[Jmol-commits] SF.net SVN: jmol: [9545] trunk/Jmol/src/org/jmol/viewer

[<hansonr@us...>]

Revision: 9545
          http://jmol.svn.sourceforge.net/jmol/?rev=9545&view=rev
Author:   hansonr
Date:     2008-07-01 09:49:39 -0700 (Tue, 01 Jul 2008)

Log Message:
-----------
version=11.5.44 # bug fix: _applet variable not initializing properly

Modified Paths:
--------------
    trunk/Jmol/src/org/jmol/viewer/Jmol.properties
    trunk/Jmol/src/org/jmol/viewer/Viewer.java

Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2008-07-01 16:26:14 UTC (rev 9544)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2008-07-01 16:49:39 UTC (rev 9545)
@@ -3,6 +3,7 @@
 
 version=11.5.44
 
+# bug fix: _applet variable not initializing properly
 # bug fix: math calculation .xyz, .color averages broken in 11.5.42
 # bug fix: select @x broken in 11.5.43
 # bug fix: integer addition not remaining integer

Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java	2008-07-01 16:26:14 UTC (rev 9544)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java	2008-07-01 16:49:39 UTC (rev 9545)
@@ -268,6 +268,7 @@
     this.syncId = (i < 0 ? "" : fullName
         .substring(i + 1, fullName.length() - 1));
     isApplet = (documentBase != null);
+
     String str = appletProxyOrCommandOptions;
     if (str == null)
       str = "";
@@ -283,6 +284,7 @@
     if (useCommandThread)
       scriptManager.startCommandWatcher(true);
     isSignedApplet = (isApplet && str.indexOf("-signed") >= 0);
+    setBooleanProperty("_applet", isApplet);
     setBooleanProperty("_signedApplet", isSignedApplet);
     setBooleanProperty("_useCommandThread", useCommandThread);
     if (!isApplet) {
@@ -3161,7 +3163,6 @@
   }
 
   public void renderScreenImage(Graphics g, Dimension size, Rectangle clip) {
-    //System.out.println("renderScreenImage");
     if (isTainted || getSlabEnabled())
       setModelVisibility();
     isTainted = false;
@@ -3325,7 +3326,6 @@
     // initiated WITHIN this applet (not sent to it) 
     // we append #NOSYNC; here so that the receiving applet does not attempt
     // to pass it back to us or any other applet.
-    //System.out.println(getHtmlName() + " evalstringquiet " + strScript);
     if (allowSyncScript && syncingScripts && strScript.indexOf("#NOSYNC;") < 0  )
       syncScript(strScript + " #NOSYNC;", null);
     boolean isInterrupt = (strScript.length() > 0 && strScript.charAt(0) == '!');
@@ -6565,7 +6565,6 @@
     boolean allButMe = (">".equals(applet));
     boolean disableSend = ("~".equals(applet));
     boolean justMe = disableSend || (".".equals(applet));
-    //System.out.println(getHtmlName() + " syncscript " + script + " --- applet " + applet);
     //null same as ">" -- "all others"
     if (!justMe) {
       statusManager.syncSend(script, (isAll || allButMe ? null : applet));


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Jmol-commits] SF.net SVN: jmol: [9544] trunk/Jmol/src/org/jmol/viewer

[<hansonr@us...>]

Revision: 9544
          http://jmol.svn.sourceforge.net/jmol/?rev=9544&view=rev
Author:   hansonr
Date:     2008-07-01 09:26:14 -0700 (Tue, 01 Jul 2008)

Log Message:
-----------
version=11.5.44 bug fixes

# bug fix: math calculation .xyz, .color averages broken in 11.5.42
# bug fix: select @x broken in 11.5.43

Modified Paths:
--------------
    trunk/Jmol/src/org/jmol/viewer/Eval.java
    trunk/Jmol/src/org/jmol/viewer/Jmol.properties

Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java	2008-07-01 12:57:03 UTC (rev 9543)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java	2008-07-01 16:26:14 UTC (rev 9544)
@@ -7836,16 +7836,20 @@
             break;
           case Token.xyz:
             pt.add(atom);
+            fv = 0;
             break;
           case Token.fracXyz:
             pt.add(atom.getFractionalCoord());
+            fv = 0;
             break;
           case Token.vibXyz:
             pt.add(viewer.getVibrationVector(i));
+            fv = 0;
             break;
           case Token.color:
             pt.add(Graphics3D.colorPointFromInt(viewer.getColixArgb(atom
                 .getColix()), ptT));
+            fv = 0;
             break;
           default:
             error(ERROR_unrecognizedAtomProperty, Token.nameOf(tok));

Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2008-07-01 12:57:03 UTC (rev 9543)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2008-07-01 16:26:14 UTC (rev 9544)
@@ -3,6 +3,7 @@
 
 version=11.5.44
 
+# bug fix: math calculation .xyz, .color averages broken in 11.5.42
 # bug fix: select @x broken in 11.5.43
 # bug fix: integer addition not remaining integer
 


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Jmol-commits] SF.net SVN: jmol: [9543] trunk/Jmol/src/org/jmol/modelset/ModelCollection. java

[<hansonr@us...>]

Revision: 9543
          http://jmol.svn.sourceforge.net/jmol/?rev=9543&view=rev
Author:   hansonr
Date:     2008-07-01 05:57:03 -0700 (Tue, 01 Jul 2008)

Log Message:
-----------
version=11.5.44

# bug fix: select @x broken in 11.5.43
# bug fix: integer addition not remaining integer

Modified Paths:
--------------
    trunk/Jmol/src/org/jmol/modelset/ModelCollection.java

Modified: trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelCollection.java	2008-07-01 12:56:30 UTC (rev 9542)
+++ trunk/Jmol/src/org/jmol/modelset/ModelCollection.java	2008-07-01 12:57:03 UTC (rev 9543)
@@ -1493,7 +1493,7 @@
           thisModelIndex = modelIndex;
         }
         indexInModel++;
-        bs = getConnectedBitSet(i);
+        bs = getConnectedBitSet(i, -1);
         atomlist.or(bs);
         if (moleculeCount == molecules.length)
           molecules = (Molecule[]) ArrayUtil.setLength(molecules,
@@ -1505,9 +1505,13 @@
       }
   }
 
-  private BitSet getConnectedBitSet(int atomIndex) {
+  public BitSet getConnectedBitSet(int atomIndex, int atomIndexNot) {
     BitSet bs = new BitSet(atomCount);
+    if (atomIndex < 0)
+      return bs;
     BitSet bsToTest = getModelAtomBitSet(atoms[atomIndex].modelIndex, true);
+    if (atomIndexNot >= 0)
+      bsToTest.clear(atomIndexNot);
     getCovalentlyConnectedBitSet(atoms[atomIndex], bs, bsToTest);
     return bs;
   }
@@ -1525,11 +1529,7 @@
       Bond bond = atom.bonds[i];
       if ((bond.order & JmolConstants.BOND_HYDROGEN_MASK) != 0)
         continue;
-      if (bond.atom1 == atom) {
-        getCovalentlyConnectedBitSet(bond.atom2, bs, bsToTest);
-      } else {
-        getCovalentlyConnectedBitSet(bond.atom1, bs, bsToTest);
-      }
+        getCovalentlyConnectedBitSet(bond.getOtherAtom(atom), bs, bsToTest);
     }
   }
 


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Jmol-commits] SF.net SVN: jmol: [9542] trunk/Jmol/src/org/jmol/viewer/Viewer.java

[<hansonr@us...>]

Revision: 9542
          http://jmol.svn.sourceforge.net/jmol/?rev=9542&view=rev
Author:   hansonr
Date:     2008-07-01 05:56:30 -0700 (Tue, 01 Jul 2008)

Log Message:
-----------
version=11.5.44

# bug fix: select @x broken in 11.5.43
# bug fix: integer addition not remaining integer

Modified Paths:
--------------
    trunk/Jmol/src/org/jmol/viewer/Viewer.java

Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java	2008-07-01 12:56:00 UTC (rev 9541)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java	2008-07-01 12:56:30 UTC (rev 9542)
@@ -2374,6 +2374,10 @@
     return modelSet.getAtomsConnected(min, max, intType, bs);
   }
 
+  BitSet getConnectedBitSet(int atomIndex, int atomIndexNot) {
+    return modelSet.getConnectedBitSet(atomIndex, atomIndexNot);  
+  }
+  
   int getAtomIndexFromAtomNumber(int atomNumber) {
     return modelSet.getAtomIndexFromAtomNumber(atomNumber);
   }


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Jmol-commits] SF.net SVN: jmol: [9541] trunk/Jmol/src/org/jmol/viewer/Token.java

[<hansonr@us...>]

Revision: 9541
          http://jmol.svn.sourceforge.net/jmol/?rev=9541&view=rev
Author:   hansonr
Date:     2008-07-01 05:56:00 -0700 (Tue, 01 Jul 2008)

Log Message:
-----------
version=11.5.44

# bug fix: select @x broken in 11.5.43
# bug fix: integer addition not remaining integer

Modified Paths:
--------------
    trunk/Jmol/src/org/jmol/viewer/Token.java

Modified: trunk/Jmol/src/org/jmol/viewer/Token.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Token.java	2008-07-01 12:20:45 UTC (rev 9540)
+++ trunk/Jmol/src/org/jmol/viewer/Token.java	2008-07-01 12:56:00 UTC (rev 9541)
@@ -284,6 +284,7 @@
   final public static int group        = expression | 8;
   final public static int chain        = expression | 9;
   final public static int sequence     = expression | 10;
+  final public static int branch       = expression | 11;
   final static int coord               = expression | 12;
   final static int none                = expression | 13;
   final static int semicolon           = expression | 14;
@@ -1253,7 +1254,8 @@
     "back",             new Token(back),    
     "backlit",          new Token(backlit),
     "bondCount",        new Token(bondcount),
-    "bottom",           new Token(bottom),    
+    "bottom",           new Token(bottom),
+    "branch",           new Token(branch),
     "carbohydrate",     new Token(carbohydrate),
     "cell",             new Token(cell),
     "chain",            new Token(chain),


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Jmol-commits] SF.net SVN: jmol: [9540] trunk/Jmol/src/org/jmol/viewer

[<hansonr@us...>]

Revision: 9540
          http://jmol.svn.sourceforge.net/jmol/?rev=9540&view=rev
Author:   hansonr
Date:     2008-07-01 05:20:45 -0700 (Tue, 01 Jul 2008)

Log Message:
-----------
version=11.5.44

# bug fix: select @x broken in 11.5.43
# bug fix: integer addition not remaining integer

Modified Paths:
--------------
    trunk/Jmol/src/org/jmol/viewer/Eval.java
    trunk/Jmol/src/org/jmol/viewer/Jmol.properties

Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java	2008-07-01 04:29:07 UTC (rev 9539)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java	2008-07-01 12:20:45 UTC (rev 9540)
@@ -12451,6 +12451,7 @@
     private boolean evaluateWithin(Token[] args) throws ScriptException {
       if (args.length < 1)
         return false;
+      int i = args.length;
       Object withinSpec = args[0].value;
       int tok = args[0].tok;
       String withinStr = "" + withinSpec;
@@ -12458,9 +12459,16 @@
       float distance = 0;
       boolean isSequence = false;
       boolean isBoundbox = false;
-      int i = args.length;
       boolean isWithinModelSet = false;
       boolean isDistance = (tok == Token.decimal || tok == Token.integer);
+      if (withinStr.equals("branch")) {
+        if (i != 3 || !(args[1].value instanceof BitSet)
+            || !(args[2].value instanceof BitSet))
+          return false;
+        return addX(viewer.getConnectedBitSet(BitSetUtil
+            .firstSetBit((BitSet) args[2].value), BitSetUtil
+            .firstSetBit((BitSet) args[1].value)));
+      }
       if (withinSpec instanceof String) {
         isSequence = !Parser.isOneOf(withinStr,
             "element;site;group;chain;structure;molecule;model;boundbox");
@@ -12499,8 +12507,9 @@
         plane = (Point4f) args[i].value;
       else if (args[i].value instanceof Point3f)
         pt = (Point3f) args[i].value;
-      
-      if (i > 0 && plane == null && pt == null && !(args[i].value instanceof BitSet))
+
+      if (i > 0 && plane == null && pt == null
+          && !(args[i].value instanceof BitSet))
         return false;
       if (isSyntaxCheck)
         return addX(bs);
@@ -12750,6 +12759,14 @@
       case Token.plus:
         if (x1.tok == Token.list || x2.tok == Token.list)
           return addX(Token.concatList(x1, x2));
+        if (x1.tok == Token.integer) {
+          if (x2.tok == Token.string) {
+            if ((s = (Token.sValue(x2)).trim()).indexOf(".") < 0
+                && s.indexOf("+") <= 0 && s.lastIndexOf("-") <= 0)
+              return addX(x1.intValue + Token.iValue(x2));
+          } else if (x2.tok != Token.decimal)
+            return addX(x1.intValue + Token.iValue(x2));
+        }
         switch (x1.tok) {
         default:
           return addX(Token.fValue(x1) + Token.fValue(x2));

Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2008-07-01 04:29:07 UTC (rev 9539)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2008-07-01 12:20:45 UTC (rev 9540)
@@ -4,7 +4,7 @@
 version=11.5.44
 
 # bug fix: select @x broken in 11.5.43
-#
+# bug fix: integer addition not remaining integer
 
 # -----------------------------------------------------------------------------
 


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Jmol-commits] SF.net SVN: jmol: [9539] trunk/Jmol/src/org/jmol/viewer

[<hansonr@us...>]

Revision: 9539
          http://jmol.svn.sourceforge.net/jmol/?rev=9539&view=rev
Author:   hansonr
Date:     2008-06-30 21:29:07 -0700 (Mon, 30 Jun 2008)

Log Message:
-----------
11.5.44 VERSION

# bug fix: select @x broken in 11.5.43

Modified Paths:
--------------
    trunk/Jmol/src/org/jmol/viewer/Compiler.java
    trunk/Jmol/src/org/jmol/viewer/Eval.java
    trunk/Jmol/src/org/jmol/viewer/Jmol.properties

Modified: trunk/Jmol/src/org/jmol/viewer/Compiler.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Compiler.java	2008-06-30 21:45:50 UTC (rev 9538)
+++ trunk/Jmol/src/org/jmol/viewer/Compiler.java	2008-07-01 04:29:07 UTC (rev 9539)
@@ -1526,7 +1526,6 @@
       if (!isImplicitExpression
           && !(isEmbeddedExpression && lastToken == Token.tokenCoordinateEnd)) {
         addTokenToPostfix(Token.tokenExpressionEnd);
-        tokenBegin.intValue = ltokenPostfix.size();
       }
       if (moreTokens()) {
         if (tokCommand != Token.select && !isEmbeddedExpression)
@@ -1534,6 +1533,7 @@
         if (tokCommand == Token.select) {
           // advanced select, with two expressions, the first
           // being an atom expression; the second being a property selector expression
+          tokenBegin.intValue = 0;
           tokCommand = Token.nada;
           isEmbeddedExpression = true;
           isImplicitExpression = true;

Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java	2008-06-30 21:45:50 UTC (rev 9538)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java	2008-07-01 04:29:07 UTC (rev 9539)
@@ -5374,7 +5374,7 @@
       error(ERROR_invalidArgument);
     }
     BitSet bs = null;
-    if (getToken(1).intValue != statementLength) {
+    if (getToken(1).intValue == 0) {
       Object v = tokenSetting(0).value;
       if (!(v instanceof BitSet))
         error(ERROR_invalidArgument);

Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2008-06-30 21:45:50 UTC (rev 9538)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2008-07-01 04:29:07 UTC (rev 9539)
@@ -1,8 +1,11 @@
 # Developers: to add a description of changes you have made,
 # add it on line starting with # below the "version=..." line
 
-version=11.5.44_dev
+version=11.5.44
 
+# bug fix: select @x broken in 11.5.43
+#
+
 # -----------------------------------------------------------------------------
 
 #version=11.5.43


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.