Revision: 18279
http://sourceforge.net/p/jmol/code/18279
Author: hansonr
Date: 2013-06-04 23:07:59 +0000 (Tue, 04 Jun 2013)
Log Message:
-----------
___JmolVersion="13.1.16_dev_2013.06.04"
bug fix: "display add" by itself should not do anything
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/adapter/smarter/Bond.java
trunk/Jmol/src/org/jmol/modelset/BondCollection.java
trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
trunk/Jmol/src/org/jmol/script/T.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 23:07:26 UTC (rev 18278)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/JmolObject.java
2013-06-04 23:07:59 UTC (rev 18279)
@@ -126,22 +126,30 @@
}
@SuppressWarnings("unchecked")
- void finalizeObject(ModelSet m, String mepList, boolean doCache) {
+ void finalizeObject(PyMOLScene pymolScene, ModelSet m, String mepList,
boolean doCache) {
ShapeManager sm = m.shapeManager;
int modelIndex = getModelIndex(m);
String sID;
SB sb = null;
switch (id) {
+ case T.hidden:
+ // bsHidden
+ sm.viewer.displayAtoms(bsAtoms, false, false, T.add, true);
+ return;
+ case T.restrict:
+ sm.viewer.select(null, false, 0, true);
+ sm.restrictSelected(false, false);
+ return;
case T.display:
case T.hide:
// from PyMOLScene after restore scene
if (bsAtoms == null) {
if (info == null) {
- sm.viewer.displayAtoms(null, true, false, null, true);
+ sm.viewer.displayAtoms(null, true, false, 0, true);
}
sm.viewer.setObjectProp((String) info, id);
} else {
- sm.viewer.displayAtoms(bsAtoms, id == T.display, false, Boolean.TRUE,
+ sm.viewer.displayAtoms(bsAtoms, id == T.display, false, T.add,
true);
}
return;
@@ -169,14 +177,21 @@
sm.viewer.saveOrientation(objectNameID,
(float[]) ((Map<String, Object>) info).get("pymolView"));
return;
- case T.hidden:
- sm.viewer.displayAtoms(bsAtoms, false, false, Boolean.TRUE, true);
- return;
case JC.SHAPE_LABELS:
sm.loadShape(id);
sm.setShapePropertyBs(id, "textLabels", info, bsAtoms);
return;
+ case T.bonds:
+ break;
+ case T.wireframe:
case JC.SHAPE_STICKS:
+ if (size != -1) {
+ sm.setShapeSizeBs(JC.SHAPE_STICKS, size, null, bsAtoms);
+
pymolScene.setUniqueBonds(((BS[])sm.getShapePropertyIndex(JC.SHAPE_STICKS,
"sets", 0))[1], id == JC.SHAPE_STICKS);
+ size = -1;
+ }
+ id = JC.SHAPE_STICKS;
+ break;
case JC.SHAPE_BALLS:
break;
case JC.SHAPE_TRACE:
@@ -197,10 +212,6 @@
}
switch (id) {
- case T.restrict:
- sm.viewer.select(null, false, null, true);
- sm.restrictSelected(false, false);
- return;
case JC.SHAPE_MEASURES:
if (modelIndex < 0)
return;
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
2013-06-04 23:07:26 UTC (rev 18278)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
2013-06-04 23:07:59 UTC (rev 18279)
@@ -40,8 +40,6 @@
import org.jmol.util.BoxInfo;
import org.jmol.util.BS;
import org.jmol.util.BSUtil;
-import org.jmol.util.C;
-//import org.jmol.util.Dimension;
import org.jmol.util.Logger;
import org.jmol.util.P3;
import org.jmol.util.TextFormat;
@@ -72,7 +70,7 @@
* 3) JmolObjects are finalized after file reading takes place by a call from
ModelLoader
* back here to finalizeModelSet(), which runs PyMOLScene.setObjects, which
runs JmolObject.finalizeObject.
*
- *
+ * TODO: Handle discrete objects, DiscreteAtmToIdx?
*
* @author Bob Hanson hans...@stolaf.edu
*
@@ -136,6 +134,8 @@
private JmolList<Object> sceneOrder;
+ private int bondCount;
+
@Override
protected void initializeReader() throws Exception {
isBinary = true;
@@ -178,8 +178,7 @@
@Override
public void finalizeModelSet(int baseModelIndex, int baseAtomIndex) {
- pymolScene.setObjects(mepList, doCache, baseModelIndex, baseAtomIndex,
- haveScenes);
+ pymolScene.setObjects(mepList, doCache, baseModelIndex, baseAtomIndex);
if (haveMeasurements) {
appendLoadNote(viewer.getMeasurementInfoAsString());
@@ -235,7 +234,7 @@
//atomSetCollection.setAtomSetCollectionAuxiliaryInfo("settings",
settings);
setUniqueSettings(getMapList(map, "unique_settings"));
pymolScene = new PyMOLScene(this, viewer, settings, uniqueSettings,
- pymolVersion);
+ pymolVersion, haveScenes);
// just log and display some information here
@@ -399,14 +398,18 @@
* This will be used later in processing molecule objects.
*
* @param list
+ * @return max id
*/
@SuppressWarnings("unchecked")
- private void setUniqueSettings(JmolList<Object> list) {
+ private int setUniqueSettings(JmolList<Object> list) {
uniqueSettings = new Hashtable<Integer, JmolList<Object>>();
+ int max = 0;
if (list != null && list.size() != 0) {
for (int i = list.size(); --i >= 0;) {
JmolList<Object> atomSettings = (JmolList<Object>) list.get(i);
int id = intAt(atomSettings, 0);
+ if (id > max)
+ max = id;
JmolList<Object> mySettings = (JmolList<Object>) atomSettings.get(1);
for (int j = mySettings.size(); --j >= 0;) {
JmolList<Object> setting = (JmolList<Object>) mySettings.get(j);
@@ -416,6 +419,7 @@
}
}
}
+ return max;
}
/**
@@ -856,9 +860,6 @@
*/
private JmolList<Bond> getBondList(JmolList<Object> bonds) {
JmolList<Bond> bondList = new JmolList<Bond>();
- int color = (int) pymolScene.floatSetting(PyMOL.stick_color);
- float radius = pymolScene.floatSetting(PyMOL.stick_radius);
- float translucency = pymolScene.floatSetting(PyMOL.stick_transparency);
boolean valence = pymolScene.booleanSetting(PyMOL.valence);
int n = bonds.size();
for (int i = 0; i < n; i++) {
@@ -866,29 +867,11 @@
int order = (valence ? intAt(b, 2) : 1);
if (order < 1 || order > 3)
order = 1;
- // TODO: hydrogen bonds?
int ia = intAt(b, 0);
int ib = intAt(b, 1);
Bond bond = new Bond(ia, ib, order);
+ bond.uniqueID = (b.size() > 6 && intAt(b, 6) != 0 ? intAt(b, 5) : -1);
bondList.addLast(bond);
- int c;
- float rad, t;
- boolean hasID = (b.size() > 6 && intAt(b, 6) != 0);
- if (hasID) {
- int id = intAt(b, 5);
- rad = pymolScene.getUniqueFloatDef(id, PyMOL.stick_radius, radius);
- c = (int) pymolScene.getUniqueFloatDef(id, PyMOL.stick_color, color);
- t = pymolScene.getUniqueFloatDef(id, PyMOL.stick_transparency,
translucency);
- } else {
- rad = radius;
- c = color;
- t = translucency;
- }
- // I think rad is being ignored, because later we set it with a script
- bond.radius = rad;
- if (c >= 0)
- bond.colix = C.getColixTranslucent3(C.getColix(PyMOL.getRGB(c)), t > 0,
- t);
}
return bondList;
}
@@ -1027,6 +1010,8 @@
float[] data = PyMOLScene.floatsAt(a, 41, new float[7], 6);
atomSetCollection.setAnisoBorU(atom, data, 12);
}
+ //if (uniqueID > 0)
+ //pymolScene.setUnique(uniqueID, atom);
pymolScene.setAtomColor(uniqueID, atomColor);
processAtom2(atom, serNo, x, y, z, formalCharge);
@@ -1060,8 +1045,10 @@
Bond bond = bonds.get(i);
bond.atomIndex1 = atomMap[bond.atomIndex1];
bond.atomIndex2 = atomMap[bond.atomIndex2];
- if (bond.atomIndex1 >= 0 && bond.atomIndex2 >= 0)
- atomSetCollection.addBond(bond);
+ if (bond.atomIndex1 < 0 || bond.atomIndex2 < 0)
+ continue;
+ pymolScene.setUniqueBond(bondCount++, bond.uniqueID);
+ atomSetCollection.addBond(bond);
}
}
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
2013-06-04 23:07:26 UTC (rev 18278)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
2013-06-04 23:07:59 UTC (rev 18279)
@@ -78,7 +78,6 @@
htStateSettings = null;
objectInfo = null;
settings = null;
- uniqueSettings = null;
occludedObjects = null;
htHiddenObjects = null;
bsHidden = bsNucleic = bsNonbonded = bsLabeled = bsHydrogen = bsNoSurface
= bsCartoon = null;
@@ -102,7 +101,18 @@
private Map<String, Map<Integer, JmolList<Object>>> htStateSettings = new
Hashtable<String, Map<Integer, JmolList<Object>>>();
private Map<Integer, JmolList<Object>> stateSettings;
private Map<Integer, JmolList<Object>> uniqueSettings;
-
+ private Map<Integer, Integer> uniqueList;
+ private BS bsUniqueBonds;
+ void setUniqueBond(int index, int uniqueID) {
+ if (uniqueID < 0)
+ return;
+ if (uniqueList == null) {
+ uniqueList = new Hashtable<Integer, Integer>();
+ bsUniqueBonds = new BS();
+ }
+ uniqueList.put(Integer.valueOf(index), Integer.valueOf(uniqueID));
+ bsUniqueBonds.set(index);
+ }
private int bgRgb;
private int surfaceMode;
private int surfaceColor;
@@ -144,8 +154,12 @@
private boolean doCache;
private boolean haveScenes;
+
private BS bsCarve;
private boolean solventAccessible;
+ private BS bsLineBonds = new BS();
+ private BS bsStickBonds = new BS();
+ private int thisState;
void setStateCount(int stateCount) {
this.stateCount = stateCount;
@@ -153,12 +167,13 @@
@SuppressWarnings("unchecked")
PyMOLScene(PymolAtomReader reader, Viewer viewer, JmolList<Object> settings,
- Map<Integer, JmolList<Object>> uniqueSettings, int pymolVersion) {
+ Map<Integer, JmolList<Object>> uniqueSettings, int pymolVersion, boolean
haveScenes) {
this.reader = reader;
this.viewer = viewer;
this.settings = settings;
this.uniqueSettings = uniqueSettings;
this.pymolVersion = pymolVersion;
+ this.haveScenes = haveScenes;
setVersionSettings();
bgRgb = colorSetting(listAt(settings, PyMOL.bg_rgb));
pointAt((JmolList<Object>) listAt(settings, PyMOL.label_position).get(2),
@@ -261,6 +276,9 @@
void buildScene(String name, JmolList<Object> thisScene,
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
@@ -271,12 +289,10 @@
// colors: [colorIndex, object list]
//
Map<String, Object> smap = new Hashtable<String, Object>();
+ smap.put("pymolFrame", frame);
smap.put("generator", this);
smap.put("name", name);
JmolList<Object> view = listAt(thisScene, 0);
- Object frame = thisScene.get(2);
- if (frame != null)
- smap.put("pymolFrame", frame);
if (view != null)
smap.put("pymolView", getPymolView(view, false));
@@ -332,14 +348,12 @@
occludedObjects.clear();
htHiddenObjects.clear();
Integer frame = (Integer) scene.get("pymolFrame");
- if (frame != null)
- addJmolObject(T.frame, null, Integer.valueOf(frame.intValue() - 1));
+ thisState = frame.intValue();
+ addJmolObject(T.frame, null, Integer.valueOf(thisState - 1));
try {
- int istate = (frame == null ? 0 : frame.intValue());
- generateVisibilities((Map<String, Object>) scene.get("visibilities"),
- istate);
- generateColors((Object[]) scene.get("colors"), istate);
- generateShapes((Object[]) scene.get("moleculeReps"), istate);
+ generateVisibilities((Map<String, Object>) scene.get("visibilities"));
+ generateColors((Object[]) scene.get("colors"));
+ generateShapes((Object[]) scene.get("moleculeReps"));
finalizeEverything();
finalizeObjects();
} catch (Exception e) {
@@ -349,7 +363,7 @@
}
@SuppressWarnings("unchecked")
- private void generateColors(Object[] colors, int istate) {
+ private void generateColors(Object[] colors) {
if (colors == null)
return;
// note that colors are for ALL STATES
@@ -358,7 +372,7 @@
int color = ((Integer) item[0]).intValue();
int icolor = PyMOL.getRGB(color);
JmolList<Object> molecules = (JmolList<Object>) item[1];
- BS bs = getSelectionAtoms(molecules, istate, new BS());
+ BS bs = getSelectionAtoms(molecules, thisState, new BS());
addJmolObject(JC.SHAPE_BALLS, bs, null).argb = icolor;
}
}
@@ -385,7 +399,7 @@
}
@SuppressWarnings("unchecked")
- private void generateVisibilities(Map<String, Object> vis, int istate) {
+ private void generateVisibilities(Map<String, Object> vis) {
if (vis == null)
return;
BS bs = new BS();
@@ -413,7 +427,7 @@
String name = e.getKey();
if (name.equals("all"))
continue;
- setObject(name, istate);
+ setObject(name, thisState);
if (objectHidden)
continue;
JmolList<Object> list = (JmolList<Object>) e.getValue();
@@ -464,14 +478,14 @@
}
@SuppressWarnings("unchecked")
- private void generateShapes(Object[] reps, int istate) {
+ private void generateShapes(Object[] reps) {
if (reps == null)
return;
- addJmolObject(T.restrict, null, null);
+ addJmolObject(T.restrict, null, null).argb = thisState - 1;
// through all molecules...
// for (int m = moleculeNames.size(); --m >= 0;) {
for (int m = 0; m < moleculeNames.size(); m++) {
- setObject(moleculeNames.get(m), istate);
+ setObject(moleculeNames.get(m), thisState);
getObjectSettings();
if (objectHidden)
continue;
@@ -483,7 +497,7 @@
Map<String, JmolList<Object>> repMap = (Map<String, JmolList<Object>>)
reps[i];
JmolList<Object> list = (repMap == null ? null :
repMap.get(objectName));
if (list != null)
- selectAllAtoms(list, istate, molReps[i]);
+ selectAllAtoms(list, thisState, molReps[i]);
}
createShapeObjects(molReps, true, -1, -1);
}
@@ -518,14 +532,17 @@
}
void setObjects(String mepList, boolean doCache, int baseModelIndex,
- int baseAtomIndex, boolean haveScenes) {
+ int baseAtomIndex) {
this.baseModelIndex = baseModelIndex;
this.baseAtomIndex = baseAtomIndex;
this.mepList = mepList;
this.doCache = doCache;
- this.haveScenes = haveScenes;
clearReaderData(!haveScenes);
finalizeObjects();
+ if (!haveScenes) {
+ uniqueSettings = null;
+ bsUniqueBonds = bsStickBonds = bsLineBonds = null;
+ }
}
private void finalizeObjects() {
@@ -533,12 +550,13 @@
try {
JmolObject obj = jmolObjects.get(i);
obj.offset(baseModelIndex, baseAtomIndex);
- obj.finalizeObject(viewer.modelSet, mepList, doCache);
+ obj.finalizeObject(this, viewer.modelSet, mepList, doCache);
} catch (Exception e) {
System.out.println(e);
e.printStackTrace();
}
}
+ finalizeUniqueBonds();
jmolObjects.clear();
}
@@ -981,7 +999,7 @@
}
if (frameObj == null)
return;
- frameObj.finalizeObject(viewer.getModelSet(), null, false);
+ frameObj.finalizeObject(this, viewer.getModelSet(), null, false);
frameObj = null;
}
@@ -1312,13 +1330,19 @@
createRibbonObject(bs);
break;
case PyMOL.REP_LINES:
- jo = addJmolObject(JC.SHAPE_STICKS, bs, null);
+ jo = addJmolObject(T.wireframe, bs, null);
jo.setSize(floatSetting(PyMOL.line_width) / 15);
+ int color = (int) floatSetting(PyMOL.line_color);
+ if (color >= 0)
+ jo.argb = PyMOL.getRGB(color);
break;
case PyMOL.REP_STICKS:
jo = addJmolObject(JC.SHAPE_STICKS, bs, null);
jo.setSize(floatSetting(PyMOL.stick_radius) * 2);
jo.translucency = stickTranslucency;
+ int col = (int) floatSetting(PyMOL.stick_color);
+ if (col >= 0)
+ jo.argb = PyMOL.getRGB(col);
break;
default:
Logger.error("Unprocessed representation type " + shapeID);
@@ -1521,4 +1545,33 @@
return haveScenes || !htCarveSets.isEmpty();
}
+ public void setUniqueBonds(BS bsBonds, boolean isSticks) {
+ if (isSticks) {
+ bsStickBonds.or(bsBonds);
+ bsStickBonds.andNot(bsLineBonds);
+ } else {
+ bsLineBonds.or(bsBonds);
+ bsLineBonds.andNot(bsStickBonds);
+ }
+ }
+
+ private void finalizeUniqueBonds() {
+ if (uniqueList == null)
+ return;
+ for (int i = bsUniqueBonds.nextSetBit(0); i >= 0; i =
bsUniqueBonds.nextSetBit(i + 1)) {
+ float rad = Float.NaN;
+ int id = uniqueList.get(Integer.valueOf(i)).intValue();
+ if (bsLineBonds.get(i)) {
+ rad = getUniqueFloatDef(id, PyMOL.line_width, Float.NaN) / 30;
+ } else if (bsStickBonds.get(i)) {
+ rad = getUniqueFloatDef(id, PyMOL.stick_radius, Float.NaN);
+ }
+ int c = (int) getUniqueFloatDef(id, PyMOL.stick_color,
Integer.MAX_VALUE);
+ if (c != Integer.MAX_VALUE)
+ c = PyMOL.getRGB(c);
+ float t = getUniqueFloatDef(id, PyMOL.stick_transparency, Float.NaN);
+ viewer.setBondParameters(thisState - 1, i, rad, c, t);
+ }
+ }
+
}
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/Bond.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/Bond.java 2013-06-04 23:07:26 UTC
(rev 18278)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/Bond.java 2013-06-04 23:07:59 UTC
(rev 18279)
@@ -29,6 +29,7 @@
public int order;
public float radius = -1;
public short colix = -1;
+ public int uniqueID = -1;
public Bond (int atomIndex1, int atomIndex2, int order) {
this.atomIndex1 = atomIndex1;
Modified: trunk/Jmol/src/org/jmol/modelset/BondCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/BondCollection.java 2013-06-04
23:07:26 UTC (rev 18278)
+++ trunk/Jmol/src/org/jmol/modelset/BondCollection.java 2013-06-04
23:07:59 UTC (rev 18279)
@@ -30,6 +30,7 @@
import org.jmol.util.ArrayUtil;
import org.jmol.util.BS;
import org.jmol.util.BSUtil;
+import org.jmol.util.C;
import org.jmol.util.JmolEdge;
import org.jmol.util.JmolMolecule;
import org.jmol.util.Logger;
@@ -847,5 +848,31 @@
bonds[i].setShapeVisibility(isDisplay);
}
+ /**
+ * used in PyMOL reader to set unique bond settings
+ * @param modelIndex
+ * @param i
+ * @param rad
+ * @param argb
+ * @param trans
+ */
+ public void setBondParameters(int modelIndex, int i, float rad, int argb,
float trans) {
+ if (i < 0 || i >= bondCount)
+ return;
+ Bond b = bonds[i];
+ if (modelIndex >= 0 && b.atom1.modelIndex != modelIndex)
+ return;
+ if (!Float.isNaN(rad))
+ b.mad = (short) (rad * 2000);
+ short colix = b.colix;
+ if (argb != Integer.MAX_VALUE)
+ colix = C.getColix(argb);
+ if (!Float.isNaN(trans))
+ b.colix = C.getColixTranslucent3(colix, trans != 0, trans);
+ else if (b.colix != colix)
+ b.colix = C.copyColixTranslucency(b.colix, colix);
+ }
+
+
}
Modified: trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2013-06-04 23:07:26 UTC
(rev 18278)
+++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2013-06-04 23:07:59 UTC
(rev 18279)
@@ -11003,13 +11003,13 @@
private void display(boolean isDisplay) throws ScriptException {
BS bs = null;
- Boolean addRemove = null;
+ int addRemove = 0;
int i = 1;
int tok;
switch (tok = tokAt(1)) {
case T.add:
case T.remove:
- addRemove = Boolean.valueOf(tok == T.add);
+ addRemove = tok;
tok = tokAt(++i);
break;
}
@@ -11144,7 +11144,7 @@
private void select(int i) throws ScriptException {
// NOTE this is called by restrict()
if (slen == 1) {
- viewer.select(null, false, null, tQuiet
+ viewer.select(null, false, 0, tQuiet
|| scriptLevel > scriptReportingLevel);
return;
}
@@ -11171,8 +11171,8 @@
}
error(ERROR_invalidArgument);
}
- BS bs = null;
- Boolean addRemove = null;
+ BS bs;
+ int addRemove = 0;
boolean isGroup = false;
if (getToken(1).intValue == 0) {
Object v = parameterExpressionToken(0).value;
@@ -11185,7 +11185,7 @@
switch (tok) {
case T.add:
case T.remove:
- addRemove = Boolean.valueOf(tok == T.add);
+ addRemove = tok;
tok = tokAt(++i);
}
isGroup = (tok == T.group);
@@ -11321,7 +11321,7 @@
boolean isQuiet = (tQuiet || scriptLevel > scriptReportingLevel);
if (!isQuiet)
scriptStatusOrBuffer(GT._("{0} atoms deleted", nDeleted));
- viewer.select(null, false, null, isQuiet);
+ viewer.select(null, false, 0, isQuiet);
}
private void zoom(boolean isZoomTo) throws ScriptException {
@@ -12000,7 +12000,7 @@
.valueOf(JmolEdge.BOND_HYDROGEN_MASK));
setShapeSizeBs(JC.SHAPE_STICKS, 0, bsAtoms);
viewer.autoHbond(bsAtoms, bsAtoms, true);
- viewer.select(bsAtoms, false, null, tQuiet);
+ viewer.select(bsAtoms, false, 0, tQuiet);
}
private void vector() throws ScriptException {
Modified: trunk/Jmol/src/org/jmol/script/T.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/T.java 2013-06-04 23:07:26 UTC (rev
18278)
+++ trunk/Jmol/src/org/jmol/script/T.java 2013-06-04 23:07:59 UTC (rev
18279)
@@ -264,7 +264,7 @@
final static int print = 1 | mathExpressionCommand;
final static int returncmd = 2 | mathExpressionCommand;
- final static int set = 3 | mathExpressionCommand | expression;
+ public final static int set = 3 | mathExpressionCommand |
expression;
final static int var = 4 | mathExpressionCommand;
final static int log = 5 | mathExpressionCommand;
//final static int prompt see mathfunc
@@ -743,7 +743,7 @@
// distance(a,b)
//so it can be a math property and it can have up to two parameters
- final static int add = 1 | 2 << 9 | mathfunc | mathproperty;
+ public final static int add = 1 | 2 << 9 | mathfunc | mathproperty;
public final static int distance = 2 | 2 << 9 | mathfunc | mathproperty;
final static int find = 4 | 3 << 9 | mathfunc | mathproperty;
final static int replace = 3 | 2 << 9 | mathfunc | mathproperty;
@@ -1241,7 +1241,7 @@
public final static int range = misc | 290;
public final static int rasmol = misc | 292;
final static int reference = misc | 294;
- final static int remove = misc | 295;
+ public final static int remove = misc | 295;
public final static int residue = misc | 296;
final static int resolution = misc | 298;
final static int reversecolor = misc | 300;
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-06-04 23:07:26 UTC
(rev 18278)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-06-04 23:07:59 UTC
(rev 18279)
@@ -9,8 +9,9 @@
# The quotes above look odd for a parameter file, but they are
# important for the JavaScript version of Jmol.
-___JmolVersion="13.1.16_dev_2013.06.01"
+___JmolVersion="13.1.16_dev_2013.06.04"
+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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