Author: scooter
Date: 2013-02-19 15:59:01 -0800 (Tue, 19 Feb 2013)
New Revision: 31129
Modified:
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/commands/ChemVizCommandHandler.java
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tasks/CreateMCSSTask.java
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tasks/SMARTSSearchTask.java
Log:
Add search structures command. Looks like there's a threading problem with
the smiles parser...
Modified:
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/commands/ChemVizCommandHandler.java
===================================================================
---
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/commands/ChemVizCommandHandler.java
2013-02-19 18:58:21 UTC (rev 31128)
+++
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/commands/ChemVizCommandHandler.java
2013-02-19 23:59:01 UTC (rev 31129)
@@ -71,6 +71,7 @@
import chemViz.tasks.CreateCompoundTableTask;
import chemViz.tasks.CreateMCSSTask;
import chemViz.tasks.CreateNodeGraphicsTask;
+import chemViz.tasks.SMARTSSearchTask;
import chemViz.ui.ChemInfoSettingsDialog;
enum Command {
@@ -98,6 +99,9 @@
REMOVE("remove",
"Remove 2D structures from nodes",
"network|nodelist|node"),
+ SEARCHSTRUCTURES("search structures",
+ "Search the designated structures using SMARTS",
+
"node|nodelist|edge|edgelist|smarts|smiles|inchi|columnlist"),
SHOWSTRUCTURES("show structures",
"Popup the 2D structures for a node/edge or group of
nodes/edges",
"node|nodelist|edge|edgelist|labelattribute|smiles|inchi"),
@@ -145,6 +149,7 @@
static final String NODELIST = "nodelist";
static final String SELECTED = "selected";
static final String SHOWRESULT = "showresult";
+ static final String SMARTS = "smarts";
static final String SMILES = "smiles";
static final String SMILESATTRIBUTE = "smilesattribute";
@@ -347,7 +352,7 @@
}
CreateMCSSTask mcssTask = new CreateMCSSTask(gObjList,
attributes, dialog, false, createGroup);
- TaskManager.executeTask(mcssTask,
mcssTask.getDefaultTaskConfig());
+ TaskManager.executeTask(mcssTask, null);
try {
while(!mcssTask.isDone()) {
@@ -390,6 +395,34 @@
TaskManager.executeTask(cngTask,
cngTask.getDefaultTaskConfig());
for (GraphObject obj: gObjList)
result.addMessage("Removed graphics from node
'"+obj+"'");
+
+ // SEARCHSTRUCTURES("search structures",
+ // "Search the designated structures using
SMARTS",
+ //
"node|nodelist|edge|edgelist|smarts|smiles|inchi|columnlist"),
+ } else if (Command.SEARCHSTRUCTURES.equals(command)) {
+ if (gObjList == null)
+ throw new RuntimeException("chemviz
"+command+": must specify node/edge or nodelist/edgelist");
+
+ if (!args.containsKey(SMARTS))
+ throw new RuntimeException("chemviz
"+command+": must specify SMARTS string");
+
+ String smarts = (String)args.get(SMARTS);
+
+ List<Compound> compoundList =
ValueUtils.getCompounds(gObjList, mstring, mtype, smilesAttrList,
inchiAttrList);
+ CyAttributes attributes = Cytoscape.getNodeAttributes();
+ if (gObjList != null && (gObjList.get(0) instanceof
CyEdge))
+ attributes = Cytoscape.getEdgeAttributes();
+
+ List<String> columnList = null;
+ if (args.containsKey(COLUMNLIST)) {
+ String[] columnSpecs =
((String)args.get(COLUMNLIST)).split(",");
+ columnList = Arrays.asList(columnSpecs);
+ }
+
+ SMARTSSearchTask searchTask =
+ new SMARTSSearchTask(smarts, gObjList,
attributes, dialog, 0, columnList);
+ TaskManager.executeTask(searchTask,
searchTask.getDefaultTaskConfig());
+ result.addMessage("Showing structures matching:
"+smarts);
// SHOWSTRUCTURES("show structures",
// "Popup the 2D structures for a node or
group of nodes",
Modified:
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tasks/CreateMCSSTask.java
===================================================================
--- csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tasks/CreateMCSSTask.java
2013-02-19 18:58:21 UTC (rev 31128)
+++ csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tasks/CreateMCSSTask.java
2013-02-19 23:59:01 UTC (rev 31129)
@@ -167,7 +167,8 @@
List<IAtomContainer> mcssList =
Collections.synchronizedList(new
ArrayList<IAtomContainer>(compoundList.size()));
for (Compound c: compoundList) {
- mcssList.add(c.getIAtomContainer());
+ if (c.getIAtomContainer() != null)
+ mcssList.add(c.getIAtomContainer());
}
int pass = 0;
Modified:
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tasks/SMARTSSearchTask.java
===================================================================
---
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tasks/SMARTSSearchTask.java
2013-02-19 18:58:21 UTC (rev 31128)
+++
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tasks/SMARTSSearchTask.java
2013-02-19 23:59:01 UTC (rev 31129)
@@ -118,6 +118,7 @@
try {
SMARTSQueryTool queryTool = new
SMARTSQueryTool(searchString);
for (Compound compound: cList) {
+ if (compound.getIAtomContainer() ==
null) continue;
boolean status =
queryTool.matches(compound.getIAtomContainer());
if (status && queryTool.countMatches()
> 0)
matches.add(compound);
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