Revision: 20875
http://sourceforge.net/p/jmol/code/20875
Author: hansonr
Date: 2015-12-01 05:14:58 +0000 (Tue, 01 Dec 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.5.0_2015.11.30"
bug fix: getProperty("JSON", "variableInfo", "x") will fail if x is an array
-- was problem with JSV_predict2 failing to properly map atoms between Jmol
and JSME
bug fix: {atomset}.sxyz gives incorrect screen coordinate when antialiased
bug fix: point(pt, true|false) also modifies pt itself
bug fix: point({atomset}, true) gives incorrect screen coordinate when
antialiased.
bug fix: point({atomset}, false) gives incorrect Cartesian coordinate when
antialiased.
bug fix: popup menu item "Surfaces...Off" resets atom selection
bug fix: files with names containing "[]" cannot be loaded.
bug fix: print {cell=555}.find("cellFormula") can fail because of 2% slop
involved in defining cell=555
bug fix: {atomset}.split() [split atomset by model] returns array of strings,
not array of atoms
bug fix: getproperty SHAPEINFO fails if CGO is present
bug fix: CGO from state deletes DRAW objects
bug fix: CGO not properly isolated to current model; "fixed" not implemented
Modified Paths:
--------------
branches/v14_4/Jmol/src/org/jmol/api/SymmetryInterface.java
branches/v14_4/Jmol/src/org/jmol/modelset/Atom.java
branches/v14_4/Jmol/src/org/jmol/popup/AwtSwingPopupHelper.java
branches/v14_4/Jmol/src/org/jmol/popup/MainPopupResourceBundle.java
branches/v14_4/Jmol/src/org/jmol/script/SV.java
branches/v14_4/Jmol/src/org/jmol/scriptext/MathExt.java
branches/v14_4/Jmol/src/org/jmol/symmetry/Symmetry.java
branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: branches/v14_4/Jmol/src/org/jmol/api/SymmetryInterface.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/api/SymmetryInterface.java 2015-12-01
05:13:30 UTC (rev 20874)
+++ branches/v14_4/Jmol/src/org/jmol/api/SymmetryInterface.java 2015-12-01
05:14:58 UTC (rev 20875)
@@ -156,10 +156,10 @@
public SymmetryInterface setPointGroup(
SymmetryInterface pointGroupPrevious,
- T3[] atomset, BS bsAtoms,
+ T3[] atomset,
+ BS bsAtoms,
boolean haveVibration,
- float distanceTolerance,
- float linearTolerance, boolean
localEnvOnly);
+ float distanceTolerance, float
linearTolerance, boolean localEnvOnly);
public void setSpaceGroup(boolean doNormalize);
Modified: branches/v14_4/Jmol/src/org/jmol/modelset/Atom.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/modelset/Atom.java 2015-12-01 05:13:30 UTC
(rev 20874)
+++ branches/v14_4/Jmol/src/org/jmol/modelset/Atom.java 2015-12-01 05:14:58 UTC
(rev 20875)
@@ -1369,8 +1369,7 @@
return (group.chain.model.isJmolDataFrame ?
getFractionalCoordPt(!vwr.g.legacyJavaFloat, false, ptTemp)
: getFractionalUnitCoordPt(!vwr.g.legacyJavaFloat, false, ptTemp));
case T.screenxyz:
- return P3.new3(sX, group.chain.model.ms.vwr.getScreenHeight()
- - sY, sZ);
+ return P3.new3(vwr.antialiased ? sX / 2 : sX, vwr.getScreenHeight() -
(vwr.antialiased ? sY / 2 : sY), vwr.antialiased ? sZ / 2 : sZ);
case T.vibxyz:
return getVibrationVector();
case T.modxyz:
Modified: branches/v14_4/Jmol/src/org/jmol/popup/AwtSwingPopupHelper.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/popup/AwtSwingPopupHelper.java
2015-12-01 05:13:30 UTC (rev 20874)
+++ branches/v14_4/Jmol/src/org/jmol/popup/AwtSwingPopupHelper.java
2015-12-01 05:14:58 UTC (rev 20875)
@@ -112,6 +112,8 @@
@Override
public int getItemType(SC m) {
+ if (m == null)
+ return 0;
JComponent jc = ((AwtSwingComponent) m).jc;
return (jc instanceof JMenu ? 4
: jc instanceof JRadioButtonMenuItem ? 3
Modified: branches/v14_4/Jmol/src/org/jmol/popup/MainPopupResourceBundle.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/popup/MainPopupResourceBundle.java
2015-12-01 05:13:30 UTC (rev 20874)
+++ branches/v14_4/Jmol/src/org/jmol/popup/MainPopupResourceBundle.java
2015-12-01 05:14:58 UTC (rev 20875)
@@ -1007,7 +1007,7 @@
"isosurface delete resolution 0 vdw color range -0.1 0.1 map MEP
translucent" },
{ "surfOpaque", "mo opaque;isosurface opaque" },
{ "surfTranslucent", "mo translucent;isosurface translucent" },
- { "surfOff", "mo delete;isosurface delete;select *;dots off" },
+ { "surfOff", "mo delete;isosurface delete;var ~~sel = {selected};select
*;dots off;select ~~sel" },
{ "FILEMOLload",
"save orientation;load \"\";restore orientation;center" },
{ "FILEUNITone",
Modified: branches/v14_4/Jmol/src/org/jmol/script/SV.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/script/SV.java 2015-12-01 05:13:30 UTC
(rev 20874)
+++ branches/v14_4/Jmol/src/org/jmol/script/SV.java 2015-12-01 05:14:58 UTC
(rev 20875)
@@ -1230,10 +1230,9 @@
*
* @param args
* @param pt 0: to JSON, 5: to base64, 12: to bytearray, 22: to array
- * @param array2D
* @return formatted string
*/
- public static Object format(SV[] args, int pt, boolean array2D) {
+ public static Object format(SV[] args, int pt) {
switch (args.length) {
case 0:
return "";
@@ -1757,4 +1756,17 @@
}
return this;
}
+
+ /**
+ * Safely create a JSON key - object pair, allowing for already-named arrays
+ *
+ * @param key
+ * @param property
+ * @return JSON object
+ */
+ public static Object safeJSON(String key, Object property) {
+ return "{"
+ + (property instanceof SV ? PT.esc(key) + " : " + format(new SV[] {
null, (SV) property },
+ 0) : PT.toJSON(key, property)) + "}";
+ }
}
Modified: branches/v14_4/Jmol/src/org/jmol/scriptext/MathExt.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/scriptext/MathExt.java 2015-12-01
05:13:30 UTC (rev 20874)
+++ branches/v14_4/Jmol/src/org/jmol/scriptext/MathExt.java 2015-12-01
05:14:58 UTC (rev 20875)
@@ -1548,7 +1548,7 @@
if (pt >= 0 && args.length != 2)
return false;
if (pt >= 0 || args.length < 2 || args[1].tok != T.varray) {
- Object o = SV.format(args, pt, false);
+ Object o = SV.format(args, pt);
return (format.equalsIgnoreCase("json") ? mp.addXStr((String)o) :
mp.addXObj(o));
}
// fill an array with applied formats
@@ -1557,7 +1557,7 @@
String[] sa = new String[a.size()];
for (int i = sa.length; --i >= 0;) {
args2[1] = a.get(i);
- sa[i] = SV.format(args2, pt, true).toString();
+ sa[i] = SV.format(args2, pt).toString();
}
return mp.addXAS(sa);
}
@@ -2093,7 +2093,7 @@
* @param mp
* @param args
* @param tok
- * @return
+ * @return true
* @throws ScriptException
*/
private boolean evaluatePlane(ScriptMathProcessor mp, SV[] args, int tok)
@@ -2272,20 +2272,34 @@
Object pt = Escape.uP(s);
return (pt instanceof P3 ? mp.addXPt((P3) pt) : mp.addXStr("" + pt));
case 2:
- // to/from screen coordinates
P3 pt3;
switch (args[1].tok) {
case T.off:
- if ((pt3 = SV.ptValue(args[0])) == null)
- return false;
- // these are screen coordinates
- vwr.tm.unTransformPoint(pt3, pt3);
- break;
case T.on:
- if ((pt3 = SV.ptValue(args[0])) == null)
+ // to/from screen coordinates
+ switch (args[0].tok) {
+ case T.point3f:
+ pt3 = P3.newP((T3) args[0].value);
+ break;
+ case T.bitset:
+ pt3 = vwr.ms.getAtomSetCenter(SV.bsSelectVar(args[0]));
+ break;
+ default:
return false;
- // this is TO screen coordinates
+ }
+ if (args[1].tok == T.on) {
+ // this is TO screen coordinates, 0 at bottom left
vwr.tm.transformPt3f(pt3, pt3);
+ pt3.y = vwr.tm.height - pt3.y;
+ if (vwr.antialiased)
+ pt3.scale(0.5f);
+ } else {
+ // this is FROM screen coordinates
+ if (vwr.antialiased)
+ pt3.scale(2f);
+ pt3.y = vwr.tm.height - pt3.y;
+ vwr.tm.unTransformPoint(pt3, pt3);
+ }
break;
case T.point3f:
// unitcell transform
Modified: branches/v14_4/Jmol/src/org/jmol/symmetry/Symmetry.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/symmetry/Symmetry.java 2015-12-01
05:13:30 UTC (rev 20874)
+++ branches/v14_4/Jmol/src/org/jmol/symmetry/Symmetry.java 2015-12-01
05:14:58 UTC (rev 20875)
@@ -96,14 +96,14 @@
@Override
public SymmetryInterface setPointGroup(SymmetryInterface siLast,
- T3[] atomset, BS bsAtoms,
+ T3[] atomset,
+ BS bsAtoms,
boolean haveVibration,
float distanceTolerance,
- float linearTolerance,
- boolean localEnvOnly) {
+ float linearTolerance, boolean
localEnvOnly) {
pointGroup = PointGroup.getPointGroup(siLast == null ? null
- : ((Symmetry) siLast).pointGroup, atomset, bsAtoms, haveVibration,
- distanceTolerance, linearTolerance, localEnvOnly);
+ : ((Symmetry) siLast).pointGroup, atomset, bsAtoms,
+ haveVibration, distanceTolerance, linearTolerance, localEnvOnly);
return this;
}
@@ -323,7 +323,7 @@
@Override
public String getSymmetryInfoStr() {
- return symmetryInfo == null ? "" : symmetryInfo.infoStr;
+ return (symmetryInfo == null ? "" : symmetryInfo.infoStr);
}
@Override
@@ -379,9 +379,9 @@
boolean isAbsolute) {
uc.toFractional(ptTemp, isAbsolute);
// {1 1 1} here is the original cell
- return (ptTemp.x >= cell.x - 1f - slop && ptTemp.x <= cell.x + slop
- && ptTemp.y >= cell.y - 1f - slop && ptTemp.y <= cell.y + slop
- && ptTemp.z >= cell.z - 1f - slop && ptTemp.z <= cell.z + slop);
+ return (ptTemp.x >= cell.x - 1f - SimpleUnitCell.SLOP && ptTemp.x <=
cell.x + SimpleUnitCell.SLOP
+ && ptTemp.y >= cell.y - 1f - SimpleUnitCell.SLOP && ptTemp.y <= cell.y
+ SimpleUnitCell.SLOP
+ && ptTemp.z >= cell.z - 1f - SimpleUnitCell.SLOP && ptTemp.z <= cell.z
+ SimpleUnitCell.SLOP);
}
@Override
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2015-12-01
05:13:30 UTC (rev 20874)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2015-12-01
05:14:58 UTC (rev 20875)
@@ -8,17 +8,18 @@
# see also http://chemapps.stolaf.edu/jmol/zip for daily updates
-Jmol.___JmolVersion="14.4.0_2015.11.29"
+Jmol.___JmolVersion="14.5.0_2015.11.30"
+bug fix: getProperty("JSON", "variableInfo", "x") will fail if x is an array
+ -- was problem with JSV_predict2 failing to properly map atoms between Jmol
and JSME
+bug fix: {atomset}.sxyz gives incorrect screen coordinate when antialiased
+bug fix: point(pt, true|false) also modifies pt itself
+bug fix: point({atomset}, true) gives incorrect screen coordinate when
antialiased.
+bug fix: point({atomset}, false) gives incorrect Cartesian coordinate when
antialiased.
+bug fix: popup menu item "Surfaces...Off" resets atom selection
bug fix: files with names containing "[]" cannot be loaded.
bug fix: print {cell=555}.find("cellFormula") can fail because of 2% slop
involved in defining cell=555
-
-JmolVersion="14.4.0_2015.11.27"
-
bug fix: {atomset}.split() [split atomset by model] returns array of strings,
not array of atoms
-
-JmolVersion="14.4.0_2015.11.26"
-
bug fix: getproperty SHAPEINFO fails if CGO is present
bug fix: CGO from state deletes DRAW objects
bug fix: CGO not properly isolated to current model; "fixed" not implemented
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