Revision: 18273
http://sourceforge.net/p/jmol/code/18273
Author: hansonr
Date: 2013-06-02 17:38:09 +0000 (Sun, 02 Jun 2013)
Log Message:
-----------
___JmolVersion="13.1.16_dev_2013.06.1"
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
trunk/Jmol/src/org/jmol/shapespecial/Dots.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/StateManager.java
trunk/Jmol/src/org/jmol/viewer/TransformManager.java
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
2013-05-31 16:16:56 UTC (rev 18272)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
2013-06-02 17:38:09 UTC (rev 18273)
@@ -922,7 +922,7 @@
s = "[x" + s.substring(s.length() - 6) + "]";
sb.append(";background " + s);
sb.append(";moveto 0 PyMOL " + Escape.eAF(pymolView));
- sb.append(";");
+ sb.append(";save orientation 'default';");
return sb;
}
Modified: trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2013-05-31 16:16:56 UTC
(rev 18272)
+++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2013-06-02 17:38:09 UTC
(rev 18273)
@@ -6813,6 +6813,9 @@
refresh();
if (!useThreads())
floatSecondsTotal = 0;
+ if (cameraDepth == 0) {
+ cameraDepth = cameraX = cameraY = Float.NaN;
+ }
if (pymolView != null)
viewer.movePyMOL(this, floatSecondsTotal, pymolView);
else
Modified: trunk/Jmol/src/org/jmol/shapespecial/Dots.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapespecial/Dots.java 2013-05-31 16:16:56 UTC
(rev 18272)
+++ trunk/Jmol/src/org/jmol/shapespecial/Dots.java 2013-06-02 17:38:09 UTC
(rev 18273)
@@ -274,7 +274,7 @@
}
// now, calculate surface for selected atoms
- if (dotsConvexMaps == null && colixes.length != atomCount) {
+ if (dotsConvexMaps == null && (colixes == null || colixes.length !=
atomCount)) {
colixes = new short[atomCount];
paletteIDs = new byte[atomCount];
}
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-05-31 16:16:56 UTC
(rev 18272)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-06-02 17:38:09 UTC
(rev 18273)
@@ -9,7 +9,7 @@
# The quotes above look odd for a parameter file, but they are
# important for the JavaScript version of Jmol.
-___JmolVersion="13.1.16_dev_2013.05.31a"
+___JmolVersion="13.1.16_dev_2013.06.1"
bug fix: Hall translation initialization problem
bug fix: JavaScript reading of old-style JVXL files
Modified: trunk/Jmol/src/org/jmol/viewer/StateManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/StateManager.java 2013-05-31 16:16:56 UTC
(rev 18272)
+++ trunk/Jmol/src/org/jmol/viewer/StateManager.java 2013-06-02 17:38:09 UTC
(rev 18273)
@@ -131,6 +131,7 @@
}
GlobalSettings getGlobalSettings(GlobalSettings gsOld, boolean
clearUserVariables) {
+ saved.clear();
return new GlobalSettings(gsOld, clearUserVariables);
}
@@ -159,7 +160,7 @@
void setJmolDefaults() {
setCommonDefaults();
- viewer.setStringProperty("defaultColorScheme", "Jmol");
+ viewer.setStringProperty("ColorScheme", "Jmol");
viewer.setBooleanProperty("axesOrientationRasmol", false);
viewer.setBooleanProperty("zeroBasedXyzRasmol", false);
viewer.setIntProperty("percentVdwAtom",
@@ -350,7 +351,7 @@
deleteSavedType("Orientation_");
return;
}
- Orientation o = new Orientation(saveName.equals("default"), pymolView);
+ Orientation o = new Orientation(saveName.equalsIgnoreCase("default"),
pymolView);
o.saveName = lastOrientation = "Orientation_" + saveName;
saved.put(o.saveName, o);
}
@@ -395,6 +396,7 @@
moveToText = "moveTo -1.0 PyMOL " + Escape.eAF(pymolView);
return;
}
+ viewer.finalizeTransformParameters();
if (asDefault) {
Matrix3f rotationMatrix = (Matrix3f) viewer
.getModelSetAuxiliaryInfoValue("defaultOrientationMatrix");
@@ -420,7 +422,11 @@
navDepth = viewer.getNavigationDepthPercent();
navCenter = P3.newP(viewer.getNavigationCenter());
}
- cameraDepth = viewer.getCameraDepth();
+ if (viewer.getCamera().z != 0) { // PyMOL mode
+ cameraDepth = viewer.getCameraDepth();
+ cameraX = viewer.getCamera().x;
+ cameraY = viewer.getCamera().y;
+ }
}
public String getMoveToText(boolean asCommand) {
Modified: trunk/Jmol/src/org/jmol/viewer/TransformManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/TransformManager.java 2013-05-31
16:16:56 UTC (rev 18272)
+++ trunk/Jmol/src/org/jmol/viewer/TransformManager.java 2013-06-02
17:38:09 UTC (rev 18273)
@@ -1757,6 +1757,7 @@
}
String getMoveToText(float timespan, boolean addComments) {
+ finalizeTransformParameters();
SB sb = new SB();
sb.append("moveto ");
if (addComments)
This was sent by the SourceForge.net collaborative development platform, the
world's largest Open Source development site.
------------------------------------------------------------------------------
Get 100% visibility into Java/.NET code with AppDynamics Lite
It's a free troubleshooting tool designed for production
Get down to code-level detail for bottlenecks, with <2% overhead.
Download for free and get started troubleshooting in minutes.
http://p.sf.net/sfu/appdyn_d2d_ap2
_______________________________________________
Jmol-commits mailing list
Jmol-commits@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-commits
