Revision: 18280
http://sourceforge.net/p/jmol/code/18280
Author: hansonr
Date: 2013-06-04 23:27:41 +0000 (Tue, 04 Jun 2013)
Log Message:
-----------
___version=13.0.16_dev_2013.06.04
bug fix: "display add" by itself should not do anything
bug fix: Gaussian reader not splitting MO set by model
bug fix: polyhedra not saved in state
Modified Paths:
--------------
branches/v13_0/Jmol/src/org/jmol/adapter/readers/quantum/GaussianReader.java
branches/v13_0/Jmol/src/org/jmol/script/ScriptEvaluator.java
branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties
branches/v13_0/Jmol/src/org/jmol/viewer/SelectionManager.java
Modified:
branches/v13_0/Jmol/src/org/jmol/adapter/readers/quantum/GaussianReader.java
===================================================================
---
branches/v13_0/Jmol/src/org/jmol/adapter/readers/quantum/GaussianReader.java
2013-06-04 23:07:59 UTC (rev 18279)
+++
branches/v13_0/Jmol/src/org/jmol/adapter/readers/quantum/GaussianReader.java
2013-06-04 23:27:41 UTC (rev 18280)
@@ -77,7 +77,9 @@
private int equivalentAtomSets = 0;
private int stepNumber;
+ private int moModelSet = -1;
+
/**
* Reads a Collection of AtomSets from a BufferedReader.
*
@@ -546,7 +548,8 @@
}
}
addMOData(nThisLine, data, mos);
- setMOData(false); // perhaps in the future we might change this to TRUE
+ setMOData(moModelSet != atomSetCollection.getAtomSetCount());
+ moModelSet = atomSetCollection.getAtomSetCount();
}
/* SAMPLE FREQUENCY OUTPUT */
Modified: branches/v13_0/Jmol/src/org/jmol/script/ScriptEvaluator.java
===================================================================
--- branches/v13_0/Jmol/src/org/jmol/script/ScriptEvaluator.java
2013-06-04 23:07:59 UTC (rev 18279)
+++ branches/v13_0/Jmol/src/org/jmol/script/ScriptEvaluator.java
2013-06-04 23:27:41 UTC (rev 18280)
@@ -15661,7 +15661,7 @@
isDesignParameter = true;
continue;
case Token.distancefactor:
- if (!needsGenerating)
+ if (nAtomSets == 0)
error(ERROR_insufficientArguments);
decimalPropertyName = "distanceFactor";
isDesignParameter = true;
Modified: branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-06-04
23:07:59 UTC (rev 18279)
+++ branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-06-04
23:27:41 UTC (rev 18280)
@@ -9,8 +9,11 @@
# Don't use ___ in your text, as that is the key for stripping out
# the information saved in the JAR version of this file.
-___version=13.0.16_dev_2013.05.20a
+___version=13.0.16_dev_2013.06.04
+bug fix: "display add" by itself should not do anything
+bug fix: Gaussian reader not splitting MO set by model
+bug fix: polyhedra not saved in state
bug fix: rockets not working for alpha polymer
bug fix: GXL added to carbohydrates
bug fix: show state/anim turns "anim" into "animation"
Modified: branches/v13_0/Jmol/src/org/jmol/viewer/SelectionManager.java
===================================================================
--- branches/v13_0/Jmol/src/org/jmol/viewer/SelectionManager.java
2013-06-04 23:07:59 UTC (rev 18279)
+++ branches/v13_0/Jmol/src/org/jmol/viewer/SelectionManager.java
2013-06-04 23:27:41 UTC (rev 18280)
@@ -79,15 +79,16 @@
}
void hide(ModelSet modelSet, BitSet bs, Boolean addRemove, boolean isQuiet) {
- if (bs == null) {
+ if (addRemove == null) {
bsHidden.clear();
- } else if (addRemove == null) {
- bsHidden.clear();
- bsHidden.or(bs);
+ if (bs != null)
+ bsHidden.or(bs);
} else if (addRemove.booleanValue()) {
- bsHidden.or(bs);
+ if (bs != null)
+ bsHidden.or(bs);
} else {
- bsHidden.andNot(bs);
+ if (bs != null)
+ bsHidden.andNot(bs);
}
if (modelSet != null)
modelSet.setBsHidden(bsHidden);
@@ -97,16 +98,17 @@
}
void display(ModelSet modelSet, BitSet bs, Boolean addRemove, boolean
isQuiet) {
- BitSet bsAll = modelSet.getModelAtomBitSetIncludingDeleted(-1, false);
- if (bs == null) {
- bsHidden.clear();
- } else if (addRemove == null) {
+ BitSet bsAll = modelSet.getModelAtomBitSetIncludingDeleted(-1, false);
+ if (addRemove == null) {
bsHidden.or(bsAll);
- bsHidden.andNot(bs);
+ if (bs != null)
+ bsHidden.andNot(bs);
} else if (addRemove.booleanValue()) {
- bsHidden.andNot(bs);
+ if (bs != null)
+ bsHidden.andNot(bs);
} else {
- bsHidden.or(bs);
+ if (bs != null)
+ bsHidden.or(bs);
}
BitSetUtil.andNot(bsHidden, bsDeleted);
modelSet.setBsHidden(bsHidden);
@@ -195,15 +197,16 @@
}
void setSelectionSet(BitSet set, Boolean addRemove) {
- if (set == null) {
+ if (addRemove == null) {
bsSelection.clear();
- } else if (addRemove == null) {
- bsSelection.clear();
- bsSelection.or(set);
+ if (set != null)
+ bsSelection.or(set);
} else if (addRemove.booleanValue()) {
- bsSelection.or(set);
+ if (set != null)
+ bsSelection.or(set);
} else {
- bsSelection.andNot(set);
+ if (set != null)
+ bsSelection.andNot(set);
}
empty = UNKNOWN;
selectionChanged(false);
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