Revision: 18281
http://sourceforge.net/p/jmol/code/18281
Author: hansonr
Date: 2013-06-04 23:48:28 +0000 (Tue, 04 Jun 2013)
Log Message:
-----------
___JmolVersion="13.1.16_dev_2013.06.04"
PyMOL: better scene restore;
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/pymol/JmolObject.java
trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pymol/JmolObject.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pymol/JmolObject.java
2013-06-04 23:27:41 UTC (rev 18280)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/JmolObject.java
2013-06-04 23:48:28 UTC (rev 18281)
@@ -137,8 +137,11 @@
sm.viewer.displayAtoms(bsAtoms, false, false, T.add, true);
return;
case T.restrict:
- sm.viewer.select(null, false, 0, true);
- sm.restrictSelected(false, false);
+ // start of generating shapes; argb is modelIndex
+ BS bs = sm.viewer.getModelUndeletedAtomsBitSet(argb);
+ BSUtil.invertInPlace(bs, sm.viewer.getAtomCount());
+ sm.viewer.select(bs, false, 0, true);
+ sm.restrictSelected(false, true);
return;
case T.display:
case T.hide:
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
2013-06-04 23:27:41 UTC (rev 18280)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
2013-06-04 23:48:28 UTC (rev 18281)
@@ -227,7 +227,7 @@
// create settings and uniqueSettings lists
JmolList<Object> settings = getMapList(map, "settings");
sceneOrder = getMapList(map, "scene_order");
- haveScenes = (sceneOrder != null && sceneOrder.size() != 0);
+ haveScenes = getFrameScenes(map);
JmolList<Object> file = listAt(settings, PyMOL.session_file);
if (file != null)
Logger.info("PyMOL session file: " + file.get(2));
@@ -394,6 +394,25 @@
}
/**
+ * remove all scenes that do not define a frame.
+ * @param map
+ * @return true if there are scenes that define a frame
+ */
+ @SuppressWarnings("unchecked")
+ private boolean getFrameScenes(Map<String, Object> map) {
+ if (sceneOrder == null)
+ return false;
+ Map<String, Object> scenes = (Map<String, Object>) map.get("scene_dict");
+ for (int i = 0; i < sceneOrder.size(); i++) {
+ String name = stringAt(sceneOrder, i);
+ JmolList<Object> thisScene = getMapList(scenes, name);
+ if (thisScene == null || thisScene.get(2) == null)
+ sceneOrder.remove(i--);
+ }
+ return (sceneOrder != null && sceneOrder.size() != 0);
+ }
+
+ /**
* Create uniqueSettings from the "unique_settings" map item.
* This will be used later in processing molecule objects.
*
@@ -1213,13 +1232,12 @@
Map<String, JmolList<Object>> htObjNames = PyMOLScene.listToMap(getMapList(
map, "names"));
if (haveScenes) {
- JmolList<Object> order = getMapList(map, "scene_order");
Map<String, Object> scenes = (Map<String, Object>) map.get("scene_dict");
finalizeSceneData();
Map<String, JmolList<Object>> htSecrets = PyMOLScene
.listToMap(getMapList(map, "selector_secrets"));
- for (int i = 0; i < order.size(); i++) {
- String name = stringAt(order, i);
+ for (int i = 0; i < sceneOrder.size(); i++) {
+ String name = stringAt(sceneOrder, i);
JmolList<Object> thisScene = getMapList(scenes, name);
if (thisScene == null)
continue;
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
2013-06-04 23:27:41 UTC (rev 18280)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
2013-06-04 23:48:28 UTC (rev 18281)
@@ -267,6 +267,8 @@
/**
*
+ * frame scenes only here
+ *
* @param name
* @param thisScene
* @param htObjNames
@@ -277,9 +279,6 @@
Map<String, JmolList<Object>> htObjNames,
Map<String, JmolList<Object>> htSecrets) {
Object frame = thisScene.get(2);
- if (frame == null)
- return; // must have frame defined; ignore other scenes
-
// generator : this
// name : scene name
// pymolFrame : specified frame
@@ -389,7 +388,7 @@
setObject(name, istate);
JmolList<Object> atomList = listAt(obj, 1);
int k0 = (istate == 0 ? 1 : istate);
- int k1 = (istate == 0 ? stateCount : istate + 1);
+ int k1 = (istate == 0 ? stateCount : istate);
for (int k = k0; k <= k1; k++) {
int[] atomMap = htAtomMap.get(fixName(name + "_" + k));
if (atomMap == null)
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-06-04 23:27:41 UTC
(rev 18280)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-06-04 23:48:28 UTC
(rev 18281)
@@ -11,6 +11,7 @@
___JmolVersion="13.1.16_dev_2013.06.04"
+PyMOL: better scene restore;
bug fix: "display add" by itself should not do anything
bug fix: Hall translation initialization problem
bug fix: JavaScript reading of old-style JVXL files
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