Author: scooter
Date: 2011-09-18 20:32:10 -0700 (Sun, 18 Sep 2011)
New Revision: 26859
Added:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/CreateNetworkDialog.java
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/actions/CyChimera.java
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/ChimeraChain.java
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/ChimeraModel.java
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/Structure.java
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/GraphObjectSelectionListener.java
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/ModelNavigatorDialog.java
Log:
Prototype of using structureViz to create a Residue Interaction Network.
Still need to layout the resulting graph and set up a more informative
VizMap.
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/actions/CyChimera.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/actions/CyChimera.java
2011-09-18 22:53:33 UTC (rev 26858)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/actions/CyChimera.java
2011-09-19 03:32:10 UTC (rev 26859)
@@ -529,9 +529,13 @@
for (GraphObject obj: goList) {
if (obj instanceof Node) {
// Handle secondary paint??
- view.getNodeView((Node)obj).setSelected(state);
+ NodeView nv = view.getNodeView((Node)obj);
+ if (nv != null)
+ nv.setSelected(state);
} else if (obj instanceof Edge) {
- view.getEdgeView((Edge)obj).setSelected(state);
+ EdgeView ev = view.getEdgeView((Edge)obj);
+ if (ev != null)
+ ev.setSelected(state);
}
if (selectedList.contains(obj))
selectedList.remove(obj);
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/ChimeraChain.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/ChimeraChain.java
2011-09-18 22:53:33 UTC (rev 26858)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/ChimeraChain.java
2011-09-19 03:32:10 UTC (rev 26859)
@@ -236,17 +236,13 @@
* @return String representation of chain
*/
public String toString() {
- String nodeName = "{none}";
- Structure structure = chimeraModel.getStructure();
- if (structure != null && structure.getIdentifier() != null)
- nodeName = structure.getIdentifier();
String displayName = chimeraModel.getModelName();
if (displayName.length() > 14)
displayName = displayName.substring(0,13)+"...";
if (chainId.equals("_")) {
- return (nodeName+"; "+displayName+" Chain (no ID)
("+getResidueCount()+" residues)");
+ return (displayName+" Chain (no ID)
("+getResidueCount()+" residues)");
} else {
- return (nodeName+"; "+displayName+" Chain "+chainId+"
("+getResidueCount()+" residues)");
+ return (displayName+" Chain "+chainId+"
("+getResidueCount()+" residues)");
}
}
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/ChimeraModel.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/ChimeraModel.java
2011-09-18 22:53:33 UTC (rev 26858)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/ChimeraModel.java
2011-09-19 03:32:10 UTC (rev 26859)
@@ -358,18 +358,23 @@
* Return a string representation for the model
*/
public String toString() {
- String nodeName = "{none}";
- if (structure != null && structure.getIdentifier() != null)
+ String nodeName = " {none}";
+ if (structure != null && structure.getIdentifier() != null) {
nodeName = structure.getIdentifier();
+ if (structure.getGraphObjectList().size() > 1)
+ nodeName = "s {"+nodeName+"}";
+ else
+ nodeName = " "+nodeName;
+ }
String displayName = name;
if (name.length() > 14)
displayName = name.substring(0,13)+"...";
if (getChainCount() > 0) {
- return ("Node "+nodeName+" [Model "+toSpec()+"
"+displayName+" ("+getChainCount()+" chains, "+getResidueCount()+"
residues)]");
+ return ("Node"+nodeName+" [Model "+toSpec()+"
"+displayName+" ("+getChainCount()+" chains, "+getResidueCount()+"
residues)]");
} else if (getResidueCount() > 0) {
- return ("Node "+nodeName+" [Model "+toSpec()+"
"+displayName+" ("+getResidueCount()+" residues)]");
+ return ("Node"+nodeName+" [Model "+toSpec()+"
"+displayName+" ("+getResidueCount()+" residues)]");
} else {
- return ("Node "+nodeName+" [Model "+toSpec()+"
"+displayName+"]");
+ return ("Node"+nodeName+" [Model "+toSpec()+"
"+displayName+"]");
}
}
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/Structure.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/Structure.java
2011-09-18 22:53:33 UTC (rev 26858)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/Structure.java
2011-09-19 03:32:10 UTC (rev 26859)
@@ -361,6 +361,11 @@
else
list += ";"+obj.getIdentifier();
}
+
+ // We really don't want this to be too long -- truncate, if
necessary
+ if (list.length() > 14) {
+ list = list.substring(0, 13).concat("...");
+ }
return list;
}
Added:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/CreateNetworkDialog.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/CreateNetworkDialog.java
(rev 0)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/CreateNetworkDialog.java
2011-09-19 03:32:10 UTC (rev 26859)
@@ -0,0 +1,379 @@
+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2006 The Regents of the University of California.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions, and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above
+ * copyright notice, this list of conditions, and the following
+ * disclaimer in the documentation and/or other materials provided
+ * with the distribution.
+ * 3. Redistributions must acknowledge that this software was
+ * originally developed by the UCSF Computer Graphics Laboratory
+ * under support by the NIH National Center for Research Resources,
+ * grant P41-RR01081.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
+package structureViz.ui;
+
+// System imports
+import java.util.List;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+
+import javax.swing.BorderFactory;
+import javax.swing.BoxLayout;
+import javax.swing.JButton;
+import javax.swing.JDialog;
+import javax.swing.JPanel;
+
+import javax.swing.border.EtchedBorder;
+
+import java.awt.Dialog;
+import java.awt.Dimension;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+// Cytoscape imports
+import cytoscape.CyEdge;
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+import cytoscape.data.CyAttributes;
+import cytoscape.data.Semantics;
+import cytoscape.layout.LayoutProperties;
+import cytoscape.layout.Tunable;
+import cytoscape.view.CyNetworkView;
+
+import giny.view.NodeView;
+
+// StructureViz imports
+import structureViz.actions.Chimera;
+import structureViz.model.ChimeraModel;
+
+/**
+ */
+public class CreateNetworkDialog extends JDialog implements ActionListener {
+ // Instance variables
+ Chimera chimeraObject;
+ LayoutProperties properties;
+ boolean includeContacts = true;
+ boolean includeClashes = false;
+ boolean includeHBonds = false;
+ int interactionBetween = 2; // Between selection & other models
+ static final int BETWEENMODELS = 0;
+ static final int BETWEENSELMODELS = 1;
+ static final int BETWEENALL = 2;
+ static final String[] interactionArray = {"Between models", "Between
selection & other models", "Between selection and all atoms"};
+ static final String CLASHCOMMAND = "findclash sel makePseudobonds false
log true namingStyle command";
+
+ /**
+ * Create a CreateNetworkDialog
+ *
+ * @param parent the Frame acting as the parent of this Dialog
+ * @param object the Chimera interface object
+ */
+ public CreateNetworkDialog (Dialog parent, Chimera object) {
+ super(parent, false);
+ chimeraObject = object;
+ properties = new LayoutProperties("CreateNetworkDialog");
+ initTunables();
+ initComponents();
+ }
+
+ /**
+ * Initialize all of the graphical components of the dialog
+ */
+ private void initComponents() {
+ this.setTitle("Create Network Dialog");
+
+ setDefaultCloseOperation(DISPOSE_ON_CLOSE);
+
+ // Create a panel for the main content
+ JPanel dataPanel = new JPanel();
+ BoxLayout layout = new BoxLayout(dataPanel,
BoxLayout.PAGE_AXIS);
+ dataPanel.setLayout(layout);
+
+ // Use Tunables for the checkboxes, etc.
+ dataPanel.add(properties.getTunablePanel());
+
+ // Add the button box
+ JPanel buttonBox = new JPanel();
+ JButton createButton = new JButton("Create network");
+ createButton.setActionCommand("create");
+ createButton.addActionListener(this);
+
+ JButton doneButton = new JButton("Cancel");
+ doneButton.setActionCommand("done");
+ doneButton.addActionListener(this);
+ buttonBox.add(createButton);
+ buttonBox.add(doneButton);
+
buttonBox.setBorder(BorderFactory.createEtchedBorder(EtchedBorder.LOWERED));
+ buttonBox.setMaximumSize(new Dimension(1000,35));
+ dataPanel.add(buttonBox);
+
+ setContentPane(dataPanel);
+ }
+
+ private void initTunables() {
+ properties.add(new Tunable("includeContacts", "Include
contacts",
+ Tunable.BOOLEAN, includeContacts));
+ properties.add(new Tunable("includeClashes", "Include clashes",
+ Tunable.BOOLEAN, includeClashes));
+ properties.add(new Tunable("includeHBonds", "Include hydrogen
bonds (overlaps with contacts)",
+ Tunable.BOOLEAN, includeHBonds));
+ properties.add(new Tunable("interaction", "Include
interactions",
+ Tunable.LIST, new
Integer(interactionBetween),
+ (Object) interactionArray, (Object)
null, 0));
+ }
+
+ private void updateTunables(boolean force) {
+ Tunable t = properties.get("includeContacts");
+ if ((t != null) && (t.valueChanged() || force))
+ includeContacts = ((Boolean)
t.getValue()).booleanValue();
+
+ t = properties.get("includeClashes");
+ if ((t != null) && (t.valueChanged() || force))
+ includeClashes = ((Boolean)
t.getValue()).booleanValue();
+
+ t = properties.get("includeHBonds");
+ if ((t != null) && (t.valueChanged() || force))
+ includeHBonds = ((Boolean) t.getValue()).booleanValue();
+
+ t = properties.get("interaction");
+ if ((t != null) && (t.valueChanged() || force))
+ interactionBetween = ((Integer)
t.getValue()).intValue();
+
+ }
+
+ /**
+ * The method called to actually execute the command.
+ */
+ public void actionPerformed(ActionEvent e) {
+ if ("done".equals(e.getActionCommand())) {
+ setVisible(false);
+ return;
+ }
+ if ("create".equals(e.getActionCommand())) {
+ updateTunables(true);
+ List<String> edgeList = null;
+ String cutoff = "";
+ String type = "Clashes";
+ // Send the commands to Chimera and get the results
+ if (includeContacts) {
+ type = "Contacts";
+ cutoff = "overlapCutoff -0.4 hbondAllowance
0.0";
+ }
+ if (includeClashes || includeContacts) {
+ String command = "findclash sel makePseudobonds
false log true namingStyle command "+cutoff ;
+ if (interactionBetween == BETWEENMODELS) {
+ } else if (interactionBetween ==
BETWEENSELMODELS)
+ command = command.concat(" test other");
+ else if (interactionBetween == BETWEENALL)
+ command = command.concat(" test model");
+
+ List<String>replyList =
chimeraObject.commandReply(command);
+ printReply(replyList);
+ edgeList = parseClashReplies(replyList, type);
+ }
+ if (includeHBonds) {
+ String command = null;
+ if (interactionBetween == BETWEENMODELS) {
+ } else if (interactionBetween ==
BETWEENSELMODELS)
+ command = "findhbond selRestrict any
intermodel true intramodel false makePseudobonds false log true namingStyle
command";
+ else if (interactionBetween == BETWEENALL)
+ command = "findhbond selRestrict any
intermodel true intramodel true makePseudobonds false log true namingStyle
command";
+ List<String>replyList =
chimeraObject.commandReply(command);
+ if (edgeList == null)
+ edgeList = parseHBondReplies(replyList);
+ else
+
edgeList.addAll(parseHBondReplies(replyList));
+ printReply(replyList);
+ }
+ // We've got a list of edges, now we need to create the
nodes and edges
+ // and assign the attributes we want, then we can
create the network as a child of the current network
+ System.out.println("edgeList has "+edgeList.size()+"
entries");
+ int[] edges = new int[edgeList.size()];
+ int[] nodes = new int[edgeList.size()*2];
+ int edgeCount = 0;
+ for (String edge: edgeList) {
+ System.out.println("Edge "+(edgeCount+1)+":
"+edge);
+ createNodesAndEdge(edge, nodes, edges,
edgeCount);
+ edgeCount++;
+ }
+
+ CyNetwork network = Cytoscape.getCurrentNetwork();
+ String name = network.getTitle();
+
+ // Create the network
+ Cytoscape.createNetwork(nodes, edges, "Interaction from
"+name, network, true);
+
+ setVisible(false);
+ return;
+ }
+ }
+
+ private void printReply(List<String> replyLog) {
+ for (String str: replyLog) System.out.println(str);
+ }
+
+ /**
+ * Clash replies look like:
+ * *preamble*
+ * *header line*
+ * *clash lines*
+ * where preamble is:
+ * Allowed overlap: -0.4
+ * H-bond overlap reduction: 0
+ * Ignore contacts between atoms separated by 4 bonds or less
+ * Ignore intra-residue contacts
+ * 44 contacts
+ * and the header line is:
+ * atom1 atom2 overlap distance
+ * and the clash lines look like:
+ * :2470.A@N :323.A@OD2 -0.394 3.454
+ */
+ private List<String> parseClashReplies(List<String> replyLog, String
type) {
+ // Scan for our header line
+ boolean foundHeader = false;
+ int index = 0;
+ for (index = 0; index < replyLog.size(); index++) {
+ String str = replyLog.get(index);
+ System.out.println("Line "+index+": "+str);
+ if (str.trim().startsWith("atom1")) {
+ foundHeader = true;
+ break;
+ }
+ }
+ if (!foundHeader) return null;
+
+ List<String> edgeList = new ArrayList<String>();
+
+ for (++index; index < replyLog.size(); index++) {
+ System.out.println("Line "+index+":
"+replyLog.get(index));
+ String[] line =
replyLog.get(index).trim().split("\\s+");
+ if (line.length != 4) continue;
+
+ System.out.println("atom1 = "+line[0]+" atom2 =
"+line[1]+" overlap = "+line[2]+" distance = "+line[3]);
+
edgeList.add(fixResidue(line[0])+"\t"+type+"\t"+fixResidue(line[1])+"\t"+line[2]+"\t"+line[3]);
+ }
+
+ return edgeList;
+
+ }
+
+
+ // H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
+ /**
+ * Finding acceptors in model '1tkk'
+ * Building search tree of acceptor atoms
+ * Finding donors in model '1tkk'
+ * Matching donors in model '1tkk' to acceptors
+ * Finding intermodel H-bonds
+ * Finding intramodel H-bonds
+ * Constraints relaxed by 0.4 angstroms and 20 degrees
+ * Models used:
+ * #0 1tkk
+ * H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
+ * ARG 24.A NH1 GLU 2471.A OE1 no hydrogen 3.536 N/A
+ * LYS 160.A NZ GLU 2471.A O no hydrogen 2.680 N/A
+ * LYS 162.A NZ ALA 2470.A O no hydrogen 3.022 N/A
+ * LYS 268.A NZ GLU 2471.A O no hydrogen 3.550 N/A
+ * ILE 298.A N GLU 2471.A OE2 no hydrogen 3.141 N/A
+ * ALA 2470.A N THR 135.A OG1 no hydrogen 2.814 N/A
+ * ALA 2470.A N ASP 321.A OD1 no hydrogen 2.860 N/A
+ * ALA 2470.A N ASP 321.A OD2 no hydrogen 3.091 N/A
+ * ALA 2470.A N ASP 323.A OD1 no hydrogen 2.596 N/A
+ * ALA 2470.A N ASP 323.A OD2 no hydrogen 3.454 N/A
+ * GLU 2471.A N SER 296.A O no hydrogen 2.698 N/A
+ * HOH 2541.A O GLU 2471.A OE1 no hydrogen 2.746 N/A
+ * HOH 2577.A O GLU 2471.A O no hydrogen 2.989 N/A
+ */
+ private List<String> parseHBondReplies(List<String> replyLog) {
+ // Scan for our header line
+ boolean foundHeader = false;
+ int index = 0;
+ for (index = 0; index < replyLog.size(); index++) {
+ String str = replyLog.get(index);
+ System.out.println("Line "+index+": "+str);
+ if (str.trim().startsWith("H-bonds")) {
+ foundHeader = true;
+ break;
+ }
+ }
+ if (!foundHeader) return null;
+
+ List<String> edgeList = new ArrayList<String>();
+
+ for (++index; index < replyLog.size(); index++) {
+ System.out.println("Line "+index+":
"+replyLog.get(index));
+ String[] line =
replyLog.get(index).trim().split("\\s+");
+ if (line.length != 6 && line.length != 7) continue;
+
+ String atom1 = line[0];
+ String atom2 = line[1];
+ String distance = line[3];
+ if (line[2].equals("no") && line[3].equals("hydrogen"))
+ distance = line[4];
+
edgeList.add(fixResidue(atom1)+"\tHBond\t"+fixResidue(atom2)+"\t\t"+distance);
+ }
+ return edgeList;
+ }
+
+ private String fixResidue(String residue) {
+ int atIndex = residue.indexOf('@');
+ if (atIndex == -1) return residue;
+ return residue.substring(0, atIndex);
+ }
+
+ private void createNodesAndEdge(String edgeSpec, int[] nodes, int[]
edges, int edgeCount) {
+ CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
+ CyAttributes edgeAttributes = Cytoscape.getEdgeAttributes();
+
+ String[] edgeParts = edgeSpec.split("\t");
+ CyNode node1 =
Cytoscape.getCyNode(makeFunctionalResidue(edgeParts[0]), true);
+ CyNode node2 =
Cytoscape.getCyNode(makeFunctionalResidue(edgeParts[2]), true);
+ nodeAttributes.setAttribute(node1.getIdentifier(),
"FunctionalResidues", node1.getIdentifier());
+ nodeAttributes.setAttribute(node2.getIdentifier(),
"FunctionalResidues", node2.getIdentifier());
+ CyEdge edge = Cytoscape.getCyEdge(node1, node2,
Semantics.INTERACTION, edgeParts[1], true);
+ if (edgeParts[3] != null && edgeParts[3].length() > 0)
+ edgeAttributes.setAttribute(edge.getIdentifier(),
"Overlap", Double.valueOf(edgeParts[3]));
+ edgeAttributes.setAttribute(edge.getIdentifier(), "Distance",
Double.valueOf(edgeParts[4]));
+ edges[edgeCount] = edge.getRootGraphIndex();
+ nodes[edgeCount*2] = node1.getRootGraphIndex();
+ nodes[edgeCount*2+1] = node2.getRootGraphIndex();
+ }
+
+ private String makeFunctionalResidue(String alias) {
+ int model = 0;
+ int submodel = 0;
+ String[] modelSplit = alias.split(":");
+ if (modelSplit[0].length() > 0) {
+ String[] subSplit =
modelSplit[0].substring(1).split(".");
+ model = Integer.parseInt(subSplit[0]);
+ if (subSplit.length > 1)
+ submodel = Integer.parseInt(subSplit[1]);
+ }
+ // Get the model
+ ChimeraModel cModel = chimeraObject.getChimeraModel(model,
submodel);
+ return "#"+cModel.getModelName()+":"+modelSplit[1];
+ }
+}
+
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/GraphObjectSelectionListener.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/GraphObjectSelectionListener.java
2011-09-18 22:53:33 UTC (rev 26858)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/GraphObjectSelectionListener.java
2011-09-19 03:32:10 UTC (rev 26859)
@@ -140,7 +140,6 @@
String command = null;
for (String selStr: selStrs) {
- System.out.println("selStr = "+selStr);
if (command == null)
command = "select "+selStr;
else
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/ModelNavigatorDialog.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/ModelNavigatorDialog.java
2011-09-18 22:53:33 UTC (rev 26858)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/ModelNavigatorDialog.java
2011-09-19 03:32:10 UTC (rev 26859)
@@ -95,6 +95,7 @@
private static final int COLLAPSEALL = 19;
private static final int EXPANDMODELS = 20;
private static final int EXPANDCHAINS = 21;
+ private static final int CREATENETWORK = 22;
private boolean ignoreSelection = false;
private int residueDisplay = ChimeraResidue.THREE_LETTER;
private boolean isCollapsing = false;
@@ -147,6 +148,7 @@
alignMenu.setEnabled(false);
chimeraObject.updateSelection();
ignoreSelection = false;
+ pack();
}
/**
@@ -422,20 +424,29 @@
JMenu clashMenu = new JMenu("Clash detection");
addMenuItem(clashMenu, "Find all clashes", FINDCLASH,
"findclash sel continuous true");
addMenuItem(clashMenu, "Find clashes within models", FINDCLASH,
"findclash sel test model continuous true");
- addMenuItem(clashMenu, "Clear clashes", COMMAND, "~findclash");
+ addMenuItem(clashMenu, "Clear clashes and contacts", COMMAND,
"~findclash");
chimeraMenu.add(clashMenu);
+ JMenu contactMenu = new JMenu("Contact detection");
+ addMenuItem(contactMenu, "Find all contacts", FINDCLASH,
"findclash sel overlapCutoff -0.4 hbondAllowance 0.0");
+ addMenuItem(contactMenu, "Find contacts within models",
FINDCLASH, "findclash sel test model overlapCutoff -0.4 hbondAllowance 0.0");
+ addMenuItem(contactMenu, "Clear clashes and contacts", COMMAND,
"~findclash");
+ chimeraMenu.add(contactMenu);
+
JMenu hBondMenu = new JMenu("Hydrogen bond detection");
JMenu fHBondMenu = new JMenu("Find hydrogen bonds");
- addMenuItem(fHBondMenu, "Between models", FINDHBOND, "findhbond
sel any intermodel true intramodel false");
- addMenuItem(fHBondMenu, "Within models", FINDHBOND, "findhbond
sel any intermodel false intramodel true");
- addMenuItem(fHBondMenu, "Both", FINDHBOND, "findhbond sel any
intermodel true intramodel true");
+ addMenuItem(fHBondMenu, "Between models", FINDHBOND, "findhbond
selRestrict any intermodel true intramodel false");
+ addMenuItem(fHBondMenu, "Within models", FINDHBOND, "findhbond
selRestrict any intermodel false intramodel true");
+ addMenuItem(fHBondMenu, "Both", FINDHBOND, "findhbond
selRestrict any intermodel true intramodel true");
hBondMenu.add(fHBondMenu);
addMenuItem(hBondMenu, "Clear hydrogen bonds", COMMAND,
"~findhbond");
chimeraMenu.add(hBondMenu);
chimeraMenu.add(new JSeparator());
+ addMenuItem(chimeraMenu, "Create interaction network from
structure...", CREATENETWORK, null);
+ chimeraMenu.add(new JSeparator());
+
addMenuItem(chimeraMenu, "Exit", EXIT, null);
menuBar.add(chimeraMenu);
@@ -669,6 +680,8 @@
JOptionPane.showMessageDialog(dialog,
"You must select something to find hydrogen bonds",
"Nothing
Selected", JOptionPane.ERROR_MESSAGE);
}
+ } else if (type == CREATENETWORK) {
+ launchNewNetworkDialog();
} else {
residueDisplay = type;
treeModel.setResidueDisplay(type);
@@ -676,6 +689,13 @@
}
}
+ private void launchNewNetworkDialog()
+ {
+ CreateNetworkDialog dialog = new
CreateNetworkDialog(null, chimeraObject);
+ dialog.pack();
+ dialog.setVisible(true);
+ }
+
/**
* Create and instantiate the align dialog
*/
--
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