Revision: 20775
http://sourceforge.net/p/jmol/code/20775
Author: hansonr
Date: 2015-09-14 22:41:00 +0000 (Mon, 14 Sep 2015)
Log Message:
-----------
fix for 2D mol file H atom addition and minimization failing; releasing 14.3.16
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/script/ScriptEval.java
trunk/Jmol/src/org/jmol/viewer/FileManager.java
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/org/jmol/script/ScriptEval.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEval.java 2015-09-14 18:19:24 UTC
(rev 20774)
+++ trunk/Jmol/src/org/jmol/script/ScriptEval.java 2015-09-14 22:41:00 UTC
(rev 20775)
@@ -4621,6 +4621,7 @@
vwr.setBooleanProperty("legacyJavaFloat", false);
if (isMutate)
htParams.put("isMutate", Boolean.TRUE);
+ htParams.put("eval", this);
errMsg = vwr.loadModelFromFile(null, filename, filenames, null, isAppend,
htParams, loadScript, sOptions, tokType, isConcat);
if (timeMsg)
Modified: trunk/Jmol/src/org/jmol/viewer/FileManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/FileManager.java 2015-09-14 18:19:24 UTC
(rev 20774)
+++ trunk/Jmol/src/org/jmol/viewer/FileManager.java 2015-09-14 22:41:00 UTC
(rev 20775)
@@ -1207,9 +1207,9 @@
void cacheClear() {
Logger.info("cache cleared");
cache.clear();
- String fileName = null;
- fileName = fileName == null ? null :
getCanonicalName(Rdr.getZipRoot(fileName));
- if (pngjCache == null || fileName != null &&
!pngjCache.containsKey(fileName))
+ //String fileName = null;
+ //fileName = fileName == null ? null :
getCanonicalName(Rdr.getZipRoot(fileName));
+ if (pngjCache == null)// || fileName != null &&
!pngjCache.containsKey(fileName))
return;
pngjCache = null;
Logger.info("PNGJ cache cleared");
@@ -1296,6 +1296,7 @@
? vwr.vwrOptions.get("codePath") + classPath + resourceName
: url.getFile());
if (vwr.async) {
+ // if we are running asynchronously, this will be a problem.
Object bytes = vwr.fm.cacheGet(resourceName, false);
if (bytes == null)
throw new JmolAsyncException(resourceName);
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-09-14 18:19:24 UTC (rev
20774)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-09-14 22:41:00 UTC (rev
20775)
@@ -1971,7 +1971,7 @@
// loadInline
if (arrayModels == null || arrayModels.length == 0)
return null;
- String ret = openStringsInlineParamsAppend(arrayModels, null, isAppend);
+ String ret = openStringsInlineParamsAppend(arrayModels, new
Hashtable<String, Object>(), isAppend);
refresh(1, "loadInline String[]");
return ret;
}
@@ -1999,7 +1999,7 @@
Object atomSetCollection = fm.createAtomSeCollectionFromArrayData(list,
setLoadParameters(null, isAppend), isAppend);
String ret = createModelSetAndReturnError(atomSetCollection, isAppend,
- null, null);
+ null, new Hashtable<String, Object>());
refresh(1, "loadInline");
return ret;
}
@@ -2109,7 +2109,7 @@
Object atomSetCollection = fm.createAtomSetCollectionFromString(strModel,
htParams, isAppend);
return createModelSetAndReturnError(atomSetCollection, isAppend,
- loadScript, null);
+ loadScript, htParams);
}
/**
@@ -2131,7 +2131,7 @@
arrayModels, loadScript, setLoadParameters(htParams, isAppend),
isAppend);
return createModelSetAndReturnError(atomSetCollection, isAppend,
- loadScript, null);
+ loadScript, htParams);
}
public char getInlineChar() {
@@ -2194,7 +2194,8 @@
String jmolScript = (String) ms.getInfoM("jmolscript");
if (ms.getMSInfoB("doMinimize"))
try {
- minimize((JmolScriptEvaluator) htParams.get("eval"),
+ JmolScriptEvaluator eval = (JmolScriptEvaluator)
htParams.get("eval");
+ minimize(eval,
Integer.MAX_VALUE, 0, bsNew, null, 0, true, true, true, true);
} catch (Exception e) {
// TODO
@@ -2222,7 +2223,7 @@
errMsg = getErrorMessage();
setFileLoadStatus(FIL.CREATED, fullPathName, fileName, ms.modelSetName,
- errMsg, htParams == null ? null : (Boolean) htParams.get("async"));
+ errMsg, (Boolean) htParams.get("async"));
if (isAppend) {
selectAll();
setTainted(true);
@@ -8427,7 +8428,8 @@
getMinimizer(true).minimize(steps, crit, bsSelected, bsMotionFixed,
haveFixed, isSilent, ff);
} catch (JmolAsyncException e) {
- eval.loadFileResourceAsync(e.getFileName());
+ if (eval != null)
+ eval.loadFileResourceAsync(e.getFileName());
} catch (Exception e) {
Logger.error("Minimization error: " + e.toString());
if (!isJS)
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