Author: scooter
Date: 2011-09-19 19:53:42 -0700 (Mon, 19 Sep 2011)
New Revision: 26869
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/StructureViz.java
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/ChimeraResidue.java
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/CreateNetworkDialog.java
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/StructureVizMenuListener.java
Log:
More work on createNetwork
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/StructureViz.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/StructureViz.java
2011-09-20 01:06:10 UTC (rev 26868)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/StructureViz.java
2011-09-20 02:53:42 UTC (rev 26869)
@@ -139,7 +139,6 @@
* @param pmenu the popup menu
*/
public void addNodeContextMenuItems (NodeView nodeView, JPopupMenu
pmenu) {
-
if (pmenu == null) {
pmenu = new JPopupMenu();
}
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/ChimeraResidue.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/ChimeraResidue.java
2011-09-20 01:06:10 UTC (rev 26868)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/ChimeraResidue.java
2011-09-20 02:53:42 UTC (rev 26869)
@@ -200,6 +200,7 @@
}
}
+
/**
* Return the Chimera specification for this Residue
*
@@ -374,6 +375,8 @@
displayType = type;
}
+ public static int getDisplayType() {return displayType;}
+
/**
* Convert the amino acid type to a full name
*
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/CreateNetworkDialog.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/CreateNetworkDialog.java
2011-09-20 01:06:10 UTC (rev 26868)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/CreateNetworkDialog.java
2011-09-20 02:53:42 UTC (rev 26869)
@@ -33,10 +33,11 @@
package structureViz.ui;
// System imports
-import java.util.List;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
import javax.swing.BorderFactory;
import javax.swing.BoxLayout;
@@ -66,7 +67,9 @@
// StructureViz imports
import structureViz.actions.Chimera;
+import structureViz.model.ChimeraChain;
import structureViz.model.ChimeraModel;
+import structureViz.model.ChimeraResidue;
/**
*/
@@ -77,12 +80,19 @@
boolean includeContacts = true;
boolean includeClashes = false;
boolean includeHBonds = false;
+ boolean includeConnectivity = 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";
+ 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
@@ -139,6 +149,8 @@
Tunable.BOOLEAN, includeClashes));
properties.add(new Tunable("includeHBonds", "Include hydrogen
bonds (overlaps with contacts)",
Tunable.BOOLEAN, includeHBonds));
+ properties.add(new Tunable("includeConnectivity", "Include
connectivity",
+ Tunable.BOOLEAN,
includeConnectivity));
properties.add(new Tunable("interaction", "Include
interactions",
Tunable.LIST, new
Integer(interactionBetween),
(Object) interactionArray, (Object)
null, 0));
@@ -157,6 +169,10 @@
if ((t != null) && (t.valueChanged() || force))
includeHBonds = ((Boolean) t.getValue()).booleanValue();
+ t = properties.get("includeConnectivity");
+ if ((t != null) && (t.valueChanged() || force))
+ includeConnectivity = ((Boolean)
t.getValue()).booleanValue();
+
t = properties.get("interaction");
if ((t != null) && (t.valueChanged() || force))
interactionBetween = ((Integer)
t.getValue()).intValue();
@@ -173,7 +189,8 @@
}
if ("create".equals(e.getActionCommand())) {
updateTunables(true);
- List<String> edgeList = null;
+ List<CyEdge> edgeList = null;
+ List<CyNode> nodeList = new ArrayList<CyNode>();
String cutoff = "";
String type = "Clashes";
// Send the commands to Chimera and get the results
@@ -190,41 +207,52 @@
command = command.concat(" test model");
List<String>replyList =
chimeraObject.commandReply(command);
- printReply(replyList);
- edgeList = parseClashReplies(replyList, type);
+ // printReply(replyList);
+ edgeList = parseClashReplies(replyList,
nodeList, type);
}
if (includeHBonds) {
- String command = null;
+ String command =
+ "findhbond selRestrict any intermodel
true makePseudobonds false log true namingStyle command";
if (interactionBetween == BETWEENMODELS) {
} else if (interactionBetween ==
BETWEENSELMODELS)
- command = "findhbond selRestrict any
intermodel true intramodel false makePseudobonds false log true namingStyle
command";
+ command = command.concat(" intramodel
false");
else if (interactionBetween == BETWEENALL)
- command = "findhbond selRestrict any
intermodel true intramodel true makePseudobonds false log true namingStyle
command";
+ command = command.concat(" intramodel
true");
List<String>replyList =
chimeraObject.commandReply(command);
if (edgeList == null)
- edgeList = parseHBondReplies(replyList);
+ edgeList = parseHBondReplies(replyList,
nodeList);
else
-
edgeList.addAll(parseHBondReplies(replyList));
- printReply(replyList);
+
edgeList.addAll(parseHBondReplies(replyList, nodeList));
+ // 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);
+ for (CyEdge edge: edgeList) {
+ edges[edgeCount] = edge.getRootGraphIndex();
+ nodes[edgeCount*2] =
edge.getSource().getRootGraphIndex();
+ nodes[edgeCount*2+1] =
edge.getTarget().getRootGraphIndex();
edgeCount++;
}
+ // Add seed information (from selection)
+
+ // Create the network
CyNetwork network = Cytoscape.getCurrentNetwork();
String name = network.getTitle();
+ CyNetwork newNetwork = Cytoscape.createNetwork(nodes,
edges, "Interaction from "+name, network, true);
+
+ // Set vizmap
- // Create the network
- Cytoscape.createNetwork(nodes, edges, "Interaction from
"+name, network, true);
+ // Do a layout
+ // Make it current
+ Cytoscape.setCurrentNetwork(newNetwork.getIdentifier());
+
Cytoscape.setCurrentNetworkView(newNetwork.getIdentifier());
+
+ // Activate structureViz on this network
+
setVisible(false);
return;
}
@@ -250,13 +278,12 @@
* 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) {
+ private List<CyEdge> parseClashReplies(List<String> replyLog,
List<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);
- System.out.println("Line "+index+": "+str);
if (str.trim().startsWith("atom1")) {
foundHeader = true;
break;
@@ -264,19 +291,26 @@
}
if (!foundHeader) return null;
- List<String> edgeList = new ArrayList<String>();
-
+ Map<CyEdge, Double> distanceMap = new HashMap<CyEdge, Double>();
+ Map<CyEdge, Double> overlapMap = new HashMap<CyEdge, Double>();
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]);
+
+ 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
}
- return edgeList;
-
+ 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());
}
@@ -306,13 +340,12 @@
* 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) {
+ private List<CyEdge> parseHBondReplies(List<String> replyLog,
List<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);
- System.out.println("Line "+index+": "+str);
if (str.trim().startsWith("H-bonds")) {
foundHeader = true;
break;
@@ -320,60 +353,127 @@
}
if (!foundHeader) return null;
- List<String> edgeList = new ArrayList<String>();
-
+ Map<CyEdge, Double> distanceMap = new HashMap<CyEdge, Double>();
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];
+ 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];
-
edgeList.add(fixResidue(atom1)+"\tHBond\t"+fixResidue(atom2)+"\t\t"+distance);
+ updateMap(distanceMap, edge, distance, -1); // We want
the smallest distance
}
- return edgeList;
+
+ 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());
}
- private String fixResidue(String residue) {
- int atIndex = residue.indexOf('@');
- if (atIndex == -1) return residue;
- return residue.substring(0, atIndex);
+ private CyEdge createEdge(List<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.add(source);
+ nodes.add(target);
+
+ // Create our edge
+ return Cytoscape.getCyEdge(source, target,
Semantics.INTERACTION, type, true);
}
- private void createNodesAndEdge(String edgeSpec, int[] nodes, int[]
edges, int edgeCount) {
+ 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 = getModel(alias);
+ if (model == null) {
+ model = chimeraObject.getChimeraModels().get(0);
+ singleModel = true;
+ }
+ ChimeraResidue residue = getResidue(alias, model);
+ boolean backbone = isBackbone(alias);
+
+ 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();
- CyAttributes edgeAttributes = Cytoscape.getEdgeAttributes();
+ 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);
- 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();
+ return node;
}
- private String makeFunctionalResidue(String alias) {
+ private ChimeraModel getModel(String alias) {
+ String[] split = alias.split(":");
+ // No model specified....
+ if (split[0].length() == 0) return null;
+
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]);
+ String[] subSplit = split[0].substring(1).split(".");
+ model = Integer.parseInt(subSplit[0]);
+ if (subSplit.length > 1)
+ submodel = Integer.parseInt(subSplit[1]);
+
+ return chimeraObject.getChimeraModel(model, submodel);
+ }
+
+ private ChimeraResidue getResidue(String alias, ChimeraModel model) {
+ String[] split = alias.split(":|@");
+
+ // Split into residue and chain
+ String[] residueChain = split[1].split("\\.");
+
+ if (residueChain.length == 1)
+ return model.getResidue(residueChain[0]); // No chain...
+
+ ChimeraChain chain = model.getChain(residueChain[1]);
+ return chain.getResidue(residueChain[0]);
+ }
+
+ private boolean isBackbone(String alias) {
+ String[] split = alias.split("@");
+ String atom = split[1];
+ if (atom.equals("C") || atom.equals("CA") || atom.equals("N")
|| atom.equals("H") ||
+ atom.equals("O"))
+ return true;
+ return false;
+ }
+
+ 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);
}
- // Get the model
- ChimeraModel cModel = chimeraObject.getChimeraModel(model,
submodel);
- return "#"+cModel.getModelName()+":"+modelSplit[1];
}
}
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/StructureVizMenuListener.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/StructureVizMenuListener.java
2011-09-20 01:06:10 UTC (rev 26868)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/StructureVizMenuListener.java
2011-09-20 02:53:42 UTC (rev 26869)
@@ -100,6 +100,7 @@
{
JMenu item = new JMenu("Open structure(s)");
List<Structure>structures =
CyChimera.getSelectedStructures(overNode, false);
+ // System.out.println("Found: "+structures.size()+"
structures for node "+overNode.getNode().getIdentifier());
if (structures.size() == 0) {
item.setEnabled(false);
} else {
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