[Jmol-commits] CVS: Jmol/src/org/jmol/viewer Viewer.java,1.82,1.83 ModelManager.java,1.34,1.35 Eval.java,1.94,1.95 StatusManager.java,1.10,1.11 Sticks.java,1.14,1.15

[Bob H. <ha...@us...>]

Update of /cvsroot/jmol/Jmol/src/org/jmol/viewer
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv2918/src/org/jmol/viewer

Modified Files:
	Viewer.java ModelManager.java Eval.java StatusManager.java 
	Sticks.java 
Log Message:
(1) returns to void applet.script()
(2) adds Script applet.scriptNoWait() for testing
(3) adds Script applet.scriptCheck() for testing
(4) all set if we want to go to frame/model difference, but this is left as is for now.
(5) adding NEW keyword in connect, to complement EXISTS -- this allows either choice -- only bonds made where no bond is present; only bonds made where bonds already present
(6) adding colix in atomInfo, just for testing purposes. 



Index: Viewer.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/jmol/viewer/Viewer.java,v
retrieving revision 1.82
retrieving revision 1.83
diff -u -r1.82 -r1.83
--- Viewer.java	20 Feb 2006 03:41:00 -0000	1.82
+++ Viewer.java	22 Feb 2006 04:38:44 -0000	1.83
@@ -1851,13 +1851,11 @@
   public String evalStringWait(String strScript) {
     if (strScript == null)
       return null;
-    getProperty("String", "jmolStatus", "all");
-    if (!getEval().loadScriptString(strScript, false))
-      return eval.getErrorMessage();
-    eval.run();
-    String str = (String) getProperty("JSON", "jmolStatus", "all");
-    getProperty("String", "jmolStatus", "none");
-    return str;
+    String statusList = statusManager.statusList;
+    getProperty("String", "jmolStatus", statusList);
+    if (getEval().loadScriptString(strScript, false))
+      eval.run();
+    return (String) getProperty("JSON", "jmolStatus", statusList);
   }
 
   int iscript = 0;
@@ -1869,6 +1867,12 @@
     return strError;
   }
 
+  public String scriptCheck(String script) {
+    iscript++;
+    String strError = evalString(script);
+    return strError;
+  }
+
   public String scriptWait(String script) {
     iscript++;
     String strInfo = evalStringWait(script);
@@ -2012,7 +2016,7 @@
 
   void setShapeSize(int shapeID, int size) {
     modelManager.setShapeSize(shapeID, size, selectionManager.bsSelection);
-    refresh(0, "Viewer:setShapeSize()");
+    refresh(0, "Viewer:setShapeSize(" +shapeID + "," + size + ")");
   }
 
   int getShapeSize(int shapeID) {

Index: ModelManager.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/jmol/viewer/ModelManager.java,v
retrieving revision 1.34
retrieving revision 1.35
diff -u -r1.34 -r1.35
--- ModelManager.java	20 Feb 2006 03:41:01 -0000	1.34
+++ ModelManager.java	22 Feb 2006 04:38:44 -0000	1.35
@@ -646,6 +646,7 @@
     info.put("visible", new Boolean(getAtomVisibility(i)));
     info.put("spacefill", new Integer(atom.madAtom >> 3));
     info.put("color", viewer.getHexColorFromIndex(atom.colixAtom));
+    info.put("colix", new Integer(atom.colixAtom));
     info.put("translucent", new Boolean(atom.isTranslucent()));
     info.put("formalCharge", new Integer(atom.getFormalCharge()));
     info.put("partialCharge", new Float(atom.getPartialCharge()));

Index: Eval.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/jmol/viewer/Eval.java,v
retrieving revision 1.94
retrieving revision 1.95
diff -u -r1.94 -r1.95
--- Eval.java	19 Feb 2006 18:42:24 -0000	1.94
+++ Eval.java	22 Feb 2006 04:38:44 -0000	1.95
@@ -455,8 +455,10 @@
         show();
         break;
       case Token.frame:
+        frame(1, false);
+        break;
       case Token.model:
-        frame();
+        frame(1, true);
         break;
       case Token.font:
         font();
@@ -2413,7 +2415,7 @@
       showAnimation();
       break;
     case Token.frame:
-      frame(2);
+      frame(2, false);
       break;
     case Token.mode:
       animationMode();
@@ -2429,11 +2431,8 @@
     }
   }
 
-  void frame() throws ScriptException {
-    frame(1);
-  }
-
-  void frame(int offset) throws ScriptException {
+  void frame(int offset, boolean useModelNumber) throws ScriptException {
+    useModelNumber = true; //for now -- as before -- remove to implement frame/model difference 
     if (statementLength <= offset)
       badArgumentCount();
     if (statement[offset].tok == Token.hyphen) {
@@ -2445,8 +2444,8 @@
       viewer.setAnimationPrevious();
       return;
     }
-    int modelNumber = -1;
-    int modelNumber2 = -1;
+    int frameNumber = -1;
+    int frameNumber2 = -1;
     boolean isPlay = false;
     boolean isRange = false;
     while (offset < statementLength) {
@@ -2458,18 +2457,16 @@
       case Token.none:
         break;
       case Token.integer:
-        if(modelNumber == -1) {
-          modelNumber = statement[offset].intValue;
+        if(frameNumber == -1) {
+          frameNumber = statement[offset].intValue;
         } else {
-          modelNumber2 = statement[offset].intValue;        
+          frameNumber2 = statement[offset].intValue;        
         }
         break;
       case Token.play:
-        //System.out.println("play");
         isPlay = true;
         break;
       case Token.range:
-        //System.out.println("play");
         isRange = true;
         break;
       default:
@@ -2478,19 +2475,19 @@
       }
       
       if (offset == statementLength - 1) {
-        int modelIndex = viewer.getModelNumberIndex(modelNumber);
+        int modelIndex = (useModelNumber ? viewer.getModelNumberIndex(frameNumber) : frameNumber - 1);
         if(! isPlay  && ! isRange || modelIndex >= 0) {
           viewer.setDisplayModelIndex(modelIndex);
         }
         if(isPlay || isRange) {
-          if (isRange || modelNumber2 >=0) {
-            int modelIndex2 = viewer.getModelNumberIndex(modelNumber2);
+          if (isRange || frameNumber2 >=0) {
+            int modelIndex2 = (useModelNumber ? viewer.getModelNumberIndex(frameNumber2) : frameNumber2 - 1);
             //System.out.println("isPlay " + modelIndex +" "+ modelIndex2);
 
             viewer.setAnimationDirection(1);
             viewer.setAnimationRange(modelIndex, modelIndex2);
           } 
-          if (! isRange)
+          if (isPlay)
             viewer.resumeAnimation();
         }
       }
@@ -3617,9 +3614,9 @@
     viewer.setShapeProperty(JmolConstants.SHAPE_STICKS,
         "connectBondOrder", new Float(1.0));
     viewer.setShapeProperty(JmolConstants.SHAPE_STICKS,
-        "connectDynamic", new Float(1.0));
+        "connectExistant", new Boolean(true));
     viewer.setShapeProperty(JmolConstants.SHAPE_STICKS,
-        "connectDynamic", new Float(1.0));
+        "connectNew", new Boolean(true));
     viewer.setShapeProperty(JmolConstants.SHAPE_STICKS,
         "sourceSet", null);
 
@@ -3659,9 +3656,12 @@
             cmd.equals("hbond")) {
           propertyName = "connectBondOrder";
           propertyValue = cmd;
-        } else if (cmd.equals("static")) {
-          propertyName = "connectStatic";
-          propertyValue = new Boolean(true);
+        } else if (cmd.equals("exists")) {
+          propertyName = "connectNew";
+          propertyValue = new Boolean(false);
+        } else if (cmd.equals("new")) {
+          propertyName = "connectExistant";
+          propertyValue = new Boolean(false);
         } else {
           unrecognizedSubcommand();
         }

Index: StatusManager.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/jmol/viewer/StatusManager.java,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -r1.10 -r1.11
--- StatusManager.java	19 Feb 2006 19:40:31 -0000	1.10
+++ StatusManager.java	22 Feb 2006 04:38:44 -0000	1.11
@@ -51,6 +51,7 @@
   Hashtable messageQueue = new Hashtable();
   int statusPtr = 0;
   static int MAXIMUM_QUEUE_LENGTH = 16;
+  String compileError;
   
   StatusManager(Viewer viewer) {
     this.viewer = viewer;
@@ -128,18 +129,18 @@
       jmolStatusListener.notityNewDefaultModeMeasurement(count, status + ": " + strMeasure);
   }
   
-  synchronized void setStatusScriptStarted(int iscript, String script, String strError) {
-    if (strError == null)
-      strError = GT._("Jmol executing script ...");
+  synchronized void setStatusScriptStarted(int iscript, String script, String compileError) {
+    this.compileError = compileError;
+    if (compileError == null)
+      compileError = GT._("Jmol executing script ...");
     setStatusChanged("scriptStarted", iscript, script, false);   
-    setStatusChanged("scriptMessage", 0, strError, false);
+    setStatusChanged("scriptMessage", 0, compileError, false);
     if (jmolStatusListener != null)
-      jmolStatusListener.notifyScriptStart(strError, script); 
+      jmolStatusListener.notifyScriptStart(compileError, script); 
   }
 
   synchronized void setStatusScriptTermination(String statusMessage, int msWalltime){
-    if(statusMessage == null) 
-      statusMessage = "Jmol script completed";
+    statusMessage = "Jmol script completed" + (compileError == null ? "" : ": " + compileError);
     setStatusChanged("scriptTerminated", msWalltime, statusMessage, false);
     if (jmolStatusListener == null)
       return;

Index: Sticks.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/jmol/viewer/Sticks.java,v
retrieving revision 1.14
retrieving revision 1.15
diff -u -r1.14 -r1.15
--- Sticks.java	18 Feb 2006 06:18:40 -0000	1.14
+++ Sticks.java	22 Feb 2006 04:38:44 -0000	1.15
@@ -35,7 +35,8 @@
   float maxBondingDistance;
   float minBondingDistance;
   short order;
-  boolean isConnectStatic;
+  boolean iConnectNew;
+  boolean iConnectExistant;
   BitSet bsSource;
   
   void setSize(int size, BitSet bsSelected) {
@@ -71,15 +72,13 @@
       }
       return;
     }
-
-    //sorry; I couldn't figure out the type-casting business! -BH
-    if ("connectStatic" == propertyName) {
-      isConnectStatic = true;
+    if ("connectNew" == propertyName) {
+      iConnectNew = ((Boolean)value).booleanValue();
       return;
     }
 
-    if ("connectDynamic" == propertyName) {
-      isConnectStatic = false;
+    if ("connectExistant" == propertyName) {
+      iConnectExistant = ((Boolean)value).booleanValue();
       return;
     }
 
@@ -127,7 +126,7 @@
       BitSet bsTarget = (BitSet)value;
       if(minBondingDistance < 0.0F) 
         minBondingDistance = 0.0F;
-      makeConnections(minBondingDistance, maxBondingDistance, (bsSource != null ? bsSource : bsSelected), bsTarget, order, isConnectStatic);
+      makeConnections(minBondingDistance, maxBondingDistance, (bsSource != null ? bsSource : bsSelected), bsTarget, order, iConnectExistant, iConnectNew);
       return;
     }
   }
@@ -151,7 +150,7 @@
 
   void setTranslucencyBond(boolean isTranslucent,
                            short bondTypeMask, BitSet bs) {
-    System.out.println("setTranslucencyBond " + isTranslucent);
+    //System.out.println("setTranslucencyBond " + isTranslucent);
     BondIterator iter = frame.getBondIterator(bondTypeMask, bs);
     while (iter.hasNext())
       iter.next().setTranslucent(isTranslucent);
@@ -173,13 +172,13 @@
     frame.deleteBonds(bsDelete);
   }
 
-  void makeConnections(float minDistance, float maxDistance, BitSet bsA, BitSet bsB, short order, boolean isStatic) {
+  void makeConnections(float minDistance, float maxDistance, BitSet bsA, BitSet bsB, short order, boolean iConnectExistant, boolean iConnectNew) {
     int atomCount = frame.atomCount;
     Atom[] atoms = frame.atoms;
     int nbonds = 0;
     boolean bondmode = viewer.getBondSelectionModeOr();
     viewer.setBondSelectionModeOr(false);
-    
+    //System.out.println(iConnectNew + "," + iConnectExistant);
     float minDistanceSquared = minDistance * minDistance;
     float maxDistanceSquared = maxDistance * maxDistance;
     //System.out.println("distances "+minDistance+" "+maxDistance);
@@ -195,11 +194,15 @@
         if (   iB == iA
             || (frame.getAtomAt(iA).getModelIndex() != frame.getAtomAt(iB).getModelIndex())
             || (iB < iA && bsA.get(iB) && bsB.get(iA))
-            || (isStatic && !atomA.isBonded(atoms[iB]))
-           )
+            )
           continue;
-        //System.out.println(iA+" "+iB+" continuing");
         Atom atomB = atoms[iB];
+        boolean isBonded = atomA.isBonded(atomB);
+        if (isBonded && !iConnectExistant 
+            || !isBonded && !iConnectNew
+            )
+          continue;
+        //System.out.println(iA+" "+iB+" continuing");
         float distanceSquared = pointA.distanceSquared(atomB.point3f);
         if (distanceSquared > minDistanceSquared && distanceSquared <= maxDistanceSquared) {
           BitSet bsTwoAtoms=new BitSet();
@@ -216,7 +219,7 @@
         }
       }
     }
-    System.out.println("Sticks.java::makeConnections: " + nbonds + " bonds " + (order == 0 ? " deleted":" formed or modified"));
+    viewer.scriptStatus(nbonds + " bonds " + (order == 0 ? " deleted":" formed or modified"));
     viewer.setBondSelectionModeOr(bondmode);
   }
 }