Revision: 18265
http://sourceforge.net/p/jmol/code/18265
Author: hansonr
Date: 2013-05-30 16:35:52 +0000 (Thu, 30 May 2013)
Log Message:
-----------
___JmolVersion="13.1.16_dev_2013.05.30b"
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
trunk/Jmol/src/org/jmol/shapespecial/Dots.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
2013-05-30 13:25:58 UTC (rev 18264)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
2013-05-30 16:35:52 UTC (rev 18265)
@@ -45,7 +45,6 @@
BS bsLabeled = new BS();
BS bsHydrogen = new BS();
BS bsNoSurface = new BS();
- BS bsCartoon = new BS();
// private -- only needed for file reading
@@ -85,6 +84,7 @@
// private -- needed for processing Scenes
+ private BS bsCartoon = new BS();
private Map<String, Boolean> htHiddenObjects = new Hashtable<String,
Boolean>();
private JmolList<String> moleculeNames = new JmolList<String>();
private JmolList<JmolObject> jmolObjects = new JmolList<JmolObject>();
@@ -419,8 +419,6 @@
String groupName = htObjectGroups.get(objectName);
objectHidden = (htHiddenObjects.containsKey(name) || groupName != null
&& !groups.get(groupName).visible);
- if (name.startsWith("1iep"))
- System.out.println(name + " " + groupName + " " + !objectHidden);
getObjectSettings();
}
@@ -601,14 +599,9 @@
viewer.setStringProperty("measurementUnits", "ANGSTROMS");
viewer.setBooleanProperty("zoomHeight", true);
setGroupVisibilities();
- for (String e: occludedObjects.keySet())
- System.out.println("occluded " + e);
-
if (groups != null) {
for (int i = jmolObjects.size(); --i >= 0;) {
JmolObject obj = jmolObjects.get(i);
- if (obj.id == T.isosurface)
- System.out.println(obj.visible + " " + obj.objectNameID);
if (obj.objectNameID != null
&& occludedObjects.containsKey(obj.objectNameID))
obj.visible = false;
@@ -625,7 +618,6 @@
for (PyMOLGroup g : list) {
if (g.parent != null)
continue;
- System.out.println("Checking " + g.name + " " + g.visible);
setGroupVisible(g, true);
}
}
@@ -1041,6 +1033,7 @@
private void fixReps(BS[] reps) {
htSpacefill.clear();
+ bsCartoon.clearAll();
for (int iAtom = objectAtoms.nextSetBit(0); iAtom >= 0; iAtom =
objectAtoms.nextSetBit(iAtom + 1)) {
float rad = 0;
int uniqueID = (reader == null ? uniqueIDs[iAtom] : reader
@@ -1096,10 +1089,13 @@
}
}
}
- cleanSingletons(reps[PyMOL.REP_CARTOON]);
+
+ reps[PyMOL.REP_CARTOON].and(bsCartoon);
+ cleanSingletons(reps[PyMOL.REP_CARTOON]);
cleanSingletons(reps[PyMOL.REP_RIBBON]);
cleanSingletons(reps[PyMOL.REP_JMOL_TRACE]);
cleanSingletons(reps[PyMOL.REP_JMOL_PUTTY]);
+ bsCartoon.and(reps[PyMOL.REP_CARTOON]);
}
/**
@@ -1111,6 +1107,9 @@
* @param bs
*/
private void cleanSingletons(BS bs) {
+ if (bs.isEmpty())
+ return;
+ bs.and(objectAtoms);
BS bsr = new BS();
int n = bs.length();
int pass = 0;
@@ -1148,8 +1147,6 @@
* Note that LINES and STICKS are done initially, then all the others are
* processed.
*
- * REP_DASHES not implemented yet.
- *
* @param shapeID
* @param bs
*/
@@ -1324,7 +1321,6 @@
if (bs == null)
return;
bs.and(bsCartoon);
- bs.and(objectAtoms);
if (bs.isEmpty())
return;
if (key.equals(" ")) {
@@ -1352,7 +1348,6 @@
boolean vis = parentVis && g.visible;
if (vis)
return;
- System.out.println("hiding " + g.name + " " + g.objectNameID);
g.visible = false;
occludedObjects.put(g.objectNameID, Boolean.TRUE);
htHiddenObjects.put(g.name, Boolean.TRUE);
Modified: trunk/Jmol/src/org/jmol/shapespecial/Dots.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapespecial/Dots.java 2013-05-30 13:25:58 UTC
(rev 18264)
+++ trunk/Jmol/src/org/jmol/shapespecial/Dots.java 2013-05-30 16:35:52 UTC
(rev 18265)
@@ -274,7 +274,7 @@
}
// now, calculate surface for selected atoms
- if (dotsConvexMaps == null) {
+ if (dotsConvexMaps == 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 2013-05-30 13:25:58 UTC
(rev 18264)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-05-30 16:35:52 UTC
(rev 18265)
@@ -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_2013.05.30a"
+___JmolVersion="13.1.16_dev_2013.05.30b"
new feature: restore SCENE "xxxx" nSec
new feature: Scene menu
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