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[Jmol-commits] SF.net SVN: jmol:[19740] trunk/Jmol/src
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From: <ha...@us...> - 2014-05-27 00:27:02
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Revision: 19740
http://sourceforge.net/p/jmol/code/19740
Author: hansonr
Date: 2014-05-27 00:26:31 +0000 (Tue, 27 May 2014)
Log Message:
-----------
Modified Paths:
--------------
trunk/Jmol/src/javajs/util/P3.java
trunk/Jmol/src/javajs/util/P4.java
trunk/Jmol/src/javajs/util/T3.java
trunk/Jmol/src/javajs/util/T4.java
trunk/Jmol/src/javajs/util/V3.java
trunk/Jmol/src/org/jmol/script/ScriptEval.java
trunk/Jmol/src/org/jmol/symmetry/Symmetry.java
trunk/Jmol/src/org/jmol/symmetry/SymmetryOperation.java
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/javajs/util/P3.java
===================================================================
--- trunk/Jmol/src/javajs/util/P3.java 2014-05-26 21:13:49 UTC (rev 19739)
+++ trunk/Jmol/src/javajs/util/P3.java 2014-05-27 00:26:31 UTC (rev 19740)
@@ -33,6 +33,10 @@
*/
public class P3 extends T3 {
+ public P3() {
+ // ignore T3
+ }
+
public static P3 newP(T3 t) {
P3 p = new P3();
p.x = t.x;
Modified: trunk/Jmol/src/javajs/util/P4.java
===================================================================
--- trunk/Jmol/src/javajs/util/P4.java 2014-05-26 21:13:49 UTC (rev 19739)
+++ trunk/Jmol/src/javajs/util/P4.java 2014-05-27 00:26:31 UTC (rev 19740)
@@ -32,6 +32,14 @@
*/
public class P4 extends T4 {
+ /**
+ *
+ * @j2sIgnore *
+ */
+ public P4() {
+ // skip T4() constructor
+ }
+
public static P4 new4(float x, float y, float z, float w) {
P4 pt = new P4();
pt.set4(x, y, z, w);
Modified: trunk/Jmol/src/javajs/util/T3.java
===================================================================
--- trunk/Jmol/src/javajs/util/T3.java 2014-05-26 21:13:49 UTC (rev 19739)
+++ trunk/Jmol/src/javajs/util/T3.java 2014-05-27 00:26:31 UTC (rev 19740)
@@ -36,6 +36,10 @@
public float x, y, z;
+ /**
+ * @j2sIgnore
+ *
+ */
public T3() {
}
Modified: trunk/Jmol/src/javajs/util/T4.java
===================================================================
--- trunk/Jmol/src/javajs/util/T4.java 2014-05-26 21:13:49 UTC (rev 19739)
+++ trunk/Jmol/src/javajs/util/T4.java 2014-05-27 00:26:31 UTC (rev 19740)
@@ -37,6 +37,8 @@
/**
* Constructs and initializes a Tuple4f to (0,0,0,0).
+ *
+ * @j2sIgnore *
*/
public T4() {
}
Modified: trunk/Jmol/src/javajs/util/V3.java
===================================================================
--- trunk/Jmol/src/javajs/util/V3.java 2014-05-26 21:13:49 UTC (rev 19739)
+++ trunk/Jmol/src/javajs/util/V3.java 2014-05-27 00:26:31 UTC (rev 19740)
@@ -32,6 +32,9 @@
*/
public class V3 extends T3 {
+ public V3() {
+ // ignore T3
+ }
public static V3 newV(T3 t) {
return V3.new3(t.x, t.y, t.z);
}
Modified: trunk/Jmol/src/org/jmol/script/ScriptEval.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEval.java 2014-05-26 21:13:49 UTC (rev 19739)
+++ trunk/Jmol/src/org/jmol/script/ScriptEval.java 2014-05-27 00:26:31 UTC (rev 19740)
@@ -7575,7 +7575,7 @@
TickInfo tickInfo = tickParamAsStr(index, true, false, false);
index = iToken;
String id = null;
- P3[] points = null;
+ P3[] oabc = null;
Object newUC = null;
boolean isOffset = false;
boolean isReset = false;
@@ -7646,7 +7646,9 @@
//$FALL-THROUGH$
default:
if (isArrayParameter(index + 1)) {
- points = getPointArray(index, 4);
+ // Origin vA vB vC
+ // these are VECTORS, though
+ oabc = getPointArray(index, 4);
index = iToken;
} else if (slen == index + 2) {
if (getToken(index + 1).tok == T.integer
@@ -7664,13 +7666,13 @@
if (mad == Integer.MAX_VALUE)
vwr.am.cai = -1;
if (newUC != null)
- points = vwr.getPts0xyz(newUC);
+ oabc = vwr.getPts0xyz(newUC);
if (icell != Integer.MAX_VALUE)
vwr.ms.setUnitCellOffset(vwr.getCurrentUnitCell(), null, icell);
else if (id != null)
vwr.setCurrentCage(id);
- else if (isReset ||points != null)
- vwr.setCurrentCagePts(points);
+ else if (isReset ||oabc != null)
+ vwr.setCurrentCagePts(oabc);
setObjectMad(JC.SHAPE_UCCAGE, "unitCell", mad);
if (pt != null)
vwr.ms.setUnitCellOffset(vwr.getCurrentUnitCell(), pt, 0);
Modified: trunk/Jmol/src/org/jmol/symmetry/Symmetry.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/Symmetry.java 2014-05-26 21:13:49 UTC (rev 19739)
+++ trunk/Jmol/src/org/jmol/symmetry/Symmetry.java 2014-05-27 00:26:31 UTC (rev 19740)
@@ -835,33 +835,23 @@
P3[] pts = new P3[4];
P3 pt = new P3();
M3 m3 = new M3();
-
m.getRotationScale(m3);
m.getTranslation(pt);
if (isRev) {
- pts[0] = P3.new3(0, 0, 0);
- pts[1] = P3.new3(1, 0, 0);
- pts[2] = P3.new3(0, 1, 0);
- pts[3] = P3.new3(0, 0, 1);
m3.invert();
m3.transpose();
m3.rotate(pt);
- for (int i = 0; i < 4; i++) {
- m3.rotate(pts[i]);
- pts[i].sub(pt);
- uc.toCartesian(pts[i], false);
- }
- } else {
- uc.toCartesian(pt, false);
- M3 m3b = new M3();
- ((Symmetry)uc).unitCell.matrixFractionalToCartesian.getRotationScale(m3b);
- m3.mul2(m3b, m3);
- m3.transpose();
- pts[0] = P3.newP(pt);
- pts[1] = P3.new3(m3.m00, m3.m01, m3.m02);
- pts[2] = P3.new3(m3.m10, m3.m11, m3.m12);
- pts[3] = P3.new3(m3.m20, m3.m21, m3.m22);
- }
+ pt.scale(-1);
+ }
+ pts[0] = P3.newP(pt);
+ pts[1] = P3.new3(1, 0, 0);
+ pts[2] = P3.new3(0, 1, 0);
+ pts[3] = P3.new3(0, 0, 1);
+ for (int i = 1; i < 4; i++) {
+ m3.rotate(pts[i]);
+ uc.toCartesian(pts[i], false);
+ System.out.println(pts[i]);
+ }
return pts;
}
Modified: trunk/Jmol/src/org/jmol/symmetry/SymmetryOperation.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/SymmetryOperation.java 2014-05-26 21:13:49 UTC (rev 19739)
+++ trunk/Jmol/src/org/jmol/symmetry/SymmetryOperation.java 2014-05-27 00:26:31 UTC (rev 19740)
@@ -357,8 +357,11 @@
linearRotTrans[linearRotTrans.length - 1] = 1;
// may be a-b,-5a-5b,-c;0,0,0 form
int transPt = xyz.indexOf(';') + 1;
- if (transPt != 0)
+ if (transPt != 0) {
allowScaling = true;
+ if (transPt == xyz.length())
+ xyz += "0,0,0";
+ }
int rotPt = -1;
String[] myLabels = (op == null || modDim == 0 ? null : op.myLabels);
if (myLabels == null)
@@ -367,6 +370,7 @@
if (modDim > 0)
for (int i = modDim + 3; --i >= 0;)
xyz = PT.rep(xyz, labelsXn[i], labelsXnSub[i]);
+ int xpt = 0;
int tpt0 = 0;
int rowPt = 0;
char ch;
@@ -406,13 +410,14 @@
case 'h':
tpt0 = rowPt * nRows;
int ipt = (ch >= 'x' ? ch - 'x' :ch - 'a' + dimOffset);
+ xpt = tpt0 + ipt;
int val = (isNegative ? -1 : 1);
if (allowScaling && iValue != 0) {
- linearRotTrans[tpt0 + ipt] = iValue;
+ linearRotTrans[xpt] = iValue;
val = (int) iValue;
iValue = 0;
} else {
- linearRotTrans[tpt0 + ipt] = val;
+ linearRotTrans[xpt] = val;
}
strT += plusMinus(strT, val, myLabels[ipt]);
break;
@@ -463,7 +468,12 @@
}
if (ich >= 0 && ich <= 9) {
if (isDenominator) {
- iValue /= ich;
+ if (iValue == 0) {
+ // a/2,....
+ linearRotTrans[xpt] /= ich;
+ } else {
+ iValue /= ich;
+ }
} else {
iValue = iValue * 10 + (isNegative ? -1 : 1) * ich;
isNegative = false;
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2014-05-26 21:13:49 UTC (rev 19739)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2014-05-27 00:26:31 UTC (rev 19740)
@@ -3102,10 +3102,10 @@
ms.setModelCage(am.cmi, (SymmetryInterface) data[1]);
}
- public void setCurrentCagePts(P3[] ptsOrMat4) {
+ public void setCurrentCagePts(T3[] originABC) {
try {
ms.setModelCage(am.cmi,
- ptsOrMat4 == null ? null : Interface.getSymmetry().getUnitCell(ptsOrMat4, false));
+ originABC == null ? null : Interface.getSymmetry().getUnitCell(originABC, false));
} catch (Exception e) {
//
}
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