jmol-commits Mailing List for Jmol

Revision: 9538
          http://jmol.svn.sourceforge.net/jmol/?rev=9538&view=rev
Author:   nicove
Date:     2008-06-30 14:45:50 -0700 (Mon, 30 Jun 2008)

Log Message:
-----------
Version

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

Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2008-06-30 18:19:44 UTC (rev 9537)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2008-06-30 21:45:50 UTC (rev 9538)
@@ -1,8 +1,12 @@
 # Developers: to add a description of changes you have made,
 # add it on line starting with # below the "version=..." line
 
-version=11.5.43
+version=11.5.44_dev
 
+# -----------------------------------------------------------------------------
+
+#version=11.5.43
+
 # bug fix -- if last helix is last atom, SHOW STRUCTURE fails to identify it.
 #
 # new feature/feature change:
@@ -105,9 +109,8 @@
 #
 #   load =1d66
 #   calculate straightness;color straightness
-#  
+
 # -----------------------------------------------------------------------------
-#
 
 #version=11.5.42
 


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Revision: 9537
          http://jmol.svn.sourceforge.net/jmol/?rev=9537&view=rev
Author:   hansonr
Date:     2008-06-30 11:19:44 -0700 (Mon, 30 Jun 2008)

Log Message:
-----------
version=11.5.43 # bug fix -- if last helix is last atom, SHOW STRUCTURE fails to identify it.

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

Modified: trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelCollection.java	2008-06-30 15:00:22 UTC (rev 9536)
+++ trunk/Jmol/src/org/jmol/modelset/ModelCollection.java	2008-06-30 18:19:44 UTC (rev 9537)
@@ -2154,7 +2154,7 @@
     int nTurn = 0;
     int nSheet = 0;
     for (int i = 0; i <= atomCount; i++)
-      if (bsAtoms == null || bsAtoms.get(i)) {
+      if (i == atomCount || bsAtoms == null || bsAtoms.get(i)) {
         id = Integer.MIN_VALUE;
         if (i == atomCount || (id = atoms[i].getProteinStructureID()) != lastId) {
           if (bs != null) {

Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2008-06-30 15:00:22 UTC (rev 9536)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2008-06-30 18:19:44 UTC (rev 9537)
@@ -3,6 +3,8 @@
 
 version=11.5.43
 
+# bug fix -- if last helix is last atom, SHOW STRUCTURE fails to identify it.
+#
 # new feature/feature change:
 #
 # selectX is no longer necessary. Simply use


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Revision: 9536
          http://jmol.svn.sourceforge.net/jmol/?rev=9536&view=rev
Author:   hansonr
Date:     2008-06-30 08:00:22 -0700 (Mon, 30 Jun 2008)

Log Message:
-----------
version=11.5.43

# new feature/feature change:
#
# selectX is no longer necessary. Simply use
#
#   select {atomExpression} (property expression)
#
# with no "x." An implied variable "_x" can be used explicitly:
#
#   select {*} (straightness < 0.995) # does not round
#   select {*.ca} (atomY < atomX)
#   select {*.ca} (phi < select(y; {*.ca}; y.resno = _x.resno + 1).phi))
#

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
    trunk/Jmol/src/org/jmol/viewer/Token.java

Modified: trunk/Jmol/src/org/jmol/viewer/Compiler.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Compiler.java	2008-06-30 05:09:59 UTC (rev 9535)
+++ trunk/Jmol/src/org/jmol/viewer/Compiler.java	2008-06-30 15:00:22 UTC (rev 9536)
@@ -1414,7 +1414,6 @@
 
   boolean isImplicitExpression;
   boolean isSetOrDefine;
-  boolean isSelectX;
   Token tokenCommand;
   int tokCommand;
 
@@ -1435,7 +1434,6 @@
     tokCommand = tokenCommand.tok;
     isImplicitExpression = tokAttr(tokCommand, Token.implicitExpression);
     isSetOrDefine = (tokCommand == Token.set || tokCommand == Token.define);
-    isSelectX = (tokCommand == Token.selectx);
     isCommaAsOrAllowed = tokAttr(tokCommand, Token.expressionCommand);
     int size = ltoken.size();
     if (size == 1 && !tokAttr(tokCommand, Token.flowCommand) 
@@ -1456,9 +1454,6 @@
 
     //compile expressions
 
-//    isEmbeddedExpression = (tokAttr(tokCommand, Token.embeddedExpression));
-//    boolean checkExpression = (tokAttrOr(tokCommand, Token.expressionCommand,
-  //      Token.embeddedExpression));
     isEmbeddedExpression = tokCommand != Token.function && (!tokAttrOr(tokCommand, Token.expressionCommand, Token.specialstring));
     boolean checkExpression = isEmbeddedExpression || (tokAttr(tokCommand, Token.expressionCommand));
 
@@ -1508,6 +1503,7 @@
     int firstToken = (isSetOrDefine && !isSetBrace ? 2 : 1);
     ltokenPostfix = new Vector();
     itokenInfix = 0;
+    Token tokenBegin = null;
     for (int i = 0; i < firstToken && addNextToken(); i++) {
     }
     while (moreTokens()) {
@@ -1523,15 +1519,27 @@
         continue;
       }
       if (!isImplicitExpression)
-        addTokenToPostfix(Token.tokenExpressionBegin);
+        addTokenToPostfix(tokenBegin = new Token(Token.expressionBegin, "implicitExpressionBegin"));
       if (!clauseOr(isCommaAsOrAllowed || !isImplicitExpression
           && tokPeek(Token.leftparen)))
         return false;
       if (!isImplicitExpression
-          && !(isEmbeddedExpression && lastToken == Token.tokenCoordinateEnd))
+          && !(isEmbeddedExpression && lastToken == Token.tokenCoordinateEnd)) {
         addTokenToPostfix(Token.tokenExpressionEnd);
-      if (!isSelectX && moreTokens() && !isEmbeddedExpression)
-        return error(ERROR_endOfExpressionExpected);
+        tokenBegin.intValue = ltokenPostfix.size();
+      }
+      if (moreTokens()) {
+        if (tokCommand != Token.select && !isEmbeddedExpression)
+          return error(ERROR_endOfExpressionExpected);
+        if (tokCommand == Token.select) {
+          // advanced select, with two expressions, the first
+          // being an atom expression; the second being a property selector expression
+          tokCommand = Token.nada;
+          isEmbeddedExpression = true;
+          isImplicitExpression = true;
+          isCommaAsOrAllowed = false;
+        }
+      }
     }
     atokenInfix = new Token[ltokenPostfix.size()];
     ltokenPostfix.copyInto(atokenInfix);

Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java	2008-06-30 05:09:59 UTC (rev 9535)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java	2008-06-30 15:00:22 UTC (rev 9536)
@@ -989,9 +989,6 @@
       case Token.select:
         select();
         break;
-      case Token.selectx:
-        selectX();
-        break;
       case Token.translate:
         translate();
         break;
@@ -5376,7 +5373,16 @@
       }
       error(ERROR_invalidArgument);
     }
-    BitSet bs = expression(1);
+    BitSet bs = null;
+    if (getToken(1).intValue != statementLength) {
+      Object v = tokenSetting(0).value;
+      if (!(v instanceof BitSet))
+        error(ERROR_invalidArgument);
+      checkStatementLength(++iToken);
+      bs = (BitSet) v;
+    } else {
+      bs = expression(1);
+    }
     if (isSyntaxCheck)
       return;
     if (isBondSet) {
@@ -5386,20 +5392,6 @@
     }
   }
 
-  private void selectX() throws ScriptException {
-    if (statementLength == 1) {
-      viewer.select(null, tQuiet || scriptLevel > scriptReportingLevel);
-      return;
-    }
-    Object v = tokenSetting(0).value;
-    if (!(v instanceof BitSet))
-      error(ERROR_invalidArgument);
-    checkStatementLength(++iToken);
-    if (isSyntaxCheck)
-      return;    
-    viewer.select((BitSet)v, tQuiet || scriptLevel > scriptReportingLevel);
-  }
-
   private void subset() throws ScriptException {
     BitSet bs = (statementLength == 1 ? null : expression(-1));
     if (isSyntaxCheck)
@@ -7034,7 +7026,9 @@
     }
     int tokProperty = Token.nada;
     if (tokAt(pt) == Token.dot) {
-      Token token = getBitsetPropertySelector(pt++, true);
+      Token token = getBitsetPropertySelector(++pt, true);
+      if (token == null)
+        error(ERROR_invalidArgument);
       if (tokAt(++pt) != Token.opEQ)
         error(ERROR_invalidArgument);
       pt++;
@@ -7212,15 +7206,17 @@
 
   private Object parameterExpression(int pt, int ptMax, String key,
                                      boolean asVector) throws ScriptException {
-    return parameterExpression(pt, ptMax, key, asVector, -1, null);
+    return parameterExpression(pt, ptMax, key, asVector, -1, null, null);
   }
 
   private Object parameterExpression(int pt, int ptMax, String key,
                                      boolean asVector, int ptAtom,
-                                     Hashtable localVars)
+                                     Hashtable localVars, String localVar)
       throws ScriptException {
     Object v;
+    boolean isSelectX = (pt == 0);
     boolean isOneExpressionOnly = (pt < 0);
+    boolean isImplicitAtomProperty = (localVar != null);
     if (isOneExpressionOnly)
       pt = -pt;
     int nParen = 0;
@@ -7230,14 +7226,18 @@
       ptMax = statementLength;
     out: for (int i = pt; i < ptMax; i++) {
       v = null;
-      switch (getToken(i).tok) {
-      case Token.selectx:
-        if (i != 0)
-          error(ERROR_invalidArgument);
-        // fall through
+      int tok = getToken(i).tok;
+      if (isImplicitAtomProperty && tokAt(i + 1) != Token.dot) {
+        if (Compiler.tokAttr(tok, Token.atomproperty)) {
+          rpn.addX((Token) localVars.get(localVar));
+          if (!rpn.addOp(new Token(Token.propselector, tok, parameterAsString(i).toLowerCase())))
+            error(ERROR_invalidArgument);
+          continue;
+        }
+      }
+      switch (tok) {
       case Token.select:
-        String dummy = "x";
-        boolean isSelectX = (theTok == Token.selectx);
+        String dummy = "_x";
         if (!isSelectX) {
           if (getToken(++i).tok != Token.leftparen
               || getToken(++i).tok != Token.identifier)
@@ -7265,8 +7265,8 @@
             bsX.clear();
             bsX.set(j);
             t.intValue2 = j;
-            if (((Boolean) parameterExpression(i, -1, null, false, j, localVars))
-                .booleanValue())
+            if (((Boolean) parameterExpression(i, -1, null, false, j, 
+                localVars, isSelectX ? dummy : null)).booleanValue())
               bsSelect.set(j);
             if (!isSelectX && tokAt(iToken) != Token.rightparen)
               error(ERROR_invalidArgument);
@@ -7317,7 +7317,9 @@
           error(ERROR_invalidArgument);
         break;
       case Token.dot:
-        Token token = getBitsetPropertySelector(i, false);
+        Token token = getBitsetPropertySelector(i + 1, false);
+        if (token == null)
+          error(ERROR_invalidArgument);
         //check for added min/max modifier
         if (tokAt(iToken + 1) == Token.dot) {
           if (tokAt(iToken + 2) == Token.all) {
@@ -7565,16 +7567,17 @@
 
   private Token getBitsetPropertySelector(int i, boolean mustBeSettable)
       throws ScriptException {
-    int tok = getToken(++i).tok;
-    String s = parameterAsString(i).toLowerCase();
+    int tok = getToken(i).tok;
+    String s = null;
     switch (tok) {
     default:
       if (Compiler.tokAttrOr(tok, Token.atomproperty, Token.mathproperty))
         break;
-      error(ERROR_invalidArgument);
+      return null; 
     case Token.property:
       break;
     case Token.identifier:
+      s = parameterAsString(i).toLowerCase();
       if (s.equals("x"))
         tok = Token.atomX;
       else if (s.equals("y"))
@@ -7584,11 +7587,13 @@
       else if (s.equals("w"))
         tok = Token.qw;
       else
-        error(ERROR_invalidArgument);
+        return null;
       break;
     }
     if (mustBeSettable && !Compiler.tokAttr(tok, Token.settable))
-      error(ERROR_invalidArgument);
+      return null;
+    if (s == null)
+      s = parameterAsString(i).toLowerCase();
     return new Token(Token.propselector, tok, s);
   }
 

Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2008-06-30 05:09:59 UTC (rev 9535)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2008-06-30 15:00:22 UTC (rev 9536)
@@ -3,6 +3,18 @@
 
 version=11.5.43
 
+# new feature/feature change:
+#
+# selectX is no longer necessary. Simply use
+#
+#   select {atomExpression} (property expression)
+#
+# with no "x." An implied variable "_x" can be used explicitly:
+#
+#   select {*} (straightness < 0.995) # does not round
+#   select {*.ca} (atomY < atomX)
+#   select {*.ca} (phi < select(y; {*.ca}; y.resno = _x.resno + 1).phi))
+#
 # new feature: quaterion % point4f --- "thetaDirected" -- 
 #   point4f is {x, y, z, w} (w ignored), where {x y z} is a
 #   preferred direction. 

Modified: trunk/Jmol/src/org/jmol/viewer/Token.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Token.java	2008-06-30 05:09:59 UTC (rev 9535)
+++ trunk/Jmol/src/org/jmol/viewer/Token.java	2008-06-30 15:00:22 UTC (rev 9536)
@@ -181,7 +181,6 @@
   final static int rotate       = command | 27 | numberOrExpression;
   final static int save         = command | 28;
 //  final static int script       = command | 29; with mathfunc 
-  final static int selectx      = command | 30 | implicitExpression;
   final static int set          = command | 31 | implicitExpression | colorparam;
   final static int show         = command | 32;
   final static int slab         = command | 33 | numberOrExpression;
@@ -463,7 +462,7 @@
 
   // ___.xxx(a)
   
-  // a.distance(b) is in a different set -- x.distance(b,c) -- because it CAN take
+  // a.distance(b) is in a different set -- distance(b,c) -- because it CAN take
   // two parameters and it CAN be a dot-function (but not both together)
   
   final static int split        = 0  | 1 << 3 | mathfunc | mathproperty;
@@ -1108,7 +1107,6 @@
     "script",            new Token(script,          varArgCount),
     "source",            null, 
     "select",            new Token(select,          varArgCount),
-    "selectX",           new Token(selectx,         varArgCount),
     "selectionHalos",    new Token(selectionHalo,    onDefault1),
     "selectionHalo",     null, 
     "set",               new Token(set,             varArgCount),


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Revision: 9535
          http://jmol.svn.sourceforge.net/jmol/?rev=9535&view=rev
Author:   hansonr
Date:     2008-06-29 22:09:59 -0700 (Sun, 29 Jun 2008)

Log Message:
-----------
version=11.5.43 quaternion, POV-RAY, more.

# new feature: quaterion % point4f --- "thetaDirected" -- 
#   point4f is {x, y, z, w} (w ignored), where {x y z} is a
#   preferred direction. 
#   Returns a point4f angle-Axis equivalent with x, y, z the normal for the quaternion
#   rotation and w = theta for the rotation, where the normal and theta are chosen
#   to be directed with a positive dot product between the input {x y z}
#   vector and the output {x y z}.
   
# bug fix: POV-RAY output of quadrilaterals.

# new feature: Ramachandran "r" --- includes third (Z) axis quaternion r difference2 X component equivalent

# bug fix: quaternion definition with dot-product check not effective -- removed
# bug fix: quaternion construction from matrix error
#
# new feature: _applet boolean
#
# new feature: extended quaternion math
#
#   q = quaternion({x y z}, angleDegrees)
#   q = quaternion(q0, q1, q2,q3)
#   q = {qx, qy, qz, qw}
#
# returning component values: 
#
#   q.x, q.y, q.z, q.w
#
# note that the Point4f equivalent stores w LAST, even though it is "q0" 
# because the Java Quat4f() and Point4f() both do that as well. We're just
# being consistent with other Java use.
#
# Modulus operator for extended information retrieval:
#
#   (q%0) -- q0 (w)
#   (q%1) -- q1 (x)
#   (q%2) -- q2 (y)
#   (q%3) -- q3 (z)
#   (q%-1) -- the vector {q1, q2, q3}
#   (q%-2) -- theta
#   (q%-3) -- equivalent rotational frame X-axis 
#   (q%-4) -- equivalent rotational frame Y-axis 
#   (q%-5) -- equivalent rotational frame Z-axis 
#   (q%{x y z})  -- rotational transform of a point or vector based on a quaternion
#
# thus, for example, (q%{1 0 0}) is the same as (q%-3)
#
#   (!q) -- quaternion inverse
#
# 
# Quaternion right division (difference "dq"):
#
#   q2 / q1 = q2 * (!q1)
#
# Quaternion left division (relative difference n):
#
#   q2 \ q1 = (!q1) * q2
#
# Examples:
#
#   q = quaternion({1 1 1},120)
#   print "" + (q%{1 0 0}) + " " + (q%{0 1 0}) + " " + (q%{0 0 1})    
#
#   {0 1.0 0} {0 0 1.0} {1.0 0 0}
#
# new feature: Numerical left division (integer divide)
#
#   3.6 \ 2 = 1
#   3.6 \ 1.3 = 2
#
# new feature: sqrt(x)
#
# bug fix: load trajectory for cases with different atom counts.
#
# experimental: "straightness" defined as 1 - 2 * acos(normal(dq[i]%-1) dot normal(dq[i+1])) / PI
# giving a measure proportional to the difference in local helical axis angle 
# and ranging from -1 (opposite direction) to 1 (same direction) for proteins 
# -- a work in progress. See
#
#   load =1d66
#   calculate straightness;color straightness
#  

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

Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2008-06-30 05:04:35 UTC (rev 9534)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2008-06-30 05:09:59 UTC (rev 9535)
@@ -10,7 +10,15 @@
 #   rotation and w = theta for the rotation, where the normal and theta are chosen
 #   to be directed with a positive dot product between the input {x y z}
 #   vector and the output {x y z}.
-   
+#
+# thus, because the negative angle switches the normal:  
+#
+#   print quaternion({1 0 0}, -20) % 1 ==> {-1 0 0}; %1 ==> 20
+#
+# but % {1 0 0 0} forces the angle associated with {1 0 0} to be reported 
+#
+#   print quaternion({1 0 0}, -20) % {1 0 0 0} ==> {1 0 0 20}
+#
 # bug fix: POV-RAY output of quadrilaterals.
 
 # new feature: Ramachandran "r" --- includes third (Z) axis quaternion r difference2 X component equivalent


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Revision: 9534
          http://jmol.svn.sourceforge.net/jmol/?rev=9534&view=rev
Author:   hansonr
Date:     2008-06-29 22:04:35 -0700 (Sun, 29 Jun 2008)

Log Message:
-----------
version=11.5.43 quaternion, POV-RAY, more.

# new feature: quaterion % point4f --- "thetaDirected" -- 
#   point4f is {x, y, z, w} (w ignored), where {x y z} is a
#   preferred direction. 
#   Returns a point4f angle-Axis equivalent with x, y, z the normal for the quaternion
#   rotation and w = theta for the rotation, where the normal and theta are chosen
#   to be directed with a positive dot product between the input {x y z}
#   vector and the output {x y z}.
   
# bug fix: POV-RAY output of quadrilaterals.

# new feature: Ramachandran "r" --- includes third (Z) axis quaternion r difference2 X component equivalent

# bug fix: quaternion definition with dot-product check not effective -- removed
# bug fix: quaternion construction from matrix error
#
# new feature: _applet boolean
#
# new feature: extended quaternion math
#
#   q = quaternion({x y z}, angleDegrees)
#   q = quaternion(q0, q1, q2,q3)
#   q = {qx, qy, qz, qw}
#
# returning component values: 
#
#   q.x, q.y, q.z, q.w
#
# note that the Point4f equivalent stores w LAST, even though it is "q0" 
# because the Java Quat4f() and Point4f() both do that as well. We're just
# being consistent with other Java use.
#
# Modulus operator for extended information retrieval:
#
#   (q%0) -- q0 (w)
#   (q%1) -- q1 (x)
#   (q%2) -- q2 (y)
#   (q%3) -- q3 (z)
#   (q%-1) -- the vector {q1, q2, q3}
#   (q%-2) -- theta
#   (q%-3) -- equivalent rotational frame X-axis 
#   (q%-4) -- equivalent rotational frame Y-axis 
#   (q%-5) -- equivalent rotational frame Z-axis 
#   (q%{x y z})  -- rotational transform of a point or vector based on a quaternion
#
# thus, for example, (q%{1 0 0}) is the same as (q%-3)
#
#   (!q) -- quaternion inverse
#
# 
# Quaternion right division (difference "dq"):
#
#   q2 / q1 = q2 * (!q1)
#
# Quaternion left division (relative difference n):
#
#   q2 \ q1 = (!q1) * q2
#
# Examples:
#
#   q = quaternion({1 1 1},120)
#   print "" + (q%{1 0 0}) + " " + (q%{0 1 0}) + " " + (q%{0 0 1})    
#
#   {0 1.0 0} {0 0 1.0} {1.0 0 0}
#
# new feature: Numerical left division (integer divide)
#
#   3.6 \ 2 = 1
#   3.6 \ 1.3 = 2
#
# new feature: sqrt(x)
#
# bug fix: load trajectory for cases with different atom counts.
#
# experimental: "straightness" defined as 1 - 2 * acos(normal(dq[i]%-1) dot normal(dq[i+1])) / PI
# giving a measure proportional to the difference in local helical axis angle 
# and ranging from -1 (opposite direction) to 1 (same direction) for proteins 
# -- a work in progress. See
#
#   load =1d66
#   calculate straightness;color straightness
#  

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

Modified: trunk/Jmol/src/org/jmol/util/Quaternion.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Quaternion.java	2008-06-30 04:34:03 UTC (rev 9533)
+++ trunk/Jmol/src/org/jmol/util/Quaternion.java	2008-06-30 05:04:35 UTC (rev 9534)
@@ -285,6 +285,17 @@
     return (float) (Math.acos(q0) * 2 * 180/Math.PI);  
   }
   
+  public void getThetaDirected(Point4f axisAngle) {
+    //fills in .w;
+    float theta = getTheta();
+    Vector3f v = getNormal();
+    if (axisAngle.x * q1 + axisAngle.y * q2 + axisAngle.z * q3 < 0) {
+      v.scale(-1);
+      theta = -theta;
+    }
+    axisAngle.set(v.x, v.y, v.z, theta);
+  }
+  
   public Point4f toPoint4f() {
     fixQ();
     return new Point4f(q1, q2, q3, q0);

Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java	2008-06-30 04:34:03 UTC (rev 9533)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java	2008-06-30 05:04:35 UTC (rev 9534)
@@ -12929,6 +12929,11 @@
           Point4f q = (Point4f) x1.value;
           if (x2.tok == Token.point3f)
             return addX((new Quaternion(q)).transform((Point3f) x2.value));
+          if (x2.tok == Token.point4f) {
+            Point4f v4 = new Point4f((Point4f) x2.value);
+            (new Quaternion(q)).getThetaDirected(v4);
+            return addX(v4);
+          }
           switch (n) {
           case 0:
             return addX(q.w);

Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2008-06-30 04:34:03 UTC (rev 9533)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2008-06-30 05:04:35 UTC (rev 9534)
@@ -1,8 +1,16 @@
 # Developers: to add a description of changes you have made,
 # add it on line starting with # below the "version=..." line
 
-version=11.5.43_dev
+version=11.5.43
 
+# new feature: quaterion % point4f --- "thetaDirected" -- 
+#   point4f is {x, y, z, w} (w ignored), where {x y z} is a
+#   preferred direction. 
+#   Returns a point4f angle-Axis equivalent with x, y, z the normal for the quaternion
+#   rotation and w = theta for the rotation, where the normal and theta are chosen
+#   to be directed with a positive dot product between the input {x y z}
+#   vector and the output {x y z}.
+   
 # bug fix: POV-RAY output of quadrilaterals.
 
 # new feature: Ramachandran "r" --- includes third (Z) axis quaternion r difference2 X component equivalent


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

Revision: 9533
          http://jmol.svn.sourceforge.net/jmol/?rev=9533&view=rev
Author:   hansonr
Date:     2008-06-29 21:34:03 -0700 (Sun, 29 Jun 2008)

Log Message:
-----------
11.5.43 VERSION 

bug fix POV-RAY output of quadrilaterals.

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

Modified: trunk/Jmol/src/org/jmol/export/_PovrayExporter.java
===================================================================
--- trunk/Jmol/src/org/jmol/export/_PovrayExporter.java	2008-06-30 03:34:09 UTC (rev 9532)
+++ trunk/Jmol/src/org/jmol/export/_PovrayExporter.java	2008-06-30 04:34:03 UTC (rev 9533)
@@ -446,7 +446,7 @@
       int nColix = 0;
       for (int i = 0; i < nVertices; i++) {
         color = color4(colixes[i]);
-        if (!htColixes.containsKey(color)) 
+        if (!htColixes.containsKey(color))
           htColixes.put(color, new Integer(nColix++));
       }
       String[] list = new String[nColix];
@@ -457,11 +457,11 @@
       }
 
       output("texture_list { " + nColix);
-      for (int i = 0; i < nColix; i++) 
-        output("\n, texture{pigment{rgbt<" + list[i] + ">}" 
-          + " translucentFinish(" 
-          + translucencyFractionalFromColix(colixes[0]) + ")}");
-          // just using the transparency of the first colix there... 
+      for (int i = 0; i < nColix; i++)
+        output("\n, texture{pigment{rgbt<" + list[i] + ">}"
+            + " translucentFinish("
+            + translucencyFractionalFromColix(colixes[0]) + ")}");
+      // just using the transparency of the first colix there... 
       output("\n}\n");
     }
     output("face_indices { " + nFaces);
@@ -480,10 +480,8 @@
         color = color4(colixes[indices[i][2]]);
         output("," + ((Integer) htColixes.get(color)).intValue());
       }
-      output(" //\n");
       if (faceVertexMax == 4 && indices[i].length == 4) {
-        output(", <" + triad(indices[i]) + ","
-            + indices[i][3] + ">");
+        output(", <" + indices[i][0] + "," + indices[i][2] + "," + indices[i][3] + ">");
         if (colixes != null) {
           color = color4(colixes[indices[i][0]]);
           output("," + ((Integer) htColixes.get(color)).intValue());
@@ -492,15 +490,15 @@
           color = color4(colixes[indices[i][3]]);
           output("," + ((Integer) htColixes.get(color)).intValue());
         }
-        output(" //\n");
       }
+      output("\n");
     }
     output("\n}\n");
 
     if (colixes == null) {
       output("pigment{rgbt<" + color4(colix) + ">}\n");
-      output("  translucentFinish("  
-        + translucencyFractionalFromColix(colix) +")\n");
+      output("  translucentFinish(" + translucencyFractionalFromColix(colix)
+          + ")\n");
     }
     output("  check_shadow()\n");
     output("  clip()\n");

Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2008-06-30 03:34:09 UTC (rev 9532)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2008-06-30 04:34:03 UTC (rev 9533)
@@ -3,6 +3,8 @@
 
 version=11.5.43_dev
 
+# bug fix: POV-RAY output of quadrilaterals.
+
 # new feature: Ramachandran "r" --- includes third (Z) axis quaternion r difference2 X component equivalent
 
 # bug fix: quaternion definition with dot-product check not effective -- removed


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

Revision: 9532
          http://jmol.svn.sourceforge.net/jmol/?rev=9532&view=rev
Author:   hansonr
Date:     2008-06-29 20:34:09 -0700 (Sun, 29 Jun 2008)

Log Message:
-----------
version=11.5.43_dev # new feature: Ramachandran "r" --- includes third (Z) axis quaternion r difference2 X component equivalent

Modified Paths:
--------------
    trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
    trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java
    trunk/Jmol/src/org/jmol/viewer/Eval.java
    trunk/Jmol/src/org/jmol/viewer/Jmol.properties
    trunk/Jmol/src/org/jmol/viewer/Token.java

Modified: trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelCollection.java	2008-06-29 13:41:08 UTC (rev 9531)
+++ trunk/Jmol/src/org/jmol/modelset/ModelCollection.java	2008-06-30 03:34:09 UTC (rev 9532)
@@ -935,7 +935,9 @@
     Model model = models[modelIndex];
     char ctype = (type.length() > 11 && type.indexOf("quaternion ") >= 0 ? type
         .charAt(11) : 'R');
-    char qtype = (ctype == 'R' ? 'R' : viewer.getQuaternionFrame());
+    char qtype = (ctype != 'R' ? viewer.getQuaternionFrame() 
+        : type.length() > 13 && type.indexOf("ramachandran ") >= 0 ?
+          type.charAt(13) : 'R');
     int derivType = (type.indexOf("diff") < 0 ? 0 : type.indexOf("2") < 0 ? 1 : 2);
     boolean isDraw = (type.indexOf("draw") >= 0);    
     BitSet bsAtoms = getModelAtomBitSet(modelIndex, false);

Modified: trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java	2008-06-29 13:41:08 UTC (rev 9531)
+++ trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java	2008-06-30 03:34:09 UTC (rev 9532)
@@ -515,6 +515,8 @@
     boolean isRelativeAlias = (ctype == 'r');
     String prefix = (derivType > 0 ? "dq" + (derivType  == 2 ? "2" : "") : "q");
     float psiLast = Float.NaN;
+    if (derivType == 2 && isRelativeAlias)
+      ctype= 'x';
     Quaternion q;
     for (int m = 0; m < p.monomerCount; m++) {
       Monomer monomer = p.monomers[m];
@@ -526,20 +528,24 @@
           z = monomer.getOmega();
           if (z < -90)
             z += 360;
-          //z -= 180;
+          z -= 180; // center on 0
           if (Float.isNaN(x) || Float.isNaN(y) || Float.isNaN(z))
             continue;
           w = a.getPartialCharge();
           float phiNext = (m == p.monomerCount - 1 ? Float.NaN : p.monomers[m + 1].getPhi());   
           float angle = y + phiNext - psiLast - x;//psi[i] + phi[i+1] - psi[i-1] - phi[i]
+          psiLast = y;
           if (Float.isNaN(angle)) {
             strExtra = "";
+            if (qtype == 'r')
+              continue;
           } else {
             q = new Quaternion (new Point3f(1, 0, 0), angle);
             strExtra = TextFormat.sprintf("%10.6f%10.6f%10.6f%10.6f  %6.2f",
                 new Object[] { new float[] { q.q0, q.q1, q.q2, q.q3, q.getTheta() } });
+            if (qtype == 'r')
+              z = angle;
           }
-          psiLast = y;
         } else {
           char cid = monomer.getChainID();
           String id = "" + monomer.getResno()

Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java	2008-06-29 13:41:08 UTC (rev 9531)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java	2008-06-30 03:34:09 UTC (rev 9532)
@@ -4461,21 +4461,22 @@
   }
 
   private void dataFrame(int datatype) throws ScriptException {
-    String type = "";
     boolean isQuaternion = false;
     boolean isDraw = (tokAt(0) == Token.draw);
     int pt0 = (isDraw ? 1 : 0);
     boolean isDerivative = false;
     boolean isSecondDerivative = false;
+    boolean isRamachandranRelative = false;
+    int pt = statementLength - 1;
+    String type = optParameterAsString(pt).toLowerCase();
     switch (datatype) {
     case JmolConstants.JMOL_DATA_RAMACHANDRAN:
-      type = "ramachandran";
+      isRamachandranRelative = (pt > pt0 && type.startsWith("r"));
+      type = "ramachandran" + (isRamachandranRelative ? " r" : "");
       break;
     case JmolConstants.JMOL_DATA_QUATERNION:
       isQuaternion = true;
       // working backward this time:
-      int pt = statementLength - 1;
-      type = optParameterAsString(pt).toLowerCase();
       if (type.equalsIgnoreCase("draw")) {
         isDraw = true;
         type = optParameterAsString(--pt).toLowerCase();
@@ -4533,12 +4534,14 @@
     switch (datatype) {
     case JmolConstants.JMOL_DATA_RAMACHANDRAN:
     default:
-      viewer.setFrameTitle(modelCount - 1, "ramachandran plot for model "
+      viewer.setFrameTitle(modelCount - 1, type + " plot for model "
           + viewer.getModelNumberDotted(modelIndex));
       script = "frame 0.0; frame last; reset;"
           + "select visible; color structure; spacefill 3.0; wireframe 0; set rotationRadius 260;"
           + "draw ramaAxisX" + modelCount + " {200 0 0} {-200 0 0} \"phi\";"
-          + "draw ramaAxisY" + modelCount + " {0 200 0} {0 -200 0} \"psi\";";
+          + "draw ramaAxisY" + modelCount + " {0 200 0} {0 -200 0} \"psi\";"
+          //+ "draw ramaAxisZ" + modelCount + " {0 0 400} {0 0 0} \"" + (isRamachandranRelative ? "theta" : "omega") +"\";"
+          ;
       break;
     case JmolConstants.JMOL_DATA_QUATERNION:
       viewer.setFrameTitle(modelCount - 1, type + " for model "

Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2008-06-29 13:41:08 UTC (rev 9531)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2008-06-30 03:34:09 UTC (rev 9532)
@@ -3,6 +3,8 @@
 
 version=11.5.43_dev
 
+# new feature: Ramachandran "r" --- includes third (Z) axis quaternion r difference2 X component equivalent
+
 # bug fix: quaternion definition with dot-product check not effective -- removed
 # bug fix: quaternion construction from matrix error
 #

Modified: trunk/Jmol/src/org/jmol/viewer/Token.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Token.java	2008-06-29 13:41:08 UTC (rev 9531)
+++ trunk/Jmol/src/org/jmol/viewer/Token.java	2008-06-30 03:34:09 UTC (rev 9532)
@@ -1091,7 +1091,7 @@
     "quaternion",        new Token(quaternion,      varArgCount),
     "quaternions",       null,
     "quit",              new Token(quit,                      0),
-    "ramachandran",      new Token(ramachandran,              0),
+    "ramachandran",      new Token(ramachandran,    varArgCount),
     "rama",              null,
     "refresh",           new Token(refresh,                   0),
     "reset",             new Token(reset,               maxArg1),


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

Revision: 9531
          http://jmol.svn.sourceforge.net/jmol/?rev=9531&view=rev
Author:   nicove
Date:     2008-06-29 06:41:08 -0700 (Sun, 29 Jun 2008)

Log Message:
-----------
Folding@Home

Added Paths:
-----------
    trunk/Jmol-FAH/projects/p4586.xyz.gz
    trunk/Jmol-FAH/projects/p4587.xyz.gz

Added: trunk/Jmol-FAH/projects/p4586.xyz.gz
===================================================================
(Binary files differ)


Property changes on: trunk/Jmol-FAH/projects/p4586.xyz.gz
___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream

Added: trunk/Jmol-FAH/projects/p4587.xyz.gz
===================================================================
(Binary files differ)


Property changes on: trunk/Jmol-FAH/projects/p4587.xyz.gz
___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream


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

Revision: 9530
          http://jmol.svn.sourceforge.net/jmol/?rev=9530&view=rev
Author:   nicove
Date:     2008-06-29 04:09:50 -0700 (Sun, 29 Jun 2008)

Log Message:
-----------
Folding@Home

Added Paths:
-----------
    trunk/Jmol-FAH/projects/p4583.xyz.gz

Added: trunk/Jmol-FAH/projects/p4583.xyz.gz
===================================================================
(Binary files differ)


Property changes on: trunk/Jmol-FAH/projects/p4583.xyz.gz
___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream


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

Revision: 9529
          http://jmol.svn.sourceforge.net/jmol/?rev=9529&view=rev
Author:   nicove
Date:     2008-06-29 02:33:01 -0700 (Sun, 29 Jun 2008)

Log Message:
-----------
Folding@Home

Added Paths:
-----------
    trunk/Jmol-FAH/projects/p3858.xyz.gz
    trunk/Jmol-FAH/projects/p4579.xyz.gz
    trunk/Jmol-FAH/projects/p4581.xyz.gz

Added: trunk/Jmol-FAH/projects/p3858.xyz.gz
===================================================================
(Binary files differ)


Property changes on: trunk/Jmol-FAH/projects/p3858.xyz.gz
___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream

Added: trunk/Jmol-FAH/projects/p4579.xyz.gz
===================================================================
(Binary files differ)


Property changes on: trunk/Jmol-FAH/projects/p4579.xyz.gz
___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream

Added: trunk/Jmol-FAH/projects/p4581.xyz.gz
===================================================================
(Binary files differ)


Property changes on: trunk/Jmol-FAH/projects/p4581.xyz.gz
___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream


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

Revision: 9528
          http://jmol.svn.sourceforge.net/jmol/?rev=9528&view=rev
Author:   nicove
Date:     2008-06-28 00:44:31 -0700 (Sat, 28 Jun 2008)

Log Message:
-----------
Folding@Home

Added Paths:
-----------
    trunk/Jmol-FAH/projects/p4577.xyz.gz
    trunk/Jmol-FAH/projects/p4580.xyz.gz
    trunk/Jmol-FAH/projects/p5102.xyz.gz

Added: trunk/Jmol-FAH/projects/p4577.xyz.gz
===================================================================
(Binary files differ)


Property changes on: trunk/Jmol-FAH/projects/p4577.xyz.gz
___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream

Added: trunk/Jmol-FAH/projects/p4580.xyz.gz
===================================================================
(Binary files differ)


Property changes on: trunk/Jmol-FAH/projects/p4580.xyz.gz
___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream

Added: trunk/Jmol-FAH/projects/p5102.xyz.gz
===================================================================
(Binary files differ)


Property changes on: trunk/Jmol-FAH/projects/p5102.xyz.gz
___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream


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Revision: 9527
          http://jmol.svn.sourceforge.net/jmol/?rev=9527&view=rev
Author:   hansonr
Date:     2008-06-26 20:58:18 -0700 (Thu, 26 Jun 2008)

Log Message:
-----------
version=11.5.43_dev quaternion tweaks

# bug fix: quaternion definition with dot-product check not effective -- removed
# bug fix: quaternion construction from matrix error
#

Modified Paths:
--------------
    trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
    trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java
    trunk/Jmol/src/org/jmol/viewer/Eval.java

Modified: trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelCollection.java	2008-06-27 02:07:03 UTC (rev 9526)
+++ trunk/Jmol/src/org/jmol/modelset/ModelCollection.java	2008-06-27 03:58:18 UTC (rev 9527)
@@ -972,9 +972,9 @@
       break;
     }
     remark += "\n\n" + getProteinStructureState(bsAtoms, ctype == 'R');
-    remark += "REMARK   6    AT GRP CH RESNO  " + data + "    Sym";
+    remark += "REMARK   6    AT GRP CH RESNO  " + data + "    Sym   q0_______ q1_______ q2_______ q3_______  theta_";
     if (ctype != 'R')
-      remark += "   q0_______ q1_______ q2_______ q3_______  centerX___ centerY___ centerZ___";
+      remark += "  centerX___ centerY___ centerZ___";
     if (qtype == 'n')
       remark += "  NHX_______ NHY_______ NYZ_______";
     remark += "\n\n";

Modified: trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java	2008-06-27 02:07:03 UTC (rev 9526)
+++ trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java	2008-06-27 03:58:18 UTC (rev 9527)
@@ -514,6 +514,8 @@
     String strExtra = "";
     boolean isRelativeAlias = (ctype == 'r');
     String prefix = (derivType > 0 ? "dq" + (derivType  == 2 ? "2" : "") : "q");
+    float psiLast = Float.NaN;
+    Quaternion q;
     for (int m = 0; m < p.monomerCount; m++) {
       Monomer monomer = p.monomers[m];
       if (bsAtoms == null || bsAtoms.get(monomer.getLeadAtomIndex())) {
@@ -528,11 +530,21 @@
           if (Float.isNaN(x) || Float.isNaN(y) || Float.isNaN(z))
             continue;
           w = a.getPartialCharge();
+          float phiNext = (m == p.monomerCount - 1 ? Float.NaN : p.monomers[m + 1].getPhi());   
+          float angle = y + phiNext - psiLast - x;//psi[i] + phi[i+1] - psi[i-1] - phi[i]
+          if (Float.isNaN(angle)) {
+            strExtra = "";
+          } else {
+            q = new Quaternion (new Point3f(1, 0, 0), angle);
+            strExtra = TextFormat.sprintf("%10.6f%10.6f%10.6f%10.6f  %6.2f",
+                new Object[] { new float[] { q.q0, q.q1, q.q2, q.q3, q.getTheta() } });
+          }
+          psiLast = y;
         } else {
           char cid = monomer.getChainID();
           String id = "" + monomer.getResno()
               + (cid == '\0' ? "" : "" + cid);
-          Quaternion q = p.getQuaternion(m, qtype);
+          q = p.getQuaternion(m, qtype);
           if (q == null) {
             qlast = null;
             atomno = Integer.MIN_VALUE;
@@ -642,9 +654,9 @@
             .append(" color ").append(qColor[derivType]).append('\n');
             continue;
           }
-          strExtra = TextFormat.sprintf("%10.6f%10.6f%10.6f%10.6f  %10.5p %10.5p %10.5p",
+          strExtra = TextFormat.sprintf("%10.6f%10.6f%10.6f%10.6f  %6.2f  %10.5p %10.5p %10.5p",
               new Object[] { 
-                new float[] { q.q0, q.q1, q.q2, q.q3 },  
+                new float[] { q.q0, q.q1, q.q2, q.q3, q.getTheta() },  
                 new Point3f[] { ptCenter }
               });
           if (qtype == 'n')

Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java	2008-06-27 02:07:03 UTC (rev 9526)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java	2008-06-27 03:58:18 UTC (rev 9527)
@@ -8812,7 +8812,7 @@
       }
       if (type != "VAR" && pt == 1)
         type = "image";
-      else if (fileName.charAt(0) == '.' && (pt == 2 || pt == 3)) {
+      else if (fileName.length() > 0 && fileName.charAt(0) == '.' && (pt == 2 || pt == 3)) {
         fileName = Token.sValue(tokenAt(pt - 1, args)) + fileName;
         if (type != "VAR" && pt == 2)
           type = "image";
@@ -12755,13 +12755,6 @@
           case Token.point4f:
             return addX(q1.mul(new Quaternion((Point4f) x2.value)).toPoint4f());
           }
-        case 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));
         case Token.point3f:
           Point3f pt = new Point3f((Point3f) x1.value);
           switch (x2.tok) {
@@ -12773,6 +12766,14 @@
             Point4f pt4 = (Point4f) x2.value;
             pt.add(new Point3f(pt4.x, pt4.y, pt4.z));
             return addX(pt);
+          case 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));
+            // fall through
           default:
             float f = Token.fValue(x2);
             return addX(new Point3f(pt.x + f, pt.y + f, pt.z + f));


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Revision: 9526
          http://jmol.svn.sourceforge.net/jmol/?rev=9526&view=rev
Author:   hansonr
Date:     2008-06-26 19:07:03 -0700 (Thu, 26 Jun 2008)

Log Message:
-----------
version=11.5.43_dev quaternion tweaks

# bug fix: quaternion definition with dot-product check not effective -- removed
# bug fix: quaternion construction from matrix error
#

Modified Paths:
--------------
    trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
    trunk/Jmol/src/org/jmol/modelset/ModelSet.java
    trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java
    trunk/Jmol/src/org/jmol/shape/MeasuresRenderer.java
    trunk/Jmol/src/org/jmol/shapespecial/Draw.java
    trunk/Jmol/src/org/jmol/util/Quaternion.java
    trunk/Jmol/src/org/jmol/viewer/Eval.java
    trunk/Jmol/src/org/jmol/viewer/Jmol.properties
    trunk/Jmol/src/org/jmol/viewer/Viewer.java

Modified: trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelCollection.java	2008-06-26 15:33:51 UTC (rev 9525)
+++ trunk/Jmol/src/org/jmol/modelset/ModelCollection.java	2008-06-27 02:07:03 UTC (rev 9526)
@@ -2131,7 +2131,7 @@
   
   //////////// state definition ///////////
 
-  protected String getProteinStructureState(BitSet bsAtoms, boolean needPhiPsi) {
+  public String getProteinStructureState(BitSet bsAtoms, boolean needPhiPsi) {
     BitSet bs = null;
     StringBuffer cmd = new StringBuffer();
     StringBuffer sbTurn = new StringBuffer();

Modified: trunk/Jmol/src/org/jmol/modelset/ModelSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelSet.java	2008-06-26 15:33:51 UTC (rev 9525)
+++ trunk/Jmol/src/org/jmol/modelset/ModelSet.java	2008-06-27 02:07:03 UTC (rev 9526)
@@ -580,12 +580,11 @@
 
     // connections
 
-    
     if (isAll) {
-      
+
       int len = stateScripts.size();
       for (int i = 0; i < len; i++) {
-        StateScript ss = (StateScript) stateScripts.get(i); 
+        StateScript ss = (StateScript) stateScripts.get(i);
         if (ss.postDefinitions && (cmd = ss.toString()).length() > 0)
           commands.append("  ").append(cmd).append("\n");
       }
@@ -594,14 +593,14 @@
         if ((bonds[i].order & JmolConstants.BOND_NEW) != 0
             || bonds[i].isHydrogen()) {
           Bond bond = bonds[i];
-          commands.append("  connect ") 
-              .append("({").append(bond.atom1.atomIndex).append("}) ") 
-              .append("({").append(bond.atom2.atomIndex).append("}) ") 
-              .append(JmolConstants.getBondOrderNameFromOrder(bond.order))
+          commands.append("  connect ").append("({").append(
+              bond.atom1.atomIndex).append("}) ").append("({").append(
+              bond.atom2.atomIndex).append("}) ").append(
+              JmolConstants.getBondOrderNameFromOrder(bond.order))
               .append(";\n");
         }
       }
-      commands.append("\n");      
+      commands.append("\n");
     }
 
     // shape construction
@@ -618,15 +617,17 @@
         commands.append(cmd);
     }
 
-    for (int i = 0; i < modelCount; i++) {
-      String t = frameTitles[i];
-      if (t != null && t.length() > 0)
-        commands.append("  frame " + getModelNumberDotted(i) + "; frame title "
-            + Escape.escape(t) + ";\n");
-    }
+    if (isAll) {
+      for (int i = 0; i < modelCount; i++) {
+        String t = frameTitles[i];
+        if (t != null && t.length() > 0)
+          commands.append("  frame " + getModelNumberDotted(i)
+              + "; frame title " + Escape.escape(t) + ";\n");
+      }
 
-    commands.append("  set fontScaling " + viewer.getFontScaling() + ";\n");
+      commands.append("  set fontScaling " + viewer.getFontScaling() + ";\n");
 
+    }
     if (sfunc != null)
       commands.append("\nend function;\n\n");
     return commands.toString();

Modified: trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java	2008-06-26 15:33:51 UTC (rev 9525)
+++ trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java	2008-06-27 02:07:03 UTC (rev 9526)
@@ -577,11 +577,6 @@
               // first deriv:
               q = dq;
             }
-            if (q.q0 < 0)
-              q = q.mul(-1);
-            if (qlast != null && q.dot(qlast) < 0)
-              q = q.mul(-1);
-
             if (derivType == 1 && aprev != null && qlast != null && ctype == 'w')
               aprev.getGroup().setStraightness(getStraightness(id, qlast, q));
             
@@ -597,13 +592,6 @@
             aprev = atemp;
             // save this dq as dq'
             dqprev = dq;
-          } else {
-             if (qlast == null && q.q0 < 0) {
-               //initialize with a positive q0
-               q = q.mul(-1);
-             }
-             if (qlast != null && q.dot(qlast) < 0)
-               q = q.mul(-1);
           }
           qlast = q;
           switch (ctype) {
@@ -642,18 +630,6 @@
               continue;
             String strV = " VECTOR " + Escape.escape(ptCenter) + " ";
             int deg = (int) (Math.acos(w) * 360 / Math.PI);
-            //this is the angle required to rotate the INITIAL FRAME to this position
-            //if (deg < 0)
-            //deg += 360;
-            if (deg > 180)
-              deg = deg - 360;
-            if (deg < -180)
-              deg = deg + 360;
-            int ndeg = -deg;
-            if (ndeg > 180)
-              ndeg = ndeg - 360;
-            if (ndeg < -180)
-              ndeg = ndeg + 360;
             if (derivType == 0)
               pdbATOM.append("draw " + prefix + "x" + id + strV + Escape.escape(q.getVector(0)))
                   .append(" color red\n")
@@ -661,12 +637,8 @@
                   .append(" color green\n")
                   .append("draw " + prefix + "z" + id + strV + Escape.escape(q.getVector(2)))
                   .append(" color blue\n");            
-            pdbATOM.append(deg >= 0 
-                ? "draw " + prefix + "a" + id + strV + " {" + (x * 2)
-                  + "," + (y * 2) + "," + (z * 2) + "}" + " \">" + deg + "\""
-                : "draw " + prefix + "b" + id + strV + " {" + (-x * 2) 
-                  + "," + (-y * 2) + "," + (-z * 2) + "}" + " \">" + ndeg + "\""
-                )
+            pdbATOM.append("draw " + prefix + "a" + id + strV + " {" + (x * 2)
+                  + "," + (y * 2) + "," + (z * 2) + "}" + " \">" + deg + "\"")
             .append(" color ").append(qColor[derivType]).append('\n');
             continue;
           }
@@ -700,6 +672,7 @@
   }
   
   private static float getStraightness(String id, Quaternion dqprev, Quaternion dq) {
+    //System.out.println(id + " " + dqprev.getTheta() + " " + dq.getTheta());
     float f = (float) (Math.acos(dqprev.getNormal().dot(dq.getNormal()))/ Math.PI);
     return 1 - 2 * f;
   }

Modified: trunk/Jmol/src/org/jmol/shape/MeasuresRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/shape/MeasuresRenderer.java	2008-06-26 15:33:51 UTC (rev 9525)
+++ trunk/Jmol/src/org/jmol/shape/MeasuresRenderer.java	2008-06-27 02:07:03 UTC (rev 9526)
@@ -64,15 +64,11 @@
       if (colix == 0)
         colix = viewer.getColixBackgroundContrast();
       g3d.setColix(colix);
-      renderMeasurement(m);
+      renderMeasurement(m.getCount(), m, true);
     }
     renderPendingMeasurement(measures.pendingMeasurement);
   }
 
-  private void renderMeasurement(Measurement measurement) {
-    renderMeasurement(measurement.getCount(), measurement, true); 
-  }
-
   Point3fi atomA, atomB, atomC, atomD;
   
   private Point3fi getAtom(int i) {
@@ -251,7 +247,7 @@
     if (pendingMeasurement.getLastIndex() == -1)
       renderPendingWithCursor(pendingMeasurement);
     else
-      renderMeasurement(pendingMeasurement);
+      renderMeasurement(pendingMeasurement.getCount(), pendingMeasurement, true);
   }
   
   private void renderPendingWithCursor(MeasurementPending pendingMeasurement) {

Modified: trunk/Jmol/src/org/jmol/shapespecial/Draw.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapespecial/Draw.java	2008-06-26 15:33:51 UTC (rev 9525)
+++ trunk/Jmol/src/org/jmol/shapespecial/Draw.java	2008-06-27 02:07:03 UTC (rev 9526)
@@ -831,10 +831,11 @@
       return null;
     Point3f v = pickedMesh.vertices[pickedMesh.polygonIndexes[pickedModel][pickedVertex]];
     if (isDrawPicking && !isPickingMode) {
-      viewer.setStatusAtomPicked(-2, "[\"draw\",\"" + pickedMesh.thisID + "\"," +
+      if (modifiers != 0) // not mouseMove
+        viewer.setStatusAtomPicked(-2, "[\"draw\",\"" + pickedMesh.thisID + "\"," +
           + pickedModel + "," + pickedVertex + "," + v.x + "," + v.y + "," + v.z+"]"
-          + (pickedMesh.title == null ? "" :      
-            "\"" + pickedMesh.title[pickedModel]+"\""));
+          + (pickedMesh.title == null ? "" 
+               : "\"" + pickedMesh.title[pickedModel]+"\""));
       return v; 
     }
     if (modifiers == 0 || pickedMesh.polygonIndexes[pickedModel][0] == pickedMesh.polygonIndexes[pickedModel][1])

Modified: trunk/Jmol/src/org/jmol/util/Quaternion.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Quaternion.java	2008-06-26 15:33:51 UTC (rev 9525)
+++ trunk/Jmol/src/org/jmol/util/Quaternion.java	2008-06-27 02:07:03 UTC (rev 9526)
@@ -36,7 +36,19 @@
 /*
  * Standard UNIT quaternion math -- for rotation.
  * 
+ * All rotations can be represented as two identical quaternions. 
+ * This is because any rotation can be considered from either end of the
+ * rotational axis -- either as a + rotation or a - rotation. This code
+ * is designed to always maintain the quaternion with a rotation in the
+ * [0, PI) range. 
  * 
+ * This ensures that the reported theta is always positive, and the normal
+ * reported is always associated with a positive theta.  
+ * 
+ * By Bob Hanson, ha...@st... 6/2008
+ * 
+ * 
+ * 
  */
 
 
@@ -50,6 +62,7 @@
     this.q1 = q1;
     this.q2 = q2;
     this.q3 = q3;
+    fixQ();
   }
 
   public Quaternion(Point4f pt) {
@@ -62,7 +75,8 @@
     q1 = pt.x / factor;
     q2 = pt.y / factor;
     q3 = pt.z / factor;
-  }
+    fixQ();
+}
 
   public Quaternion(Tuple3f pt, float theta) {
     if (pt.x == 0 && pt.y == 0 && pt.z == 0) {
@@ -74,8 +88,19 @@
     q1 = pt.x * fact;
     q2 = pt.y * fact;
     q3 = pt.z * fact;
+    fixQ();
   }
   
+  private Quaternion fixQ() {
+    if (q0 < 0) {
+      q0 = -q0;
+      q1 = -q1;
+      q2 = -q2;
+      q3 = -q3;
+    }
+    return this;
+  }
+
   public Quaternion(Matrix3f mat) {
 
     /*
@@ -92,44 +117,37 @@
 
     float tr = mat.m00 + mat.m11 + mat.m22; /* Matrix trace */
     float s;
+    float[] q = new float[4];
     if (tr > 0) {
       s = (float) Math.sqrt(tr + 1);
       q0 = 0.5f * s;
       s = 0.5f / s;
-      q1 = (mat.m12 - mat.m21) * s;
-      q2 = (mat.m20 - mat.m02) * s;
-      q3 = (mat.m01 - mat.m10) * s;
-      
-      q1 = -q1;
-      q2 = -q2;
-      q3 = -q3;
-      
+      q1 = (mat.m21 - mat.m12) * s;
+      q2 = (mat.m02 - mat.m20) * s;
+      q3 = (mat.m10 - mat.m01) * s;
     } else {
       float[][] m = new float[][] { new float[3], new float[3], new float[3] };
       mat.getRow(0, m[0]);
       mat.getRow(1, m[1]);
       mat.getRow(2, m[2]);
 
-      /* Find out the bigger element from diagonal */
+      /* Find out the biggest element along the diagonal */
       float max = Math.max(mat.m11, mat.m00);
-      int i = (max == mat.m00 ? 0 : mat.m22 > max ? 2 : 1);
+      int i = (mat.m22 > max ? 2 : max == mat.m11 ? 1 : 0);
       int j = (i + 1) % 3;
       int k = (j + 1) % 3;
-      s = (float) Math.sqrt((m[i][i] - (m[j][j] + m[k][k])) + 1);
-      float[] q = new float[4];
+      s = -(float) Math.sqrt((m[i][i] - (m[j][j] + m[k][k])) + 1);
       q[i] = s * 0.5f;
       if (s != 0)
         s = 0.5f / s;
       q[j] = (m[i][j] + m[j][i]) * s;
       q[k] = (m[i][k] + m[k][i]) * s;
-      q[3] = (m[j][k] - m[k][j]) * s;
-
-      q1 = -q[0];  // x
-      q2 = -q[1];  // y
-      q3 = -q[2];  // z  
-      q0 = q[3];  // w
-
+      q0 = (m[k][j] - m[j][k]) * s;
+      q1 = q[0];  // x
+      q2 = q[1];  // y
+      q3 = q[2];  // z  
     }
+    fixQ();
   }
   
   public static final Quaternion getQuaternionFrame(Vector3f vA, Vector3f vB, Vector3f vC) {
@@ -243,6 +261,7 @@
   }
   
   public String toString() {
+    fixQ();
     return "{" + q0 + " " + q1 + " " + q2 + " " + q3 + "}";
   }
   
@@ -255,16 +274,19 @@
   }
   
   public Vector3f getNormal() {
+    fixQ();
     Vector3f v = new Vector3f(q1, q2, q3);
     v.normalize();
     return v;
   }
   
   public float getTheta() {
+    fixQ();
     return (float) (Math.acos(q0) * 2 * 180/Math.PI);  
   }
   
   public Point4f toPoint4f() {
+    fixQ();
     return new Point4f(q1, q2, q3, q0);
   }
   
@@ -284,4 +306,4 @@
     return vNew;
   }
 
-}
+}
\ No newline at end of file

Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java	2008-06-26 15:33:51 UTC (rev 9525)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java	2008-06-27 02:07:03 UTC (rev 9526)
@@ -4547,7 +4547,7 @@
           + "select visible; wireframe 0; "
           + "isosurface quatSphere" + modelCount
           + " resolution 1.0 sphere 10.0 mesh nofill translucent 0.8;set rotationRadius 12;"
-          + (isDerivative ? "color structure" : "trace 0.1; color trace structure;");
+          + "color structure";
       break;
     }
     runScript(script);
@@ -9148,7 +9148,7 @@
     case Token.structure:
       if ((len = statementLength) == 2) {
         if (!isSyntaxCheck)
-          msg = viewer.getStructureState();
+          msg = viewer.getProteinStructureState();
         break;
       }
       String shape = parameterAsString(2);

Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2008-06-26 15:33:51 UTC (rev 9525)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2008-06-27 02:07:03 UTC (rev 9526)
@@ -3,6 +3,9 @@
 
 version=11.5.43_dev
 
+# bug fix: quaternion definition with dot-product check not effective -- removed
+# bug fix: quaternion construction from matrix error
+#
 # new feature: _applet boolean
 #
 # new feature: extended quaternion math
@@ -64,7 +67,10 @@
 # experimental: "straightness" defined as 1 - 2 * acos(normal(dq[i]%-1) dot normal(dq[i+1])) / PI
 # giving a measure proportional to the difference in local helical axis angle 
 # and ranging from -1 (opposite direction) to 1 (same direction) for proteins 
-# -- a work in progress.
+# -- a work in progress. See
+#
+#   load =1d66
+#   calculate straightness;color straightness
 #  
 # -----------------------------------------------------------------------------
 #

Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java	2008-06-26 15:33:51 UTC (rev 9525)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java	2008-06-27 02:07:03 UTC (rev 9526)
@@ -2525,6 +2525,10 @@
     return modelSet.getState(null, false);
   }
 
+  String getProteinStructureState() {
+    return modelSet.getProteinStructureState(selectionManager.bsSelection, false);
+  }
+
   public String getCoordinateState(BitSet bsSelected) {
     return modelSet.getAtomicPropertyState(AtomCollection.TAINT_COORD, bsSelected);
   }
@@ -6737,4 +6741,5 @@
   void setQuaternionFrame(String qType) {
     global.quaternionFrame = "" + (qType.toLowerCase()+"c").charAt(0);
   }
+
 }


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

Revision: 9525
          http://jmol.svn.sourceforge.net/jmol/?rev=9525&view=rev
Author:   hansonr
Date:     2008-06-26 08:33:51 -0700 (Thu, 26 Jun 2008)

Log Message:
-----------
version=11.5.43_dev quaternions, mostly

# new feature: _applet boolean
#
# new feature: extended quaternion math
#
#   q = quaternion({x y z}, angleDegrees)
#   q = quaternion(q0, q1, q2,q3)
#   q = {qx, qy, qz, qw}
#
# returning component values: 
#
#   q.x, q.y, q.z, q.w
#
# note that the Point4f equivalent stores w LAST, even though it is "q0" 
# because the Java Quat4f() and Point4f() both do that as well. We're just
# being consistent with other Java use.
#
# Modulus operator for extended information retrieval:
#
#   (q%0) -- q0 (w)
#   (q%1) -- q1 (x)
#   (q%2) -- q2 (y)
#   (q%3) -- q3 (z)
#   (q%-1) -- the vector {q1, q2, q3}
#   (q%-2) -- theta
#   (q%-3) -- equivalent rotational frame X-axis 
#   (q%-4) -- equivalent rotational frame Y-axis 
#   (q%-5) -- equivalent rotational frame Z-axis 
#   (q%{x y z})  -- rotational transform of a point or vector based on a quaternion
#
# thus, for example, (q%{1 0 0}) is the same as (q%-3)
#
#   (!q) -- quaternion inverse
#
# 
# Quaternion right division (difference "dq"):
#
#   q2 / q1 = q2 * (!q1)
#
# Quaternion left division (relative difference n):
#
#   q2 \ q1 = (!q1) * q2
#
# Examples:
#
#   q = quaternion({1 1 1},120)
#   print "" + (q%{1 0 0}) + " " + (q%{0 1 0}) + " " + (q%{0 0 1})    
#
#   {0 1.0 0} {0 0 1.0} {1.0 0 0}
#
# new feature: Numerical left division (integer divide)
#
#   3.6 \ 2 = 1
#   3.6 \ 1.3 = 2
#
# new feature: sqrt(x)
#
# bug fix: load trajectory for cases with different atom counts.
#
# experimental: "straightness" defined as 1 - 2 * acos(normal(dq[i]%-1) dot normal(dq[i+1])) / PI
# giving a measure proportional to the difference in local helical axis angle 
# and ranging from -1 (opposite direction) to 1 (same direction) for proteins 
# -- a work in progress.
#  

Modified Paths:
--------------
    trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java
    trunk/Jmol/src/org/jmol/util/Quaternion.java
    trunk/Jmol/src/org/jmol/viewer/Compiler.java
    trunk/Jmol/src/org/jmol/viewer/Eval.java
    trunk/Jmol/src/org/jmol/viewer/Jmol.properties
    trunk/Jmol/src/org/jmol/viewer/Token.java

Modified: trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java	2008-06-25 19:55:12 UTC (rev 9524)
+++ trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java	2008-06-26 15:33:51 UTC (rev 9525)
@@ -700,9 +700,8 @@
   }
   
   private static float getStraightness(String id, Quaternion dqprev, Quaternion dq) {
-    float f = Math.abs(dqprev.getNormal().dot(dq.getNormal()));
-    //System.out.println(id + " " + f + " " + dqprev.getNormal() + " " + dq.getNormal());
-    return (2 * f - 1);
+    float f = (float) (Math.acos(dqprev.getNormal().dot(dq.getNormal()))/ Math.PI);
+    return 1 - 2 * f;
   }
 
   Quaternion getQuaternion(int m, char qtype) {

Modified: trunk/Jmol/src/org/jmol/util/Quaternion.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Quaternion.java	2008-06-25 19:55:12 UTC (rev 9524)
+++ trunk/Jmol/src/org/jmol/util/Quaternion.java	2008-06-26 15:33:51 UTC (rev 9525)
@@ -33,12 +33,19 @@
 //import javax.vecmath.Point3f;
 //import javax.vecmath.Quat4f;
 
+/*
+ * Standard UNIT quaternion math -- for rotation.
+ * 
+ * 
+ */
+
+
 public class Quaternion {
   public float q0, q1, q2, q3;
 
   public Matrix3f mat;
   // create a new object with the given components
-  public Quaternion(float q0, float q1, float q2, float q3) {
+  private Quaternion(float q0, float q1, float q2, float q3) {
     this.q0 = q0;
     this.q1 = q1;
     this.q2 = q2;
@@ -46,10 +53,15 @@
   }
 
   public Quaternion(Point4f pt) {
-    q0 = pt.w;
-    q1 = pt.x;
-    q2 = pt.y;
-    q3 = pt.z;
+    float factor = pt.distance(new Point4f(0,0,0,0));
+    if (factor == 0) {
+      q0 = 1;
+      return;
+    }
+    q0 = pt.w / factor;
+    q1 = pt.x / factor;
+    q2 = pt.y / factor;
+    q3 = pt.z / factor;
   }
 
   public Quaternion(Tuple3f pt, float theta) {
@@ -191,8 +203,16 @@
     mat.m22 = q0 * q0 - q1 * q1 - q2 * q2 + q3 * q3;
   }
   
+  public Quaternion add(float x) {
+    // UNIT addition 
+    return new Quaternion(getNormal(), getTheta() + x);
+  }
+
   public Quaternion mul(float x) {
-    return new Quaternion(q0 * x, q1 * x, q2 * x, q3 * x);
+    // UNIT multiplication
+    if (x == 1 || x == -1)
+      return new Quaternion(q0 * x, q1 * x, q2 * x, q3 * x);
+    return new Quaternion(getNormal(), getTheta() * x);
   }
   
   public Quaternion mul(Quaternion p) {
@@ -204,6 +224,16 @@
         );
   }
   
+  public Quaternion div(Quaternion p) {
+    // unit quaternions assumed -- otherwise would scale by 1/p.dot(p)
+    return mul(p.inv());
+  }
+  
+  public Quaternion divLeft(Quaternion p) {
+    // unit quaternions assumed -- otherwise would scale by 1/p.dot(p)
+    return p.inv().mul(this);
+  }
+  
   public float dot(Quaternion q) {
     return this.q0*q.q0 + this.q1*q.q1 + this.q2*q.q2 + this.q3*q.q3;
   }

Modified: trunk/Jmol/src/org/jmol/viewer/Compiler.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Compiler.java	2008-06-25 19:55:12 UTC (rev 9524)
+++ trunk/Jmol/src/org/jmol/viewer/Compiler.java	2008-06-26 15:33:51 UTC (rev 9525)
@@ -1359,6 +1359,7 @@
     case '%':
     case '[':
     case ']':
+    case '\\':  // leftdivide
     break;
     case '&':
     case '|':

Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java	2008-06-25 19:55:12 UTC (rev 9524)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java	2008-06-26 15:33:51 UTC (rev 9525)
@@ -12304,10 +12304,11 @@
           return false;
         if (isSyntaxCheck)
           return addX(new Point4f(0, 0, 0, 1));
-        return addX(args.length == 4 ? new Point4f(Token.fValue(args[0]), Token
-            .fValue(args[1]), Token.fValue(args[2]), Token.fValue(args[3]))
-            : (new Quaternion((Point3f) args[0].value, Token.fValue(args[1]))
-                .toPoint4f()));
+        return addX(args.length == 4 ? (new Quaternion(new Point4f(
+            Token.fValue(args[1]), Token.fValue(args[2]),
+            Token.fValue(args[3]),Token.fValue(args[0])))).toPoint4f() 
+            : (new Quaternion(
+            (Point3f) args[0].value, Token.fValue(args[1])).toPoint4f()));
       }
       if (args.length != 1)
         return false;
@@ -12637,15 +12638,13 @@
       if (x2.tok == Token.list)
         x2 = Token.selectItem(x2);
 
-      if (op.tok == Token.opNot) 
-        return (isScriptCheck ? addX(true)
-            : x2.tok == Token.point4f ? // quaternion
-                addX((new Quaternion((Point4f) x2.value)).inv().toPoint4f())                
-            : x2.tok == Token.bitset ? 
-              addX(BitSetUtil.copyInvert(Token.bsSelect(x2), 
-                (x2.value instanceof BondSet ? viewer.getBondCount() 
-                    : viewer.getAtomCount()))) 
-            : addX(!Token.bValue(x2)));
+      if (op.tok == Token.opNot)
+        return (isScriptCheck ? addX(true) : x2.tok == Token.point4f ? // quaternion
+            addX((new Quaternion((Point4f) x2.value)).inv().toPoint4f())
+            : x2.tok == Token.bitset ? addX(BitSetUtil.copyInvert(Token
+                .bsSelect(x2), (x2.value instanceof BondSet ? viewer
+                .getBondCount() : viewer.getAtomCount()))) : addX(!Token
+                .bValue(x2)));
       int iv = op.intValue & ~Token.minmaxmask;
       if (op.tok == Token.propselector) {
         switch (iv) {
@@ -12743,29 +12742,34 @@
       case Token.plus:
         if (x1.tok == Token.list || x2.tok == Token.list)
           return addX(Token.concatList(x1, x2));
-        if (x1.tok == Token.string)
+        switch (x1.tok) {
+        default:
+          return addX(Token.fValue(x1) + Token.fValue(x2));
+        case Token.string:
           return addX(Token.sValue(x1) + Token.sValue(x2));
-        if (x1.tok == Token.string && x2.tok == Token.integer) {
-          if ((s = (Token.sValue(x1)).trim()).indexOf(".") < 0
-              && s.indexOf("+") <= 0 && s.lastIndexOf("-") <= 0)
-            return addX(Token.iValue(x1) + x2.intValue);
-        }
-        if (x1.tok == Token.integer) {
+        case Token.point4f:
+          Quaternion q1 = new Quaternion((Point4f) x1.value);
+          switch (x2.tok) {
+          default:
+            return addX(q1.add(Token.fValue(x2)).toPoint4f());
+          case Token.point4f:
+            return addX(q1.mul(new Quaternion((Point4f) x2.value)).toPoint4f());
+          }
+        case 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));
-        }
-        if (x1.tok == Token.point3f) {
+        case Token.point3f:
           Point3f pt = new Point3f((Point3f) x1.value);
           switch (x2.tok) {
           case Token.point3f:
             pt.add((Point3f) x2.value);
             return addX(pt);
           case Token.point4f:
-           //extract {xyz}
+            //extract {xyz}
             Point4f pt4 = (Point4f) x2.value;
             pt.add(new Point3f(pt4.x, pt4.y, pt4.z));
             return addX(pt);
@@ -12774,7 +12778,6 @@
             return addX(new Point3f(pt.x + f, pt.y + f, pt.z + f));
           }
         }
-        return addX(Token.fValue(x1) + Token.fValue(x2));
       case Token.minus:
         if (x1.tok == Token.integer) {
           if (x2.tok == Token.string) {
@@ -12789,34 +12792,38 @@
               && s.indexOf("+") <= 0 && s.lastIndexOf("-") <= 0)
             return addX(Token.iValue(x1) - x2.intValue);
         }
-        if (x1.tok == Token.integer && x2.tok == Token.integer)
-          return addX(x1.intValue - Token.iValue(x2));
-        if (x1.tok == Token.point3f) {
+        switch (x1.tok) {
+        default:
+          return addX(Token.fValue(x1) - Token.fValue(x2));
+        case Token.point3f:
           Point3f pt = new Point3f((Point3f) x1.value);
           switch (x2.tok) {
+          default:
+            float f = Token.fValue(x2);
+            return addX(new Point3f(pt.x - f, pt.y - f, pt.z - f));
           case Token.point3f:
             pt.sub((Point3f) x2.value);
             return addX(pt);
           case Token.point4f:
             //extract {xyz}
-             Point4f pt4 = (Point4f) x2.value;
-             pt.sub(new Point3f(pt4.x, pt4.y, pt4.z));
-             return addX(pt);
+            Point4f pt4 = (Point4f) x2.value;
+            pt.sub(new Point3f(pt4.x, pt4.y, pt4.z));
+            return addX(pt);
+          }
+        case Token.point4f:
+          Quaternion q1 = new Quaternion((Point4f) x1.value);
+          switch (x2.tok) {
           default:
-            float f = Token.fValue(x2);
-            return addX(new Point3f(pt.x - f, pt.y - f, pt.z - f));
-          }
-        }
-        if (x1.tok == Token.point4f) {
-          if (x2.tok == Token.point4f) {
-            Quaternion q1 = new Quaternion((Point4f)x1.value);
-            Quaternion q2 = new Quaternion((Point4f)x2.value);
+            return addX(q1.add(-Token.fValue(x2)).toPoint4f());
+          case Token.point4f:
+            Quaternion q2 = new Quaternion((Point4f) x2.value);
             return addX(q2.mul(q1.inv()).toPoint4f());
           }
         }
-        return addX(Token.fValue(x1) - Token.fValue(x2));
       case Token.unaryMinus:
         switch (x2.tok) {
+        default:
+          return addX(-Token.fValue(x2));
         case Token.integer:
           return addX(-Token.iValue(x2));
         case Token.point3f:
@@ -12828,14 +12835,17 @@
           plane.scale(-1f);
           return addX(plane);
         case Token.bitset:
-          return addX(BitSetUtil.copyInvert(Token.bsSelect(x2), 
-              (x2.value instanceof BondSet ? viewer.getBondCount() : viewer.getAtomCount())));
+          return addX(BitSetUtil.copyInvert(Token.bsSelect(x2),
+              (x2.value instanceof BondSet ? viewer.getBondCount() : viewer
+                  .getAtomCount())));
         }
-        return addX(-Token.fValue(x2));
       case Token.times:
         if (x1.tok == Token.integer && x2.tok != Token.decimal)
           return addX(x1.intValue * Token.iValue(x2));
-        if (x1.tok == Token.point3f) {
+        switch (x1.tok) {
+        default:
+          return addX(Token.fValue(x1) * Token.fValue(x2));
+        case Token.point3f:
           Point3f pt = new Point3f((Point3f) x1.value);
           switch (x2.tok) {
           case Token.point3f:
@@ -12845,17 +12855,19 @@
             float f = Token.fValue(x2);
             return addX(new Point3f(pt.x * f, pt.y * f, pt.z * f));
           }
+        case Token.point4f:
+          if (x2.tok == Token.point4f) {
+            //quaternion multiplication
+            // note that Point4f is {x,y,z,w} so we use that for
+            // quaternion notation as well here.
+            Quaternion q1 = new Quaternion((Point4f) x1.value);
+            Quaternion q = new Quaternion((Point4f) x2.value);
+            q = q1.mul(q);
+            return addX(new Point4f(q.q1, q.q2, q.q3, q.q0));
+          }
+          return addX(new Quaternion((Point4f) x1.value).mul(Token.fValue(x2))
+              .toPoint4f());
         }
-        if (x1.tok == Token.point4f && x2.tok == Token.point4f) {
-          //quaternion multiplication
-          // note that Point4f is {x,y,z,w} so we use that for
-          // quaternion notation as well here. 
-          Quaternion q1 = new Quaternion((Point4f)x1.value);
-          Quaternion q = new Quaternion((Point4f)x2.value);
-          q = q1.mul(q);
-          return addX(new Point4f(q.q1, q.q2, q.q3, q.q0));
-        }
-        return addX(Token.fValue(x1) * Token.fValue(x2));
       case Token.percent:
         // more than just modulus
 
@@ -12875,6 +12887,7 @@
         case Token.on:
         case Token.off:
         case Token.integer:
+        default:
           if (n == 0)
             return addX((int) 0);
           return addX(Token.iValue(x1) % n);
@@ -12911,8 +12924,8 @@
         case Token.point4f:
           Point4f q = (Point4f) x1.value;
           if (x2.tok == Token.point3f)
-            return addX((new Quaternion(q)).transform((Point3f)x2.value));
-          switch(n) {
+            return addX((new Quaternion(q)).transform((Point3f) x2.value));
+          switch (n) {
           case 0:
             return addX(q.w);
           case 1:
@@ -12941,20 +12954,43 @@
         if (x1.tok == Token.integer && x2.tok == Token.integer
             && x2.intValue != 0)
           return addX(x1.intValue / x2.intValue);
-        if (x1.tok == Token.point3f) {
+        float f2 = Token.fValue(x2);
+        switch (x1.tok) {
+        default:
+          float f1 = Token.fValue(x1);
+          if (f2 == 0)
+            return addX(f1 == 0 ? 0f : f1 < 0 ? Float.POSITIVE_INFINITY
+                : Float.POSITIVE_INFINITY);
+          return addX(f1 / f2);
+        case Token.point3f:
           Point3f pt = new Point3f((Point3f) x1.value);
-          float f = Token.fValue(x2);
-          if (f == 0)
+          if (f2 == 0)
             return addX(new Point3f(Float.NaN, Float.NaN, Float.NaN));
-          return addX(new Point3f(pt.x / f, pt.y / f, pt.z / f));
+          return addX(new Point3f(pt.x / f2, pt.y / f2, pt.z / f2));
+        case Token.point4f:
+          if (f2 == 0)
+            return addX(new Point4f(Float.NaN, Float.NaN, Float.NaN, Float.NaN));
+          if (x2.tok == Token.point4f)
+            return addX(new Quaternion((Point4f) x1.value).div(
+                new Quaternion((Point4f) x2.value)).toPoint4f());
+          return addX(new Quaternion((Point4f) x1.value).mul(1 / f2)
+              .toPoint4f());
         }
-        float f1 = Token.fValue(x1);
-        float f2 = Token.fValue(x2);
-        if (f2 == 0)
-          return addX(f1 == 0 ? 0f : f1 < 0 ? Float.POSITIVE_INFINITY
-              : Float.POSITIVE_INFINITY);
-        return addX(f1 / f2);
+    case Token.leftdivide:
+      float f = Token.fValue(x2);
+      switch (x1.tok) {
+      default:
+        return addX(f == 0 ? 0 : (int) (Token.fValue(x1) / Token.fValue(x2)));
+      case Token.point4f:
+        if (f == 0)
+          return addX(new Point4f(Float.NaN, Float.NaN, Float.NaN, Float.NaN));
+        if (x2.tok == Token.point4f)
+          return addX(new Quaternion((Point4f) x1.value).divLeft(
+              new Quaternion((Point4f) x2.value)).toPoint4f());
+        return addX(new Quaternion((Point4f) x1.value).mul(1 / f)
+            .toPoint4f());
       }
+    }
       return true;
     }
 

Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2008-06-25 19:55:12 UTC (rev 9524)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2008-06-26 15:33:51 UTC (rev 9525)
@@ -3,9 +3,12 @@
 
 version=11.5.43_dev
 
+# new feature: _applet boolean
+#
 # new feature: extended quaternion math
 #
 #   q = quaternion({x y z}, angleDegrees)
+#   q = quaternion(q0, q1, q2,q3)
 #   q = {qx, qy, qz, qw}
 #
 # returning component values: 
@@ -32,14 +35,15 @@
 # thus, for example, (q%{1 0 0}) is the same as (q%-3)
 #
 #   (!q) -- quaternion inverse
+#
 # 
-# Quaternion difference "dq":
+# Quaternion right division (difference "dq"):
 #
-#   q2 * (!q1)
+#   q2 / q1 = q2 * (!q1)
 #
-# Quaternion relative difference:
+# Quaternion left division (relative difference n):
 #
-#   (!q1) * q2
+#   q2 \ q1 = (!q1) * q2
 #
 # Examples:
 #
@@ -48,10 +52,22 @@
 #
 #   {0 1.0 0} {0 0 1.0} {1.0 0 0}
 #
+# new feature: Numerical left division (integer divide)
 #
+#   3.6 \ 2 = 1
+#   3.6 \ 1.3 = 2
+#
+# new feature: sqrt(x)
+#
 # bug fix: load trajectory for cases with different atom counts.
 #
+# experimental: "straightness" defined as 1 - 2 * acos(normal(dq[i]%-1) dot normal(dq[i+1])) / PI
+# giving a measure proportional to the difference in local helical axis angle 
+# and ranging from -1 (opposite direction) to 1 (same direction) for proteins 
+# -- a work in progress.
+#  
 # -----------------------------------------------------------------------------
+#
 
 #version=11.5.42
 
@@ -154,7 +170,7 @@
 # (with corrected 40_dev draw scale)
 # new feature: new command:
 #
-# selectx {atomExpression} booleanEvaluation
+# selectX {atomExpression} booleanEvaluation
 #
 #   same as select() function, but simpler to implement   
 #
@@ -163,8 +179,10 @@
 #
 #   select(x;{atomexpression};booleanEvaluation)
 #
-#  for example:
+# for example:
+#
 #  x = select(x;{*};x.distance({atomno=3}) / 3 > x.distance({atomno=2}))
+#  x = select(x;{*.ca};x.phi < select(y; {*.ca}; y.resno = x.resno + 1).phi)
 #
 # bug fix: H1 and H3 in DNA are NOT backbone 
 # new feature: quaternion derivative2 (2nd derivative) and quaternion e derivative [experimental]

Modified: trunk/Jmol/src/org/jmol/viewer/Token.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Token.java	2008-06-25 19:55:12 UTC (rev 9524)
+++ trunk/Jmol/src/org/jmol/viewer/Token.java	2008-06-26 15:33:51 UTC (rev 9525)
@@ -364,6 +364,7 @@
   final static int divide       = 0  | mathop | 8 << 3;
   final static int times        = 1  | mathop | 8 << 3;
   final static int percent      = 2  | mathop | 8 << 3;
+  final static int leftdivide   = 3  | mathop | 8 << 3;  //   quaternion1 \ quaternion2
   
   final static int unaryMinus   = 0  | mathop | 9 << 3;
   
@@ -484,7 +485,6 @@
   final static int random       = 1  | 2 << 3 | mathfunc;
   final static int data         = 2  | 2 << 3 | mathfunc | command;
   final static int cross        = 3  | 2 << 3 | mathfunc;
-  final static int quaternion   = 4  | 2 << 3 | mathfunc | command;
 
   // ___.xxx(a,b)
 
@@ -506,6 +506,7 @@
   final static int angle        = 1  | 4 << 3 | mathfunc;
   final static int plane        = 2  | 4 << 3 | mathfunc | specialstring; //may appear as string alone
   final static int point        = 3  | 4 << 3 | mathfunc;
+  final static int quaternion   = 4  | 4 << 3 | mathfunc | command;
 
   // xxx(a,b,c,d,e)
   
@@ -1227,6 +1228,7 @@
     "-",            tokenMinus,
     "*",            tokenTimes,
     "/",            tokenDivide,
+    "\\",           new Token(leftdivide),
 
     // misc
         


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

Revision: 9524
          http://jmol.svn.sourceforge.net/jmol/?rev=9524&view=rev
Author:   nicove
Date:     2008-06-25 12:55:12 -0700 (Wed, 25 Jun 2008)

Log Message:
-----------
Folding@Home

Added Paths:
-----------
    trunk/Jmol-FAH/projects/p4570.xyz.gz
    trunk/Jmol-FAH/projects/p4571.xyz.gz
    trunk/Jmol-FAH/projects/p4572.xyz.gz
    trunk/Jmol-FAH/projects/p4574.xyz.gz
    trunk/Jmol-FAH/projects/p4578.xyz.gz

Added: trunk/Jmol-FAH/projects/p4570.xyz.gz
===================================================================
(Binary files differ)


Property changes on: trunk/Jmol-FAH/projects/p4570.xyz.gz
___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream

Added: trunk/Jmol-FAH/projects/p4571.xyz.gz
===================================================================
(Binary files differ)


Property changes on: trunk/Jmol-FAH/projects/p4571.xyz.gz
___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream

Added: trunk/Jmol-FAH/projects/p4572.xyz.gz
===================================================================
(Binary files differ)


Property changes on: trunk/Jmol-FAH/projects/p4572.xyz.gz
___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream

Added: trunk/Jmol-FAH/projects/p4574.xyz.gz
===================================================================
(Binary files differ)


Property changes on: trunk/Jmol-FAH/projects/p4574.xyz.gz
___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream

Added: trunk/Jmol-FAH/projects/p4578.xyz.gz
===================================================================
(Binary files differ)


Property changes on: trunk/Jmol-FAH/projects/p4578.xyz.gz
___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream


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

Revision: 9523
          http://jmol.svn.sourceforge.net/jmol/?rev=9523&view=rev
Author:   nicove
Date:     2008-06-25 10:54:50 -0700 (Wed, 25 Jun 2008)

Log Message:
-----------
Folding@Home

Modified Paths:
--------------
    trunk/Jmol-web/cache.properties
    trunk/Jmol-web/source/doc/fah/fah-projects.xml

Modified: trunk/Jmol-web/cache.properties
===================================================================
--- trunk/Jmol-web/cache.properties	2008-06-25 17:43:51 UTC (rev 9522)
+++ trunk/Jmol-web/cache.properties	2008-06-25 17:54:50 UTC (rev 9523)
@@ -239,23 +239,23 @@
 download/index.fr.html=501a49c1d17b64265c6b57ea12d59c79
 download/index.nl.html=2b51aa4ac32868a75dbbf40e37929b56
 fah/FAHlogoButton.jpg=7c3af4cc2f5a35c1a063ae8115e1dc4f
-fah/availableProjects.txt=bb83652a11c38eb3606dda7fc2d72d07
-fah/createProjectList.js=f6aacf825728b545700887c579a76bae
-fah/fah-projects.xml=ee9b782ff6b8daefbfd5c48c31710a18
+fah/availableProjects.txt=22cc8f1e751dbdd7c90489fb5f482e75
+fah/createProjectList.js=e5b42c1c87bdc06ae5ce76ec85122c8f
+fah/fah-projects.xml=89230e061b63fa36c02ccea84f986bd3
 fah/fah-projects.xsd=d989d0314017e1e2c609616a0f478956
 fah/fah.js=901f9e1bd08cca13ebbdbc48c1f5bef5
-fah/index.de.html=59f150eea73e76b68f63cf1bba83b8a5
-fah/index.en.html=68bdba51969efe362912bf4a2d7969b8
-fah/index.es.html=dec6dafe7c433471c8a34e638ff63ee0
-fah/index.et.html=bbed8648d0ccba2881b41aa4ddb42ca1
-fah/index.fr.html=bea569b69720df9d6107441f92108f38
-fah/index.hu.html=0f3b4081756c37ed23ae7f99b2663ba7
-fah/index.it.html=1c44d57eecb865245e616c48aa9689f2
-fah/index.nl.html=156729fa3c74b7d63e6fb44499db1ece
-fah/index.pt.html=ac062c97c10af1e3ebbf66d53c58a58f
-fah/index.pt_BR.html=e5eec6c334b2a18f8a655bd2513bcaa9
-fah/index.ro.html=a6eb9348416b356846fdae502c306fe9
-fah/missingProjects.txt=c3ce4c90c23d8f672aaefb2f6af61b24
+fah/index.de.html=08c2f8a1b5880243818458fe1b0ad062
+fah/index.en.html=cb6bf12a80943846d251375c7534b425
+fah/index.es.html=85fee63e1ab7ebdcb29cc6280f91b4b0
+fah/index.et.html=c9157ee54a5be172b98943d7bda87f98
+fah/index.fr.html=e8bd7e141483b34f03f713071d2e2b8d
+fah/index.hu.html=0d35751ec73ca642f032798106df409b
+fah/index.it.html=6f6c0bd33ed7f7f152b05cae137a76e6
+fah/index.nl.html=915895d88966587019447f0fe6a7d260
+fah/index.pt.html=06f3c95aab97b5f5cbc3b58b71e5b9fa
+fah/index.pt_BR.html=fccb465dee10903da40f75fbe3b10093
+fah/index.ro.html=1e6c0bc09f48e9554f5fd1e28141a730
+fah/missingProjects.txt=8752aa1ca6e85e205fc2cee8e695b456
 fah/projects/Jmol_translation.zip=f05e7804b12274e58299bd1ae4fecae0
 fah/projects/p1001.xyz.gz=f092439792dc8f05d1e143264bdd14ee
 fah/projects/p1002.xyz.gz=9327be24296aa7f57a644d2818e3adfd
@@ -932,6 +932,7 @@
 fah/projects/p2169.xyz.gz=977aa3b87d8430afa7cb6c24452e5f40
 fah/projects/p217.xyz.gz=e1aaa13d78f90a7c882cf8114cb16c87
 fah/projects/p2170.xyz.gz=78340ca35d4d1dff0c6d48ee362c20c4
+fah/projects/p2171.xyz.gz=969ccda502d6074dc84d598e0cee17b3
 fah/projects/p218.xyz.gz=75eef3a8804bc47ceeda07c4e1eb040b
 fah/projects/p219.xyz.gz=c2e4c58828dad26254679641712ef6eb
 fah/projects/p220.xyz.gz=ee6b551db7a6a4d1eccb3f515c19d350
@@ -1093,6 +1094,8 @@
 fah/projects/p2588.xyz.gz=fbc2dd05c1a16fe93f6e4ff7b68efbc5
 fah/projects/p2589.xyz.gz=c4d5a0a7b0e10a1f805da70efc87eae1
 fah/projects/p259.xyz.gz=fe41226cb0bf5227a2f1d28161e7d1f9
+fah/projects/p2590.xyz.gz=6f19e07d49d6fb4ae085d6c1dee0d1b6
+fah/projects/p2592.xyz.gz=99d22203a6b54cf08ab5a0566f7b7fb1
 fah/projects/p260.xyz.gz=b5ce97604e247680bec8de79da1eade5
 fah/projects/p2602.xyz.gz=5aea4babe634e85a50550bb9f0030c7c
 fah/projects/p2603.xyz.gz=925c5d2704e7311d4a5ea3c56910e317
@@ -1476,9 +1479,31 @@
 fah/projects/p4549.xyz.gz=b204fffc1fc4e7134f8671a228f050b6
 fah/projects/p4550.xyz.gz=0ecfb8499b812e5f153765d249480835
 fah/projects/p4551.xyz.gz=9caba3f323e9c7b3081d97bea2f30ee9
+fah/projects/p4552.xyz.gz=b171df4067bffe79e79f19cd0ec0c796
+fah/projects/p4553.xyz.gz=8e18e1bfa7c013124e2d0fd145917124
+fah/projects/p4554.xyz.gz=7357d4e00ce728577c7c32ca7f2760d3
+fah/projects/p4555.xyz.gz=5324e3ebb45f5fb8441be6918e8be314
+fah/projects/p4556.xyz.gz=b3f7675a3f2e8cdd64555ea000b12745
+fah/projects/p4557.xyz.gz=f47fbfba666598346f93f3b1929e0372
+fah/projects/p4558.xyz.gz=554869e7a15dee6d31850f2190f6a64b
+fah/projects/p4559.xyz.gz=7533004a1165670c12305c33d5ce81f7
+fah/projects/p4560.xyz.gz=fbef37881af2128513b4fa6de4264216
+fah/projects/p4561.xyz.gz=777b2cb7e480264c44fc2ab4781198ff
+fah/projects/p4562.xyz.gz=cc09234d0f49be29750a08d3c8eda07a
+fah/projects/p4563.xyz.gz=e6da9eab0de814bf5a8b95e8223f5882
+fah/projects/p4564.xyz.gz=1cc1751de55616548d61c82e31362c09
+fah/projects/p4565.xyz.gz=83624c5577e0229ea0c5666561f0af03
+fah/projects/p4566.xyz.gz=b7354f9cde2149d5e091d6f9a799b518
+fah/projects/p4567.xyz.gz=38b9f6cbf8f1afee9acda07c96fc7f54
+fah/projects/p4568.xyz.gz=33aea13b2cf586bd1519bd42bc64b41c
+fah/projects/p4569.xyz.gz=4207fb74058b6cb41a6128f661f939d4
+fah/projects/p4573.xyz.gz=0a658a7f088ad15a7f9d6fadafab9553
+fah/projects/p4575.xyz.gz=ac0d0e880874573ff215d9136753049a
+fah/projects/p4576.xyz.gz=3096bca1c20d107ca2ee86bbafdd4f7e
 fah/projects/p501.xyz.gz=09c6eb4ff9f727fdc6fad87d3c05ad64
 fah/projects/p506.xyz.gz=fcaa3a6b6c6733f9344be3de7ab07a09
 fah/projects/p507.xyz.gz=56fa33e680c4bc668f7e8fafe8b11ffe
+fah/projects/p5101.xyz.gz=1853a92fb818527d8ccd2ebff54a9512
 fah/projects/p513.xyz.gz=a1b7bd21244ff7fbbbdc4ae6f4fe4b42
 fah/projects/p515.xyz.gz=18a05cce9f49037ec7ddc5b8feddca0f
 fah/projects/p516.xyz.gz=e79397a8c44933b1e56f7dd7c318e39b
@@ -1667,6 +1692,12 @@
 fah/projects/p775.xyz.gz=1de1502023818bf5e3e634f6a2040048
 fah/projects/p776.xyz.gz=feb25d7431ce72289e7d71741eaf8dd8
 fah/projects/p780.xyz.gz=f49714b672896dcaa57528eff9982242
+fah/projects/p781.xyz.gz=8225be2a7ab96f4ead04ea641a5c3aba
+fah/projects/p782.xyz.gz=a202bfa011bb6d2da4dd0be421cb23b7
+fah/projects/p783.xyz.gz=0b93c722fad45d11d01d630b89c72cfe
+fah/projects/p784.xyz.gz=b9c3a6aa93ca43b6a18e7ba270e25cb4
+fah/projects/p785.xyz.gz=e88a6cfb570e5f51d2930706aa1448d8
+fah/projects/p786.xyz.gz=a92f34aca4d1fcefd5143723510b3e36
 fah/projects/p800.xyz.gz=21111f1643623cfd927ffbec62492f9d
 fah/projects/p801.xyz.gz=b2ee3d32646c92aaf4c8437ddd95bc43
 fah/projects/p802.xyz.gz=ec23f2f76734d4289fe50c086aadda0f
@@ -1743,6 +1774,8 @@
 fah/projects/p891.xyz.gz=312266903c966f57dbf3aac32a73f0b0
 fah/projects/p892.xyz.gz=7bb11d26114eefdcbc7ee30531b9cd43
 fah/projects/p893.xyz.gz=d7d8500d0a9ed0a04bf9df8ba3833c2d
+fah/projects/p894.xyz.gz=40311466de9bfa0a38c2150da833b618
+fah/projects/p895.xyz.gz=33cacacc62c4938f5edd8ba34522a1cc
 fah/projects/p905.xyz.gz=46e9aef2093d4e3538584fab170822ff
 fah/projects/p906.xyz.gz=c8f5e1ace10b2b1fef5e78276340da76
 fah/projects/p907.xyz.gz=00dfb8e7b9011e2d1f490c13bab4b177
@@ -1856,23 +1889,23 @@
 index.fr.html=0cc2d847ee0533240cfe9071d5a651ad
 index.nl.html=a618c45f49ccaaadb4d0760a5f0ebdad
 jmol/Jmol.js=bd5f687d2965577b770861a1effd1328
-jmol/JmolApplet.jar=09952a355ac21acf36592aa6b97d965e
-jmol/JmolApplet0.jar=0633178cec8fa2d746053912bb37a46f
-jmol/JmolApplet0_Core.jar=3b9ed141bf1167f3dac5c502e2fc759e
-jmol/JmolApplet0_Jars.jar=5ce9a51d2ba613fa5ed4538b56fa9766
-jmol/JmolApplet0_Jvxl.jar=9eee5215e86a9f75f57c090f731d8cfe
-jmol/JmolApplet0_Main.jar=77bc866ede643edc6aea7c415d5497dc
-jmol/JmolApplet0_Popup.jar=d032560052e2b130617a895b85dbd9a7
-jmol/JmolApplet0_Quantum.jar=0129fd218151f602244d5e04902e8018
-jmol/JmolApplet0_ReadersCifPdb.jar=a40c4b782a64bef74effabda472a3e6f
-jmol/JmolApplet0_ReadersMolXyz.jar=09b53d37b59d88588b8a7cda590ea8b2
-jmol/JmolApplet0_ReadersMore.jar=aed9d1fe970f869753fb4160d82d34ff
-jmol/JmolApplet0_ReadersXml.jar=832f52e46c4c8eb9123c6db8cbeb923b
-jmol/JmolApplet0_ShapeBio.jar=e130e665193aeeb71fe315a03c3d5b09
-jmol/JmolApplet0_ShapeSpecial.jar=ace5c2098c4ba270c208c73aec984304
-jmol/JmolApplet0_Smiles.jar=7044c07a318b0a3189d921d6ff420ef5
-jmol/JmolApplet0_Viewer.jar=7c10dc2ff6601a3d5fcba51d0742f17a
-jmol/JmolApplet0_i18n.jar=0566502e54264a35f634232b24a9d196
+jmol/JmolApplet.jar=f84fe676c1be47415de0230fd69db21b
+jmol/JmolApplet0.jar=08db64b2d59cdcd559c210ae26a3f47f
+jmol/JmolApplet0_Core.jar=dcef80f177305116b2140edea1874086
+jmol/JmolApplet0_Jars.jar=3ae2bc203da3b6ec70c8ba086ad73a9b
+jmol/JmolApplet0_Jvxl.jar=1e7f96bc016fc2fc7b3d2363dbbb36a8
+jmol/JmolApplet0_Main.jar=9f005df500ad57c2896d128cbc53f489
+jmol/JmolApplet0_Popup.jar=39665f9f0c8489136225df5e18fe8da1
+jmol/JmolApplet0_Quantum.jar=c074499ce77094894230269cf807442c
+jmol/JmolApplet0_ReadersCifPdb.jar=7034e737459e1f8b5e001ca44b7695a6
+jmol/JmolApplet0_ReadersMolXyz.jar=cb1bbe3b02d9d809a4caccb85ebd2119
+jmol/JmolApplet0_ReadersMore.jar=55a5affd2aba07be3583de574a4d479a
+jmol/JmolApplet0_ReadersXml.jar=50dc3952f866abb90bfbe7e60744d741
+jmol/JmolApplet0_ShapeBio.jar=bcea6bef826489533beeb88c64f1fdd6
+jmol/JmolApplet0_ShapeSpecial.jar=7e641aaaa728bdaab9d48b37cdf0d5f8
+jmol/JmolApplet0_Smiles.jar=30832c043649bb0c67bc88a0a1b45eb1
+jmol/JmolApplet0_Viewer.jar=776dff97bce0d636157f5e2ff0f38e5b
+jmol/JmolApplet0_i18n.jar=758d18e0c8b380d3096427d7e52a048e
 jscolors/colors.js=ade68c0fba732e2c9420e48a32b23c28
 jscolors/gradients.png=5bc2889b4a3ebeebdf238b9829642e98
 jscolors/index.en.html=98e0bb9623501f5932b12d86f07176ba
@@ -1882,8 +1915,8 @@
 jscolors/jmol_colors_layout.js=dcb062410de32efd569bcdd310314de9
 jscolors/jmol_constants.js=4418e7d10cc1f49aa3b96f499a954297
 jscolors/jsColorNames.js=994ed21d92bb14f3eb9395c5bc7ee476
-jslibrary/index.en.html=0a148b744ed19ea457aa6fa1c215be86
-jslibrary/index.es.html=a443983c054dfebb514bc7c2460cb638
+jslibrary/index.en.html=65709bbb3e022619bed7ddde4d588134
+jslibrary/index.es.html=e0ca7e5849b14a14948826df84fd0c86
 jslibrary/index.fr.html=40032d17fb18713648b1952c7b7442ed
 lists/index.en.html=1ce1bc89a0acd03b1f906d02e10d0cb3
 lists/index.es.html=869f949188016e230247796f509a9cf7

Modified: trunk/Jmol-web/source/doc/fah/fah-projects.xml
===================================================================
--- trunk/Jmol-web/source/doc/fah/fah-projects.xml	2008-06-25 17:43:51 UTC (rev 9522)
+++ trunk/Jmol-web/source/doc/fah/fah-projects.xml	2008-06-25 17:54:50 UTC (rev 9523)
@@ -1835,24 +1835,24 @@
   <fah_proj number="780" name="p780_Minichap_0kT" public="n" file="y"
     server="171.64.122.138" atoms="43460" preferred="20" deadline="154"
     credit="565" frames="100" code="A0" contact="dlucent" contrib="v00d00"/>
-  <fah_proj number="781" name="p781_Minichap_1kT" public="n"
+  <fah_proj number="781" name="p781_Minichap_1kT" public="n" file="y"
     server="171.64.122.138" atoms="43460" preferred="20" deadline="154"
-    credit="565" frames="100" code="A0" contact="dlucent"/>
-  <fah_proj number="782" name="p782_Minichap_2.0kT" public="n"
+    credit="565" frames="100" code="A0" contact="dlucent" contrib="Hyperlife"/>
+  <fah_proj number="782" name="p782_Minichap_2.0kT" public="n" file="y"
     server="171.64.122.138" atoms="43460" preferred="20" deadline="154"
-    credit="565" frames="100" code="A0" contact="dlucent"/>
-  <fah_proj number="783" name="p783_Minichap_0.3kT" public="n"
+    credit="565" frames="100" code="A0" contact="dlucent" contrib="Ivoshiee"/>
+  <fah_proj number="783" name="p783_Minichap_0.3kT" public="n" file="y"
     server="171.64.122.138" atoms="43460" preferred="20" deadline="154"
-    credit="565" frames="100" code="A0" contact="dlucent"/>
-  <fah_proj number="784" name="p784_Minichap_0.6kT" public="n"
+    credit="565" frames="100" code="A0" contact="dlucent" contrib="Ivoshiee"/>
+  <fah_proj number="784" name="p784_Minichap_0.6kT" public="n" file="y"
     server="171.64.122.138" atoms="43460" preferred="20" deadline="154"
-    credit="565" frames="100" code="A0" contact="dlucent"/>
-  <fah_proj number="785" name="p785_Minichap_1.3kT" public="n"
+    credit="565" frames="100" code="A0" contact="dlucent" contrib="Ivoshiee"/>
+  <fah_proj number="785" name="p785_Minichap_1.3kT" public="n" file="y"
     server="171.64.122.138" atoms="43460" preferred="20" deadline="154"
-    credit="565" frames="100" code="A0" contact="dlucent"/>
-  <fah_proj number="786" name="p786_Minichap_1.6kT" public="n"
+    credit="565" frames="100" code="A0" contact="dlucent" contrib="uncle_fungus"/>
+  <fah_proj number="786" name="p786_Minichap_1.6kT" public="n" file="y"
     server="171.64.122.138" atoms="43460" preferred="20" deadline="154"
-    credit="565" frames="100" code="A0" contact="dlucent"/>
+    credit="565" frames="100" code="A0" contact="dlucent" contrib="Ivoshiee"/>
   <!-- This is Genome@Home
   <fah_proj number="799" public="y"/>
   -->
@@ -2140,6 +2140,15 @@
   <fah_proj number="893" name="p893_p53peptides893" public="y" file="y"
     server="130.49.240.80" atoms="10528" preferred="118" deadline="176"
     credit="647" frames="100" code="A0" contact="ltchong" contrib="v00d00"/>
+  <fah_proj number="894" name="p894_p53MDM2_gb" public="y" file="y"
+    server="130.49.240.81" atoms="1681" preferred="135" deadline="203"
+    credit="743" frames="100" code="A" contact="ltchong" contrib="Torstein"/>
+  <fah_proj number="895" name="p895_p53peptides_gb" public="y" file="y"
+    server="130.49.240.81" atoms="227" preferred="30" deadline="45"
+    credit="165" frames="100" code="A" contact="ltchong" contrib="konpas1986"/>
+  <fah_proj number="896" name="p896_p53longpeptides_GB" public="y"
+    server="130.49.240.81" atoms="260" preferred="31" deadline="47"
+    credit="171" frames="100" code="A" contact="ltchong"/>
 
   <!-- Projects 900 to 999 -->
   <fah_proj number="901" public="y"
@@ -3861,16 +3870,16 @@
   <fah_proj number="1731" name="p1731_A21nat_d26_VAC" public="y" file="y"
     server="171.65.103.155" atoms="4018" preferred="27" deadline="40"
     credit="139" frames="100" code="G" contact="esorin" contrib="Macaholic"/>
-  <fah_proj number="1732" name="p1732_nat_305_03" public="n" file="y"
+  <fah_proj number="1732" name="p1732_nat_305_03" public="y" file="y"
     server="134.139.127.31" atoms="6414" preferred="18" deadline="36"
     credit="57" frames="100" code="G" contact="esorin" contrib="Bruce"/>
-  <fah_proj number="1733" name="p1733_unf_305_03" public="n" file="y"
+  <fah_proj number="1733" name="p1733_unf_305_03" public="y" file="y"
     server="134.139.127.31" atoms="6384" preferred="18" deadline="36"
     credit="57" frames="100" code="G" contact="esorin" contrib="John Deas"/>
-  <fah_proj number="1734" name="p1734_A21nat_305_03" public="n" file="y"
+  <fah_proj number="1734" name="p1734_A21nat_305_03" public="y" file="y"
     server="134.139.127.32" atoms="6426" preferred="18" deadline="36"
     credit="57" frames="100" code="G" contact="esorin" contrib="John Deas"/>
-  <fah_proj number="1735" name="p1735_A21unf_305_03" public="n" file="y"
+  <fah_proj number="1735" name="p1735_A21unf_305_03" public="y" file="y"
     server="134.139.127.32" atoms="6399" preferred="18" deadline="36"
     credit="57" frames="100" code="G" contact="esorin" contrib="John Deas"/>
 
@@ -4448,9 +4457,9 @@
   <fah_proj number="2170" name="p2170_lambda_obc_300K" public="y" file="y"
     server="171.65.103.160" atoms="1258" preferred="45" deadline="66"
     credit="234" frames="100" code="A" contact="densign" contrib="John Deas"/>
-  <fah_proj number="2171" name="p2171_T113V" public="y"
+  <fah_proj number="2171" name="p2171_T113V" public="y" file="y"
     server="171.64.122.141" atoms="86182" preferred="44.8" deadline="66.3"
-    credit="429" frames="100" code="G" contact="densign"/>
+    credit="429" frames="100" code="G" contact="densign" contrib="Bruce"/>
   <fah_proj number="2172" name="p2172_T113V" public="y"
     server="171.64.122.141" atoms="86182" preferred="34.9" deadline="51.3"
     credit="329" frames="100" code="G" contact="densign"/>
@@ -4954,6 +4963,18 @@
   <fah_proj number="2589" name="p2589_BBA5" public="y" file="y"
     server="171.64.122.70" atoms="12200" preferred="26" deadline="38"
     credit="134" frames="100" code="G" contact="luttmann" contrib="Bruce"/>
+  <fah_proj number="2590" name="p2590_BBA5_ext" public="y" file="y"
+    server="171.64.122.139" atoms="12200" preferred="55" deadline="82"
+    credit="293" frames="100" code="DG" contact="luttmann" contrib="konpas1986"/>
+  <fah_proj number="2591" name="p2591_p2556_fs_ambers" public="y"
+    server="171.64.65.42" atoms="264" preferred="1.2" deadline="6"
+    credit="308" frames="100" code="G3" contact="luttmann"/>
+  <fah_proj number="2592" name="p2592_BBA5_ext" public="n" file="y"
+    server="171.64.122.139" atoms="12200" preferred="34" deadline="50"
+    credit="176" frames="100" code="DG" contact="luttmann" contrib="John Deas"/>
+  <fah_proj number="2593" name="p2593_BBA5_ext" public="n"
+    server="171.64.122.139" atoms="12200" preferred="38" deadline="56"
+    credit="198" frames="100" code="DG" contact="luttmann"/>
 
   <!-- Projects 2600 to 2699 -->
   <fah_proj number="2602" name="p2602_Protein in POPC" public="n" file="y"
@@ -6183,6 +6204,12 @@
   <fah_proj number="3856" name="p3856_fkbprelative_ligand" public="y" file="y"
     server="128.59.74.4" atoms="2722" preferred="40" deadline="60"
     credit="401" frames="100" code="DC" contact="mrshirts" contrib="toTOW"/>
+  <fah_proj number="3858" name="p3858_p3855_fkbprelative_complex" public="n"
+    server="128.59.74.4" atoms="14907" preferred="40" deadline="60"
+    credit="450" frames="100" code="DC" contact="mrshirts"/>
+  <fah_proj number="3859" name="p3859_p3856_fkbprelative_ligand" public="n"
+    server="128.59.74.4" atoms="2722" preferred="40" deadline="60"
+    credit="401" frames="100" code="DC" contact="mrshirts"/>
 
   <!-- Projects 3900 to 3999 -->
   <fah_proj number="3900" name="p3900_Protein in POPC" public="n"
@@ -6613,6 +6640,87 @@
   <fah_proj number="4551" name="p4551_T0415-12_minout" public="y" file="y"
     server="169.230.26.30" atoms="186" preferred="15.4" deadline="23.1"
     credit="84.7" frames="100" code="A" contact="vvoelz" contrib="Flathead74"/>
+  <fah_proj number="4552" name="p4552_T0432-16_minout" public="y" file="y"
+    server="169.230.26.30" atoms="297" preferred="21.7" deadline="32.5"
+    credit="119.3" frames="100" code="A" contact="vvoelz" contrib="Smoking2000,toTOW"/>
+  <fah_proj number="4553" name="p4553_T0432-8_minout" public="y" file="y"
+    server="169.230.26.30" atoms="133" preferred="8.5" deadline="12.8"
+    credit="47" frames="100" code="A" contact="vvoelz" contrib="Flathead74,Smoking2000"/>
+  <fah_proj number="4554" name="p4554_T0432-12_minout" public="y" file="y"
+    server="169.230.26.30" atoms="215" preferred="15.4" deadline="23.1"
+    credit="84.7" frames="100" code="A" contact="vvoelz" contrib="Flathead74"/>
+  <fah_proj number="4555" name="p4555_T0437-8_minout" public="y" file="y"
+    server="169.230.26.30" atoms="140" preferred="8.5" deadline="12.8"
+    credit="47" frames="100" code="A" contact="vvoelz"/>
+  <fah_proj number="4556" name="p4556_T0437-16_minout" public="y" file="y"
+    server="169.230.26.30" atoms="246" preferred="21.7" deadline="32.5"
+    credit="119.3" frames="100" code="A" contact="vvoelz" contrib="Smoking2000"/>
+  <fah_proj number="4557" name="p4557_T0437-12_minout" public="y" file="y"
+    server="169.230.26.30" atoms="194" preferred="15.4" deadline="23.1"
+    credit="84.7" frames="100" code="A" contact="vvoelz" contrib="Smoking2000"/>
+  <fah_proj number="4558" name="p4558_T0446-12_minout" public="y" file="y"
+    server="169.230.26.30" atoms="173" preferred="15.4" deadline="23.1"
+    credit="84.7" frames="100" code="A" contact="vvoelz" contrib="Chris Meyer,Smoking2000"/>
+  <fah_proj number="4559" name="p4559_T0446-8_minout" public="y" file="y"
+    server="169.230.26.30" atoms="132" preferred="8.5" deadline="12.8"
+    credit="47" frames="100" code="A" contact="vvoelz" contrib="Smoking2000"/>
+  <fah_proj number="4560" name="p4560_T0446-16_minout" public="y" file="y"
+    server="169.230.26.30" atoms="237" preferred="21.7" deadline="32.5"
+    credit="119.3" frames="100" code="A" contact="vvoelz" contrib="Smoking2000"/>
+  <fah_proj number="4561" name="p4561_T0453-16_minout" public="y" file="y"
+    server="169.230.26.30" atoms="252" preferred="21.7" deadline="32.5"
+    credit="119.3" frames="100" code="A" contact="vvoelz" contrib="Chris Meyer,Smoking2000"/>
+  <fah_proj number="4562" name="p4562_T0453-8_minout" public="y" file="y"
+    server="169.230.26.30" atoms="123" preferred="8.5" deadline="12.8"
+    credit="47" frames="100" code="A" contact="vvoelz" contrib="Smoking2000"/>
+  <fah_proj number="4563" name="p4563_T0453-12_minout" public="y" file="y"
+    server="169.230.26.30" atoms="191" preferred="15.4" deadline="23.1"
+    credit="84.7" frames="100" code="A" contact="vvoelz"/>
+  <fah_proj number="4564" name="p4564_T0459-16_minout" public="y" file="y"
+    server="169.230.26.30" atoms="251" preferred="21.7" deadline="32.5"
+    credit="119.3" frames="100" code="A" contact="vvoelz" contrib="Smoking2000"/>
+  <fah_proj number="4565" name="p4565_T0459-8_minout" public="y" file="y"
+    server="169.230.26.30" atoms="135" preferred="8.5" deadline="12.8"
+    credit="47" frames="100" code="A" contact="vvoelz" contrib="7im"/>
+  <fah_proj number="4566" name="p4566_T0459-12_minout" public="y" file="y"
+    server="169.230.26.30" atoms="195" preferred="15.4" deadline="23.1"
+    credit="84.7" frames="100" code="A" contact="vvoelz" contrib="Smoking2000"/>
+  <fah_proj number="4567" name="p4567_T0460-12_minout" public="y" file="y"
+    server="169.230.26.30" atoms="207" preferred="15.4" deadline="23.1"
+    credit="84.7" frames="100" code="A" contact="vvoelz" contrib="7im"/>
+  <fah_proj number="4568" name="p4568_T0460-16_minout" public="y" file="y"
+    server="169.230.26.30" atoms="260" preferred="21.7" deadline="32.5"
+    credit="119.3" frames="100" code="A" contact="vvoelz" contrib="7im"/>
+  <fah_proj number="4569" name="p4569_T0460-8_minout" public="y" file="y"
+    server="169.230.26.30" atoms="141" preferred="8.5" deadline="12.8"
+    credit="47" frames="100" code="A" contact="vvoelz" contrib="Flathead74"/>
+  <fah_proj number="4570" name="p4570_T0464-8_minout" public="y"
+    server="169.230.26.30" atoms="161" preferred="8.5" deadline="12.8"
+    credit="47" frames="100" code="A" contact="vvoelz"/>
+  <fah_proj number="4571" name="p4571_T0467-8_minout" public="y"
+    server="169.230.26.30" atoms="144" preferred="8.5" deadline="12.8"
+    credit="47" frames="100" code="A" contact="vvoelz"/>
+  <fah_proj number="4572" name="p4572_T0464-16_minout" public="y"
+    server="169.230.26.30" atoms="283" preferred="21.7" deadline="32.5"
+    credit="119.3" frames="100" code="A" contact="vvoelz"/>
+  <fah_proj number="4573" name="p4573_T0467-16_minout" public="y" file="y"
+    server="169.230.26.30" atoms="279" preferred="21.7" deadline="32.5"
+    credit="119.3" frames="100" code="A" contact="vvoelz"/>
+  <fah_proj number="4574" name="p4574_T0464-12_minout" public="y"
+    server="169.230.26.30" atoms="216" preferred="15.4" deadline="23.1"
+    credit="84.7" frames="100" code="A" contact="vvoelz"/>
+  <fah_proj number="4575" name="p4575_T0467-12_minout" public="y" file="y"
+    server="169.230.26.30" atoms="213" preferred="15.4" deadline="23.1"
+    credit="84.7" frames="100" code="A" contact="vvoelz" contrib="7im"/>
+  <fah_proj number="4576" name="p4576_T0469-16_minout" public="y" file="y"
+    server="169.230.26.30" atoms="274" preferred="21.7" deadline="32.5"
+    credit="119.3" frames="100" code="A" contact="vvoelz" contrib="7im"/>
+  <fah_proj number="4577" name="p4577_T0469-8_minout" public="y"
+    server="169.230.26.30" atoms="150" preferred="8.5" deadline="12.8"
+    credit="47" frames="100" code="A" contact="vvoelz"/>
+  <fah_proj number="4578" name="p4578_T0469-12_minout" public="y"
+    server="169.230.26.30" atoms="211" preferred="15.4" deadline="23.1"
+    credit="84.7" frames="100" code="A" contact="vvoelz"/>
 
   <!-- Projects 4700 to 4799 -->
   <fah_proj number="4700" name="p4700_N68H_AM03" public="y"
@@ -6651,6 +6759,9 @@
   <fah_proj number="4714" name="p4714_supervillin_e1" public="n"
     server="171.64.65.103" atoms="576" preferred="2" deadline="3"
     credit="98" frames="100" code="GG2" contact="densign"/>
+  <fah_proj number="4715" name="p4715_supervillin_e1" public="y"
+    server="171.64.65.103" atoms="576" preferred="2" deadline="3"
+    credit="122" frames="100" code="GG2" contact="densign"/>
   <fah_proj number="4716" name="p4716_fip35_ww_domain" public="y"
     server="171.64.65.103" atoms="544" preferred="3.6" deadline="5.4"
     credit="1820" frames="100" code="GG2" contact="densign"/>
@@ -6672,6 +6783,30 @@
   <fah_proj number="4722" name="p4722_lam5w_370K" public="y"
     server="171.64.65.103" atoms="1254" preferred="2" deadline="3"
     credit="300" frames="100" code="GG2" contact="densign"/>
+  <fah_proj number="4724" name="p4724_fip35_ww_domain" public="y"
+    server="171.64.65.103" atoms="544" preferred="2" deadline="3"
+    credit="177" frames="100" code="GG2" contact="densign"/>
+  <fah_proj number="4725" name="p4725_p4709_fip35_ww_domain" public="y"
+    server="171.64.65.103" atoms="544" preferred="2" deadline="3"
+    credit="182" frames="100" code="GG2" contact="densign"/>
+  <fah_proj number="4726" name="p4726_p4709_fip35_ww_domain" public="y"
+    server="171.64.65.103" atoms="544" preferred="2" deadline="3"
+    credit="192" frames="100" code="GG2" contact="densign"/>
+  <fah_proj number="4727" name="p4727_p4708_fip35_ww_domain" public="y"
+    server="171.64.65.103" atoms="544" preferred="2" deadline="3"
+    credit="192" frames="100" code="GG2" contact="densign"/>
+  <fah_proj number="4728" name="p4728_p4724_fip35_ww_domain" public="y"
+    server="171.64.65.103" atoms="544" preferred="2" deadline="3"
+    credit="192" frames="100" code="GG2" contact="densign"/>
+  <fah_proj number="4729" name="p4729_p4709_fip35_ww_domain" public="y"
+    server="171.64.65.103" atoms="544" preferred="2" deadline="3"
+    credit="224" frames="100" code="GG2" contact="densign"/>
+  <fah_proj number="4730" name="p4730_supervillin_e1" public="y"
+    server="171.64.65.103" atoms="576" preferred="2" deadline="3"
+    credit="111" frames="100" code="GG2" contact="densign"/>
+  <fah_proj number="4731" name="p4731_fip35_ww_domain" public="y"
+    server="171.64.65.103" atoms="544" preferred="2" deadline="3"
+    credit="193" frames="100" code="GG2" contact="densign"/>
 
   <!-- Projects 4800 to 4899 -->
   <fah_proj number="4800" name="p4800_" public="y"
@@ -6687,7 +6822,50 @@
   <fah_proj number="5000" name="p5000_supervillin_e1" public="y"
     server="171.64.65.20" atoms="576" preferred="2" deadline="3"
     credit="98" frames="100" code="GG2" contact="densign"/>
+  <fah_proj number="5001" name="p5001_supervillin_e1" public="y"
+    server="171.64.65.20" atoms="576" preferred="2" deadline="3"
+    credit="98" frames="100" code="GG2" contact="densign"/>
+  <fah_proj number="5002" name="p5002_supervillin_e1" public="y"
+    server="171.64.65.20" atoms="576" preferred="2" deadline="3"
+    credit="98" frames="100" code="GG2" contact="densign"/>
+  <fah_proj number="5003" name="p5003_p5002_supervillin_e1" public="y"
+    server="171.64.65.20" atoms="576" preferred="2" deadline="3"
+    credit="479" frames="100" code="GG2" contact="densign"/>
+  <fah_proj number="5004" name="p5004_p5002_supervillin_e1" public="n"
+    server="171.64.65.20" atoms="576" preferred="2" deadline="3"
+    credit="479" frames="100" code="GG2" contact="densign"/>
 
+  <!-- Projects 5000 to 5099 -->
+  <fah_proj number="5101" name="p5101_Calmodulin CMF" public="y" file="y"
+    server="171.64.65.64" atoms="26014" preferred="5" deadline="5"
+    credit="2165" frames="100" code="GS" contact="kasson" contrib="Ivoshiee"/>
+  <fah_proj number="5102" name="p5102_Calmodulin in water" public="y"
+    server="171.64.65.64" atoms="42727" preferred="5" deadline="5"
+    credit="2165" frames="100" code="GS" contact="kasson"/>
+  <fah_proj number="5104" name="p5104_Calmodulin CMG" public="n"
+    server="171.64.65.56" atoms="42813" preferred="6" deadline="6"
+    credit="2165" frames="100" code="GC" contact="kasson"/>
+  <fah_proj number="5107" name="p5107_Calmodulin CMG" public="n"
+    server="171.64.65.64" atoms="42813" preferred="6" deadline="6"
+    credit="1" frames="100" code="GC" contact="kasson"/>
+
+  <!-- Projects 5200 to 5299 -->
+  <fah_proj number="5200" name="p5200_supervillin_e1" public="y"
+    server="171.64.122.74" atoms="576" preferred="2" deadline="3"
+    credit="98" frames="100" code="GG2" contact="densign"/>
+  <fah_proj number="5201" name="p5201_supervillin_e1" public="y"
+    server="171.64.122.74" atoms="576" preferred="2" deadline="3"
+    credit="122" frames="100" code="GG2" contact="densign"/>
+  <fah_proj number="5202" name="p5202_supervillin_e1" public="y"
+    server="171.64.122.74" atoms="576" preferred="2" deadline="3"
+    credit="111" frames="100" code="GG2" contact="densign"/>
+  <fah_proj number="5203" name="p5203_supervillin_e1" public="y"
+    server="171.64.122.74" atoms="576" preferred="2" deadline="3"
+    credit="98" frames="100" code="GG2" contact="densign"/>
+  <fah_proj number="5205" name="p5205_supervillin_e1" public="n"
+    server="171.64.122.74" atoms="576" preferred="2" deadline="3"
+    credit="479" frames="100" code="GG2" contact="densign"/>
+
   <!-- Projects 9900 to 9999 -->
   <fah_proj number="9994" name="p9994_A21_agbnp_amber99" public="n"
     server="171.64.122.137" atoms="222" preferred="1.2" deadline="3.5"


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

Revision: 9522
          http://jmol.svn.sourceforge.net/jmol/?rev=9522&view=rev
Author:   nicove
Date:     2008-06-25 10:43:51 -0700 (Wed, 25 Jun 2008)

Log Message:
-----------
Folding@Home

Added Paths:
-----------
    trunk/Jmol-FAH/projects/p2592.xyz.gz
    trunk/Jmol-FAH/projects/p4573.xyz.gz
    trunk/Jmol-FAH/projects/p4575.xyz.gz
    trunk/Jmol-FAH/projects/p4576.xyz.gz
    trunk/Jmol-FAH/projects/p5101.xyz.gz
    trunk/Jmol-FAH/projects/p781.xyz.gz

Added: trunk/Jmol-FAH/projects/p2592.xyz.gz
===================================================================
(Binary files differ)


Property changes on: trunk/Jmol-FAH/projects/p2592.xyz.gz
___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream

Added: trunk/Jmol-FAH/projects/p4573.xyz.gz
===================================================================
(Binary files differ)


Property changes on: trunk/Jmol-FAH/projects/p4573.xyz.gz
___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream

Added: trunk/Jmol-FAH/projects/p4575.xyz.gz
===================================================================
(Binary files differ)


Property changes on: trunk/Jmol-FAH/projects/p4575.xyz.gz
___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream

Added: trunk/Jmol-FAH/projects/p4576.xyz.gz
===================================================================
(Binary files differ)


Property changes on: trunk/Jmol-FAH/projects/p4576.xyz.gz
___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream

Added: trunk/Jmol-FAH/projects/p5101.xyz.gz
===================================================================
(Binary files differ)


Property changes on: trunk/Jmol-FAH/projects/p5101.xyz.gz
___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream

Added: trunk/Jmol-FAH/projects/p781.xyz.gz
===================================================================
(Binary files differ)


Property changes on: trunk/Jmol-FAH/projects/p781.xyz.gz
___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream


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

Revision: 9521
          http://jmol.svn.sourceforge.net/jmol/?rev=9521&view=rev
Author:   hansonr
Date:     2008-06-24 16:51:18 -0700 (Tue, 24 Jun 2008)

Log Message:
-----------
version=11.5.43_dev # new feature: extended quaternion math
#
#   q = quaternion({x y z}, angleDegrees)
#   q = {qx, qy, qz, qw}
#
# returning component values: 
#
#   q.x, q.y, q.z, q.w
#
# note that the Point4f equivalent stores w LAST, even though it is "q0" 
# because the Java Quat4f() and Point4f() both do that as well. We're just
# being consistent with other Java use.
#
# Modulus operator for extended information retrieval:
#
#   (q%0) -- q0 (w)
#   (q%1) -- q1 (x)
#   (q%2) -- q2 (y)
#   (q%3) -- q3 (z)
#   (q%-1) -- the vector {q1, q2, q3}
#   (q%-2) -- theta
#   (q%-3) -- equivalent rotational frame X-axis 
#   (q%-4) -- equivalent rotational frame Y-axis 
#   (q%-5) -- equivalent rotational frame Z-axis 
#   (q%{x y z})  -- rotational transform of a point or vector based on a quaternion
#
# thus, for example, (q%{1 0 0}) is the same as (q%-3)
#
#   (!q) -- quaternion inverse
# 
# Quaternion difference "dq":
#
#   q2 * (!q1)
#
# Quaternion relative difference:
#
#   (!q1) * q2
#
# Examples:
#
#   q = quaternion({1 1 1},120)
#   print "" + q%{1 0 0} + " " + q%{0 1 0} + " " + q%{0 0 1}    
#
#   {0 1.0 0} {0 0 1.0} {1.0 0 0}
#
#
# bug fix: load trajectory for cases with different atom counts.

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

Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2008-06-24 23:48:46 UTC (rev 9520)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2008-06-24 23:51:18 UTC (rev 9521)
@@ -44,7 +44,7 @@
 # Examples:
 #
 #   q = quaternion({1 1 1},120)
-#   print "" + q%{1 0 0} + " " + q%{0 1 0} + " " + q%{0 0 1}    
+#   print "" + (q%{1 0 0}) + " " + (q%{0 1 0}) + " " + (q%{0 0 1})    
 #
 #   {0 1.0 0} {0 0 1.0} {1.0 0 0}
 #


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

Revision: 9520
          http://jmol.svn.sourceforge.net/jmol/?rev=9520&view=rev
Author:   hansonr
Date:     2008-06-24 16:48:46 -0700 (Tue, 24 Jun 2008)

Log Message:
-----------
version=11.5.43_dev # new feature: extended quaternion math
#
#   q = quaternion({x y z}, angleDegrees)
#   q = {qx, qy, qz, qw}
#
# returning component values: 
#
#   q.x, q.y, q.z, q.w
#
# note that the Point4f equivalent stores w LAST, even though it is "q0" 
# because the Java Quat4f() and Point4f() both do that as well. We're just
# being consistent with other Java use.
#
# Modulus operator for extended information retrieval:
#
#   (q%0) -- q0 (w)
#   (q%1) -- q1 (x)
#   (q%2) -- q2 (y)
#   (q%3) -- q3 (z)
#   (q%-1) -- the vector {q1, q2, q3}
#   (q%-2) -- theta
#   (q%-3) -- equivalent rotational frame X-axis 
#   (q%-4) -- equivalent rotational frame Y-axis 
#   (q%-5) -- equivalent rotational frame Z-axis 
#   (q%{x y z})  -- rotational transform of a point or vector based on a quaternion
#
# thus, for example, (q%{1 0 0}) is the same as (q%-3)
#
#   (!q) -- quaternion inverse
# 
# Quaternion difference "dq":
#
#   q2 * (!q1)
#
# Quaternion relative difference:
#
#   (!q1) * q2
#
# Examples:
#
#   q = quaternion({1 1 1},120)
#   print "" + q%{1 0 0} + " " + q%{0 1 0} + " " + q%{0 0 1}    
#
#   {0 1.0 0} {0 0 1.0} {1.0 0 0}
#
#
# bug fix: load trajectory for cases with different atom counts.

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

Modified: trunk/Jmol/src/org/jmol/util/Quaternion.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Quaternion.java	2008-06-24 04:00:39 UTC (rev 9519)
+++ trunk/Jmol/src/org/jmol/util/Quaternion.java	2008-06-24 23:48:46 UTC (rev 9520)
@@ -24,6 +24,7 @@
 package org.jmol.util;
 
 import javax.vecmath.Matrix3f;
+import javax.vecmath.Point3f;
 import javax.vecmath.Point4f;
 import javax.vecmath.Tuple3f;
 import javax.vecmath.Vector3f;
@@ -236,4 +237,21 @@
   public Point4f toPoint4f() {
     return new Point4f(q1, q2, q3, q0);
   }
+  
+  public Point3f transform(Point3f pt) {
+    if (mat == null)
+      setMatrix();
+    Point3f ptNew = new Point3f(pt);
+    mat.transform(ptNew);
+    return ptNew;
+  }
+
+  public Vector3f transform(Vector3f v) {
+    if (mat == null)
+      setMatrix();
+    Vector3f vNew = new Vector3f(v);
+    mat.transform(vNew);
+    return vNew;
+  }
+
 }

Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java	2008-06-24 04:00:39 UTC (rev 9519)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java	2008-06-24 23:48:46 UTC (rev 9520)
@@ -7578,6 +7578,8 @@
         tok = Token.atomY;
       else if (s.equals("z"))
         tok = Token.atomZ;
+      else if (s.equals("w"))
+        tok = Token.qw;
       else
         error(ERROR_invalidArgument);
       break;
@@ -11550,6 +11552,8 @@
         return addX(((Float) x).floatValue());
       if (x instanceof String)
         return addX((String) x);
+      if (x instanceof Vector3f)
+        return addX(new Point3f((Vector3f) x));
       if (x instanceof Point3f)
         return addX((Point3f) x);
       if (x instanceof Point4f)
@@ -12033,10 +12037,11 @@
     }
     
     private boolean evaluatePoint(Token[] args) throws ScriptException {
-      if (args.length != 1 && args.length != 3)
+      if (args.length != 1 && args.length != 3 && args.length != 4)
         return false;
-      if (isSyntaxCheck)
-        return addX(new Point3f(0, 0, 0));
+      if (isSyntaxCheck) {
+        return addX(args.length == 4 ? (Object) new Point4f() : (Object) new Point3f());
+      }
 
       switch (args.length) {
       case 1:
@@ -12045,10 +12050,9 @@
           return addX((Point3f) pt);
         return addX("" + pt);
       case 3:
-        float x = Token.fValue(args[0]);
-        float y = Token.fValue(args[1]);
-        float z = Token.fValue(args[2]);
-        return addX(new Point3f(x, y, z));
+        return addX(new Point3f(Token.fValue(args[0]), Token.fValue(args[1]), Token.fValue(args[2])));
+      case 4:
+        return addX(new Point4f(Token.fValue(args[0]), Token.fValue(args[1]), Token.fValue(args[2]), Token.fValue(args[3])));
       }
       return false;
     }
@@ -12803,6 +12807,13 @@
             return addX(new Point3f(pt.x - f, pt.y - f, pt.z - f));
           }
         }
+        if (x1.tok == Token.point4f) {
+          if (x2.tok == Token.point4f) {
+            Quaternion q1 = new Quaternion((Point4f)x1.value);
+            Quaternion q2 = new Quaternion((Point4f)x2.value);
+            return addX(q2.mul(q1.inv()).toPoint4f());
+          }
+        }
         return addX(Token.fValue(x1) - Token.fValue(x2));
       case Token.unaryMinus:
         switch (x2.tok) {
@@ -12899,6 +12910,8 @@
           return addX(pt);
         case Token.point4f:
           Point4f q = (Point4f) x1.value;
+          if (x2.tok == Token.point3f)
+            return addX((new Quaternion(q)).transform((Point3f)x2.value));
           switch(n) {
           case 0:
             return addX(q.w);
@@ -12911,8 +12924,15 @@
           case -1:
             return addX(new Point3f(q.x, q.y, q.z));
           case -2:
+            return addX((new Quaternion(q)).getTheta());
+          case -3:
+            return addX((new Quaternion(q)).getVector(0));
+          case -4:
+            return addX((new Quaternion(q)).getVector(1));
+          case -5:
+            return addX((new Quaternion(q)).getVector(2));
           default:
-            return addX((new Quaternion(q)).getTheta());
+            return addX(q);
           }
         case Token.bitset:
           return addX(Token.bsSelect(x1, n));
@@ -12980,6 +13000,18 @@
               : op.intValue == Token.fracY ? ptf.y : ptf.z);
         }
         break;
+      case Token.point4f:
+        switch (op.intValue) {
+        case Token.atomX:
+          return addX(((Point4f) x2.value).x);
+        case Token.atomY:
+          return addX(((Point4f) x2.value).y);
+        case Token.atomZ:
+          return addX(((Point4f) x2.value).z);
+        case Token.qw:
+          return addX(((Point4f) x2.value).w);
+        }
+        break;
       case Token.bitset:
         if (op.intValue == Token.bonds && x2.value instanceof BondSet)
           return addX(x2);

Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2008-06-24 04:00:39 UTC (rev 9519)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2008-06-24 23:48:46 UTC (rev 9520)
@@ -3,8 +3,54 @@
 
 version=11.5.43_dev
 
+# new feature: extended quaternion math
+#
+#   q = quaternion({x y z}, angleDegrees)
+#   q = {qx, qy, qz, qw}
+#
+# returning component values: 
+#
+#   q.x, q.y, q.z, q.w
+#
+# note that the Point4f equivalent stores w LAST, even though it is "q0" 
+# because the Java Quat4f() and Point4f() both do that as well. We're just
+# being consistent with other Java use.
+#
+# Modulus operator for extended information retrieval:
+#
+#   (q%0) -- q0 (w)
+#   (q%1) -- q1 (x)
+#   (q%2) -- q2 (y)
+#   (q%3) -- q3 (z)
+#   (q%-1) -- the vector {q1, q2, q3}
+#   (q%-2) -- theta
+#   (q%-3) -- equivalent rotational frame X-axis 
+#   (q%-4) -- equivalent rotational frame Y-axis 
+#   (q%-5) -- equivalent rotational frame Z-axis 
+#   (q%{x y z})  -- rotational transform of a point or vector based on a quaternion
+#
+# thus, for example, (q%{1 0 0}) is the same as (q%-3)
+#
+#   (!q) -- quaternion inverse
+# 
+# Quaternion difference "dq":
+#
+#   q2 * (!q1)
+#
+# Quaternion relative difference:
+#
+#   (!q1) * q2
+#
+# Examples:
+#
+#   q = quaternion({1 1 1},120)
+#   print "" + q%{1 0 0} + " " + q%{0 1 0} + " " + q%{0 0 1}    
+#
+#   {0 1.0 0} {0 0 1.0} {1.0 0 0}
+#
+#
 # bug fix: load trajectory for cases with different atom counts.
-
+#
 # -----------------------------------------------------------------------------
 
 #version=11.5.42

Modified: trunk/Jmol/src/org/jmol/viewer/Token.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Token.java	2008-06-24 04:00:39 UTC (rev 9519)
+++ trunk/Jmol/src/org/jmol/viewer/Token.java	2008-06-24 23:48:46 UTC (rev 9520)
@@ -499,13 +499,13 @@
 
   // xxx(a,b,c)
   
-  final static int point        = 1  | 3 << 3 | mathfunc;
-  final static int select       = 2  | 3 << 3 | mathfunc | expressionCommand;
+  final static int select       = 1  | 3 << 3 | mathfunc | expressionCommand;
   
   // xxx(a,b,c,d)
   
   final static int angle        = 1  | 4 << 3 | mathfunc;
   final static int plane        = 2  | 4 << 3 | mathfunc | specialstring; //may appear as string alone
+  final static int point        = 3  | 4 << 3 | mathfunc;
 
   // xxx(a,b,c,d,e)
   
@@ -962,6 +962,7 @@
   final static int triangles    = misc | 63;
   final static int url          = misc | 64; 
   final static int user         = misc | 65; //color option
+  final static int qw           = misc | 66;
 
 
   // predefined Tokens: 


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Revision: 9519
          http://jmol.svn.sourceforge.net/jmol/?rev=9519&view=rev
Author:   nicove
Date:     2008-06-23 21:00:39 -0700 (Mon, 23 Jun 2008)

Log Message:
-----------
Folding@Home

Added Paths:
-----------
    trunk/Jmol-FAH/projects/p894.xyz.gz

Added: trunk/Jmol-FAH/projects/p894.xyz.gz
===================================================================
(Binary files differ)


Property changes on: trunk/Jmol-FAH/projects/p894.xyz.gz
___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream


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Revision: 9518
          http://jmol.svn.sourceforge.net/jmol/?rev=9518&view=rev
Author:   hansonr
Date:     2008-06-23 13:43:49 -0700 (Mon, 23 Jun 2008)

Log Message:
-----------
version=11.5.43_dev # bug fix: load trajectory for cases with different atom counts.

Modified Paths:
--------------
    trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
    trunk/Jmol/src/org/jmol/modelset/ModelSet.java
    trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java
    trunk/Jmol/src/org/jmol/viewer/Jmol.properties

Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java	2008-06-23 17:33:46 UTC (rev 9517)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java	2008-06-23 20:43:49 UTC (rev 9518)
@@ -1033,8 +1033,10 @@
   ////////////////////////////////////////////////////////////////
   
   void addTrajectory() {
-    if (trajectory.length == 0) //done with FIRST atom set
-      trajectory = new Point3f[atomCount];
+    //System.out.println(atomCount);
+    if (trajectory.length == 0 || trajectory.length < atomCount) {
+      trajectory = new Point3f[atomCount];      
+    }
     for (int i = 0; i < atomCount; i++)
       trajectory[i] = new Point3f(atoms[i]);
     trajectories.addElement(trajectory);

Modified: trunk/Jmol/src/org/jmol/modelset/ModelSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelSet.java	2008-06-23 17:33:46 UTC (rev 9517)
+++ trunk/Jmol/src/org/jmol/modelset/ModelSet.java	2008-06-23 20:43:49 UTC (rev 9518)
@@ -195,7 +195,7 @@
     Point3f[] trajectory = (Point3f[]) trajectories.get(modelIndex);
     BitSet bs = new BitSet();
     int nAtoms = getAtomCountInModel(modelIndex);
-    for (int pt = 0, i = iFirst; i < nAtoms && pt < trajectory.length; i++) {
+    for (int pt = 0, i = iFirst; i < nAtoms && pt < trajectory.length && trajectory[pt]!= null; i++) {
       atoms[i].set(trajectory[pt++]);
       atoms[i].modelIndex = (short) modelIndex;
       bs.set(i);

Modified: trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java	2008-06-23 17:33:46 UTC (rev 9517)
+++ trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java	2008-06-23 20:43:49 UTC (rev 9518)
@@ -524,7 +524,7 @@
           z = monomer.getOmega();
           if (z < -90)
             z += 360;
-          z -= 180;
+          //z -= 180;
           if (Float.isNaN(x) || Float.isNaN(y) || Float.isNaN(z))
             continue;
           w = a.getPartialCharge();

Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2008-06-23 17:33:46 UTC (rev 9517)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2008-06-23 20:43:49 UTC (rev 9518)
@@ -3,6 +3,8 @@
 
 version=11.5.43_dev
 
+# bug fix: load trajectory for cases with different atom counts.
+
 # -----------------------------------------------------------------------------
 
 #version=11.5.42


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Revision: 9517
          http://jmol.svn.sourceforge.net/jmol/?rev=9517&view=rev
Author:   nicove
Date:     2008-06-23 10:33:46 -0700 (Mon, 23 Jun 2008)

Log Message:
-----------
Version

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

Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2008-06-23 17:11:18 UTC (rev 9516)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2008-06-23 17:33:46 UTC (rev 9517)
@@ -1,8 +1,12 @@
 # Developers: to add a description of changes you have made,
 # add it on line starting with # below the "version=..." line
 
-version=11.5.42
+version=11.5.43_dev
 
+# -----------------------------------------------------------------------------
+
+#version=11.5.42
+
 # code: modified Jmol encoded PDB data output
 
 # bug fix: color of NaN float values changed from "center of color scheme" to GRAY
@@ -82,7 +86,7 @@
 #    selectX {*} x.straightness < 0.995 # does not round
 # 
 # new feature: "%T" label format for straightness
-#
+
 # -----------------------------------------------------------------------------
 
 #version=11.5.41


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Revision: 9516
          http://jmol.svn.sourceforge.net/jmol/?rev=9516&view=rev
Author:   nicove
Date:     2008-06-23 10:11:18 -0700 (Mon, 23 Jun 2008)

Log Message:
-----------
Folding@Home

Added Paths:
-----------
    trunk/Jmol-FAH/projects/p895.xyz.gz

Added: trunk/Jmol-FAH/projects/p895.xyz.gz
===================================================================
(Binary files differ)


Property changes on: trunk/Jmol-FAH/projects/p895.xyz.gz
___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream


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Revision: 9515
          http://jmol.svn.sourceforge.net/jmol/?rev=9515&view=rev
Author:   hansonr
Date:     2008-06-23 07:04:29 -0700 (Mon, 23 Jun 2008)

Log Message:
-----------
11.5.42 VERSION (d) 

Modified Paths:
--------------
    trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
    trunk/Jmol/src/org/jmol/modelset/ModelLoader.java
    trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java
    trunk/Jmol/src/org/jmol/viewer/Eval.java
    trunk/Jmol/src/org/jmol/viewer/Jmol.properties

Modified: trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelCollection.java	2008-06-23 01:45:09 UTC (rev 9514)
+++ trunk/Jmol/src/org/jmol/modelset/ModelCollection.java	2008-06-23 14:04:29 UTC (rev 9515)
@@ -892,29 +892,6 @@
   /* ONLY from one model 
    * 
    */
-  /* ONLY from one model 
-   * 
-   */
-  private String getPdbData(int modelIndex, char ctype, int derivType, 
-                            boolean isDraw, BitSet bsSelected) {
-    if (isJmolDataFrame(modelIndex))
-      modelIndex = getJmolDataSourceFrame(modelIndex);
-    if (modelIndex < 0)
-      return "";
-    char qtype = (ctype == 'R' ? 'R' : viewer.getQuaternionFrame());
-    Model model = models[modelIndex];
-    BitSet bsAtoms = getModelAtomBitSet(modelIndex, false);
-    int nPoly = model.getBioPolymerCount();
-    StringBuffer pdbATOM = new StringBuffer();
-    StringBuffer pdbCONECT = new StringBuffer();
-    if (!isDraw)
-      pdbATOM.append(getProteinStructureState(bsAtoms, ctype == 'R'));
-    for (int p = 0; p < nPoly; p++)
-        model.bioPolymers[p].getPdbData(ctype, qtype, derivType, isDraw,
-            bsAtoms, pdbATOM, pdbCONECT, bsSelected);
-    pdbATOM.append(pdbCONECT);
-    return pdbATOM.toString();
-  }
 
   public String getPdbAtomData(BitSet bs) {
     if (atomCount == 0)
@@ -949,39 +926,58 @@
    *****************************/
 
   public String getPdbData(int modelIndex, String type, BitSet bsSelected) {
+    if (isJmolDataFrame(modelIndex))
+      modelIndex = getJmolDataSourceFrame(modelIndex);
+    if (modelIndex < 0)
+      return "";
     if (!models[modelIndex].isPDB)
       return null;
+    Model model = models[modelIndex];
     char ctype = (type.length() > 11 && type.indexOf("quaternion ") >= 0 ? type
         .charAt(11) : 'R');
-    String s = getPdbData(modelIndex, ctype, 
-        (type.indexOf("diff") < 0 ? 0 : type.indexOf("2") < 0 ? 1 : 2),
-        (type.indexOf("draw") >= 0), bsSelected);
-    if (s.length() == 0 || type.indexOf("draw") >= 0)
+    char qtype = (ctype == 'R' ? 'R' : viewer.getQuaternionFrame());
+    int derivType = (type.indexOf("diff") < 0 ? 0 : type.indexOf("2") < 0 ? 1 : 2);
+    boolean isDraw = (type.indexOf("draw") >= 0);    
+    BitSet bsAtoms = getModelAtomBitSet(modelIndex, false);
+    int nPoly = model.getBioPolymerCount();
+    StringBuffer pdbATOM = new StringBuffer();
+    StringBuffer pdbCONECT = new StringBuffer();
+    for (int p = 0; p < nPoly; p++)
+        model.bioPolymers[p].getPdbData(ctype, qtype, derivType, isDraw,
+            bsAtoms, pdbATOM, pdbCONECT, bsSelected);
+    pdbATOM.append(pdbCONECT);
+    String s = pdbATOM.toString();
+    if (isDraw || s.length() == 0)
       return s;
-    String remark = "REMARK   6 Jmol PDB-encoded data: " + type
-        + " data(x,y,z,charge)=";
+    String remark = "REMARK   6 Jmol PDB-encoded data: " + type + ";";
+    if (ctype != 'R')
+      remark += "  quaternionFrame = \"" + qtype + "\""; 
+    String data;
     switch (ctype) {
     default:
     case 'w':
-      remark += "(x,y,z,w)";
+      data = "x*10___ y*10___ z*10___      w*10__       ";
       break;
     case 'x':
-      remark += "(y,z,w,x)";
+      data = "y*10___ z*10___ w*10___      x*10__       ";
       break;
     case 'y':
-      remark += "(z,w,x,y)";
+      data = "z*10___ w*10___ x*10___      y*10__       ";
       break;
     case 'z':
-      remark += "(w,x,y,z)";
+      data = "w*10___ x*10___ y*10___      z*10__       ";
       break;
     case 'R':
-      remark += "(phi,psi,omega,partialCharge)";
+      data = "phi____ psi____ omega-180    PartialCharge";
       break;
-    case 's':
-      remark = "# draw sequence for quaternions";
-      break;
     }
-    remark += "\n";
+    remark += "\n\n" + getProteinStructureState(bsAtoms, ctype == 'R');
+    remark += "REMARK   6    AT GRP CH RESNO  " + data + "    Sym";
+    if (ctype != 'R')
+      remark += "   q0_______ q1_______ q2_______ q3_______  centerX___ centerY___ centerZ___";
+    if (qtype == 'n')
+      remark += "  NHX_______ NHY_______ NYZ_______";
+    remark += "\n\n";
     return remark + s;
   }
 

Modified: trunk/Jmol/src/org/jmol/modelset/ModelLoader.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelLoader.java	2008-06-23 01:45:09 UTC (rev 9514)
+++ trunk/Jmol/src/org/jmol/modelset/ModelLoader.java	2008-06-23 14:04:29 UTC (rev 9515)
@@ -349,7 +349,7 @@
           clientFile, i);
       if (modelName == null)
         modelName = (jmolData != null ? jmolData.substring(jmolData
-            .indexOf(":") + 2, jmolData.indexOf("data("))
+            .indexOf(":") + 2, jmolData.indexOf(";"))
             : modelNumber == Integer.MAX_VALUE ? "" : "" + (modelNumber % 1000000));
       boolean isPDBModel = setModelNameNumberProperties(ipt, iTrajectory, modelName,
           modelNumber, modelProperties, modelAuxiliaryInfo, isPDB, jmolData);

Modified: trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java	2008-06-23 01:45:09 UTC (rev 9514)
+++ trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java	2008-06-23 14:04:29 UTC (rev 9515)
@@ -606,17 +606,6 @@
                q = q.mul(-1);
           }
           qlast = q;
-          Point3f ptCenter = (p instanceof AminoPolymer ? AminoPolymer
-              .getQuaternionFrameCenter((AminoMonomer) a.getGroup(), qtype)
-              : p instanceof NucleicPolymer ? NucleicPolymer
-                  .getQuaternionFrameCenter((NucleicMonomer) a.getGroup(),
-                      qtype) : new Point3f());
-          strExtra = TextFormat.sprintf("%8.3p%8.3p%8.3p",
-              new Object[] { new Point3f[] { ptCenter } });
-          if (qtype == 'n')
-            strExtra += TextFormat.sprintf(" %8.3p%8.3p%8.3p",
-                new Object[] { new Point3f[] { ((AminoPolymer) p)
-                    .getNHPoint((AminoMonomer) a.getGroup()) } });
           switch (ctype) {
           default:
             x = q.q1;
@@ -643,6 +632,11 @@
             w = q.q1;
             break;
           }
+          Point3f ptCenter = (p instanceof AminoPolymer ? AminoPolymer
+              .getQuaternionFrameCenter((AminoMonomer) a.getGroup(), qtype)
+              : p instanceof NucleicPolymer ? NucleicPolymer
+                  .getQuaternionFrameCenter((NucleicMonomer) a.getGroup(),
+                      qtype) : new Point3f());
           if (isDraw) {
             if (bsSelected != null && !bsSelected.get(a.getAtomIndex()))
               continue;
@@ -676,12 +670,21 @@
             .append(" color ").append(qColor[derivType]).append('\n');
             continue;
           }
-        }
+          strExtra = TextFormat.sprintf("%10.6f%10.6f%10.6f%10.6f  %10.5p %10.5p %10.5p",
+              new Object[] { 
+                new float[] { q.q0, q.q1, q.q2, q.q3 },  
+                new Point3f[] { ptCenter }
+              });
+          if (qtype == 'n')
+            strExtra += TextFormat.sprintf("  %10.5p %10.5p %10.5p",
+                new Object[] { new Point3f[] { ((AminoPolymer) p)
+                    .getNHPoint((AminoMonomer) a.getGroup()) } });
+        } 
         if (pdbATOM == null)
           continue;
         pdbATOM.append(a.formatLabel("ATOM  %5i %4a%1A%3n %1c%4R%1E   "));
         pdbATOM.append(TextFormat.sprintf(
-            "%8.3f%8.3f%8.3f%6.2f                %2s    %s\n", new String[] {
+            "%8.2f%8.2f%8.2f      %6.3f          %2s    %s\n", new String[] {
                 a.getElementSymbol().toUpperCase(), strExtra }, new float[] {
                 x * factor, y * factor, z * factor, w * factor }));
         if (atomno != Integer.MIN_VALUE) {

Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java	2008-06-23 01:45:09 UTC (rev 9514)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java	2008-06-23 14:04:29 UTC (rev 9515)
@@ -4491,7 +4491,7 @@
         evalError("QUATERNION [w,x,y,z,a,r] [difference][2]");
       type = "quaternion " + type + (isDerivative ? " difference" : "")
           + (isSecondDerivative ? "2" : "") 
-          + (isDraw ? " draw" : " (quaternionFrame " + viewer.getQuaternionFrame() + ")");
+          + (isDraw ? " draw" : "");
       break;
     }
     if (isSyntaxCheck) //just in case we later add parameter options to this

Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2008-06-23 01:45:09 UTC (rev 9514)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2008-06-23 14:04:29 UTC (rev 9515)
@@ -3,6 +3,8 @@
 
 version=11.5.42
 
+# code: modified Jmol encoded PDB data output
+
 # bug fix: color of NaN float values changed from "center of color scheme" to GRAY
 # bug fix: connect "_1" was inadvertently dropped in 11.5.26.
 # bug fix: state script fails to save data for atoms created using the quaternion command


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Revision: 9514
          http://jmol.svn.sourceforge.net/jmol/?rev=9514&view=rev
Author:   hansonr
Date:     2008-06-22 18:45:09 -0700 (Sun, 22 Jun 2008)

Log Message:
-----------


Modified Paths:
--------------
    trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java
    trunk/Jmol/src/org/jmol/applet/Jmol.java

Modified: trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java	2008-06-23 01:03:03 UTC (rev 9513)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java	2008-06-23 01:45:09 UTC (rev 9514)
@@ -114,7 +114,7 @@
         return "unrecognized file format for file " + fullName + "\n"
             + atomSetCollectionReaderName;
       if (atomSetCollectionReaderName.equals("spt"))
-        return "file recognized as a script file: " + fullName + "\n";
+        return "NOTE: file recognized as a script file: " + fullName + "\n";
       Logger.info("The Resolver thinks " + atomSetCollectionReaderName);
     }
     if (htParams == null)

Modified: trunk/Jmol/src/org/jmol/applet/Jmol.java
===================================================================
--- trunk/Jmol/src/org/jmol/applet/Jmol.java	2008-06-23 01:03:03 UTC (rev 9513)
+++ trunk/Jmol/src/org/jmol/applet/Jmol.java	2008-06-23 01:45:09 UTC (rev 9514)
@@ -966,7 +966,7 @@
         String errorMsg = (String) data[4];
         //data[5] = (String) null; // don't pass reference to clientFile reference
         if (errorMsg != null) {
-          showStatusAndConsole(GT._("File Error:") + errorMsg);
+          showStatusAndConsole((errorMsg.indexOf("NOTE:") >= 0 ? "" : GT._("File Error:")) + errorMsg);
           return;
         }
         break;


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