/**
* Returns all residues relate to a BIRD molecule. Since BIRD molecules can span multiple internal
* chains, we need to search all chains with a particular BIRD instance
*
* @param structure
* @param chain
* @return
*/
private Residue[] getBirdResidues(Structure structure, Chain chain) {
List<Residue> residues = new ArrayList<Residue>();
Bird bird = chain.getBird();
for (Chain c : structure.getStructureMap().getChains()) {
Bird b = c.getBird();
if (b != null && b.isSameInstance(bird)) {
residues.addAll(c.getResidues());
}
}
return residues.toArray(new Residue[residues.size()]);
}
/**
* Returns true if the initialLigand matches a PRD ID (i.e., PRD_000223)
*
* @param residue
* @param initialLigand Specification of PRD molecule to be highlighted in Ligand Explorer upon
* startup
* @return
*/
private boolean isInitialBirdChain(Chain chain, String initialLigand) {
if (chain.getClassification() == Classification.BIRD) {
Residue r = chain.getResidue(0);
if (r != null) {
Bird bird = r.getBird();
if (bird == null) {
return false;
}
if (initialLigand.toUpperCase().startsWith("PRD_")) {
return bird.getPrdId().equalsIgnoreCase(initialLigand);
} else {
String chainId = initialLigand.substring(0, 1);
String prdId = initialLigand.substring(2, initialLigand.length());
return chain.getAuthorChainId().equalsIgnoreCase(chainId)
&& bird.getPrdId().equalsIgnoreCase(prdId);
}
}
}
return false;
}
public LigandSideBar(LXDocumentFrame mainFrame) {
super();
final StructureModel model = LigandExplorer.sgetModel();
if (!model.hasStructures()) {
this.setBackground(LXDocumentFrame.sidebarColor);
this.setLayout(new BorderLayout());
final JPanel pdbPanel = new JPanel();
pdbPanel.setLayout(new FlowLayout());
pdbPanel.setBackground(LXDocumentFrame.sidebarColor);
final JLabel pdbLabel = new JLabel("PDB id");
pdbLabel.setFont(pdbLabel.getFont().deriveFont(Font.BOLD));
pdbLabel.setBackground(LXDocumentFrame.sidebarColor);
mainFrame.getPdbIdList().setBackground(LXDocumentFrame.sidebarColor);
pdbPanel.add(pdbLabel);
pdbPanel.add(mainFrame.getPdbIdList());
this.add(pdbPanel, BorderLayout.NORTH);
} else {
this.ligandList = this.getLigandList(model.getStructures().get(0));
final Comparator<Chain> chainComparator =
new Comparator<Chain>() {
public int compare(Chain c1, Chain c2) {
return c1.getAuthorChainId().compareTo(c2.getAuthorChainId());
}
};
Collections.sort(ligandList, chainComparator);
this.setLayout(null);
final JLabel centerView = new JLabel("Choose a ligand to analyze...");
centerView.setFont(centerView.getFont().deriveFont(Font.BOLD + Font.ITALIC));
this.add(centerView);
if (this.ligandList.size() > 0) {
DefaultMutableTreeNode root = new DefaultMutableTreeNode("Ligands:");
ligandJList = new JTree(root);
ligandJList
.getSelectionModel()
.setSelectionMode(TreeSelectionModel.CONTIGUOUS_TREE_SELECTION);
ligandJList.setCellRenderer(new LigandTreeCellRenderer());
ligandJList.setExpandsSelectedPaths(true);
ligandJList.setRootVisible(false);
ligandJList.setShowsRootHandles(true);
String chainId = "";
DefaultMutableTreeNode chainNode = null;
DefaultMutableTreeNode birdNode = null;
Bird prevBird = null;
for (Chain chain : ligandList) {
// create new node only if chain id is different from previous chain id
if (!chain.getAuthorChainId().equals(chainId)) {
// chainNode = new DefaultMutableTreeNode(chain);
chainNode = new DefaultMutableTreeNode(chain.getAuthorChainId());
root.add(chainNode);
chainId = chain.getAuthorChainId();
}
if (chain.getClassification() == Residue.Classification.LIGAND) {
for (Residue residue : chain.getResidues()) {
chainNode.add(new DefaultMutableTreeNode(residue));
}
} else if (chain.getClassification() == Residue.Classification.BIRD) {
Bird currBird = chain.getBird();
if (prevBird == null && currBird != null) {
birdNode = new DefaultMutableTreeNode(chain);
chainNode.add(birdNode);
prevBird = currBird;
} else if (!prevBird.isSameInstance(currBird)) {
birdNode = new DefaultMutableTreeNode(chain);
chainNode.add(birdNode);
prevBird = currBird;
}
for (Residue residue : chain.getResidues()) {
birdNode.add(new DefaultMutableTreeNode(residue));
}
} else if (chain.hasModifiedResidues()) {
for (Residue residue : chain.getModifiedResidues()) {
chainNode.add(new DefaultMutableTreeNode(residue));
}
}
}
ligandJList
.getSelectionModel()
.addTreeSelectionListener(
new TreeSelectionListener() {
public void valueChanged(TreeSelectionEvent e) {
applyButton.doClick();
Structure structure = AppBase.sgetModel().getStructures().get(0);
if (structure.getStructureMap().getSurfaceCount() > 0) {
LigandExplorer.sgetGlGeometryViewer().ligandViewWithSurface(structure);
} else {
LigandExplorer.sgetGlGeometryViewer().ligandView(structure);
}
}
});
ligandScroller = new JScrollPane(this.ligandJList);
add(ligandScroller);
} else centerView.setText("No ligands in this structure");
final JLabel displayView = new JLabel("Choose interactions & thresholds...");
displayView.setFont(displayView.getFont().deriveFont(Font.BOLD + Font.ITALIC));
this.add(displayView);
final JCheckBox hydrophilicBox = new JCheckBox(InteractionConstants.hydrogenBondType);
final LegendPanel hydrophilicPanel =
new LegendPanel(InteractionConstants.hydrogenBondColor, LXDocumentFrame.sidebarColor);
final FloatLimitField philicFLF2 = new FloatLimitField("3.3");
this.add(hydrophilicBox);
this.add(philicFLF2);
this.add(hydrophilicPanel);
final JCheckBox hydrophobicBox = new JCheckBox(InteractionConstants.hydrophobicType);
final LegendPanel hydrophobicPanel =
new LegendPanel(InteractionConstants.hydrophobicBondColor, LXDocumentFrame.sidebarColor);
final FloatLimitField phobicFLF2 = new FloatLimitField("3.9");
this.add(hydrophobicBox);
this.add(phobicFLF2);
this.add(hydrophobicPanel);
final JCheckBox l_h2o_pBox = new JCheckBox(InteractionConstants.waterMediatedType);
l_h2o_pBox.setBackground(LXDocumentFrame.sidebarColor);
final LegendPanel l_h2o_pPanel =
new LegendPanel(InteractionConstants.waterMediatedColor, LXDocumentFrame.sidebarColor);
l_h2o_pBox.setBackground(LXDocumentFrame.sidebarColor);
final FloatLimitField l_h2o_pFLF2 = new FloatLimitField("3.3");
this.add(l_h2o_pBox);
this.add(l_h2o_pFLF2);
this.add(l_h2o_pPanel);
final JCheckBox otherBox = new JCheckBox(InteractionConstants.metalInteractionType);
final LegendPanel otherPanel =
new LegendPanel(InteractionConstants.metalInteractionColor, LXDocumentFrame.sidebarColor);
final FloatLimitField otherFLF2 = new FloatLimitField("3.5");
this.add(otherBox);
this.add(otherFLF2);
this.add(otherPanel);
final JCheckBox neighborBox = new JCheckBox(InteractionConstants.neighborInteractionType);
final FloatLimitField neighborFLF1 = new FloatLimitField("4.0");
this.add(neighborBox);
this.add(neighborFLF1);
// new: added this separator
final JSeparator separator = new JSeparator();
this.add(separator);
final JCheckBox distanceBox = new JCheckBox("Label interactions by distance");
distanceBox.setBackground(LXDocumentFrame.sidebarColor);
distanceBox.setSelected(true);
this.add(distanceBox);
// System.out.println("Adding BindingSiteSurfacePanel");
final JPanel surfacePanel = new BindingSiteSurfacePanel(hasMacromoleculeChain());
surfacePanel.setBackground(LXDocumentFrame.sidebarColor);
this.add(surfacePanel);
// this button should eventually be removed. Its still used
// to fire some update events
applyButton = new JButton("Apply");
this.add(applyButton);
this.setLayout(
new LayoutManager() {
public void addLayoutComponent(String arg0, Component arg1) {}
private Dimension layoutSize = null;
public void layoutContainer(Container parent) {
final int visualBuffer = 3;
Insets parentInsets = parent.getInsets();
if (ligandList == null || ligandList.size() == 0) {
Dimension preferred = centerView.getPreferredSize();
centerView.setBounds(
parentInsets.left + visualBuffer,
parentInsets.top + visualBuffer,
preferred.width,
preferred.height);
} else {
Dimension step1Preferred = centerView.getPreferredSize();
Dimension step2Preferred = displayView.getPreferredSize();
;
Dimension hydrophilicBoxPreferred = hydrophilicBox.getPreferredSize();
Dimension hydrophobicBoxPreferred = hydrophobicBox.getPreferredSize();
Dimension l_h2o_pBoxPreferred = l_h2o_pBox.getPreferredSize();
Dimension otherBoxPreferred = otherBox.getPreferredSize();
Dimension neighborBoxPreferred = neighborBox.getPreferredSize();
Dimension distancePreferred = distanceBox.getPreferredSize();
Dimension hydrophilicFLF2Preferred = philicFLF2.getPreferredSize();
Dimension hydrophobicFLF2Preferred = phobicFLF2.getPreferredSize();
Dimension l_h2o_pFLF2Preferred = l_h2o_pFLF2.getPreferredSize();
Dimension otherFLF2Preferred = otherFLF2.getPreferredSize();
Dimension neighborFLF1Preferred = neighborFLF1.getPreferredSize();
Dimension separatorPreferred = separator.getPreferredSize();
Dimension surfacePanelPreferred = surfacePanel.getPreferredSize();
int parentHeight = parent.getHeight();
int parentWidth = parent.getWidth();
int fullWidth =
parentWidth - parentInsets.left - parentInsets.right - visualBuffer * 2;
int listHeight =
parentHeight
- parentInsets.top
- parentInsets.bottom
- (step1Preferred.height
+ step2Preferred.height
+ hydrophilicBoxPreferred.height
+ hydrophobicBoxPreferred.height
+ l_h2o_pBoxPreferred.height
+ otherBoxPreferred.height
+ neighborBoxPreferred.height
+ separatorPreferred.height
+ distancePreferred.height
+ surfacePanelPreferred.height
+ visualBuffer * 13);
int curY = parentInsets.top + visualBuffer;
int curX = parentInsets.left + visualBuffer;
int maxWidth = 0;
centerView.setBounds(curX, curY, step1Preferred.width, step1Preferred.height);
curY += step1Preferred.height + visualBuffer;
maxWidth = step1Preferred.width;
ligandScroller.setBounds(curX, curY, fullWidth, listHeight);
curY += listHeight + visualBuffer;
displayView.setBounds(curX, curY, step2Preferred.width, step2Preferred.height);
curY += step2Preferred.height + visualBuffer;
maxWidth = Math.max(maxWidth, step2Preferred.width);
int maxCheckboxWidth = 0;
int hydrophilicBoxStartY = curY;
hydrophilicBox.setBounds(
curX, curY, hydrophilicBoxPreferred.width, hydrophilicBoxPreferred.height);
curY += hydrophilicBoxPreferred.height + visualBuffer;
maxWidth = Math.max(maxWidth, hydrophilicBoxPreferred.width);
maxCheckboxWidth = Math.max(maxCheckboxWidth, hydrophilicBoxPreferred.width);
int hydrophobicBoxStartY = curY;
hydrophobicBox.setBounds(
curX, curY, hydrophobicBoxPreferred.width, hydrophobicBoxPreferred.height);
curY += hydrophobicBoxPreferred.height + visualBuffer;
maxWidth = Math.max(maxWidth, hydrophobicBoxPreferred.width);
maxCheckboxWidth = Math.max(maxCheckboxWidth, hydrophobicBoxPreferred.width);
int l_h2o_pBoxStartY = curY;
l_h2o_pBox.setBounds(
curX, curY, l_h2o_pBoxPreferred.width, l_h2o_pBoxPreferred.height);
curY += l_h2o_pBoxPreferred.height + visualBuffer;
maxWidth = Math.max(maxWidth, l_h2o_pBoxPreferred.width);
maxCheckboxWidth = Math.max(maxCheckboxWidth, l_h2o_pBoxPreferred.width);
int otherBoxStartY = curY;
otherBox.setBounds(curX, curY, otherBoxPreferred.width, otherBoxPreferred.height);
curY += otherBoxPreferred.height + visualBuffer;
maxWidth = Math.max(maxWidth, otherBoxPreferred.width);
maxCheckboxWidth = Math.max(maxCheckboxWidth, otherBoxPreferred.width);
int neighborBoxStartY = curY;
neighborBox.setBounds(
curX, curY, neighborBoxPreferred.width, neighborBoxPreferred.height);
curY += neighborBoxPreferred.height + visualBuffer;
maxWidth = Math.max(maxWidth, neighborBoxPreferred.width);
maxCheckboxWidth = Math.max(maxCheckboxWidth, neighborBoxPreferred.width);
// now align the constraint boxes to a grid defined by the check boxes.
final int legendWidth = 50;
curX += maxCheckboxWidth + visualBuffer * 2;
neighborFLF1.setBounds(
curX,
neighborBoxStartY,
neighborFLF1Preferred.width,
neighborFLF1Preferred.height);
philicFLF2.setBounds(
curX,
hydrophilicBoxStartY,
hydrophilicFLF2Preferred.width,
hydrophilicFLF2Preferred.height);
phobicFLF2.setBounds(
curX,
hydrophobicBoxStartY,
hydrophobicFLF2Preferred.width,
hydrophobicFLF2Preferred.height);
l_h2o_pFLF2.setBounds(
curX,
l_h2o_pBoxStartY,
l_h2o_pFLF2Preferred.width,
l_h2o_pFLF2Preferred.height);
otherFLF2.setBounds(
curX, otherBoxStartY, otherFLF2Preferred.width, otherFLF2Preferred.height);
curX += philicFLF2.getWidth() + visualBuffer;
hydrophilicPanel.setBounds(
curX, hydrophilicBoxStartY, legendWidth, hydrophilicFLF2Preferred.height);
hydrophobicPanel.setBounds(
curX, hydrophobicBoxStartY, legendWidth, hydrophobicFLF2Preferred.height);
l_h2o_pPanel.setBounds(
curX, l_h2o_pBoxStartY, legendWidth, l_h2o_pFLF2Preferred.height);
otherPanel.setBounds(curX, otherBoxStartY, legendWidth, otherFLF2Preferred.height);
curX = parentInsets.left + visualBuffer;
separator.setBounds(
curX, curY, separatorPreferred.width, separatorPreferred.height);
curY += separatorPreferred.height + 3 * visualBuffer;
maxWidth = Math.max(maxWidth, separatorPreferred.width);
distanceBox.setBounds(
curX, curY, distancePreferred.width, distancePreferred.height);
curY += distancePreferred.height + visualBuffer;
maxWidth = Math.max(maxWidth, distancePreferred.width);
surfacePanel.setBounds(
curX, curY, surfacePanelPreferred.width, surfacePanelPreferred.height);
curY += surfacePanelPreferred.height + visualBuffer;
maxWidth = Math.max(maxWidth, surfacePanelPreferred.width);
// this.layoutSize.width = maxWidth + parentInsets.left + parentInsets.right +
// visualBuffer * 2;
// TODO check width on Mac OSX
this.layoutSize.width =
maxWidth + parentInsets.left + parentInsets.right + visualBuffer * 2;
}
}
public Dimension minimumLayoutSize(Container parent) {
if (this.layoutSize == null) {
this.layoutSize = new Dimension();
this.layoutContainer(parent);
}
return this.layoutSize;
}
public Dimension preferredLayoutSize(Container parent) {
if (this.layoutSize == null) {
this.layoutSize = new Dimension();
this.layoutContainer(parent);
}
return this.layoutSize;
}
public void removeLayoutComponent(Component comp) {}
});
// set colors and initial state
this.setBackground(LXDocumentFrame.sidebarColor);
hydrophilicBox.setBackground(LXDocumentFrame.sidebarColor);
hydrophilicBox.setSelected(false);
hydrophobicBox.setBackground(LXDocumentFrame.sidebarColor);
hydrophobicBox.setSelected(false);
otherBox.setBackground(LXDocumentFrame.sidebarColor);
otherBox.setSelected(false);
neighborBox.setBackground(LXDocumentFrame.sidebarColor);
neighborBox.setSelected(false);
// separator is not visible, why ??
separator.setBackground(Color.BLACK);
separator.setForeground(Color.BLACK);
separator.setVisible(true);
interactionListener =
new InteractionListener(
l_h2o_pBox,
hydrophilicBox,
hydrophobicBox,
otherBox,
neighborBox,
distanceBox,
l_h2o_pFLF2,
philicFLF2,
phobicFLF2,
otherFLF2,
neighborFLF1);
applyButton.addActionListener(interactionListener);
hydrophilicBox.addActionListener(interactionListener);
hydrophobicBox.addActionListener(interactionListener);
l_h2o_pBox.addActionListener(interactionListener);
otherBox.addActionListener(interactionListener);
neighborBox.addActionListener(interactionListener);
distanceBox.addActionListener(interactionListener);
// add action listener to the distance threshold text boxes
l_h2o_pFLF2.addActionListener(interactionListener);
philicFLF2.addActionListener(interactionListener);
phobicFLF2.addActionListener(interactionListener);
otherFLF2.addActionListener(interactionListener);
neighborFLF1.addActionListener(interactionListener);
;
}
}