Author: scooter
Date: 2011-10-04 21:10:38 -0700 (Tue, 04 Oct 2011)
New Revision: 27062
Added:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/actions/CreateNetworkAction.java
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/CreateNetworkDialog.java
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/ModelNavigatorDialog.java
Log:
Did a little refactoring....
Added:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/actions/CreateNetworkAction.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/actions/CreateNetworkAction.java
(rev 0)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/actions/CreateNetworkAction.java
2011-10-05 04:10:38 UTC (rev 27062)
@@ -0,0 +1,535 @@
+/* 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.actions;
+
+// System imports
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+// Cytoscape imports
+import cytoscape.CyEdge;
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+import cytoscape.data.CyAttributes;
+import cytoscape.data.Semantics;
+import cytoscape.task.Task;
+import cytoscape.task.TaskMonitor;
+import cytoscape.task.ui.JTaskConfig;
+import cytoscape.view.CyNetworkView;
+
+import giny.view.NodeView;
+
+// StructureViz imports
+import structureViz.actions.Chimera;
+import structureViz.actions.CyChimera;
+import structureViz.model.ChimeraChain;
+import structureViz.model.ChimeraModel;
+import structureViz.model.ChimeraResidue;
+import structureViz.model.ChimeraStructuralObject;
+import structureViz.model.Structure;
+import structureViz.model.StructureUtils;
+import structureViz.model.Structure.StructureType;
+import structureViz.ui.CreateNetworkDialog;
+
+/**
+ */
+public class CreateNetworkAction implements Task {
+ // Instance variables
+ Chimera chimeraObject;
+ TaskMonitor monitor;
+ boolean includeContacts = true;
+ boolean includeClashes = false;
+ boolean includeHBonds = false;
+ boolean includeConnectivity = false;
+ boolean includeConnectivityDistance = false;
+ boolean canceled = false;
+ int interactionBetween = 2; // Between selection & other models
+
+ static final String DISTANCE_ATTR = "MinimumDistance";
+ static final String OVERLAP_ATTR = "MaximumOverlap";
+ static final String RESIDUE_ATTR = "FunctionalResidues";
+ static final String SEED_ATTR = "SeedResidue";
+ static final String BACKBONE_ATTR = "BackboneInteraction";
+ static final String SIDECHAIN_ATTR = "SideChainInteraction";
+
+ public CreateNetworkAction(Chimera chimeraObject) {
+ this.chimeraObject = chimeraObject;
+ }
+
+ public void halt() { canceled = true; }
+
+ public void setTaskMonitor(TaskMonitor monitor) {
+ this.monitor = monitor;
+ }
+
+ public void setIncludeContacts(boolean value) { includeContacts =
value; }
+ public void setIncludeClashes(boolean value) { includeClashes = value; }
+ public void setIncludeHBonds(boolean value) { includeHBonds = value; }
+ public void setIncludeConnectivity(boolean value) { includeConnectivity
= value; }
+ public void setIncludeConnectivityDistance(boolean value) {
includeConnectivityDistance = value; }
+ public void setInteractionBetween(int value) { interactionBetween =
value; }
+
+ public String getTitle() { return "Create Interaction Network"; }
+
+ public void run() {
+
+ List<CyEdge> edgeList = null;
+ Map<CyNode, CyNode> nodeMap = new HashMap<CyNode, CyNode>();
+ String cutoff = "";
+ String type = "Clashes";
+ // Send the commands to Chimera and get the results
+ if (includeContacts) {
+ monitor.setStatus("Getting contacts");
+ type = "Contacts";
+ cutoff = "overlapCutoff -0.4 hbondAllowance 0.0";
+ } else {
+ monitor.setStatus("Getting clashes");
+ }
+ if (includeClashes || includeContacts) {
+ String command = "findclash sel makePseudobonds false
log true namingStyle command "+cutoff ;
+ if (interactionBetween ==
CreateNetworkDialog.BETWEENMODELS) {
+ // Get the first model
+ ChimeraModel model =
chimeraObject.getChimeraModels().get(0);
+ int modelNumber = model.getModelNumber();
+ // Create the command
+ command = "findclash #"+modelNumber+"
makePseudobonds false log true namingStyle command test other "+cutoff;
+ } else if (interactionBetween ==
CreateNetworkDialog.BETWEENSELMODELS)
+ command = command.concat(" test other");
+ else if (interactionBetween ==
CreateNetworkDialog.BETWEENALL)
+ command = command.concat(" test model");
+
+ List<String>replyList =
chimeraObject.commandReply(command);
+ if (canceled) return;
+ // printReply(replyList);
+ edgeList = parseClashReplies(replyList, nodeMap, type);
+ }
+ if (includeHBonds) {
+ monitor.setStatus("Getting Hydrogen Bonds");
+ // Get the first model
+ ChimeraModel model =
chimeraObject.getChimeraModels().get(0);
+ int modelNumber = model.getModelNumber();
+ String command =
+ "findhbond spec #"+modelNumber+" intramodel
false intermodel true makePseudobonds false log true namingStyle command";
+ if (interactionBetween ==
CreateNetworkDialog.BETWEENMODELS) {
+ command = "findhbond selRestrict any intermodel
true makePseudobonds false log true namingStyle command";
+ } else if (interactionBetween ==
CreateNetworkDialog.BETWEENSELMODELS)
+ command = command.concat(" intramodel false");
+ else if (interactionBetween ==
CreateNetworkDialog.BETWEENALL)
+ command = command.concat(" intramodel true");
+ List<String>replyList =
chimeraObject.commandReply(command);
+ if (canceled) return;
+ if (edgeList == null)
+ edgeList = parseHBondReplies(replyList,
nodeMap);
+ else
+ edgeList.addAll(parseHBondReplies(replyList,
nodeMap));
+ // printReply(replyList);
+ }
+ if (includeConnectivity) {
+ System.out.println("Getting Connectivity");
+ monitor.setStatus("Getting Connectivity");
+ String command = "listphysicalchains";
+ List<String>replyList =
chimeraObject.commandReply(command);
+ if (canceled) return;
+ System.out.println("Getting Connectivity Edges");
+ edgeList.addAll(parseConnectivityReplies(replyList, new
ArrayList<CyNode>(nodeMap.keySet())));
+ }
+
+ if (canceled) return;
+
+ int[] edges = new int[edgeList.size()];
+ int[] nodes = new int[edgeList.size()*2];
+ int edgeCount = 0;
+ for (CyEdge edge: edgeList) {
+ edges[edgeCount] = edge.getRootGraphIndex();
+ nodes[edgeCount*2] =
edge.getSource().getRootGraphIndex();
+ nodes[edgeCount*2+1] =
edge.getTarget().getRootGraphIndex();
+ edgeCount++;
+ }
+
+ if (canceled) return;
+
+ // Create the network
+ CyNetwork network = Cytoscape.getCurrentNetwork();
+ String name = network.getTitle();
+ CyNetwork newNetwork = Cytoscape.createNetwork(nodes, edges,
"Interaction from "+name, network, true);
+
+ // Set vizmap
+
+ // Do a layout
+
+ // Make it current
+ Cytoscape.setCurrentNetwork(newNetwork.getIdentifier());
+ Cytoscape.setCurrentNetworkView(newNetwork.getIdentifier());
+
+ // Activate structureViz for all of our nodes
+ CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
+ for (CyNode node: nodeMap.keySet()) {
+ String residueSpec =
nodeAttributes.getStringAttribute(node.getIdentifier(), RESIDUE_ATTR);
+ String structure =
CyChimera.findStructures(residueSpec);
+ Structure s = Structure.getStructure(structure, node,
StructureType.PDB_MODEL);
+ s.setResidueList(node, residueSpec);
+ }
+ }
+
+ public JTaskConfig getDefaultTaskConfig() {
+ JTaskConfig config = new JTaskConfig();
+ config.displayCancelButton(true);
+ config.displayStatus(true);
+ config.displayTimeElapsed(false);
+ config.displayTimeRemaining(false);
+ config.setAutoDispose(true);
+ return config;
+ }
+
+ 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<CyEdge> parseClashReplies(List<String> replyLog,
Map<CyNode, CyNode>nodes, 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);
+ if (str.trim().startsWith("atom1")) {
+ foundHeader = true;
+ break;
+ }
+ }
+ if (!foundHeader) return null;
+
+ Map<CyEdge, Double> distanceMap = new HashMap<CyEdge, Double>();
+ Map<CyEdge, Double> overlapMap = new HashMap<CyEdge, Double>();
+ for (++index; index < replyLog.size(); index++) {
+ String[] line =
replyLog.get(index).trim().split("\\s+");
+ if (line.length != 4) continue;
+
+ CyEdge edge = createEdge(nodes, line[0], line[1], type);
+
+ updateMap(distanceMap, edge, line[3], -1); // We want
the smallest distance
+ updateMap(overlapMap, edge, line[2], 1); // We want the
largest overlap
+ }
+
+ CyAttributes edgeAttributes = Cytoscape.getEdgeAttributes();
+ // OK, now update the edge attributes we want
+ for (CyEdge edge: distanceMap.keySet()) {
+ edgeAttributes.setAttribute(edge.getIdentifier(),
DISTANCE_ATTR, distanceMap.get(edge));
+ edgeAttributes.setAttribute(edge.getIdentifier(),
OVERLAP_ATTR, overlapMap.get(edge));
+ }
+
+ return new ArrayList<CyEdge>(distanceMap.keySet());
+ }
+
+
+ // 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<CyEdge> parseHBondReplies(List<String> replyLog,
Map<CyNode, CyNode>nodes) {
+ // Scan for our header line
+ boolean foundHeader = false;
+ int index = 0;
+ for (index = 0; index < replyLog.size(); index++) {
+ String str = replyLog.get(index);
+ if (str.trim().startsWith("H-bonds")) {
+ foundHeader = true;
+ break;
+ }
+ }
+ if (!foundHeader) return null;
+
+ Map<CyEdge, Double> distanceMap = new HashMap<CyEdge, Double>();
+ for (++index; index < replyLog.size(); index++) {
+ String[] line =
replyLog.get(index).trim().split("\\s+");
+ if (line.length != 6 && line.length != 7) continue;
+
+ CyEdge edge = createEdge(nodes, line[0], line[1],
"HBond");
+
+ String distance = line[3];
+ if (line[2].equals("no") && line[3].equals("hydrogen"))
+ distance = line[4];
+ updateMap(distanceMap, edge, distance, -1); // We want
the smallest distance
+ }
+
+ CyAttributes edgeAttributes = Cytoscape.getEdgeAttributes();
+ // OK, now update the edge attributes we want
+ for (CyEdge edge: distanceMap.keySet()) {
+ edgeAttributes.setAttribute(edge.getIdentifier(),
DISTANCE_ATTR, distanceMap.get(edge));
+ }
+
+ return new ArrayList<CyEdge>(distanceMap.keySet());
+ }
+
+ /**
+ * Parse the connectivity information from Chimera. The data is of the
form:
+ * physical chain #0:283.A #0:710.A
+ * physical chain #0:283.B #0:710.B
+ * physical chain #0:283.C #0:710.C
+ *
+ * We don't use this data to create new nodes -- only new edges. If
two nodes are within the
+ * same physical chain, we connect them with a "Connected" edge
+ */
+ private List<CyEdge> parseConnectivityReplies(List<String> replyLog,
List<CyNode>nodes) {
+ List<CyEdge> edgeList = new ArrayList<CyEdge>();
+ List<ChimeraResidue[]> rangeList = new
ArrayList<ChimeraResidue[]>();
+ for (String line: replyLog) {
+ String[] tokens = line.split(" ");
+ if (tokens.length != 4) continue;
+ String start = tokens[2];
+ String end = tokens[3];
+
+ ChimeraResidue[] range = new ChimeraResidue[2];
+
+ // Get the residues from the reside spec
+ range[0] = StructureUtils.getResidue(start,
chimeraObject);
+ range[1] = StructureUtils.getResidue(end,
chimeraObject);
+ rangeList.add(range);
+ }
+
+ // If we don't have any nodes, get all of the residues in the
connectivity
+ // list and create them as nodes
+
+ // For each node pair, figure out if the pair is connected
+ for (int i = 0; i < nodes.size(); i++) {
+ CyNode node1 = nodes.get(i);
+ // System.out.println("Getting the range for the first
node..."+node1);
+ ChimeraResidue[] range = getRange(rangeList, node1);
+ if (range == null) continue;
+ for (int j = i+1; j < nodes.size(); j++) {
+ if (canceled) return edgeList;
+ CyNode node2 = nodes.get(j);
+ // System.out.println("Seeing if node2
"+node2+" is in the range...");
+ if (inRange(range, node2)) {
+ // System.out.println("....it is");
+ // These two nodes are connected
+ CyEdge edge =
Cytoscape.getCyEdge(node1, node2, Semantics.INTERACTION, "connected", true);
+
edgeList.add(createConnectivityEdge(node1, node2));
+ }
+ }
+ }
+
+ // Now, make the edges based on whether any pair of nodes are
in the same range
+ return edgeList;
+ }
+
+ private CyEdge createEdge(Map<CyNode, CyNode>nodes, String sourceAlias,
String targetAlias, String type) {
+ // Create our two nodes. Note that makeResidueNode also adds
three attributes:
+ // 1) FunctionalResidues
+ // 2) Seed
+ // 3) SideChainOnly
+ CyNode source = makeResidueNode(sourceAlias);
+ CyNode target = makeResidueNode(targetAlias);
+ nodes.put(source, source);
+ nodes.put(target, target);
+
+ // Create our edge
+ return Cytoscape.getCyEdge(source, target,
Semantics.INTERACTION, type, true);
+ }
+
+ private CyEdge createConnectivityEdge(CyNode node1, CyNode node2) {
+ CyEdge edge = Cytoscape.getCyEdge(node1, node2,
Semantics.INTERACTION, "connected", true);
+
+ // Get the residue for node1 and node2 and ask Chimera to
calculate the distance
+ CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
+ String residueAttr =
nodeAttributes.getStringAttribute(node1.getIdentifier(), RESIDUE_ATTR);
+ ChimeraStructuralObject cso1 =
StructureUtils.fromAttribute(residueAttr, chimeraObject);
+ residueAttr =
nodeAttributes.getStringAttribute(node2.getIdentifier(), RESIDUE_ATTR);
+ ChimeraStructuralObject cso2 =
StructureUtils.fromAttribute(residueAttr, chimeraObject);
+ if (cso1 instanceof ChimeraResidue && cso2 instanceof
ChimeraResidue && includeConnectivityDistance) {
+ String spec1 = cso1.toSpec()+"@CA";
+ String spec2 = cso2.toSpec()+"@CA";
+ monitor.setStatus("Getting distance between "+spec1+"
and "+spec2);
+
+ List<String>replyList =
chimeraObject.commandReply("distance "+spec1+" "+spec2+"; ~distance "+spec1+"
"+spec2);
+ int offset = replyList.get(0).indexOf(':');
+ Double distance =
Double.valueOf(replyList.get(0).substring(offset+1));
+ CyAttributes edgeAttributes =
Cytoscape.getEdgeAttributes();
+ edgeAttributes.setAttribute(edge.getIdentifier(),
DISTANCE_ATTR, distance);
+ // chimeraObject.chimeraSend("~distance "+spec1+"
"+spec2);
+ }
+ return edge;
+ }
+
+ private CyNode makeResidueNode(String alias) {
+ // alias is a atomSpec of the form [#model]:residueNumber@atom
+ // We want to convert that to a node identifier of [pdbid#]ABC
nnn
+ // and add FunctionalResidues and BackboneOnly attributes
+ boolean singleModel = false;
+ ChimeraModel model = StructureUtils.getModel(alias,
chimeraObject);
+ if (model == null) {
+ model = chimeraObject.getChimeraModels().get(0);
+ singleModel = true;
+ }
+ ChimeraResidue residue = StructureUtils.getResidue(alias,
model, chimeraObject);
+ boolean backbone = StructureUtils.isBackbone(alias,
chimeraObject);
+
+ int displayType = ChimeraResidue.getDisplayType();
+ ChimeraResidue.setDisplayType(ChimeraResidue.THREE_LETTER);
+ // OK, now we have everything we need, create the node
+ String nodeName =
residue.toString().trim()+"."+residue.getChainId();
+ ChimeraResidue.setDisplayType(displayType);
+
+ if (!singleModel)
+ nodeName = model.getModelName()+"#"+nodeName;
+
+ // Create the node
+ CyNode node = Cytoscape.getCyNode(nodeName, true);
+
+ // Add our attributes
+ CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
+ nodeAttributes.setAttribute(nodeName, RESIDUE_ATTR,
+
model.getModelName()+"#"+residue.getIndex()+"."+residue.getChainId());
+ nodeAttributes.setAttribute(nodeName, SEED_ATTR,
Boolean.valueOf(residue.isSelected()));
+ if (backbone)
+ nodeAttributes.setAttribute(nodeName, BACKBONE_ATTR,
Boolean.TRUE);
+ else
+ nodeAttributes.setAttribute(nodeName, SIDECHAIN_ATTR,
Boolean.TRUE);
+
+ return node;
+ }
+
+ private void updateMap(Map<CyEdge, Double>map, CyEdge edge, String
value, int comparison) {
+ // Save the minimum distance between atoms
+ Double v = Double.valueOf(value);
+ if (map.containsKey(edge)) {
+ if (comparison < 0 && map.get(edge).compareTo(v) > 0)
+ map.put(edge, v);
+ else if (comparison > 0 && map.get(edge).compareTo(v) <
0)
+ map.put(edge, v);
+ } else {
+ map.put(edge, v);
+ }
+ }
+
+ private ChimeraResidue[] getRange(List<ChimeraResidue[]> rangeList,
CyNode node) {
+ for (ChimeraResidue[] range: rangeList) {
+ if (inRange(range, node)) return range;
+ }
+ return null;
+ }
+
+ private boolean inRange(ChimeraResidue[] range, CyNode node) {
+ CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
+ String residueAttr =
nodeAttributes.getStringAttribute(node.getIdentifier(), RESIDUE_ATTR);
+ ChimeraStructuralObject cso =
StructureUtils.fromAttribute(residueAttr, chimeraObject);
+ // Models can't be in a range...
+ if (cso == null || cso instanceof ChimeraModel) return false;
+
+ // A chain might be in a range -- check this
+ if (cso instanceof ChimeraChain) {
+ String chainID = ((ChimeraChain)cso).getChainId();
+ return inChainRange(range, chainID);
+ }
+
+ // OK, we have a residue, but we need to be careful to make
+ // sure that the chains match
+ ChimeraResidue residue = (ChimeraResidue)cso;
+ if (inChainRange(range, residue.getChainId())) {
+ return true;
+ }
+
+ int startIndex = Integer.parseInt(range[0].getIndex());
+ int endIndex = Integer.parseInt(range[1].getIndex());
+ int residueIndex = Integer.parseInt(residue.getIndex());
+
+ if (endIndex < startIndex) {
+ if (endIndex <= residueIndex && residueIndex <=
startIndex) return true;
+ } else {
+ if (startIndex <= residueIndex && residueIndex <=
endIndex) return true;
+ }
+
+ return false;
+
+ }
+
+ private boolean inChainRange(ChimeraResidue[] range, String chainID) {
+ String start = range[0].getChainId();
+ String end = range[1].getChainId();
+
+ if (start == null || end == null) return false;
+
+ if (start.equals(end)) return false;
+
+ if (start.compareTo(end) > 0) {
+ end = range[0].getChainId();
+ start = range[1].getChainId();
+ }
+
+ if (start.compareTo(chainID) <= 0 && chainID.compareTo(end) <=
0) return true;
+
+ return false;
+ }
+}
+
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/CreateNetworkDialog.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/CreateNetworkDialog.java
2011-10-04 23:33:06 UTC (rev 27061)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/CreateNetworkDialog.java
2011-10-05 04:10:38 UTC (rev 27062)
@@ -53,29 +53,14 @@
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.layout.TunableListener;
-import cytoscape.view.CyNetworkView;
+import cytoscape.task.util.TaskManager;
-import giny.view.NodeView;
-
// StructureViz imports
import structureViz.actions.Chimera;
-import structureViz.actions.CyChimera;
-import structureViz.model.ChimeraChain;
-import structureViz.model.ChimeraModel;
-import structureViz.model.ChimeraResidue;
-import structureViz.model.ChimeraStructuralObject;
-import structureViz.model.Structure;
-import structureViz.model.StructureUtils;
-import structureViz.model.Structure.StructureType;
+import structureViz.actions.CreateNetworkAction;
/**
*/
@@ -89,17 +74,10 @@
boolean includeConnectivity = false;
boolean includeConnectivityDistance = false;
int interactionBetween = 2; // Between selection & other models
- static final int BETWEENMODELS = 0;
- static final int BETWEENSELMODELS = 1;
- static final int BETWEENALL = 2;
+ public static final int BETWEENMODELS = 0;
+ public static final int BETWEENSELMODELS = 1;
+ public 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";
- static final String DISTANCE_ATTR = "MinimumDistance";
- static final String OVERLAP_ATTR = "MaximumOverlap";
- static final String RESIDUE_ATTR = "FunctionalResidues";
- static final String SEED_ATTR = "SeedResidue";
- static final String BACKBONE_ATTR = "BackboneInteraction";
- static final String SIDECHAIN_ATTR = "SideChainInteraction";
/**
* Create a CreateNetworkDialog
@@ -207,89 +185,15 @@
}
if ("create".equals(e.getActionCommand())) {
updateTunables(true);
- List<CyEdge> edgeList = null;
- Map<CyNode, CyNode> nodeMap = new HashMap<CyNode,
CyNode>();
- 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) {
- // Get the first model
- ChimeraModel model =
chimeraObject.getChimeraModels().get(0);
- int modelNumber =
model.getModelNumber();
- // Create the command
- command = "findclash #"+modelNumber+"
makePseudobonds false log true namingStyle command test other "+cutoff;
- } 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,
nodeMap, type);
- }
- if (includeHBonds) {
- // Get the first model
- ChimeraModel model =
chimeraObject.getChimeraModels().get(0);
- int modelNumber = model.getModelNumber();
- String command =
- "findhbond spec #"+modelNumber+"
intramodel false intermodel true makePseudobonds false log true namingStyle
command";
- if (interactionBetween == BETWEENMODELS) {
- command = "findhbond selRestrict any
intermodel true makePseudobonds false log true namingStyle command";
- } else if (interactionBetween ==
BETWEENSELMODELS)
- command = command.concat(" intramodel
false");
- else if (interactionBetween == BETWEENALL)
- command = command.concat(" intramodel
true");
- List<String>replyList =
chimeraObject.commandReply(command);
- if (edgeList == null)
- edgeList = parseHBondReplies(replyList,
nodeMap);
- else
-
edgeList.addAll(parseHBondReplies(replyList, nodeMap));
- // printReply(replyList);
- }
- if (includeConnectivity) {
- String command = "listphysicalchains";
- List<String>replyList =
chimeraObject.commandReply(command);
-
edgeList.addAll(parseConnectivityReplies(replyList, new
ArrayList<CyNode>(nodeMap.keySet())));
- }
+ CreateNetworkAction action = new
CreateNetworkAction(chimeraObject);
+ action.setIncludeContacts(includeContacts);
+ action.setIncludeClashes(includeClashes);
+ action.setIncludeHBonds(includeHBonds);
+ action.setIncludeConnectivity(includeConnectivity);
+
action.setIncludeConnectivityDistance(includeConnectivityDistance);
+ action.setInteractionBetween(interactionBetween);
+ TaskManager.executeTask(action,
action.getDefaultTaskConfig());
- int[] edges = new int[edgeList.size()];
- int[] nodes = new int[edgeList.size()*2];
- int edgeCount = 0;
- for (CyEdge edge: edgeList) {
- edges[edgeCount] = edge.getRootGraphIndex();
- nodes[edgeCount*2] =
edge.getSource().getRootGraphIndex();
- nodes[edgeCount*2+1] =
edge.getTarget().getRootGraphIndex();
- edgeCount++;
- }
-
- // Create the network
- CyNetwork network = Cytoscape.getCurrentNetwork();
- String name = network.getTitle();
- CyNetwork newNetwork = Cytoscape.createNetwork(nodes,
edges, "Interaction from "+name, network, true);
-
- // Set vizmap
-
- // Do a layout
-
- // Make it current
- Cytoscape.setCurrentNetwork(newNetwork.getIdentifier());
-
Cytoscape.setCurrentNetworkView(newNetwork.getIdentifier());
-
- // Activate structureViz for all of our nodes
- CyAttributes nodeAttributes =
Cytoscape.getNodeAttributes();
- for (CyNode node: nodeMap.keySet()) {
- String residueSpec =
nodeAttributes.getStringAttribute(node.getIdentifier(), RESIDUE_ATTR);
- String structure =
CyChimera.findStructures(residueSpec);
- Structure s = Structure.getStructure(structure,
node, StructureType.PDB_MODEL);
- s.setResidueList(node, residueSpec);
- }
-
setVisible(false);
return;
}
@@ -305,321 +209,5 @@
}
}
}
-
- 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<CyEdge> parseClashReplies(List<String> replyLog,
Map<CyNode, CyNode>nodes, 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);
- if (str.trim().startsWith("atom1")) {
- foundHeader = true;
- break;
- }
- }
- if (!foundHeader) return null;
-
- Map<CyEdge, Double> distanceMap = new HashMap<CyEdge, Double>();
- Map<CyEdge, Double> overlapMap = new HashMap<CyEdge, Double>();
- for (++index; index < replyLog.size(); index++) {
- String[] line =
replyLog.get(index).trim().split("\\s+");
- if (line.length != 4) continue;
-
- CyEdge edge = createEdge(nodes, line[0], line[1], type);
-
- updateMap(distanceMap, edge, line[3], -1); // We want
the smallest distance
- updateMap(overlapMap, edge, line[2], 1); // We want the
largest overlap
- }
-
- CyAttributes edgeAttributes = Cytoscape.getEdgeAttributes();
- // OK, now update the edge attributes we want
- for (CyEdge edge: distanceMap.keySet()) {
- edgeAttributes.setAttribute(edge.getIdentifier(),
DISTANCE_ATTR, distanceMap.get(edge));
- edgeAttributes.setAttribute(edge.getIdentifier(),
OVERLAP_ATTR, overlapMap.get(edge));
- }
-
- return new ArrayList<CyEdge>(distanceMap.keySet());
- }
-
-
- // 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<CyEdge> parseHBondReplies(List<String> replyLog,
Map<CyNode, CyNode>nodes) {
- // Scan for our header line
- boolean foundHeader = false;
- int index = 0;
- for (index = 0; index < replyLog.size(); index++) {
- String str = replyLog.get(index);
- if (str.trim().startsWith("H-bonds")) {
- foundHeader = true;
- break;
- }
- }
- if (!foundHeader) return null;
-
- Map<CyEdge, Double> distanceMap = new HashMap<CyEdge, Double>();
- for (++index; index < replyLog.size(); index++) {
- String[] line =
replyLog.get(index).trim().split("\\s+");
- if (line.length != 6 && line.length != 7) continue;
-
- CyEdge edge = createEdge(nodes, line[0], line[1],
"HBond");
-
- String distance = line[3];
- if (line[2].equals("no") && line[3].equals("hydrogen"))
- distance = line[4];
- updateMap(distanceMap, edge, distance, -1); // We want
the smallest distance
- }
-
- CyAttributes edgeAttributes = Cytoscape.getEdgeAttributes();
- // OK, now update the edge attributes we want
- for (CyEdge edge: distanceMap.keySet()) {
- edgeAttributes.setAttribute(edge.getIdentifier(),
DISTANCE_ATTR, distanceMap.get(edge));
- }
-
- return new ArrayList<CyEdge>(distanceMap.keySet());
- }
-
- /**
- * Parse the connectivity information from Chimera. The data is of the
form:
- * physical chain #0:283.A #0:710.A
- * physical chain #0:283.B #0:710.B
- * physical chain #0:283.C #0:710.C
- *
- * We don't use this data to create new nodes -- only new edges. If
two nodes are within the
- * same physical chain, we connect them with a "Connected" edge
- */
- private List<CyEdge> parseConnectivityReplies(List<String> replyLog,
List<CyNode>nodes) {
- List<CyEdge> edgeList = new ArrayList<CyEdge>();
- List<ChimeraResidue[]> rangeList = new
ArrayList<ChimeraResidue[]>();
- for (String line: replyLog) {
- String[] tokens = line.split(" ");
- if (tokens.length != 4) continue;
- String start = tokens[2];
- String end = tokens[3];
-
- ChimeraResidue[] range = new ChimeraResidue[2];
-
- // Get the residues from the reside spec
- range[0] = StructureUtils.getResidue(start,
chimeraObject);
- range[1] = StructureUtils.getResidue(end,
chimeraObject);
- rangeList.add(range);
- }
-
- // If we don't have any nodes, get all of the residues in the
connectivity
- // list and create them as nodes
-
- // For each node pair, figure out if the pair is connected
- for (int i = 0; i < nodes.size(); i++) {
- CyNode node1 = nodes.get(i);
- // System.out.println("Getting the range for the first
node..."+node1);
- ChimeraResidue[] range = getRange(rangeList, node1);
- if (range == null) continue;
- for (int j = i+1; j < nodes.size(); j++) {
- CyNode node2 = nodes.get(j);
- // System.out.println("Seeing if node2
"+node2+" is in the range...");
- if (inRange(range, node2)) {
- // System.out.println("....it is");
- // These two nodes are connected
- CyEdge edge =
Cytoscape.getCyEdge(node1, node2, Semantics.INTERACTION, "connected", true);
-
edgeList.add(createConnectivityEdge(node1, node2));
- }
- }
- }
-
- // Now, make the edges based on whether any pair of nodes are
in the same range
- return edgeList;
- }
-
- private CyEdge createEdge(Map<CyNode, CyNode>nodes, String sourceAlias,
String targetAlias, String type) {
- // Create our two nodes. Note that makeResidueNode also adds
three attributes:
- // 1) FunctionalResidues
- // 2) Seed
- // 3) SideChainOnly
- CyNode source = makeResidueNode(sourceAlias);
- CyNode target = makeResidueNode(targetAlias);
- nodes.put(source, source);
- nodes.put(target, target);
-
- // Create our edge
- return Cytoscape.getCyEdge(source, target,
Semantics.INTERACTION, type, true);
- }
-
- private CyEdge createConnectivityEdge(CyNode node1, CyNode node2) {
- CyEdge edge = Cytoscape.getCyEdge(node1, node2,
Semantics.INTERACTION, "connected", true);
-
- // Get the residue for node1 and node2 and ask Chimera to
calculate the distance
- CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
- String residueAttr =
nodeAttributes.getStringAttribute(node1.getIdentifier(), RESIDUE_ATTR);
- ChimeraStructuralObject cso1 =
StructureUtils.fromAttribute(residueAttr, chimeraObject);
- residueAttr =
nodeAttributes.getStringAttribute(node2.getIdentifier(), RESIDUE_ATTR);
- ChimeraStructuralObject cso2 =
StructureUtils.fromAttribute(residueAttr, chimeraObject);
- if (cso1 instanceof ChimeraResidue && cso2 instanceof
ChimeraResidue) {
- String spec1 = cso1.toSpec()+"@CA";
- String spec2 = cso2.toSpec()+"@CA";
- System.out.println("Getting distance between "+spec1+"
and "+spec2);
-
- List<String>replyList =
chimeraObject.commandReply("distance "+spec1+" "+spec2);
- int offset = replyList.get(0).indexOf(':');
- Double distance =
Double.valueOf(replyList.get(0).substring(offset+1));
- CyAttributes edgeAttributes =
Cytoscape.getEdgeAttributes();
- edgeAttributes.setAttribute(edge.getIdentifier(),
DISTANCE_ATTR, distance);
- chimeraObject.chimeraSend("~distance "+spec1+" "+spec2);
- }
- return edge;
- }
-
- private CyNode makeResidueNode(String alias) {
- // alias is a atomSpec of the form [#model]:residueNumber@atom
- // We want to convert that to a node identifier of [pdbid#]ABC
nnn
- // and add FunctionalResidues and BackboneOnly attributes
- boolean singleModel = false;
- ChimeraModel model = StructureUtils.getModel(alias,
chimeraObject);
- if (model == null) {
- model = chimeraObject.getChimeraModels().get(0);
- singleModel = true;
- }
- ChimeraResidue residue = StructureUtils.getResidue(alias,
model, chimeraObject);
- boolean backbone = StructureUtils.isBackbone(alias,
chimeraObject);
-
- int displayType = ChimeraResidue.getDisplayType();
- ChimeraResidue.setDisplayType(ChimeraResidue.THREE_LETTER);
- // OK, now we have everything we need, create the node
- String nodeName =
residue.toString().trim()+"."+residue.getChainId();
- ChimeraResidue.setDisplayType(displayType);
-
- if (!singleModel)
- nodeName = model.getModelName()+"#"+nodeName;
-
- // Create the node
- CyNode node = Cytoscape.getCyNode(nodeName, true);
-
- // Add our attributes
- CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
- nodeAttributes.setAttribute(nodeName, RESIDUE_ATTR,
-
model.getModelName()+"#"+residue.getIndex()+"."+residue.getChainId());
- nodeAttributes.setAttribute(nodeName, SEED_ATTR,
Boolean.valueOf(residue.isSelected()));
- if (backbone)
- nodeAttributes.setAttribute(nodeName, BACKBONE_ATTR,
Boolean.TRUE);
- else
- nodeAttributes.setAttribute(nodeName, SIDECHAIN_ATTR,
Boolean.TRUE);
-
- return node;
- }
-
- private void updateMap(Map<CyEdge, Double>map, CyEdge edge, String
value, int comparison) {
- // Save the minimum distance between atoms
- Double v = Double.valueOf(value);
- if (map.containsKey(edge)) {
- if (comparison < 0 && map.get(edge).compareTo(v) > 0)
- map.put(edge, v);
- else if (comparison > 0 && map.get(edge).compareTo(v) <
0)
- map.put(edge, v);
- } else {
- map.put(edge, v);
- }
- }
-
- private ChimeraResidue[] getRange(List<ChimeraResidue[]> rangeList,
CyNode node) {
- for (ChimeraResidue[] range: rangeList) {
- if (inRange(range, node)) return range;
- }
- return null;
- }
-
- private boolean inRange(ChimeraResidue[] range, CyNode node) {
- CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
- String residueAttr =
nodeAttributes.getStringAttribute(node.getIdentifier(), RESIDUE_ATTR);
- ChimeraStructuralObject cso =
StructureUtils.fromAttribute(residueAttr, chimeraObject);
- // Models can't be in a range...
- if (cso == null || cso instanceof ChimeraModel) return false;
-
- // A chain might be in a range -- check this
- if (cso instanceof ChimeraChain) {
- String chainID = ((ChimeraChain)cso).getChainId();
- return inChainRange(range, chainID);
- }
-
- // OK, we have a residue, but we need to be careful to make
- // sure that the chains match
- ChimeraResidue residue = (ChimeraResidue)cso;
- if (inChainRange(range, residue.getChainId())) {
- return true;
- }
-
- int startIndex = Integer.parseInt(range[0].getIndex());
- int endIndex = Integer.parseInt(range[1].getIndex());
- int residueIndex = Integer.parseInt(residue.getIndex());
-
- if (endIndex < startIndex) {
- if (endIndex <= residueIndex && residueIndex <=
startIndex) return true;
- } else {
- if (startIndex <= residueIndex && residueIndex <=
endIndex) return true;
- }
-
- return false;
-
- }
-
- private boolean inChainRange(ChimeraResidue[] range, String chainID) {
- String start = range[0].getChainId();
- String end = range[1].getChainId();
-
- if (start == null || end == null) return false;
-
- if (start.equals(end)) return false;
-
- if (start.compareTo(end) > 0) {
- end = range[0].getChainId();
- start = range[1].getChainId();
- }
-
- if (start.compareTo(chainID) <= 0 && chainID.compareTo(end) <=
0) return true;
-
- return false;
- }
}
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/ModelNavigatorDialog.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/ModelNavigatorDialog.java
2011-10-04 23:33:06 UTC (rev 27061)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/ModelNavigatorDialog.java
2011-10-05 04:10:38 UTC (rev 27062)
@@ -96,6 +96,7 @@
private static final int EXPANDMODELS = 20;
private static final int EXPANDCHAINS = 21;
private static final int CREATENETWORK = 22;
+ private static final int SELECT = 23;
private boolean ignoreSelection = false;
private int residueDisplay = ChimeraResidue.THREE_LETTER;
private boolean isCollapsing = false;
@@ -566,7 +567,7 @@
JMenuItem menuItem = new JMenuItem(label);
{
String command = "preset apply "+com[0];
- MenuActionListener va = new
MenuActionListener(this, COMMAND, command);
+ MenuActionListener va = new
MenuActionListener(this, SELECT, command);
menuItem.addActionListener(va);
}
menu.add(menuItem);
@@ -646,6 +647,8 @@
List<ChimeraStructuralObject> selectedObjects =
chimeraObject.getSelectionList();
if (type == COMMAND) {
// System.out.println("Command: "+command);
+ chimeraObject.chimeraSend(command);
+ } else if (type == SELECT) {
chimeraObject.select(command);
} else if (type == CLEAR) {
chimeraObject.select("~select");
--
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