Revision: 18442
http://sourceforge.net/p/jmol/code/18442
Author: hansonr
Date: 2013-07-10 12:52:33 +0000 (Wed, 10 Jul 2013)
Log Message:
-----------
JS fix; draw symmetry fix
Modified Paths:
--------------
trunk/Jmol/appletweb/jsmol.zip
trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java
trunk/Jmol/src/org/jmol/script/ScriptCompilationTokenParser.java
trunk/Jmol/src/org/jmol/shapespecial/Polyhedra.java
trunk/Jmol/src/org/jmol/symmetry/SymmetryOperation.java
trunk/Jmol/src/org/jmol/util/Elements.java
trunk/Jmol/src/org/jmol/util/Geodesic.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/appletweb/jsmol.zip
===================================================================
(Binary files differ)
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2013-07-08
05:53:00 UTC (rev 18441)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2013-07-10
12:52:33 UTC (rev 18442)
@@ -723,7 +723,7 @@
{"ZMatrix", "#ZMATRIX"};
private final static String[] magresFileStartRecords =
- {"Magres", "#$magres"};
+ {"Magres", "#$magres", "# magres"};
private final static String[] pymolStartRecords =
{"PyMOL", "}q" };
Modified: trunk/Jmol/src/org/jmol/script/ScriptCompilationTokenParser.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptCompilationTokenParser.java
2013-07-08 05:53:00 UTC (rev 18441)
+++ trunk/Jmol/src/org/jmol/script/ScriptCompilationTokenParser.java
2013-07-10 12:52:33 UTC (rev 18442)
@@ -829,7 +829,8 @@
if (addNextTokenIf(T.decimal))
if (!addNextTokenIf(T.comma))
break;
- String strOrder = (String) getToken().value;
+ Object o = getToken().value;
+ String strOrder = (o instanceof String ? (String) o : " ");
int intType = ScriptEvaluator.getBondOrderFromString(strOrder);
if (intType == JmolEdge.BOND_ORDER_NULL) {
returnToken();
Modified: trunk/Jmol/src/org/jmol/shapespecial/Polyhedra.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapespecial/Polyhedra.java 2013-07-08 05:53:00 UTC
(rev 18441)
+++ trunk/Jmol/src/org/jmol/shapespecial/Polyhedra.java 2013-07-10 12:52:33 UTC
(rev 18442)
@@ -368,8 +368,7 @@
while (!isOK && factor < 10.0f) {
distMax = dAverage * factor;
- for (int i = 0; i < ptCenter; i++)
- bs.set(i);
+ bs.setBits(0, ptCenter);
for (int i = 0; i < ptCenter - 2; i++)
for (int j = i + 1; j < ptCenter - 1; j++) {
if (points[i].distance(points[j]) > distMax)
@@ -397,6 +396,7 @@
}
}
+
/* Start by defining a face to be when all three distances
* are < distanceFactor * (longest central) but if a vertex is missed,
* then expand the range. The collapsed trick is to introduce
@@ -437,9 +437,13 @@
if (points[i].distance(points[j]) > distMax)
continue;
for (int k = j + 1; k < ptCenter; k++) {
+ System.out.println("checking poly " + i + " " + j + " " + k);
+ System.out.println("checking poly " + points[i] + " " + points[j] +
" " + points[k]);
+
if (points[i].distance(points[k]) > distMax
|| points[j].distance(points[k]) > distMax)
continue;
+ System.out.println("checking poly " + i + " " + j + " " + k + " ok
");
if (planeCount >= FACE_COUNT_MAX) {
Logger.error("Polyhedron error: maximum face(" + FACE_COUNT_MAX
Modified: trunk/Jmol/src/org/jmol/symmetry/SymmetryOperation.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/SymmetryOperation.java 2013-07-08
05:53:00 UTC (rev 18441)
+++ trunk/Jmol/src/org/jmol/symmetry/SymmetryOperation.java 2013-07-10
12:52:33 UTC (rev 18442)
@@ -1063,7 +1063,7 @@
// returns triangles and lines
for (int i = v.size(); --i >= 0;) {
P3[] pts = (P3[]) v.get(i);
- draw1.append(drawid).append("planep").appendI(i).append(
+ draw1.append(drawid).append("planep").appendI(i).append(" ").append(
Escape.eP(pts[0])).append(Escape.eP(pts[1]));
if (pts.length == 3)
draw1.append(Escape.eP(pts[2]));
Modified: trunk/Jmol/src/org/jmol/util/Elements.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Elements.java 2013-07-08 05:53:00 UTC (rev
18441)
+++ trunk/Jmol/src/org/jmol/util/Elements.java 2013-07-10 12:52:33 UTC (rev
18442)
@@ -216,7 +216,7 @@
int pt = elementSymbol.length() - 2;
if (pt >= 0 && Character.isDigit(elementSymbol.charAt(pt)))
pt++;
- int isotope = Parser.parseInt(elementSymbol.substring(0, pt));
+ int isotope = (pt > 0 ? Parser.parseInt(elementSymbol.substring(0, pt))
: 0);
if (isotope > 0) {
int n = elementNumberFromSymbol(elementSymbol.substring(pt), true);
if (n > 0) {
Modified: trunk/Jmol/src/org/jmol/util/Geodesic.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Geodesic.java 2013-07-08 05:53:00 UTC (rev
18441)
+++ trunk/Jmol/src/org/jmol/util/Geodesic.java 2013-07-10 12:52:33 UTC (rev
18442)
@@ -112,7 +112,14 @@
* it would be easier to take advantage of symmetry in the process of
* converting from normal to normix.
*/
+
+/**
+ *
+ * J2SRequireImport is needed because we use ArrayUtil in a static method
+ *
+ */
+@J2SRequireImport({org.jmol.util.ArrayUtil.class})
public class Geodesic {
private final static float halfRoot5 = (float)(0.5 * Math.sqrt(5));
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-07-08 05:53:00 UTC
(rev 18441)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-07-10 12:52:33 UTC
(rev 18442)
@@ -9,7 +9,7 @@
# The quotes above look odd for a parameter file, but they are
# important for the JavaScript version of Jmol.
-___JmolVersion="13.1.19_dev_2013.07.07"
+___JmolVersion="13.1.19_dev_2013.07.09"
code: org.jmol.quantum.NMRCalculation smoothly handles J-coupling and dipolar
coupling constant display.
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