[Jmol-commits] SF.net SVN: jmol:[10366] branches/v11_6/Jmol/src/org/jmol

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

Revision: 10366
          http://jmol.svn.sourceforge.net/jmol/?rev=10366&view=rev
Author:   hansonr
Date:     2008-11-25 21:34:13 +0000 (Tue, 25 Nov 2008)

Log Message:
-----------
11.6.7 VERSION

Modified Paths:
--------------
    branches/v11_6/Jmol/src/org/jmol/modelsetbio/BioPolymer.java
    branches/v11_6/Jmol/src/org/jmol/viewer/Jmol.properties

Modified: branches/v11_6/Jmol/src/org/jmol/modelsetbio/BioPolymer.java
===================================================================
--- branches/v11_6/Jmol/src/org/jmol/modelsetbio/BioPolymer.java	2008-11-25 21:30:36 UTC (rev 10365)
+++ branches/v11_6/Jmol/src/org/jmol/modelsetbio/BioPolymer.java	2008-11-25 21:34:13 UTC (rev 10366)
@@ -693,7 +693,7 @@
                  */
                 q = dq.rightDifference(dqprev); //q = dq.mul(dqprev.inv());
                 if (ctype == 's')
-                  a.getGroup().setStraightness(getStraightness(id, dqprev, dq));
+                  a.getGroup().setStraightness(getQuaternionStraightness(id, dqprev, dq));
               }
               dqprev = dq;
             }
@@ -793,19 +793,13 @@
     }
   }
   
-  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;
-    // absolute value added, because we are dotting the vector normals. Two vector normals
-    // that are colinear, despite their angle of rotation, should give the same straightness
+  private static float getQuaternionStraightness(String id, Quaternion dqprev, Quaternion dq) {
     // 
-    // straightness = 1 - acos(|n1.n2|)/(PI/2)
+    // Dan Kohler's quaternion straightness = 1 - acos(|dq1.dq2|)/(PI/2)
     //
     // alignment = near 0 or near 180 --> same - just different rotations. 
     // It's a 90-degree change in direction that corresponds to 0.
     //
-    float f = (float) (Math.acos(Math.abs(dqprev.getNormal().dot(dq.getNormal())))/ Math.PI);
-    return 1 - 2 * f;
+    return (float) (1 - 2 * Math.acos(Math.abs(dqprev.dot(dq))) / Math.PI);
   }
 }

Modified: branches/v11_6/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v11_6/Jmol/src/org/jmol/viewer/Jmol.properties	2008-11-25 21:30:36 UTC (rev 10365)
+++ branches/v11_6/Jmol/src/org/jmol/viewer/Jmol.properties	2008-11-25 21:34:13 UTC (rev 10366)
@@ -1,8 +1,9 @@
 # Developers: to add a description of changes you have made,
 # add it on a line starting with # below the "version=..." line
 
-version=11.6.7_dev
+version=11.6.7
 
+# quaternion straightness update
 # bug fix: applet improperly reporting status of "quiet" commands
 # bug fix: stereo not in state
 # bug fix: stereoDegrees parameter not reported correctly


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