Revision: 20166
http://sourceforge.net/p/jmol/code/20166
Author: hansonr
Date: 2014-12-19 14:16:33 +0000 (Fri, 19 Dec 2014)
Log Message:
-----------
Jmol.___JmolVersion="14.3.11_2014.12.19"
bug fix: JavaScript connect broken
due to j2s failure to create bsAromatic when BondCollection created
(14.3.7)
due to j2s bug in instantiating global definitions in super classes
using Clazz_prepareFields
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/quantum/GenNBOReader.java
trunk/Jmol/src/org/jmol/modelset/BondCollection.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/adapter/readers/quantum/GenNBOReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/quantum/GenNBOReader.java
2014-12-19 13:06:49 UTC (rev 20165)
+++ trunk/Jmol/src/org/jmol/adapter/readers/quantum/GenNBOReader.java
2014-12-19 14:16:33 UTC (rev 20166)
@@ -487,7 +487,7 @@
String type = tokens[i];
mo.put("type", moType + " " + type);
// TODO: does not account for SOMO
- mo.put("occupancy", Float.valueOf(type.indexOf("*") >= 0 ? 0 : 2));
+ mo.put("occupancy", Float.valueOf(type.indexOf("*") >= 0 ||
type.indexOf("(ry)") >= 0 ? 0 : 2));
}
return true;
}
Modified: trunk/Jmol/src/org/jmol/modelset/BondCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/BondCollection.java 2014-12-19
13:06:49 UTC (rev 20165)
+++ trunk/Jmol/src/org/jmol/modelset/BondCollection.java 2014-12-19
14:16:33 UTC (rev 20166)
@@ -53,7 +53,7 @@
private BS bsAromaticSingle;
private BS bsAromaticDouble;
- protected BS bsAromatic = new BS();
+ protected BS bsAromatic;
public boolean haveHiddenBonds;
@@ -63,6 +63,7 @@
protected final static int MAX_NUM_TO_CACHE = 200;
protected void setupBC() {
+ bsAromatic = new BS();
numCached = new int[MAX_BONDS_LENGTH_TO_CACHE];
freeBonds = new Bond[MAX_BONDS_LENGTH_TO_CACHE][][];
for (int i = MAX_BONDS_LENGTH_TO_CACHE; --i > 0;) // NOT >= 0
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2014-12-19 13:06:49 UTC
(rev 20165)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2014-12-19 14:16:33 UTC
(rev 20166)
@@ -18,6 +18,10 @@
Jmol.___JmolVersion="14.3.11_2014.12.19"
+bug fix: JavaScript connect broken
+ due to j2s failure to create bsAromatic when BondCollection created
(14.3.7)
+ due to j2s bug in instantiating global definitions in super classes
using Clazz_prepareFields
+
bug fix: label, echo, and measurement text should not display when deeper
than zSlab with zShade is TRUE
bug fix: mmCIF reader load filter biomolecule 1
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