Revision: 18393
http://sourceforge.net/p/jmol/code/18393
Author: hansonr
Date: 2013-07-01 20:03:33 +0000 (Mon, 01 Jul 2013)
Log Message:
-----------
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java
trunk/Jmol/src/org/jmol/util/Quaternion.java
trunk/Jmol/src/org/jmol/util/Tensor.java
Modified: trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2013-07-01
18:38:26 UTC (rev 18392)
+++ trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2013-07-01
20:03:33 UTC (rev 18393)
@@ -282,7 +282,7 @@
}
public JmolList<Tensor> getAllAtomTensors(String type) {
- return atomTensors.get(type.toLowerCase());
+ return (atomTensors == null ? null : atomTensors.get(type.toLowerCase()));
}
private Tensor[] getTensorList(JmolList<Tensor> list) {
Modified: trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java 2013-07-01
18:38:26 UTC (rev 18392)
+++ trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java 2013-07-01
20:03:33 UTC (rev 18393)
@@ -3367,6 +3367,8 @@
// q%2 y
// q%3 z
// q%4 normal
+ // q%5 EulerZXZ (degrees)
+ // q%6 EulerZYZ (degrees)
// q%-1 vector(1)
// q%-2 theta
// q%-3 Matrix column 0
@@ -3374,7 +3376,6 @@
// q%-5 Matrix column 2
// q%-6 AxisAngle format
// q%-9 Matrix format
- // q%-10 EulerZXZ (degrees)
case 0:
return addXFloat(pt4.w);
case 1:
@@ -3391,7 +3392,7 @@
case 5:
return addXAF(q.getEulerZXZ());
case 6:
- return addXAF(q.getEulerZXZ());
+ return addXAF(q.getEulerZYZ());
case -1:
return addXPt(P3.newP(q.getVector(-1)));
case -2:
Modified: trunk/Jmol/src/org/jmol/util/Quaternion.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Quaternion.java 2013-07-01 18:38:26 UTC
(rev 18392)
+++ trunk/Jmol/src/org/jmol/util/Quaternion.java 2013-07-01 20:03:33 UTC
(rev 18393)
@@ -37,10 +37,8 @@
* This ensures that the reported theta is always positive, and the normal
* reported is always associated with a positive theta.
*
- * By Bob Hanson, hans...@stolaf.edu 6/2008
+ * @author Bob Hanson, hans...@stolaf.edu 6/2008
*
- *
- *
*/
public class Quaternion {
@@ -315,11 +313,23 @@
q3 *= -1;
}
- public static final Quaternion getQuaternionFrame(P3 center, Tuple3f x,
Tuple3f y) {
+ /**
+ * returns a quaternion frame based on three points (center, x, and any
point in xy plane)
+ * or two vectors (vA, vB).
+ *
+ * @param center (null for vA/vB option)
+ * @param x
+ * @param xy
+ * @return quaternion for frame
+ */
+ public static final Quaternion getQuaternionFrame(P3 center, Tuple3f x,
+ Tuple3f xy) {
V3 vA = V3.newV(x);
- vA.sub(center);
- V3 vB = V3.newV(y);
- vB.sub(center);
+ V3 vB = V3.newV(xy);
+ if (center != null) {
+ vA.sub(center);
+ vB.sub(center);
+ }
return getQuaternionFrameV(vA, vB, null, false);
}
@@ -804,16 +814,21 @@
}
public float[] getEulerZYZ() {
- return null;
+ // http://www.swarthmore.edu/NatSci/mzucker1/e27/diebel2006attitude.pdf
+ double rA, rB, rG;
+ rA = Math.atan2(2 * (q2 * q3 - q0 * q1), 2 * (q1 * q3 + q0 * q2 ));
+ rB = Math.acos(q3 * q3 - q2 * q2 - q1 * q1 + q0 * q0);
+ rG = Math.atan2( 2 * (q2 * q3 + q0 * q1), 2 * (q0 * q2 - q1 * q3));
+ return new float[] {(float) (rA / RAD_PER_DEG), (float) (rB /
RAD_PER_DEG), (float) (rG / RAD_PER_DEG)};
}
public float[] getEulerZXZ() {
// NOT
http://en.wikipedia.org/wiki/Conversion_between_quaternions_and_Euler_angles
// http://www.swarthmore.edu/NatSci/mzucker1/e27/diebel2006attitude.pdf
double rA, rB, rG;
+ rA = Math.atan2(2 * (q1 * q3 + q0 * q2), 2 * (q0 * q1 - q2 * q3 ));
+ rB = Math.acos(q3 * q3 - q2 * q2 - q1 * q1 + q0 * q0);
rG = Math.atan2( 2 * (q1 * q3 - q0 * q2), 2 * (q2 * q3 + q0 * q1));
- rB = Math.acos(q3 * q3 - q2 * q2 - q1 * q1 + q0 * q0);
- rA = Math.atan2(2 * (q1 * q3 + q0 * q2), 2 * (q0 * q1 - q2 * q3 ));
return new float[] {(float) (rA / RAD_PER_DEG), (float) (rB /
RAD_PER_DEG), (float) (rG / RAD_PER_DEG)};
}
Modified: trunk/Jmol/src/org/jmol/util/Tensor.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Tensor.java 2013-07-01 18:38:26 UTC (rev
18392)
+++ trunk/Jmol/src/org/jmol/util/Tensor.java 2013-07-01 20:03:33 UTC (rev
18393)
@@ -29,7 +29,7 @@
/**
* @author Bob Hanson hans...@stolaf.edu 6/30/2013
- *
+ * @author Simone Sturniolo
*/
public class Tensor {
@@ -125,7 +125,8 @@
switch ((";............." + ";eigenvalues.." + ";eigenvectors."
+ ";asymmetric..." + ";symmetric...." + ";trace........"
+ ";haeberlen...." + ";eulerzyz....." + ";eulerzxz....."
- + ";indices......" + ";type.........").indexOf(infoType) / 14) {
+ + ";quaternion..." + ";indices......" + ";type.........")
+ .indexOf(infoType) / 14) {
case 1:
return eigenValues;
case 2:
@@ -159,14 +160,15 @@
/ (eigenValues[2] - haeb[0]));
return haeb;
case 7: // eulerzyz
- return Quaternion.getQuaternionFrame(P3.new3(0, 0, 0),
- eigenVectors[0], eigenVectors[1]).getEulerZYZ();
+ return ((Quaternion) getInfo("quaternion")).getEulerZYZ();
case 8: // eulerzxz
- return Quaternion.getQuaternionFrame(P3.new3(0, 0, 0),
- eigenVectors[0], eigenVectors[1]).getEulerZXZ();
- case 9: //
+ return ((Quaternion) getInfo("quaternion")).getEulerZXZ();
+ case 9: // quaternion
+ return Quaternion.getQuaternionFrame(null, eigenVectors[0],
+ eigenVectors[1]);
+ case 10: //
return new int[] { modelIndex, atomIndex1, atomIndex2 };
- case 10:
+ case 11:
return type;
default:
return null;
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