Author: scooter
Date: 2012-11-25 16:47:18 -0800 (Sun, 25 Nov 2012)
New Revision: 30838
Modified:
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/model/Compound.java
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tasks/TanimotoScorerTask.java
Log:
Improve performance of network creation
Modified: csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/model/Compound.java
===================================================================
--- csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/model/Compound.java
2012-11-23 22:07:50 UTC (rev 30837)
+++ csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/model/Compound.java
2012-11-26 00:47:18 UTC (rev 30838)
@@ -155,10 +155,10 @@
HBONDDONOR ("HBond Donors", "donors", Integer.class),
LOBMAX ("Length over Breadth Max", "lobmax", Double.class),
LOBMIN ("Length over Breadth Min", "lobmin", Double.class),
+ RULEOFFIVE ("Lipinski's Rule of Five Failures", "roff",
Double.class),
AMR ("Molar refractivity", "refractivity", Double.class),
RINGCOUNT ("Ring count", "nrings", Integer.class),
RBONDS ("Rotatable Bonds Count", "rotbonds", Integer.class),
- RULEOFFIVE ("Rule of Five Failures", "roff", Double.class),
TPSA ("Topological Polar Surface Area", "polarsurface",
Double.class),
WEINERPATH ("Wiener Path", "wienerpath", Double.class),
WEINERPOL ("Wiener Polarity", "weinerpolarity", Double.class),
@@ -186,17 +186,26 @@
static private CyLogger logger = CyLogger.getLogger(Compound.class);
static private Fingerprinter fingerprinter = Fingerprinter.PUBCHEM;
static private DescriptorType[] descriptorTypes = {
- DescriptorType.IMAGE, DescriptorType.ATTRIBUTE,
DescriptorType.IDENTIFIER, DescriptorType.WEIGHT,
+ DescriptorType.IMAGE, DescriptorType.ATTRIBUTE,
DescriptorType.IDENTIFIER,
+ DescriptorType.LIPINSKI, DescriptorType.SDF,
+ DescriptorType.ALOGP,
+ DescriptorType.ALOGP2,
+ DescriptorType.AROMATICRINGSCOUNT,
DescriptorType.MASS,
- DescriptorType.ALOGP,DescriptorType.ALOGP2,DescriptorType.AMR,
- DescriptorType.HBONDACCEPTOR,DescriptorType.HBONDDONOR,
- DescriptorType.LIPINSKI,
- // Exclude the LengthOverBreadth Descriptors until CDK gets
better ring templates
- DescriptorType.LOBMAX,DescriptorType.LOBMIN,
- DescriptorType.RBONDS,DescriptorType.RULEOFFIVE,
- DescriptorType.SDF, DescriptorType.TPSA,
- DescriptorType.RINGCOUNT, DescriptorType.AROMATICRINGSCOUNT,
- DescriptorType.WEINERPATH,DescriptorType.WEINERPOL
+ DescriptorType.HEAVYATOMCOUNT,
+ DescriptorType.HBONDACCEPTOR,
+ DescriptorType.HBONDDONOR,
+ DescriptorType.LOBMAX,
+ DescriptorType.LOBMIN,
+ DescriptorType.RULEOFFIVE,
+ DescriptorType.AMR,
+ DescriptorType.WEIGHT,
+ DescriptorType.RINGCOUNT,
+ DescriptorType.RBONDS,
+ DescriptorType.TPSA,
+ DescriptorType.WEINERPATH,
+ DescriptorType.WEINERPOL,
+ DescriptorType.XLOGP
};
static private DescriptorType[] SDFTypes = {
Modified:
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tasks/TanimotoScorerTask.java
===================================================================
---
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tasks/TanimotoScorerTask.java
2012-11-23 22:07:50 UTC (rev 30837)
+++
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tasks/TanimotoScorerTask.java
2012-11-26 00:47:18 UTC (rev 30838)
@@ -108,17 +108,10 @@
objectCount = 0;
totalObjects = selection.size();
+ List<CyEdge> edgeList = new ArrayList<CyEdge>();
updateMonitor();
- if (createNewNetwork) {
- // Create a new network if we're supposed to
- newNet = Cytoscape.createNetwork(selection, new
ArrayList(), origNetwork.getTitle()+" copy",
-
origNetwork, true);
- newNetworkView =
Cytoscape.getNetworkView(newNet.getIdentifier());
- vs =
Cytoscape.getVisualMappingManager().getVisualStyle();
- }
-
for (int index1 = 0; index1 < totalObjects; index1++) {
CyNode node1 = (CyNode)selection.get(index1);
if (canceled) break;
@@ -171,7 +164,7 @@
// System.out.print(" Creating and
edge between "+node1.getIdentifier()+" and "+node2.getIdentifier());
edge = Cytoscape.getCyEdge(node1,
node2, "interaction", "similarity", true, true);
// Add it to our new network
- newNet.addEdge(edge);
+ edgeList.add(edge);
// System.out.println("...done");
} else {
// Otherwise, get the edges connecting
these nodes (if any)
@@ -190,17 +183,24 @@
}
}
- if (createNewNetwork) {
- NodeView orig =
origNetworkView.getNodeView(node1);
- NodeView newv =
newNetworkView.getNodeView(node1);
+ updateMonitor();
+ }
+
+ if (createNewNetwork) {
+ // Create a new network if we're supposed to
+ newNet = Cytoscape.createNetwork(selection, edgeList,
origNetwork.getTitle()+" copy",
+
origNetwork, true);
+ newNetworkView =
Cytoscape.getNetworkView(newNet.getIdentifier());
+ vs =
Cytoscape.getVisualMappingManager().getVisualStyle();
+
+ for (GraphObject go: selection) {
+ CyNode node = (CyNode)go;
+ NodeView orig =
origNetworkView.getNodeView(node);
+ NodeView newv =
newNetworkView.getNodeView(node);
newv.setXPosition(orig.getXPosition());
newv.setYPosition(orig.getYPosition());
}
- updateMonitor();
- }
-
- if (createNewNetwork) {
// All done -- create and update the view
newNetworkView.fitContent();
newNetworkView.setVisualStyle(vs.getName());
--
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