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Add a Show Electron Density menu item, listener and demo
Puts the feature in reach from the alignment viewer's View menu. The fetch runs on a SwingWorker: even the smallest source is a few hundred kilobytes and a full-resolution map can be far larger, so fetching on the event dispatch thread would freeze the window for the duration. Requests are built with allowNonRenderableFormats(false), which keeps the map coefficient source out of the chain automatically rather than relying on the viewer to notice it cannot draw the result. When nothing is available the dialog explains why rather than listing HTTP codes: for an entry whose every source returns 404 the likely reason is that no structure factors were deposited and there is no associated EMDB map, which is worth saying plainly. The per-source detail is still shown underneath. AbstractAlignmentJmol gains getFrame() and setStatus() so a listener in the neighbouring package can own its dialogs and report progress; both were previously reachable only as protected fields. DemoShowElectronDensity displays 1CBS with both maps clipped around the bound retinoic acid.
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‎biojava-structure-gui/src/main/java/demo/DemoShowElectronDensity.java‎

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/**
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* BioJava development code
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*
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* This code may be freely distributed and modified under the terms of the GNU
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* Lesser General Public Licence. This should be distributed with the code. If
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* you do not have a copy, see:
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*
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* http://www.gnu.org/copyleft/lesser.html
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*
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* Copyright for this code is held jointly by the individual authors. These
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* should be listed in @author doc comments.
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*
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* For more information on the BioJava project and its aims, or to join the
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* biojava-l mailing list, visit the home page at:
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*
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* http://www.biojava.org/
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*/
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package demo;
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import org.biojava.nbio.structure.PdbId;
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import org.biojava.nbio.structure.Structure;
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import org.biojava.nbio.structure.StructureIO;
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import org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol;
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import org.biojava.nbio.structure.io.density.DensityMapCache;
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import org.biojava.nbio.structure.io.density.DensityMapKind;
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import org.biojava.nbio.structure.io.density.DensityMapResult;
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/**
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* Shows 1CBS with its electron density drawn around the bound retinoic acid.
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* <p>
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* Both maps are displayed: the 2mFo-DFc map in blue at 1 sigma, which should hug
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* the ligand closely, and the mFo-DFc difference map as a red and green pair at
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* 3 sigma, which for a well refined structure should show very little.
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* <p>
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* Once the window is up, the map can be manipulated from the Rasmol command box
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* at the bottom, for instance
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* <pre>
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* isosurface ID "bj_density_2fofc" delete
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* </pre>
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* to remove just the blue surface. Pressing Reset Display keeps the maps, since
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* they are folded into the saved state when they are drawn.
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*
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* @author Amr ALHOSSARY
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* @since 7.3.0
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*/
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public class DemoShowElectronDensity {
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/**
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* @param args an optional PDB ID to display instead of the default
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* @throws Exception if the structure or the map could not be fetched
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*/
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public static void main(String[] args) throws Exception {
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String id = args.length > 0 ? args[0] : "1cbs";
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Structure structure = StructureIO.getStructure(id);
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StructureAlignmentJmol viewer = new StructureAlignmentJmol();
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viewer.setStructure(structure);
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viewer.evalString("select all; cartoon on; color chain; "
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+ "select ligand; wireframe 0.16; spacefill 0.4; color cpk;");
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DensityMapCache cache = new DensityMapCache();
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System.out.println("Density cache: " + cache.getCachePath());
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// Clipping to the ligand keeps the surface readable and, for a large map,
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// keeps the contouring quick enough not to stall the interface.
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for (DensityMapKind kind : new DensityMapKind[] {DensityMapKind.TWO_FO_FC, DensityMapKind.FO_FC}) {
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cache.findDensityMap(new PdbId(id), kind).ifPresent(map -> {
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System.out.printf("%-8s from %-20s %s (%,d bytes)%n",
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map.getKind(), map.getSource(), map.getFile().getName(), map.getFileSizeBytes());
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viewer.getJmolPanel().loadDensityMap(map, "{ligand}", 5.0);
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});
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}
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DensityMapResult any = cache.findDensityMap(new PdbId(id), DensityMapKind.AUTO).orElse(null);
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if (any == null) {
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System.out.println("No density is available for " + id
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+ " - try an entry with deposited structure factors, such as 1cbs.");
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}
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}
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}

‎biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MenuCreator.java‎

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@@ -66,6 +66,8 @@ public class MenuCreator {
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public static final String PAIRWISE_ALIGN = "New Pairwise Alignment";
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public static final String MULTIPLE_ALIGN = "New Multiple Alignment";
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public static final String PHYLOGENETIC_TREE = "Phylogenetic Tree";
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/** @since 7.3.0 */
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public static final String SHOW_DENSITY = "Show Electron Density";
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protected static final int keyMask =
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Toolkit.getDefaultToolkit().getMenuShortcutKeyMask();
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@@ -169,6 +171,8 @@ public static JMenuBar initJmolMenu(JFrame frame,
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distMax.setMnemonic(KeyEvent.VK_D);
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distMax.addActionListener(new MyDistMaxListener(parent));
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view.add(distMax);
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//Electron density
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view.add(getShowDensityMenuItem(parent));
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//Dot Plot - only if the alignment was an afpChain
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if (afpChain != null){
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JMenuItem dotplot = new JMenuItem(DOT_PLOT);
@@ -229,6 +233,22 @@ public static JMenuItem getOpenPDBMenuItem() {
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return openI;
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}
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/**
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* Menu item that fetches and displays the electron density or cryo-EM map for
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* the structure currently on screen.
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*
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* @param parent the viewer to draw the map into
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* @return the menu item
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* @author Amr ALHOSSARY
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* @since 7.3.0
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*/
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public static JMenuItem getShowDensityMenuItem(AbstractAlignmentJmol parent) {
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JMenuItem densityI = new JMenuItem(SHOW_DENSITY);
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densityI.setMnemonic(KeyEvent.VK_E);
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densityI.addActionListener(new MyShowDensityListener(parent));
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return densityI;
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}
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public static JMenuItem getLoadMenuItem() {
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‎biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MyShowDensityListener.java‎

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/**
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* BioJava development code
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*
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* This code may be freely distributed and modified under the terms of the GNU
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* Lesser General Public Licence. This should be distributed with the code. If
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* you do not have a copy, see:
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*
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* http://www.gnu.org/copyleft/lesser.html
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*
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* Copyright for this code is held jointly by the individual authors. These
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* should be listed in @author doc comments.
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*
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* For more information on the BioJava project and its aims, or to join the
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* biojava-l mailing list, visit the home page at:
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*
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* http://www.biojava.org/
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*/
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package org.biojava.nbio.structure.align.gui;
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import java.awt.event.ActionEvent;
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import java.awt.event.ActionListener;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.Map;
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import java.util.concurrent.ExecutionException;
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import javax.swing.JOptionPane;
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import javax.swing.SwingWorker;
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import org.biojava.nbio.structure.PdbId;
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import org.biojava.nbio.structure.Structure;
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import org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol;
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import org.biojava.nbio.structure.io.density.DensityMapCache;
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import org.biojava.nbio.structure.io.density.DensityMapKind;
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import org.biojava.nbio.structure.io.density.DensityMapRequest;
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import org.biojava.nbio.structure.io.density.DensityMapResult;
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import org.biojava.nbio.structure.io.density.DensityMapSource;
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import org.biojava.nbio.structure.io.density.NoDensityMapException;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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/**
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* Fetches the density map for the structure on screen and draws it.
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* <p>
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* The download happens on a {@link SwingWorker} rather than the event dispatch
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* thread. Even the smallest source runs to a few hundred kilobytes and a
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* full-resolution map can be far larger, so fetching inline would freeze the
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* interface for as long as it took.
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*
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* @author Amr ALHOSSARY
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* @since 7.3.0
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*/
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public class MyShowDensityListener implements ActionListener {
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private static final Logger logger = LoggerFactory.getLogger(MyShowDensityListener.class);
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private static final String OPTION_2FOFC = "2Fo-Fc (electron density)";
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private static final String OPTION_FOFC = "Fo-Fc (difference)";
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private static final String OPTION_BOTH = "Both";
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private static final String OPTION_AUTO = "Whatever is available";
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private final AbstractAlignmentJmol parent;
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/**
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* @param parent the viewer to draw into
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*/
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public MyShowDensityListener(AbstractAlignmentJmol parent) {
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this.parent = parent;
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}
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@Override
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public void actionPerformed(ActionEvent e) {
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Structure structure = parent == null ? null : parent.getStructure();
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if (structure == null) {
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JOptionPane.showMessageDialog(parent == null ? null : parent.getFrame(),
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"There is no structure on screen to fetch a density map for.",
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"Show Electron Density", JOptionPane.INFORMATION_MESSAGE);
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return;
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}
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PdbId pdbId = structure.getPdbId();
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if (pdbId == null) {
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String typed = JOptionPane.showInputDialog(parent.getFrame(),
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"This structure has no PDB ID. Enter one to look up its density map:",
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"Show Electron Density", JOptionPane.QUESTION_MESSAGE);
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if (typed == null || typed.trim().isEmpty()) {
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return;
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}
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try {
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pdbId = new PdbId(typed.trim());
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} catch (IllegalArgumentException ex) {
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JOptionPane.showMessageDialog(parent.getFrame(), typed + " is not a valid PDB ID.",
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"Show Electron Density", JOptionPane.ERROR_MESSAGE);
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return;
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}
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}
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Object[] options = {OPTION_2FOFC, OPTION_FOFC, OPTION_BOTH, OPTION_AUTO};
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Object choice = JOptionPane.showInputDialog(parent.getFrame(),
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"Which map would you like to see for " + pdbId.getId() + "?",
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"Show Electron Density", JOptionPane.QUESTION_MESSAGE, null, options, OPTION_2FOFC);
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if (choice == null) {
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return;
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}
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List<DensityMapKind> kinds = new ArrayList<>(2);
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if (OPTION_BOTH.equals(choice)) {
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kinds.add(DensityMapKind.TWO_FO_FC);
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kinds.add(DensityMapKind.FO_FC);
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} else if (OPTION_FOFC.equals(choice)) {
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kinds.add(DensityMapKind.FO_FC);
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} else if (OPTION_AUTO.equals(choice)) {
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kinds.add(DensityMapKind.AUTO);
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} else {
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kinds.add(DensityMapKind.TWO_FO_FC);
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}
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fetchAndShow(pdbId, kinds);
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}
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private void fetchAndShow(PdbId pdbId, List<DensityMapKind> kinds) {
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parent.setStatus("Fetching density map for " + pdbId.getId() + " ...");
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new SwingWorker<List<DensityMapResult>, Void>() {
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private NoDensityMapException missing;
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@Override
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protected List<DensityMapResult> doInBackground() throws Exception {
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DensityMapCache cache = DensityMapCache.getInstance();
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List<DensityMapResult> results = new ArrayList<>(kinds.size());
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for (DensityMapKind kind : kinds) {
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try {
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// Restricting to displayable formats also excludes the map
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// coefficient source automatically.
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results.add(cache.getDensityMap(DensityMapRequest.builder(pdbId)
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.kind(kind)
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.allowNonRenderableFormats(false)
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.build()));
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} catch (NoDensityMapException ex) {
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missing = ex;
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}
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}
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return results;
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}
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@Override
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protected void done() {
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List<DensityMapResult> results;
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try {
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results = get();
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} catch (InterruptedException ex) {
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Thread.currentThread().interrupt();
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return;
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} catch (ExecutionException ex) {
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logger.error("Could not fetch a density map for {}", pdbId.getId(), ex.getCause());
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parent.setStatus("Could not fetch density map");
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JOptionPane.showMessageDialog(parent.getFrame(),
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"Could not fetch the density map:\n" + ex.getCause().getMessage(),
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"Show Electron Density", JOptionPane.ERROR_MESSAGE);
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return;
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}
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for (DensityMapResult result : results) {
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parent.getJmolPanel().loadDensityMap(result);
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}
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if (results.isEmpty()) {
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parent.setStatus("No density map available");
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JOptionPane.showMessageDialog(parent.getFrame(), explain(pdbId, missing),
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"Show Electron Density", JOptionPane.INFORMATION_MESSAGE);
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} else {
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DensityMapResult first = results.get(0);
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parent.setStatus(String.format("Density from %s (%,d kB)",
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first.getSource(), first.getFileSizeBytes() / 1024));
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}
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}
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}.execute();
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}
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/**
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* Turns the per-source reasons into something a user can act on, rather than a
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* list of HTTP codes.
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*/
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private static String explain(PdbId pdbId, NoDensityMapException missing) {
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StringBuilder sb = new StringBuilder("No density map is available for ")
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.append(pdbId.getId()).append(".\n\n");
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if (missing == null) {
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return sb.toString();
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}
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Map<DensityMapSource, String> attempts = missing.getAttempts();
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boolean allNotFound = !attempts.isEmpty() && attempts.values().stream()
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.allMatch(reason -> reason.startsWith("HTTP 404") || reason.startsWith("no "));
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if (allNotFound) {
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sb.append("The most likely reason is that no structure factors were deposited\n")
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.append("for this entry, and that it has no associated EMDB map.\n\n");
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}
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sb.append("Sources tried:\n");
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attempts.forEach((source, reason) -> sb.append(" ").append(source).append(": ").append(reason).append('\n'));
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return sb.toString();
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}
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}

‎biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/AbstractAlignmentJmol.java‎

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@@ -194,6 +194,29 @@ public Structure getStructure(){
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*/
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public abstract List<Matrix> getDistanceMatrices();
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/**
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* The window this viewer lives in, for use as the owner of dialogs raised from
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* outside this package.
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*
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* @return the frame, which may be <code>null</code> before the window is built
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* @since 7.3.0
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*/
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public JFrame getFrame() {
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return frame;
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}
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/**
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* Writes a short message into the viewer's status field.
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*
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* @param message the message; ignored if there is no status field yet
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* @since 7.3.0
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*/
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public void setStatus(String message) {
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if (status != null) {
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status.setText(message);
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}
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}
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/**
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* Set the title of the AlignmentJmol window.
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* @param title

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