Author: scooter
Date: 2010-12-30 12:10:14 -0800 (Thu, 30 Dec 2010)
New Revision: 23284
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/actions/Chimera.java
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/ChimeraModel.java
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/Structure.java
Log:
Submodels not working properly....
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/actions/Chimera.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/actions/Chimera.java
2010-12-30 19:18:28 UTC (rev 23283)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/actions/Chimera.java
2010-12-30 20:10:14 UTC (rev 23284)
@@ -360,6 +360,7 @@
* @param structure the Structure to open
*/
public void open(Structure structure) {
+ // System.out.println("Opening "+structure);
structure.setModelNumber(Structure.getNextModel(), 0);
if (structure.getType() ==
Structure.StructureType.MODBASE_MODEL)
chimeraSend("listen stop models; listen stop selection;
open "+structure.modelNumber()+" modbase:"+structure.name());
@@ -378,7 +379,7 @@
// Get our properties (default color scheme, etc.)
// Make the molecule look decent
- chimeraSend("repr stick "+newModel.toSpec());
+ // chimeraSend("repr stick "+newModel.toSpec());
if (structure.getType() !=
Structure.StructureType.SMILES) {
// Create the information we need for the
navigator
@@ -660,17 +661,24 @@
String name = structure.name();
int modelNumber = structure.modelNumber();
int subModelNumber = structure.subModelNumber();
- List<ChimeraModel>infoList = new ArrayList();
+ List<ChimeraModel>infoList = new ArrayList<ChimeraModel>();
- for (String modelLine: commandReply("listm type molecule spec
#"+modelNumber+"."+subModelNumber)) {
- // System.out.println("ModelList: "+modelLine);
- if (modelLine.contains("id
#"+modelNumber+"."+subModelNumber)) {
- // System.out.println("Found: "+name);
+ List<String>replyList = null;
+
+ if (subModelNumber == 0)
+ replyList = commandReply("listm type molecule spec
#"+modelNumber);
+ else
+ replyList = commandReply("listm type molecule spec
#"+modelNumber+"."+subModelNumber);
+
+ for (String modelLine: replyList) {
+ if (subModelNumber == 0 && modelLine.contains("id
#"+modelNumber)) {
// got the right model, now get the model number
ChimeraModel chimeraModel = new
ChimeraModel(structure, modelLine);
-
structure.setModelNumber(chimeraModel.getModelNumber(),
chimeraModel.getSubModelNumber());
// System.out.println("Identified model as
"+chimeraModel);
infoList.add(chimeraModel);
+ } else if (modelLine.contains("id
#"+modelNumber+"."+subModelNumber)) {
+ ChimeraModel chimeraModel = new
ChimeraModel(structure, modelLine);
+ infoList.add(chimeraModel);
}
}
if (infoList.size() > 0)
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/ChimeraModel.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/ChimeraModel.java
2010-12-30 19:18:28 UTC (rev 23283)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/ChimeraModel.java
2010-12-30 20:10:14 UTC (rev 23284)
@@ -106,8 +106,10 @@
*/
public ChimeraModel (Structure structure, String inputLine) {
this.name = structure.name();
- this.structure = structure;
this.modelNumber = parseModelNumber(inputLine);
+ // Do we need to create a submodel of the structure?
+ this.structure = structure.makeSubModel(this.subModelNumber);
+ this.structure.setModelNumber(this.modelNumber,
this.subModelNumber);
this.chains = new TreeMap();
this.residues = new TreeMap();
this.residueMap = new HashMap();
@@ -369,8 +371,8 @@
try {
subModelNumber = 0;
if (decimal > 0) {
- subModelNumber =
Integer.parseInt(inputLine.substring(decimal+1, space));
- space = decimal;
+ subModelNumber =
Integer.parseInt(inputLine.substring(decimal+hash+2, space));
+ space = decimal+hash+1;
}
modelNumber =
Integer.parseInt(inputLine.substring(hash+1, space));
return modelNumber;
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/Structure.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/Structure.java
2010-12-30 19:18:28 UTC (rev 23283)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/Structure.java
2010-12-30 20:10:14 UTC (rev 23284)
@@ -75,6 +75,12 @@
this.type = type;
}
+ public Structure makeSubModel(int subModelNumber) {
+ Structure st = new Structure(this.structureName,
this.cytoscapeNode, this.type);
+ st.setModelNumber(this.modelNumber, subModelNumber);
+ return st;
+ }
+
/**
* Get the name of the structure
*
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