Revision: 20337
http://sourceforge.net/p/jmol/code/20337
Author: hansonr
Date: 2015-02-26 15:23:18 +0000 (Thu, 26 Feb 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.2.12_2015.02.26"
bug fix: writing image of MO fails to write info (Jmol 12 or before)
bug fix: legacy non-XML JVXL reading does not color map
Modified Paths:
--------------
branches/v14_2/Jmol/src/org/jmol/jvxl/readers/JvxlReader.java
branches/v14_2/Jmol/src/org/jmol/script/ScriptEval.java
branches/v14_2/Jmol/src/org/jmol/scriptext/MathExt.java
branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties
branches/v14_2/Jmol/src/org/jmol/viewer/PropertyManager.java
branches/v14_2/Jmol/src/org/jmol/viewer/TransformManager.java
branches/v14_2/Jmol/src/org/jmol/viewer/Viewer.java
Modified: branches/v14_2/Jmol/src/org/jmol/jvxl/readers/JvxlReader.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/jvxl/readers/JvxlReader.java
2015-02-25 20:13:56 UTC (rev 20336)
+++ branches/v14_2/Jmol/src/org/jmol/jvxl/readers/JvxlReader.java
2015-02-26 15:23:18 UTC (rev 20337)
@@ -233,6 +233,8 @@
|| param3 < 0);
params.isBicolorMap = (param1 > 0 && param2 < 0);
jvxlDataIsColorMapped = (param3 != 0);
+ if (jvxlDataIsColorMapped)
+ jvxlData.colorScheme = "RGB"; // legacy
jvxlDataIs2dContour = (jvxlDataIsColorMapped && params.isContoured);
if (params.isBicolorMap || params.colorBySign)
Modified: branches/v14_2/Jmol/src/org/jmol/script/ScriptEval.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/script/ScriptEval.java 2015-02-25
20:13:56 UTC (rev 20336)
+++ branches/v14_2/Jmol/src/org/jmol/script/ScriptEval.java 2015-02-26
15:23:18 UTC (rev 20337)
@@ -5822,7 +5822,7 @@
q = getQuaternionParameter(i);
if (q != null) {
if (tok == T.best && !(isMolecular = isSelected)) // yes, setting
isMolecular here.
- q = q.mulQ(Quat.newM(vwr.tm.matrixRotate).mul(-1));
+ q = q.mulQ(vwr.tm.getRotationQ().mul(-1));
rotAxis.setT(q.getNormal());
endDegrees = q.getTheta();
}
Modified: branches/v14_2/Jmol/src/org/jmol/scriptext/MathExt.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/scriptext/MathExt.java 2015-02-25
20:13:56 UTC (rev 20336)
+++ branches/v14_2/Jmol/src/org/jmol/scriptext/MathExt.java 2015-02-26
15:23:18 UTC (rev 20337)
@@ -1958,7 +1958,7 @@
P4 p4 = null;
switch (nArgs) {
case 0:
- return mp.addXPt4(Quat.newM(vwr.tm.matrixRotate).toPoint4f());
+ return mp.addXPt4(vwr.tm.getRotationQ().toPoint4f());
case 1:
default:
if (tok == T.quaternion && args[0].tok == T.varray) {
Modified: branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties 2015-02-25
20:13:56 UTC (rev 20336)
+++ branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties 2015-02-26
15:23:18 UTC (rev 20337)
@@ -5,8 +5,13 @@
# THIS IS THE RELEASE BRANCH
# BUG FIXES ONLY, PLEASE
-Jmol.___JmolVersion="14.2.12_2015.02.22b"
+Jmol.___JmolVersion="14.2.12_2015.02.26"
+bug fix: writing image of MO fails to write info (Jmol 12 or before)
+bug fix: legacy non-XML JVXL reading does not color map
+
+JmolVersion="14.2.12_2015.02.22b"
+
bug fix: end-on bonds may appear to disappear
bug fix: JavaScript -2.format("%8.3") gives 2.000 not -2.000
bug fix: WRITE PDB broken
Modified: branches/v14_2/Jmol/src/org/jmol/viewer/PropertyManager.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/viewer/PropertyManager.java
2015-02-25 20:13:56 UTC (rev 20336)
+++ branches/v14_2/Jmol/src/org/jmol/viewer/PropertyManager.java
2015-02-26 15:23:18 UTC (rev 20337)
@@ -930,7 +930,7 @@
if (!asXYZVIB && bsAtoms.cardinality() == 0)
return "";
boolean isOK = true;
- Quat q = (doTransform ? Quat.newM(vwr.tm.matrixRotate) : null);
+ Quat q = (doTransform ? vwr.tm.getRotationQ() : null);
if (asSDF) {
String header = mol.toString();
mol = new SB();
Modified: branches/v14_2/Jmol/src/org/jmol/viewer/TransformManager.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/viewer/TransformManager.java
2015-02-25 20:13:56 UTC (rev 20336)
+++ branches/v14_2/Jmol/src/org/jmol/viewer/TransformManager.java
2015-02-26 15:23:18 UTC (rev 20337)
@@ -649,12 +649,16 @@
return info;
}
+ public Quat getRotationQ() {
+ return Quat.newM(matrixRotate);
+ }
+
String getOrientationText(int type) {
switch (type) {
case T.moveto:
return getMoveToText(1, false);
case T.rotation:
- return Quat.newM(vwr.tm.matrixRotate).toString();
+ return getRotationQ().toString();
case T.translation:
SB sb = new SB();
truncate2(sb, getTranslationXPercent());
@@ -674,7 +678,7 @@
A4 aa = new A4();
aa.setM(matrixRotate);
info.put("axisAngle", aa);
- info.put("quaternion", Quat.newM(matrixRotate).toPoint4f());
+ info.put("quaternion", getRotationQ().toPoint4f());
info.put("rotationMatrix", matrixRotate);
info.put("rotateZYZ", getRotateZyzText(false));
info.put("rotateXYZ", getRotateXyzText());
@@ -1171,11 +1175,11 @@
// in these renderers.
P3 ptCamera = P3.new3(screenWidth / 2, screenHeight / 2, 0);
- vwr.tm.unTransformPoint(ptCamera, ptCamera);
+ unTransformPoint(ptCamera, ptCamera);
ptCamera.sub(fixedRotationCenter);
P3 pt = P3.new3(screenWidth / 2, screenHeight / 2, cameraDistanceFromCenter
* scalePixelsPerAngstrom);
- vwr.tm.unTransformPoint(pt, pt);
+ unTransformPoint(pt, pt);
pt.sub(fixedRotationCenter);
ptCamera.add(pt);
Modified: branches/v14_2/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/viewer/Viewer.java 2015-02-25 20:13:56 UTC
(rev 20336)
+++ branches/v14_2/Jmol/src/org/jmol/viewer/Viewer.java 2015-02-26 15:23:18 UTC
(rev 20337)
@@ -823,24 +823,35 @@
* @return enough data to update a WebGL view
*
*/
+ @SuppressWarnings("unused")
public Object getGLmolView() {
- @SuppressWarnings("unused")
- TransformManager tm = this.tm;
+ T3 center = tm.fixedRotationCenter;
+ Quat q = tm.getRotationQ();
+ float xtrans = tm.xTranslationFraction;
+ float ytrans = tm.yTranslationFraction;
+ float scale = tm.scalePixelsPerAngstrom;
+ float zoom = tm.zmPctSet;
+ float cd = tm.cameraDistance;
+ float pc = tm.screenPixelCount;
+ boolean pd = tm.perspectiveDepth;
+ int width = tm.width;
+ int height = tm.height;
+
/**
* @j2sNative
*
* return {
- * center:tm.fixedRotationCenter,
- * quaternion:tm.getRotationQuaternion(),
- * xtrans:tm.xTranslationFraction,
- * ytrans:tm.yTranslationFraction,
- * scale:tm.scalePixelsPerAngstrom,
- * zoom:tm.zoomPercent,
- * cameraDistance:tm.cameraDistance,
- * pixelCount:tm.screenPixelCount,
- * perspective:tm.perspectiveDepth,
- * width:tm.width,
- * height:tm.height
+ * center:center,
+ * quaternion:q,
+ * xtrans:xtrans,
+ * ytrans:ytrans,
+ * scale:scale,
+ * zoom:zoom,
+ * cameraDistance:cd,
+ * pixelCount:pc,
+ * perspective:pd,
+ * width:width,
+ * height:height
* };
*/
{
@@ -3311,9 +3322,7 @@
&& checkMotionRendering(T.antialiasdisplay)
: isImageWrite && !isExport ? g.antialiasImages : false);
imageFontScaling = (isReset || width <= 0 ? 1
- : (g.zoomLarge == (height > width) ? height : width)
- / getScreenDim())
- * (antialiased ? 2 : 1);
+ : (antialiased ? 2 : 1) * (g.zoomLarge == (height > width) ? height :
width) / getScreenDim());
if (width > 0) {
dimScreen.width = width;
dimScreen.height = height;
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