypePattern(mtp.getMolecularType().getName(), mtp.getIndex());
            MolecularComponentPattern mcpFrom = mtpFrom.getMolecularComponentPattern(mc);
            MolecularTypePattern mtpTo = spBond.getMolecularTypePattern(b.molecularTypePattern.getMolecularType().getName(), b.molecularTypePattern.getIndex());
            MolecularComponentPattern mcpTo = mtpTo.getMolecularComponentPattern(b.molecularComponentPattern.getMolecularComponent());
            spBond.setBond(mtpTo, mcpTo, mtpFrom, mcpFrom);
            Icon icon = new SpeciesPatternSmallShape(3, 4, spBond, gc, observable, false, issueManager);
            ((SpeciesPatternSmallShape) icon).setDisplayRequirements(DisplayRequirements.highlightBonds);
            menuItem.setIcon(icon);
            editBondMenu.add(menuItem);
        // } else {
        // if(index == 0) {
        // menuItem.setForeground(Color.blue);
        // }
        // popupFromShapeMenu.add(menuItem);
        }
        menuItem.addActionListener(new ActionListener() {

            public void actionPerformed(ActionEvent e) {
                String name = e.getActionCommand();
                BondType btBefore = mcp.getBondType();
                if (name.equals(noneString)) {
                    if (btBefore == BondType.Specified) {
                        // specified -> not specified
                        // change the partner to possible
                        mcp.getBond().molecularComponentPattern.setBondType(BondType.Possible);
                        mcp.getBond().molecularComponentPattern.setBond(null);
                    }
                    mcp.setBondType(BondType.None);
                    mcp.setBond(null);
                    SwingUtilities.invokeLater(new Runnable() {

                        public void run() {
                            observableTreeModel.populateTree();
                        }
                    });
                } else if (name.equals(existsString)) {
                    if (btBefore == BondType.Specified) {
                        // specified -> exists
                        // change the partner to possible
                        mcp.getBond().molecularComponentPattern.setBondType(BondType.Possible);
                        mcp.getBond().molecularComponentPattern.setBond(null);
                    }
                    mcp.setBondType(BondType.Exists);
                    mcp.setBond(null);
                    SwingUtilities.invokeLater(new Runnable() {

                        public void run() {
                            observableTreeModel.populateTree();
                        }
                    });
                } else if (name.equals(possibleString)) {
                    if (btBefore == BondType.Specified) {
                        // specified -> possible
                        // change the partner to possible
                        mcp.getBond().molecularComponentPattern.setBondType(BondType.Possible);
                        mcp.getBond().molecularComponentPattern.setBond(null);
                    }
                    mcp.setBondType(BondType.Possible);
                    mcp.setBond(null);
                    SwingUtilities.invokeLater(new Runnable() {

                        public void run() {
                            observableTreeModel.populateTree();
                        }
                    });
                } else {
                    if (btBefore != BondType.Specified) {
                        // if we go from a non-specified to a specified we need to find the next available
                        // bond id, so that we can choose the color for displaying the bond
                        // a bad bond id, like -1, will crash badly when trying to choose the color
                        int bondId = sp.nextBondId();
                        mcp.setBondId(bondId);
                    } else {
                        // specified -> specified
                        // change the old partner to possible, continue using the bond id
                        mcp.getBond().molecularComponentPattern.setBondType(BondType.Possible);
                        mcp.getBond().molecularComponentPattern.setBond(null);
                    }
                    mcp.setBondType(BondType.Specified);
                    Bond b = itemMap.get(name);
                    mcp.setBond(b);
                    mcp.getBond().molecularComponentPattern.setBondId(mcp.getBondId());
                    sp.resolveBonds();
                    SwingUtilities.invokeLater(new Runnable() {

                        public void run() {
                            observableTreeModel.populateTree();
                        }
                    });
                }
            }
        });
        index++;
    }
    popupFromShapeMenu.add(editBondMenu);
}

Example 4 with Bond

use of org.vcell.model.rbm.SpeciesPattern.Bond in project vcell by virtualcell.

the class RbmTreeCellRenderer method toHtmlWorkShort.

private static final String toHtmlWorkShort(BondLocal bl) {
    // used for tooltips
    MolecularComponentPattern mcp = bl.getMolecularComponentPattern();
    String bondText = "";
    String colorTextStart = "<font color=" + "\"rgb(" + GraphConstants.red.getRed() + "," + GraphConstants.red.getGreen() + "," + GraphConstants.red.getBlue() + ")\">";
    String colorTextEnd = "</font>";
    bondText = colorTextStart + "<b>" + "(unbound)" + "</b>" + colorTextEnd;
    if (mcp != null) {
        BondType bondType = mcp.getBondType();
        if (bondType == BondType.Specified) {
            Bond bond = mcp.getBond();
            if (bond == null) {
                colorTextStart = "<font color=" + "\"rgb(" + GraphConstants.red.getRed() + "," + GraphConstants.red.getGreen() + "," + GraphConstants.red.getBlue() + ")\">";
                colorTextEnd = "</font>";
                bondText = colorTextStart + "<b>" + "bond (missing)" + "</b>" + colorTextEnd;
            } else {
                int id = mcp.getBondId();
                colorTextStart = "<font color=" + "\"rgb(" + GraphConstants.bondHtmlColors[id].getRed() + "," + GraphConstants.bondHtmlColors[id].getGreen() + "," + GraphConstants.bondHtmlColors[id].getBlue() + ")\">";
                colorTextEnd = "</font>";
                // <sub>&nbsp;</sub>
                bondText = colorTextStart + "<b>" + "Bond<sub>" + id + "</sub></b>" + colorTextEnd;
            }
        } else if (bondType == BondType.None) {
            bondText = "Unbound";
        // bondText =  "<b>" + "unbound" + "</b>";
        } else if (bondType == BondType.Exists) {
            Color c = AbstractComponentShape.plusSignGreen;
            colorTextStart = "<font color=" + "\"rgb(" + c.getRed() + "," + c.getGreen() + "," + c.getBlue() + ")\">";
            colorTextEnd = "</font>";
            // green '+'
            bondText = colorTextStart + "<b>" + mcp.getBondType().symbol + "</b>" + colorTextEnd;
            bondText = "Bond: '" + bondText + "'";
        } else if (bondType == BondType.Possible) {
            Color c = Color.gray;
            colorTextStart = "<font color=" + "\"rgb(" + c.getRed() + "," + c.getGreen() + "," + c.getBlue() + ")\">";
            colorTextEnd = "</font>";
            // gray '?'
            bondText = colorTextStart + "<b>" + mcp.getBondType().symbol + "</b>" + colorTextEnd;
            bondText = "Bond: '" + bondText + "'";
        }
    }
    return bondText;
}

Example 5 with Bond

use of org.vcell.model.rbm.SpeciesPattern.Bond in project vcell by virtualcell.

the class SpeciesPropertiesPanel method manageComponentPatternFromShape.

public void manageComponentPatternFromShape(final RbmElementAbstract selectedObject, PointLocationInShapeContext locationContext, ShowWhat showWhat) {
    popupFromShapeMenu.removeAll();
    final MolecularComponentPattern mcp = (MolecularComponentPattern) selectedObject;
    final MolecularComponent mc = mcp.getMolecularComponent();
    // ------------------------------------------------------------------- State
    if (showWhat == ShowWhat.ShowState && mc.getComponentStateDefinitions().size() != 0) {
        String prefix = "State:  ";
        final Map<String, String> itemMap = new LinkedHashMap<String, String>();
        // itemList.add(ComponentStatePattern.strAny);			// any is not an option for state
        String csdCurrentName;
        for (final ComponentStateDefinition csd : mc.getComponentStateDefinitions()) {
            csdCurrentName = "";
            if (mcp.getComponentStatePattern() != null && !mcp.getComponentStatePattern().isAny()) {
                ComponentStateDefinition csdCurrent = mcp.getComponentStatePattern().getComponentStateDefinition();
                csdCurrentName = csdCurrent.getName();
            }
            String name = csd.getName();
            if (name.equals(csdCurrentName)) {
                // currently selected menu item is shown in bold
                name = "<html>" + prefix + "<b>" + name + "</b></html>";
            } else {
                name = "<html>" + prefix + name + "</html>";
            }
            itemMap.put(name, csd.getName());
        }
        for (String name : itemMap.keySet()) {
            JMenuItem menuItem = new JMenuItem(name);
            popupFromShapeMenu.add(menuItem);
            menuItem.setIcon(VCellIcons.rbmComponentStateIcon);
            menuItem.addActionListener(new ActionListener() {

                public void actionPerformed(ActionEvent e) {
                    String key = e.getActionCommand();
                    String name = itemMap.get(key);
                    if (name.equals(ComponentStatePattern.strAny)) {
                        ComponentStatePattern csp = new ComponentStatePattern();
                        mcp.setComponentStatePattern(csp);
                    } else {
                        ComponentStateDefinition csd = mcp.getMolecularComponent().getComponentStateDefinition(name);
                        if (csd == null) {
                            throw new RuntimeException("Missing ComponentStateDefinition " + name + " for Component " + mcp.getMolecularComponent().getName());
                        }
                        ComponentStatePattern csp = new ComponentStatePattern(csd);
                        mcp.setComponentStatePattern(csp);
                    }
                }
            });
        }
    }
    if (showWhat == ShowWhat.ShowState) {
        return;
    }
    // ---------------------------------------------------------------------------- Bonds
    final MolecularTypePattern mtp = locationContext.getMolecularTypePattern();
    final SpeciesPattern sp = locationContext.getSpeciesPattern();
    JMenu editBondMenu = new JMenu();
    final String specifiedString = mcp.getBondType() == BondType.Specified ? "<html><b>" + "Site bond specified" + "</b></html>" : "<html>" + "Site bond specified" + "</html>";
    editBondMenu.setText(specifiedString);
    editBondMenu.setToolTipText("Specified");
    editBondMenu.removeAll();
    final Map<String, Bond> itemMap = new LinkedHashMap<String, Bond>();
    String noneString = mcp.getBondType() == BondType.None ? "<html><b>" + "Site is unbound" + "</b></html>" : "<html>" + "Site is unbound" + "</html>";
    itemMap.put(noneString, null);
    // itemMap.put(possibleString, null);	// not a valid option for species
    if (mtp != null && sp != null) {
        List<Bond> bondPartnerChoices = sp.getAllBondPartnerChoices(mtp, mc);
        for (Bond b : bondPartnerChoices) {
            // if(b.equals(mcp.getBond())) {
            // continue;	// if the mcp has a bond already we don't offer it
            // }
            int index = 0;
            if (mcp.getBondType() == BondType.Specified) {
                index = mcp.getBondId();
            } else {
                index = sp.nextBondId();
            }
            itemMap.put(b.toHtmlStringLong(sp, mtp, mc, index), b);
        // itemMap.put(b.toHtmlStringLong(sp, index), b);
        }
    }
    int index = 0;
    Graphics gc = shapePanel.getGraphics();
    for (String name : itemMap.keySet()) {
        JMenuItem menuItem = new JMenuItem(name);
        if (index == 0) {
            menuItem.setIcon(VCellIcons.rbmBondNoneIcon);
            menuItem.setToolTipText("None");
            popupFromShapeMenu.add(menuItem);
        } else {
            Bond b = itemMap.get(name);
            // clone of the sp, with only the bond of interest
            SpeciesPattern spBond = new SpeciesPattern(bioModel.getModel(), sp);
            spBond.resetBonds();
            spBond.resetStates();
            MolecularTypePattern mtpFrom = spBond.getMolecularTypePattern(mtp.getMolecularType().getName(), mtp.getIndex());
            MolecularComponentPattern mcpFrom = mtpFrom.getMolecularComponentPattern(mc);
            MolecularTypePattern mtpTo = spBond.getMolecularTypePattern(b.molecularTypePattern.getMolecularType().getName(), b.molecularTypePattern.getIndex());
            MolecularComponentPattern mcpTo = mtpTo.getMolecularComponentPattern(b.molecularComponentPattern.getMolecularComponent());
            spBond.setBond(mtpTo, mcpTo, mtpFrom, mcpFrom);
            Icon icon = new SpeciesPatternSmallShape(3, 4, spBond, gc, fieldSpeciesContext, false, issueManager);
            ((SpeciesPatternSmallShape) icon).setDisplayRequirements(DisplayRequirements.highlightBonds);
            menuItem.setIcon(icon);
            editBondMenu.add(menuItem);
        }
        menuItem.addActionListener(new ActionListener() {

            public void actionPerformed(ActionEvent e) {
                String name = e.getActionCommand();
                BondType btBefore = mcp.getBondType();
                if (name.equals(noneString)) {
                    if (btBefore == BondType.Specified) {
                        // specified -> not specified
                        // change the partner to none since this is the only option
                        mcp.getBond().molecularComponentPattern.setBondType(BondType.None);
                        mcp.getBond().molecularComponentPattern.setBond(null);
                    }
                    mcp.setBondType(BondType.None);
                    mcp.setBond(null);
                    SwingUtilities.invokeLater(new Runnable() {

                        public void run() {
                            speciesPropertiesTreeModel.populateTree();
                        }
                    });
                } else {
                    if (btBefore != BondType.Specified) {
                        // if we go from a non-specified to a specified we need to find the next available
                        // bond id, so that we can choose the color for displaying the bond
                        // a bad bond id, like -1, will crash badly when trying to choose the color
                        int bondId = sp.nextBondId();
                        mcp.setBondId(bondId);
                    } else {
                        // specified -> specified
                        // change the old partner to none since it's the only available option, continue using the bond id
                        mcp.getBond().molecularComponentPattern.setBondType(BondType.None);
                        mcp.getBond().molecularComponentPattern.setBond(null);
                    }
                    mcp.setBondType(BondType.Specified);
                    Bond b = itemMap.get(name);
                    mcp.setBond(b);
                    mcp.getBond().molecularComponentPattern.setBondId(mcp.getBondId());
                    sp.resolveBonds();
                    SwingUtilities.invokeLater(new Runnable() {

                        public void run() {
                            speciesPropertiesTreeModel.populateTree();
                        }
                    });
                }
            }
        });
        index++;
    }
    popupFromShapeMenu.add(editBondMenu);
}