jmol-commits

[Jmol-commits] SF.net SVN: jmol:[21235] trunk/Jmol/src/org/jmol/viewer

[<ha...@us...>]

Revision: 21235
          http://sourceforge.net/p/jmol/code/21235
Author:   hansonr
Date:     2016-08-29 16:26:49 +0000 (Mon, 29 Aug 2016)
Log Message:
-----------
Jmol.___JmolVersion="14.6.2_2016.08.29"

bug fix: load FILES does not deliver _modelFileName for individual models
bug fix: NCI/CADD reader not escaping "\" in SMILES (javajs.util.PT.escapeUrl)

Modified Paths:
--------------
    branches/v14_6/Jmol/src/org/jmol/adapter/smarter/SmarterJmolAdapter.java
    branches/v14_6/Jmol/src/org/jmol/viewer/Jmol.properties
    trunk/Jmol/src/org/jmol/adapter/smarter/SmarterJmolAdapter.java
    trunk/Jmol/src/org/jmol/viewer/Jmol.properties

Modified: branches/v14_6/Jmol/src/org/jmol/adapter/smarter/SmarterJmolAdapter.java
===================================================================
--- branches/v14_6/Jmol/src/org/jmol/adapter/smarter/SmarterJmolAdapter.java	2016-08-29 14:47:37 UTC (rev 21234)
+++ branches/v14_6/Jmol/src/org/jmol/adapter/smarter/SmarterJmolAdapter.java	2016-08-29 16:26:49 UTC (rev 21235)
@@ -237,12 +237,13 @@
 
     for (int i = 0; i < size; i++) {
       try {
-        if (r != null)
-          htParams.put("vwr", vwr);
+        htParams.put("vwr", vwr);
         if (reader == null)
           reader = filesReader.getBufferedReaderOrBinaryDocument(i, false);
         if (!(reader instanceof BufferedReader || reader instanceof GenericBinaryDocument))
           return reader;
+        String fullPathName = names[i];
+        htParams.put("fullPathName", fullPathName);
         Object ret = Resolver.getAtomCollectionReader(names[i],
             (types == null ? null : types[i]), reader, htParams, i);
         if (!(ret instanceof AtomSetCollectionReader))

Modified: branches/v14_6/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v14_6/Jmol/src/org/jmol/viewer/Jmol.properties	2016-08-29 14:47:37 UTC (rev 21234)
+++ branches/v14_6/Jmol/src/org/jmol/viewer/Jmol.properties	2016-08-29 16:26:49 UTC (rev 21235)
@@ -8,6 +8,7 @@
 
 Jmol.___JmolVersion="14.6.2_2016.08.29"
 
+bug fix: load FILES does not deliver _modelFileName for individual models
 bug fix: NCI/CADD reader not escaping "\" in SMILES (javajs.util.PT.escapeUrl)
 
 JmolVersion="14.6.2_2016.08.28"

Modified: trunk/Jmol/src/org/jmol/adapter/smarter/SmarterJmolAdapter.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/SmarterJmolAdapter.java	2016-08-29 14:47:37 UTC (rev 21234)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/SmarterJmolAdapter.java	2016-08-29 16:26:49 UTC (rev 21235)
@@ -237,12 +237,13 @@
 
     for (int i = 0; i < size; i++) {
       try {
-        if (r != null)
-          htParams.put("vwr", vwr);
+        htParams.put("vwr", vwr);
         if (reader == null)
           reader = filesReader.getBufferedReaderOrBinaryDocument(i, false);
         if (!(reader instanceof BufferedReader || reader instanceof GenericBinaryDocument))
           return reader;
+        String fullPathName = names[i];
+        htParams.put("fullPathName", fullPathName);
         Object ret = Resolver.getAtomCollectionReader(names[i],
             (types == null ? null : types[i]), reader, htParams, i);
         if (!(ret instanceof AtomSetCollectionReader))

Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2016-08-29 14:47:37 UTC (rev 21234)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2016-08-29 16:26:49 UTC (rev 21235)
@@ -49,6 +49,7 @@
  
 Jmol.___JmolVersion="14.7.2_2016.08.29"
 
+bug fix: load FILES does not deliver _modelFileName for individual models
 bug fix: NCI/CADD reader not escaping "\" in SMILES (javajs.util.PT.escapeUrl)
 
 JmolVersion="14.6.2_2016.08.28"

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[Jmol-commits] SF.net SVN: jmol:[21238] trunk/Jmol/src/org/jmol/viewer

[<ha...@us...>]

Revision: 21238
          http://sourceforge.net/p/jmol/code/21238
Author:   hansonr
Date:     2016-09-01 00:29:23 +0000 (Thu, 01 Sep 2016)
Log Message:
-----------
Jmol.___JmolVersion="14.6.2_2016.08.31"

bug fix: COMPARE {1.1} {2.1} SMILES  should be ignoring stereochemistry
bug fix: CIF subsystem reader broken

Modified Paths:
--------------
    branches/v14_6/Jmol/src/org/jmol/symmetry/SpaceGroup.java
    branches/v14_6/Jmol/src/org/jmol/viewer/Jmol.properties
    trunk/Jmol/src/org/jmol/symmetry/SpaceGroup.java
    trunk/Jmol/src/org/jmol/viewer/Jmol.properties

Modified: branches/v14_6/Jmol/src/org/jmol/symmetry/SpaceGroup.java
===================================================================
--- branches/v14_6/Jmol/src/org/jmol/symmetry/SpaceGroup.java	2016-08-31 18:41:33 UTC (rev 21237)
+++ branches/v14_6/Jmol/src/org/jmol/symmetry/SpaceGroup.java	2016-09-01 00:29:23 UTC (rev 21238)
@@ -167,7 +167,7 @@
    */
   private static SpaceGroup createSGFromList(String name, Lst<?> data) {
     // try unconventional Hall symbol
-    SpaceGroup sg = new SpaceGroup(-1, "0;--;--;--", true);
+    SpaceGroup sg = new SpaceGroup(-1, "0;0;--;--;--", true);
     sg.doNormalize = false;
     sg.name = name;
     int n = data.size();

Modified: branches/v14_6/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v14_6/Jmol/src/org/jmol/viewer/Jmol.properties	2016-08-31 18:41:33 UTC (rev 21237)
+++ branches/v14_6/Jmol/src/org/jmol/viewer/Jmol.properties	2016-09-01 00:29:23 UTC (rev 21238)
@@ -9,6 +9,7 @@
 Jmol.___JmolVersion="14.6.2_2016.08.31"
 
 bug fix: COMPARE {1.1} {2.1} SMILES  should be ignoring stereochemistry
+bug fix: CIF subsystem reader broken
 
 JmolVersion="14.6.2_2016.08.30"
 

Modified: trunk/Jmol/src/org/jmol/symmetry/SpaceGroup.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/SpaceGroup.java	2016-08-31 18:41:33 UTC (rev 21237)
+++ trunk/Jmol/src/org/jmol/symmetry/SpaceGroup.java	2016-09-01 00:29:23 UTC (rev 21238)
@@ -167,7 +167,7 @@
    */
   private static SpaceGroup createSGFromList(String name, Lst<?> data) {
     // try unconventional Hall symbol
-    SpaceGroup sg = new SpaceGroup(-1, "0;--;--;--", true);
+    SpaceGroup sg = new SpaceGroup(-1, "0;0;--;--;--", true);
     sg.doNormalize = false;
     sg.name = name;
     int n = data.size();

Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2016-08-31 18:41:33 UTC (rev 21237)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2016-09-01 00:29:23 UTC (rev 21238)
@@ -50,6 +50,7 @@
 Jmol.___JmolVersion="14.7.2_2016.08.31"
 
 bug fix: COMPARE {1.1} {2.1} SMILES  should be ignoring stereochemistry
+bug fix: CIF subsystem reader broken
 
 JmolVersion="14.7.2_2016.08.30"
 

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[Jmol-commits] SF.net SVN: jmol:[21239] trunk/Jmol/src/org/jmol/viewer

[<ha...@us...>]

Revision: 21239
          http://sourceforge.net/p/jmol/code/21239
Author:   hansonr
Date:     2016-09-01 19:52:05 +0000 (Thu, 01 Sep 2016)
Log Message:
-----------
Jmol.___JmolVersion="14.6.2_2016.09.01"

bug fix: show vdw USER broken
bug fix: COMPARE {1.1} {2.1} SMILES  should be ignoring stereochemistry
bug fix: CIF subsystem reader broken

Modified Paths:
--------------
    branches/v14_6/Jmol/src/org/jmol/scriptext/CmdExt.java
    branches/v14_6/Jmol/src/org/jmol/viewer/Jmol.properties
    trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
    trunk/Jmol/src/org/jmol/viewer/Jmol.properties

Modified: branches/v14_6/Jmol/src/org/jmol/scriptext/CmdExt.java
===================================================================
--- branches/v14_6/Jmol/src/org/jmol/scriptext/CmdExt.java	2016-09-01 00:29:23 UTC (rev 21238)
+++ branches/v14_6/Jmol/src/org/jmol/scriptext/CmdExt.java	2016-09-01 19:52:05 UTC (rev 21239)
@@ -4347,6 +4347,7 @@
     case T.vanderwaals:
       VDW vdwType = null;
       if (slen > 2) {
+        len = slen;
         vdwType = VDW.getVdwType(paramAsStr(2));
         if (vdwType == null)
           invArg();

Modified: branches/v14_6/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v14_6/Jmol/src/org/jmol/viewer/Jmol.properties	2016-09-01 00:29:23 UTC (rev 21238)
+++ branches/v14_6/Jmol/src/org/jmol/viewer/Jmol.properties	2016-09-01 19:52:05 UTC (rev 21239)
@@ -6,8 +6,9 @@
 
 # see also http://chemapps.stolaf.edu/jmol/zip for daily updates	
 
-Jmol.___JmolVersion="14.6.2_2016.08.31"
+Jmol.___JmolVersion="14.6.2_2016.09.01"
 
+bug fix: show vdw USER broken
 bug fix: COMPARE {1.1} {2.1} SMILES  should be ignoring stereochemistry
 bug fix: CIF subsystem reader broken
 

Modified: trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/CmdExt.java	2016-09-01 00:29:23 UTC (rev 21238)
+++ trunk/Jmol/src/org/jmol/scriptext/CmdExt.java	2016-09-01 19:52:05 UTC (rev 21239)
@@ -4347,6 +4347,7 @@
     case T.vanderwaals:
       VDW vdwType = null;
       if (slen > 2) {
+        len = slen;
         vdwType = VDW.getVdwType(paramAsStr(2));
         if (vdwType == null)
           invArg();

Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2016-09-01 00:29:23 UTC (rev 21238)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2016-09-01 19:52:05 UTC (rev 21239)
@@ -47,8 +47,9 @@
  -- sets the echo offset to a specific screen pixel offset
  -- TODO not saved in state
  
-Jmol.___JmolVersion="14.7.2_2016.08.31"
+Jmol.___JmolVersion="14.7.2_2016.09.01"
 
+bug fix: show vdw USER broken
 bug fix: COMPARE {1.1} {2.1} SMILES  should be ignoring stereochemistry
 bug fix: CIF subsystem reader broken
 

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[Jmol-commits] SF.net SVN: jmol:[21251] trunk/Jmol/src/org/jmol/viewer

[<ha...@us...>]

Revision: 21251
          http://sourceforge.net/p/jmol/code/21251
Author:   hansonr
Date:     2016-09-21 12:39:02 +0000 (Wed, 21 Sep 2016)
Log Message:
-----------
Jmol.___JmolVersion="14.6.3_2016.09.21"

bug fix: print compare({1.1}, {2.1}, "MAP", "H") broken in 14.6.0_2016.06.14

Modified Paths:
--------------
    branches/v14_6/Jmol/src/org/jmol/smiles/SmilesMatcher.java
    branches/v14_6/Jmol/src/org/jmol/viewer/Jmol.properties
    trunk/Jmol/src/org/jmol/smiles/SmilesMatcher.java
    trunk/Jmol/src/org/jmol/viewer/Jmol.properties

Modified: branches/v14_6/Jmol/src/org/jmol/smiles/SmilesMatcher.java
===================================================================
--- branches/v14_6/Jmol/src/org/jmol/smiles/SmilesMatcher.java	2016-09-19 01:16:37 UTC (rev 21250)
+++ branches/v14_6/Jmol/src/org/jmol/smiles/SmilesMatcher.java	2016-09-21 12:39:02 UTC (rev 21251)
@@ -194,6 +194,7 @@
     InvalidSmilesException.clear();
     target = SmilesParser.cleanPattern(target);
     pattern = SmilesParser.cleanPattern(pattern);
+    // search flags will be set in findPriv
     SmilesSearch search = SmilesParser.newSearch(target, false, true); /// smiles chirality is fixed here
     int[][] array = (int[][]) findPriv(pattern, search, flags, MODE_MAP);
     for (int i = array.length; --i >= 0;) {
@@ -496,7 +497,7 @@
         return search.atropKeys;
       case MODE_MAP:
         search.getMaps = true;
-        search.setFlags(flags); // important for COMPARE command - no stereochem
+        search.setFlags(flags | search.flags); // important for COMPARE command - no stereochem
         Lst<int[]> vl = (Lst<int[]>) search.search();
         return vl.toArray(AU.newInt2(vl.size()));
       }

Modified: branches/v14_6/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v14_6/Jmol/src/org/jmol/viewer/Jmol.properties	2016-09-19 01:16:37 UTC (rev 21250)
+++ branches/v14_6/Jmol/src/org/jmol/viewer/Jmol.properties	2016-09-21 12:39:02 UTC (rev 21251)
@@ -6,7 +6,12 @@
 
 # see also http://chemapps.stolaf.edu/jmol/zip for daily updates	
 
+Jmol.___JmolVersion="14.6.3_2016.09.21"
+
+bug fix: print compare({1.1}, {2.1}, "MAP", "H") broken in 14.6.0_2016.06.14
+
 Jmol.___JmolVersion="14.6.3_2016.09.18"
+released
 
 bug fix: write MENU broken for non-English language (UTF-8 strings not correctly encoded using base64)
 bug fix: write PNGJ should not store "#_DOCACHE_" in PNGJ file

Modified: trunk/Jmol/src/org/jmol/smiles/SmilesMatcher.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmilesMatcher.java	2016-09-19 01:16:37 UTC (rev 21250)
+++ trunk/Jmol/src/org/jmol/smiles/SmilesMatcher.java	2016-09-21 12:39:02 UTC (rev 21251)
@@ -497,7 +497,7 @@
         return search.atropKeys;
       case MODE_MAP:
         search.getMaps = true;
-        search.setFlags(flags); // important for COMPARE command - no stereochem
+        search.setFlags(flags | search.flags); // important for COMPARE command - no stereochem
         Lst<int[]> vl = (Lst<int[]>) search.search();
         return vl.toArray(AU.newInt2(vl.size()));
       }

Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2016-09-19 01:16:37 UTC (rev 21250)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2016-09-21 12:39:02 UTC (rev 21251)
@@ -47,8 +47,12 @@
  -- sets the echo offset to a specific screen pixel offset
  -- TODO not saved in state
  
+Jmol.___JmolVersion="14.7.3_2016.09.21"
+
+bug fix: print compare({1.1}, {2.1}, "MAP", "H") broken in 14.6.0_2016.06.14
+
 Jmol.___JmolVersion="14.7.3_2016.09.18"
-
+released
 new feature: show chemical formula reads formula from CIF
 
 bug fix: write MENU broken for non-English language (UTF-8 strings not correctly encoded using base64)

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[Jmol-commits] SF.net SVN: jmol:[21269] trunk/Jmol/src/org/jmol/viewer

[<ha...@us...>]

Revision: 21269
          http://sourceforge.net/p/jmol/code/21269
Author:   hansonr
Date:     2016-10-18 04:02:03 +0000 (Tue, 18 Oct 2016)
Log Message:
-----------
Jmol.___JmolVersion="14.6.4_2016.10.17"

bug fix: IDTF exporter broken in Jmol 14.6.4_2016.10.02

Modified Paths:
--------------
    branches/v14_6/Jmol/src/org/jmol/export/_IdtfExporter.java
    branches/v14_6/Jmol/src/org/jmol/viewer/Jmol.properties
    trunk/Jmol/src/org/jmol/export/_IdtfExporter.java
    trunk/Jmol/src/org/jmol/viewer/Jmol.properties

Modified: branches/v14_6/Jmol/src/org/jmol/export/_IdtfExporter.java
===================================================================
--- branches/v14_6/Jmol/src/org/jmol/export/_IdtfExporter.java	2016-10-15 16:12:09 UTC (rev 21268)
+++ branches/v14_6/Jmol/src/org/jmol/export/_IdtfExporter.java	2016-10-18 04:02:03 UTC (rev 21269)
@@ -598,7 +598,7 @@
     int[][] faces = new int[nFaces][3];
     for (int i = 0, p = 0; i < nFaces; i++)
       for (int j = 0; j < 3; j++)
-        faces[i][j] = f[++p];
+        faces[i][j] = f[p++];
     V3[] vertexes = new V3[vertexCount];
     for (int i = 0; i < vertexCount;i++)
       vertexes[i] = Geodesic.getVertexVector(i);

Modified: branches/v14_6/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v14_6/Jmol/src/org/jmol/viewer/Jmol.properties	2016-10-15 16:12:09 UTC (rev 21268)
+++ branches/v14_6/Jmol/src/org/jmol/viewer/Jmol.properties	2016-10-18 04:02:03 UTC (rev 21269)
@@ -6,8 +6,13 @@
 
 # see also http://chemapps.stolaf.edu/jmol/zip for daily updates	
 
-Jmol.___JmolVersion="14.6.4_2016.10.15"
 
+Jmol.___JmolVersion="14.6.4_2016.10.17"
+
+bug fix: IDTF exporter broken in Jmol 14.6.4_2016.10.02
+
+JmolVersion="14.6.4_2016.10.15"
+
 bug fix: (JSmolJavaExt.js) JSmol/HTML5  WRITE xxx.stl not working.
 bug fix: STL export can place two endcaps in the same location
 

Modified: trunk/Jmol/src/org/jmol/export/_IdtfExporter.java
===================================================================
--- trunk/Jmol/src/org/jmol/export/_IdtfExporter.java	2016-10-15 16:12:09 UTC (rev 21268)
+++ trunk/Jmol/src/org/jmol/export/_IdtfExporter.java	2016-10-18 04:02:03 UTC (rev 21269)
@@ -598,7 +598,7 @@
     int[][] faces = new int[nFaces][3];
     for (int i = 0, p = 0; i < nFaces; i++)
       for (int j = 0; j < 3; j++)
-        faces[i][j] = f[++p];
+        faces[i][j] = f[p++];
     V3[] vertexes = new V3[vertexCount];
     for (int i = 0; i < vertexCount;i++)
       vertexes[i] = Geodesic.getVertexVector(i);

Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2016-10-15 16:12:09 UTC (rev 21268)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2016-10-18 04:02:03 UTC (rev 21269)
@@ -47,8 +47,12 @@
  -- sets the echo offset to a specific screen pixel offset
  -- TODO not saved in state
 
-Jmol.___JmolVersion="14.7.4_2016.10.15"
+Jmol.___JmolVersion="14.7.4_2016.10.17"
 
+bug fix: IDTF exporter broken in Jmol 14.7.4_2016.10.02
+
+JmolVersion="14.7.4_2016.10.15"
+
 bug fix: (JSmolJavaExt.js) JSmol/HTML5  WRITE xxx.stl not working.
 bug fix: STL export can place two endcaps in the same location
 

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[Jmol-commits] SF.net SVN: jmol:[21270] trunk/Jmol/src/org/jmol/viewer

[<ha...@us...>]

Revision: 21270
          http://sourceforge.net/p/jmol/code/21270
Author:   hansonr
Date:     2016-10-19 04:54:45 +0000 (Wed, 19 Oct 2016)
Log Message:
-----------
Jmol.___JmolVersion="14.6.4_2016.10.17"

bug fix: load "@x" not saved in state properly
bug fix: IDTF exporter broken in Jmol 14.6.4_2016.10.02

Modified Paths:
--------------
    branches/v14_6/Jmol/src/org/jmol/script/ScriptEval.java
    branches/v14_6/Jmol/src/org/jmol/viewer/Jmol.properties
    trunk/Jmol/src/org/jmol/script/ScriptEval.java
    trunk/Jmol/src/org/jmol/viewer/Jmol.properties

Modified: branches/v14_6/Jmol/src/org/jmol/script/ScriptEval.java
===================================================================
--- branches/v14_6/Jmol/src/org/jmol/script/ScriptEval.java	2016-10-18 04:02:03 UTC (rev 21269)
+++ branches/v14_6/Jmol/src/org/jmol/script/ScriptEval.java	2016-10-19 04:54:45 UTC (rev 21270)
@@ -4601,7 +4601,7 @@
 
       loadScript.append(" ");
       if (isVariable || isInline) {
-        loadScript.append(filename.indexOf('\n') >= 0 ? PT.esc(filename) : filename);
+        loadScript.append(filename.indexOf('\n') >= 0 || isVariable ? PT.esc(filename) : filename);
       } else if (!isData) {
         if (localName != null)
           localName = vwr.fm.getFilePath(localName, false, false);

Modified: branches/v14_6/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v14_6/Jmol/src/org/jmol/viewer/Jmol.properties	2016-10-18 04:02:03 UTC (rev 21269)
+++ branches/v14_6/Jmol/src/org/jmol/viewer/Jmol.properties	2016-10-19 04:54:45 UTC (rev 21270)
@@ -9,6 +9,7 @@
 
 Jmol.___JmolVersion="14.6.4_2016.10.17"
 
+bug fix: load "@x" not saved in state properly
 bug fix: IDTF exporter broken in Jmol 14.6.4_2016.10.02
 
 JmolVersion="14.6.4_2016.10.15"

Modified: trunk/Jmol/src/org/jmol/script/ScriptEval.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEval.java	2016-10-18 04:02:03 UTC (rev 21269)
+++ trunk/Jmol/src/org/jmol/script/ScriptEval.java	2016-10-19 04:54:45 UTC (rev 21270)
@@ -4601,7 +4601,7 @@
 
       loadScript.append(" ");
       if (isVariable || isInline) {
-        loadScript.append(filename.indexOf('\n') >= 0 ? PT.esc(filename) : filename);
+        loadScript.append(filename.indexOf('\n') >= 0 || isVariable ? PT.esc(filename) : filename);
       } else if (!isData) {
         if (localName != null)
           localName = vwr.fm.getFilePath(localName, false, false);

Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2016-10-18 04:02:03 UTC (rev 21269)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2016-10-19 04:54:45 UTC (rev 21270)
@@ -49,6 +49,7 @@
 
 Jmol.___JmolVersion="14.7.4_2016.10.17"
 
+bug fix: load "@x" not saved in state properly
 bug fix: IDTF exporter broken in Jmol 14.7.4_2016.10.02
 
 JmolVersion="14.7.4_2016.10.15"

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[Jmol-commits] SF.net SVN: jmol:[21278] trunk/Jmol/src/org/jmol/viewer

[<ha...@us...>]

Revision: 21278
          http://sourceforge.net/p/jmol/code/21278
Author:   hansonr
Date:     2016-10-26 17:26:02 +0000 (Wed, 26 Oct 2016)
Log Message:
-----------
Jmol.___JmolVersion="14.6.4_2016.10.26"

bug fix: POV-Ray output spheres too large -- somehow broken in 14.6.4_2016.10.15 

Modified Paths:
--------------
    branches/v14_6/Jmol/src/org/jmol/export/__RayTracerExporter.java
    branches/v14_6/Jmol/src/org/jmol/viewer/Jmol.properties
    trunk/Jmol/src/org/jmol/export/__RayTracerExporter.java
    trunk/Jmol/src/org/jmol/viewer/Jmol.properties

Modified: branches/v14_6/Jmol/src/org/jmol/export/__RayTracerExporter.java
===================================================================
--- branches/v14_6/Jmol/src/org/jmol/export/__RayTracerExporter.java	2016-10-22 15:27:05 UTC (rev 21277)
+++ branches/v14_6/Jmol/src/org/jmol/export/__RayTracerExporter.java	2016-10-26 17:26:02 UTC (rev 21278)
@@ -124,7 +124,7 @@
 
   @Override
   void drawAtom(Atom atom, float radius) {
-    outputSphere(atom.sX, atom.sY, atom.sZ, atom.sD, atom.colixAtom);
+    outputSphere(atom.sX, atom.sY, atom.sZ, atom.sD / 2f, atom.colixAtom);
   }
 
   @Override

Modified: branches/v14_6/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v14_6/Jmol/src/org/jmol/viewer/Jmol.properties	2016-10-22 15:27:05 UTC (rev 21277)
+++ branches/v14_6/Jmol/src/org/jmol/viewer/Jmol.properties	2016-10-26 17:26:02 UTC (rev 21278)
@@ -7,8 +7,12 @@
 # see also http://chemapps.stolaf.edu/jmol/zip for daily updates	
 
 
-Jmol.___JmolVersion="14.6.4_2016.10.23"
+Jmol.___JmolVersion="14.6.4_2016.10.26"
 
+bug fix: POV-Ray output spheres too large -- somehow broken in 14.6.4_2016.10.15 
+
+JmolVersion="14.6.4_2016.10.23"
+
 code: netscape.jar references isolated to org.jmol.applet.Jmol
 
 JmolVersion="14.6.4_2016.10.21"

Modified: trunk/Jmol/src/org/jmol/export/__RayTracerExporter.java
===================================================================
--- trunk/Jmol/src/org/jmol/export/__RayTracerExporter.java	2016-10-22 15:27:05 UTC (rev 21277)
+++ trunk/Jmol/src/org/jmol/export/__RayTracerExporter.java	2016-10-26 17:26:02 UTC (rev 21278)
@@ -124,7 +124,7 @@
 
   @Override
   void drawAtom(Atom atom, float radius) {
-    outputSphere(atom.sX, atom.sY, atom.sZ, atom.sD, atom.colixAtom);
+    outputSphere(atom.sX, atom.sY, atom.sZ, atom.sD / 2f, atom.colixAtom);
   }
 
   @Override

Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2016-10-22 15:27:05 UTC (rev 21277)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2016-10-26 17:26:02 UTC (rev 21278)
@@ -47,6 +47,10 @@
  -- sets the echo offset to a specific screen pixel offset
  -- TODO not saved in state
 
+Jmol.___JmolVersion="14.7.4_2016.10.26"
+
+bug fix: POV-Ray output spheres too large -- somehow broken in 14.6.4_2016.10.15 
+
 Jmol.___JmolVersion="14.7.4_2016.10.23"
 
 code: netscape.jar references isolated to org.jmol.applet.Jmol

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[Jmol-commits] SF.net SVN: jmol:[21283] trunk/Jmol/src/org/jmol/viewer

[<ha...@us...>]

Revision: 21283
          http://sourceforge.net/p/jmol/code/21283
Author:   hansonr
Date:     2016-11-03 03:06:39 +0000 (Thu, 03 Nov 2016)
Log Message:
-----------
Jmol.___JmolVersion="14.6.4_2016.11.02"
load x.cif {1 1 1} (where that file has no unitcell) throws a loading error

Modified Paths:
--------------
    branches/v14_6/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
    branches/v14_6/Jmol/src/org/jmol/viewer/Jmol.properties
    trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
    trunk/Jmol/src/org/jmol/viewer/Jmol.properties

Modified: branches/v14_6/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
===================================================================
--- branches/v14_6/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java	2016-10-26 17:40:59 UTC (rev 21282)
+++ branches/v14_6/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java	2016-11-03 03:06:39 UTC (rev 21283)
@@ -883,6 +883,8 @@
       getNewSymmetry().setUnitCell(unitCellParams, false);
       checkUnitCellOffset();
     }
+    if (symmetry == null) // cif file with no symmetry triggers exception on LOAD {1 1 1}
+      iHaveUnitCell = false;
     return symmetry;
   }
   private void checkUnitCellOffset() {
@@ -898,7 +900,8 @@
   }
 
   protected void fractionalizeCoordinates(boolean toFrac) {
-    getSymmetry();
+    if (getSymmetry() == null)
+      return;
     Atom[] a = asc.atoms;
     if (toFrac)
       for (int i = asc.ac; --i >= 0;)

Modified: branches/v14_6/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v14_6/Jmol/src/org/jmol/viewer/Jmol.properties	2016-10-26 17:40:59 UTC (rev 21282)
+++ branches/v14_6/Jmol/src/org/jmol/viewer/Jmol.properties	2016-11-03 03:06:39 UTC (rev 21283)
@@ -7,8 +7,12 @@
 # see also http://chemapps.stolaf.edu/jmol/zip for daily updates	
 
 
-Jmol.___JmolVersion="14.6.4_2016.10.26"
+Jmol.___JmolVersion="14.6.4_2016.11.02"
+load x.cif {1 1 1} (where that file has no unitcell) throws a loading error
 
+JmolVersion="14.6.4_2016.10.26"
+released
+
 bug fix: POV-Ray output spheres too large -- somehow broken in 14.6.4_2016.10.15 
 
 JmolVersion="14.6.4_2016.10.23"

Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java	2016-10-26 17:40:59 UTC (rev 21282)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java	2016-11-03 03:06:39 UTC (rev 21283)
@@ -883,6 +883,8 @@
       getNewSymmetry().setUnitCell(unitCellParams, false);
       checkUnitCellOffset();
     }
+    if (symmetry == null) // cif file with no symmetry triggers exception on LOAD {1 1 1}
+      iHaveUnitCell = false;
     return symmetry;
   }
   private void checkUnitCellOffset() {
@@ -898,7 +900,8 @@
   }
 
   protected void fractionalizeCoordinates(boolean toFrac) {
-    getSymmetry();
+    if (getSymmetry() == null)
+      return;
     Atom[] a = asc.atoms;
     if (toFrac)
       for (int i = asc.ac; --i >= 0;)

Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2016-10-26 17:40:59 UTC (rev 21282)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2016-11-03 03:06:39 UTC (rev 21283)
@@ -47,16 +47,18 @@
  -- sets the echo offset to a specific screen pixel offset
  -- TODO not saved in state
 
-Jmol.___JmolVersion="14.7.4_2016.10.26"
+Jmol.___JmolVersion="14.7.4_2016.11.02"
+load x.cif {1 1 1} (where that file has no unitcell) throws a loading error
 
+JmolVersion="14.7.4_2016.10.26"
+
 bug fix: POV-Ray output spheres too large -- somehow broken in 14.6.4_2016.10.15 
 
-Jmol.___JmolVersion="14.7.4_2016.10.23"
+JmolVersion="14.7.4_2016.10.23"
 
 code: netscape.jar references isolated to org.jmol.applet.Jmol
 
 JmolVersion="14.7.4_2016.10.21"
-released
 
 bug fix: menu item for X3D export delivers STL; item for STL not functional 
 bug fix: X3D export includes extraneous VRML text

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[Jmol-commits] SF.net SVN: jmol:[21637] trunk/Jmol/src/org/jmol/viewer

[<ha...@us...>]

Revision: 21637
          http://sourceforge.net/p/jmol/code/21637
Author:   hansonr
Date:     2017-06-20 04:06:22 +0000 (Tue, 20 Jun 2017)
Log Message:
-----------
Jmol.___JmolVersion="14.19.1"

new feature: WRITE "SDF" implements atom value V  nnn ... information
 -- requires assigning the data property name "atom_values" in the model's molData property
 -- for example:
 
  $ load $2,3-dichlorobutane
  $ molData = {"atom_values":"chirality"}
  $ model properties "molData" molData
  $ write diol.sdf

 -- note that if the model already has a molData property, then use the following to append to it:
 
  $ molData = (_M.molData ? _M.molData : {})
  $ molData.atom_values = "chirality"
  $ model properties "molData" molData
   
   
   
new feature: x = load("filename","JSON")
 -- loads JSON data into variable
 
bug fix: SET ANTIALIASDISPLAY requires click [via resizeImage()]
bug fix: CIP gives wrong alkene root distance for cyclopropene
bug fix: WRITE of structure file does not report number of atoms and warn if selected is different from this molecule
bug fix: WRITE MOL using format 10f.5 instead of 10f.4 for x, y, z coordinates
bug fix: MOL/SDF files should truncate lines at 80 characters.

Modified Paths:
--------------
    trunk/Jmol/src/org/jmol/viewer/Jmol.properties
    trunk/Jmol/src/org/jmol/viewer/Viewer.java

Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2017-06-17 12:04:50 UTC (rev 21636)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2017-06-20 04:06:22 UTC (rev 21637)
@@ -77,6 +77,8 @@
    
 new feature: x = load("filename","JSON")
  -- loads JSON data into variable
+ 
+bug fix: SET ANTIALIASDISPLAY requires click [via resizeImage()]
 bug fix: CIP gives wrong alkene root distance for cyclopropene
 bug fix: WRITE of structure file does not report number of atoms and warn if selected is different from this molecule
 bug fix: WRITE MOL using format 10f.5 instead of 10f.4 for x, y, z coordinates

Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java	2017-06-17 12:04:50 UTC (rev 21636)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java	2017-06-20 04:06:22 UTC (rev 21637)
@@ -7057,8 +7057,10 @@
       g.antialiasImages = TF;
       return;
     }
-    if (isChanged)
+    if (isChanged) {
+      resizeImage(0, 0, false, false, true); // for antialiasdisplay
       refresh(3, "Viewer:setAntialias()");
+    }
 //    resizeImage(0, 0, false, false, true);
   }
 

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[Jmol-commits] SF.net SVN: jmol:[21667] trunk/Jmol/src/org/jmol/viewer

[<ha...@us...>]

Revision: 21667
          http://sourceforge.net/p/jmol/code/21667
Author:   hansonr
Date:     2017-07-20 14:06:47 +0000 (Thu, 20 Jul 2017)
Log Message:
-----------
Jmol.___JmolVersion="14.20.3" // 2017.07.20

bug fix: ROTATE should not stop spin if it does not initiate a spin
bug fix: CIPChirality tests for CIP1966#31,#32 douple spirans and C3 compounds
bug fix: CIPChirality for Rule 2 using atomic masses and not for duplicate atoms
bug fix: MOL file reading where isotope is indicated in atom line and V item
bug fix: MOL reader fails for H1, D, T isotopes indicated as symbols along with isotope difference

Modified Paths:
--------------
    trunk/Jmol/src/org/jmol/viewer/Jmol.properties
    trunk/Jmol/src/org/jmol/viewer/TransformManager.java

Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2017-07-20 13:40:04 UTC (rev 21666)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2017-07-20 14:06:47 UTC (rev 21667)
@@ -58,6 +58,7 @@
 
 Jmol.___JmolVersion="14.20.3" // 2017.07.20
 
+bug fix: ROTATE should not stop spin if it does not initiate a spin
 bug fix: CIPChirality tests for CIP1966#31,#32 douple spirans and C3 compounds
 bug fix: CIPChirality for Rule 2 using atomic masses and not for duplicate atoms
 bug fix: MOL file reading where isotope is indicated in atom line and V item

Modified: trunk/Jmol/src/org/jmol/viewer/TransformManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/TransformManager.java	2017-07-20 13:40:04 UTC (rev 21666)
+++ trunk/Jmol/src/org/jmol/viewer/TransformManager.java	2017-07-20 14:06:47 UTC (rev 21667)
@@ -376,7 +376,8 @@
     if (rotCenter != null)
       moveRotationCenter(rotCenter, true);
 
-    setSpinOff();
+    if (isSpin)
+      setSpinOff();
     setNavOn(false);
 
     if (vwr.headless) {
@@ -448,7 +449,8 @@
 
     // *THE* Viewer INTERNAL frame rotation entry point
 
-    setSpinOff();
+    if (isSpin)
+      setSpinOff();
     setNavOn(false);
 
     if (dihedralList == null

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[Jmol-commits] SF.net SVN: jmol:[22189] trunk/Jmol/src/org/jmol/viewer

[<ha...@us...>]

Revision: 22189
          http://sourceforge.net/p/jmol/code/22189
Author:   hansonr
Date:     2021-08-05 17:09:56 +0000 (Thu, 05 Aug 2021)
Log Message:
-----------

Jmol.___JmolVersion="14.31.49"
  also 15.1.49

bug fix: JSpecView not using ##FIRSTX for diff-dup x values after first.
bug fix: JSpecView version not showing
bug fix: Jmol not reading EBI cryo-EM files from density server.

new feature: isosurface "*em"
 - same as *emdb, just simpler.

Modified Paths:
--------------
    trunk/Jmol/src/org/jmol/viewer/JC.java
    trunk/Jmol/src/org/jmol/viewer/Jmol.properties
    trunk/Jmol/src/org/jmol/viewer/Viewer.java

Modified: trunk/Jmol/src/org/jmol/viewer/JC.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/JC.java	2021-08-05 16:23:01 UTC (rev 22188)
+++ trunk/Jmol/src/org/jmol/viewer/JC.java	2021-08-05 17:09:56 UTC (rev 22189)
@@ -45,7 +45,8 @@
 @J2SRequireImport({ javajs.util.SB.class })
 public final class JC {
 
-  public static final String NBO_TYPES = ";" + "AO;;;;" // 31
+  public static final String   NBO_TYPES = ";"
+      + "AO;;;;" // 31
       + "PNAO;;" // 32
       + "NAO;;;" // 33
       + "PNHO;;" // 34
@@ -218,19 +219,17 @@
       "pdb0", "https://files.rcsb.org/download/%FILE.pdb", // used in JSmol
       "pdbe", "https://www.ebi.ac.uk/pdbe/entry-files/download/%FILE.cif",
       "pdbe2", "https://www.ebi.ac.uk/pdbe/static/entry/%FILE_updated.cif",
-      "pubchem",
-      "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/%FILE/SDF?record_type=3d",
-      "map",
-      "https://www.ebi.ac.uk/pdbe/api/%TYPE/%FILE?pretty=false&metadata=true",
+    "pubchem", "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/%FILE/SDF?record_type=3d",
+    "map", "https://www.ebi.ac.uk/pdbe/api/%TYPE/%FILE?pretty=false&metadata=true", 
       "pdbemap", "https://www.ebi.ac.uk/pdbe/coordinates/files/%file.ccp4",
-      "pdbemapdiff",
-      "https://www.ebi.ac.uk/pdbe/coordinates/files/%file_diff.ccp4",
-      "pdbemapserver",
-      "https://www.ebi.ac.uk/pdbe/densities/x-ray/%file/box/0,0,0/0,0,0?space=cartesian&encoding=bcif",
-      "pdbemapdiffserver",
-      "https://www.ebi.ac.uk/pdbe/densities/x-ray/%file/box/0,0,0/0,0,0?space=cartesian&encoding=bcif&diff=1", /// last bit is just mine
-      "emdbmap", "http://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-%file/map/emd_%file.map.gz", // https did not work in Java due to certificate issues
+    "pdbemapdiff", "https://www.ebi.ac.uk/pdbe/coordinates/files/%file_diff.ccp4",
+    "pdbemapserver", "https://www.ebi.ac.uk/pdbe/densities/x-ray/%file/box/0,0,0/0,0,0?space=cartesian&encoding=bcif",
+    "pdbemapdiffserver", "https://www.ebi.ac.uk/pdbe/densities/x-ray/%file/box/0,0,0/0,0,0?space=cartesian&encoding=bcif&diff=1", // last bit is just mine
+    //"emdbmap", "https://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-%file/map/emd_%file.map.gz", // https did not work in Java due to certificate issues
+ // was considerably slower
+    "emdbmap", "https://www.ebi.ac.uk/pdbe/densities/emd/emd-%file/cell?detail=6&space=cartesian&encoding=bcif",
       "emdbquery", "https://www.ebi.ac.uk/emdb/api/search/fitted_pdbs:%file?fl=emdb_id,map_contour_level_value&wt=csv", // to get the EMDB id from the PDB id
+    "emdbmapserver", "https://www.ebi.ac.uk/pdbe/densities/emd/emd-%file/box/0,0,0/0,0,0?space=cartesian&encoding=bcif",
       "resolverResolver", "https://chemapps.stolaf.edu/resolver",
       };
 

Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2021-08-05 16:23:01 UTC (rev 22188)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2021-08-05 17:09:56 UTC (rev 22189)
@@ -57,7 +57,17 @@
 # TODO: isosurface cavity delivers nonsense volume due to unclosed surface
 
 
-Jmol.___JmolVersion="14.31.48"
+Jmol.___JmolVersion="14.31.49"
+  also 15.1.49
+
+bug fix: JSpecView not using ##FIRSTX for diff-dup x values after first.
+bug fix: JSpecView version not showing
+bug fix: Jmol not reading EBI cryo-EM files from density server.
+
+new feature: isosurface "*em"
+ - same as *emdb, just simpler.
+
+JmolVersion="14.31.48"
   also 15.1.48
   
   bug fix: JavaScript isosurface asynchronous file loader 

Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java	2021-08-05 16:23:01 UTC (rev 22188)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java	2021-08-05 17:09:56 UTC (rev 22189)
@@ -3246,6 +3246,11 @@
           try {
             JmolScriptEvaluator eval = (JmolScriptEvaluator) htParams
                 .get("eval");
+            BS stereo = getAtomBitSet("_C & connected(3) & !connected(double)");
+            stereo.and(bsNew);
+            if (stereo.nextSetBit(0) >= 0) {
+              bsNew.or(addHydrogens(stereo,MIN_NO_RANGE | MIN_SILENT | MIN_QUICK));
+            }
             minimize(eval, Integer.MAX_VALUE, 0, bsNew, null, 0,
                 MIN_ADDH | MIN_NO_RANGE | MIN_SILENT | MIN_QUICK);
           } catch (Exception e) {
@@ -4975,8 +4980,10 @@
         ciftype = id.substring(pt + 1);
         id = id.substring(0, pt);
       }
-      if (id.equals("emdb"))
+      if (id.equals("emdb") || id.equals("em"))
         id += "/";
+      if (id.startsWith("em/"))
+        id = "emdb" + id.substring(2);
       if (id.startsWith("emdb/")) {
         // *emdb/9357
         // *emdb/=6nef
@@ -5012,7 +5019,7 @@
             id = id.substring(0, pt);
           }
         }
-        return JC.resolveDataBase("emdbmap", id, null) + ext;
+        return JC.resolveDataBase("emdbmap" + (type == '-' ? "server" : ""), id, null) + ext;
       }
       id = JC.resolveDataBase(
           (isDiff ? "pdbemapdiff" : "pdbemap") + (type == '-' ? "server" : ""),
@@ -8942,10 +8949,12 @@
     if (bsSelected == null)
       bsSelected = getModelUndeletedAtomsBitSet(
           getVisibleFramesBitSet().length() - 1);
-    else
+    else if (!isQuick)
       bsSelected.and(bsInFrame);
-    if (isQuick)
+    if (isQuick) {
       getAuxiliaryInfoForAtoms(bsSelected).put("dimension", "3D");
+      bsInFrame = bsSelected;
+    }
 
     if (rangeFixed <= 0)
       rangeFixed = JC.MINIMIZE_FIXED_RANGE;
@@ -8974,6 +8983,8 @@
     bsMotionFixed.and(bsInFrame);
     flags |= ((haveFixed ? MIN_HAVE_FIXED : 0)
         | (getBooleanProperty("minimizationSilent") ? MIN_SILENT : 0));
+    if (isQuick && getBoolean(T.testflag2))
+      return;
     if (isQuick) {
       {
         // carry out a preliminary UFF no-hydrogen calculation
@@ -8990,8 +9001,6 @@
 
       }
     }
-    if (isQuick && getBoolean(T.testflag2))
-      return;
     if (addHydrogen) {
       BS bsH = addHydrogens(bsSelected, flags);
       if (!isQuick)
@@ -9014,6 +9023,7 @@
       if (isQuick) {
         g.forceField = "MMFF";
         setHydrogens(bsSelected);
+        showString("Minimized by Jmol",  false);
       }
     } catch (JmolAsyncException e) {
       if (eval != null)

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[Jmol-commits] SF.net SVN: jmol:[22259] trunk/Jmol/src/org/jmol/viewer

[<ha...@us...>]

Revision: 22259
          http://sourceforge.net/p/jmol/code/22259
Author:   hansonr
Date:     2021-11-25 14:48:06 +0000 (Thu, 25 Nov 2021)
Log Message:
-----------
Jmol.___JmolVersion="14.31.63" 
  also 15.1.63

bug fix: JavaScript broken for $ -- NCI legacy resolver

Modified Paths:
--------------
    trunk/Jmol/src/org/jmol/viewer/Jmol.properties
    trunk/Jmol/src/org/jmol/viewer/Viewer.java

Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2021-11-24 23:37:34 UTC (rev 22258)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2021-11-25 14:48:06 UTC (rev 22259)
@@ -57,7 +57,17 @@
 # TODO: isosurface cavity delivers nonsense volume due to unclosed surface
 
 
-Jmol.___JmolVersion="14.31.62"
+
+
+
+
+
+Jmol.___JmolVersion="14.31.63" 
+  also 15.1.63
+
+bug fix: JavaScript broken for $ -- NCI legacy resolver
+
+JmolVersion="14.31.62"
   also 15.1.62
 
 new feature: LOAD APPEND n ...  

Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java	2021-11-24 23:37:34 UTC (rev 22258)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java	2021-11-25 14:48:06 UTC (rev 22259)
@@ -4818,6 +4818,13 @@
     String format = null;
     String id = name.substring(1);
     switch (type) {
+    case 'c': // cache:local//... legacyResolver....
+      return name;
+    case 'h':
+      // legacy resolver https://
+      checkCIR(false);
+      return g.nihResolverFormat
+          + name.substring(name.indexOf("/structure") + 10);
     case '=':
       if (name.startsWith("==")) {
         id = id.substring(1);
@@ -4914,11 +4921,6 @@
         }
       }
       return PT.formatStringS(format, "FILE", id);
-    case 'h':
-      // legacy resolver
-      checkCIR(false);
-      return g.nihResolverFormat
-          + name.substring(name.indexOf("/structure") + 10);
     case '$':
       checkCIR(false);
       if (name.equals("$")) {

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[Jmol-commits] SF.net SVN: jmol:[22263] trunk/Jmol/src/org/jmol/viewer

[<ha...@us...>]

Revision: 22263
          http://sourceforge.net/p/jmol/code/22263
Author:   hansonr
Date:     2021-11-28 01:02:49 +0000 (Sun, 28 Nov 2021)
Log Message:
-----------
Jmol.___JmolVersion="14.31.63" 
  also 15.1.63

bug fix: JavaScript broken for $ -- NCI legacy resolver in 14.31.61
bug fix: _modelFile includes xxx:: type prefix
bug fix: JavaScript save JMOL after PNG setting load file to PNG rather than MOL

Modified Paths:
--------------
    trunk/Jmol/src/org/jmol/viewer/FileManager.java
    trunk/Jmol/src/org/jmol/viewer/OutputManager.java

Modified: trunk/Jmol/src/org/jmol/viewer/FileManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/FileManager.java	2021-11-27 14:06:43 UTC (rev 22262)
+++ trunk/Jmol/src/org/jmol/viewer/FileManager.java	2021-11-28 01:02:49 UTC (rev 22263)
@@ -250,8 +250,6 @@
       int pt = fileNames[i].indexOf("::");
       String nameAsGiven = (pt >= 0 ? fileNames[i].substring(pt + 2)
           : fileNames[i]);
-      
-      System.out.println(i + " FM " + nameAsGiven);
       String fileType = (pt >= 0 ? fileNames[i].substring(0, pt) : null);
       String[] names = getClassifiedName(nameAsGiven, true);
       if (names.length == 1)
@@ -707,18 +705,14 @@
   }
 
   public Object getFileAsBytes(String name, OC out) {
-    return getFileAsBytesW(name, out, false);
-  }
-  
-  public Object getFileAsBytesW(String name, OC out, boolean isWrite) {
-
-    // ?? used by eval of "WRITE FILE"
+    // used by OutputManager.createZipSet"
     // will be full path name
     if (name == null)
       return null;
     String fullName = name;
     String[] subFileList = null;
-    if (name.indexOf("|") >= 0 && !isWrite) {
+    boolean isCached = name.startsWith("cache://");
+    if (name.indexOf("|") >= 0 && !isCached) {
       subFileList = PT.split(name, "|");
       name = subFileList[0];
     }
@@ -726,7 +720,7 @@
     // but in that case we can get the bytes directly and not
     // fool with a BufferedInputStream, and we certainly do not want to 
     // open it twice in the case of the returned interior file being another PNGJ file
-    Object bytes = (subFileList == null ? null : getPngjOrDroppedBytes(
+    Object bytes = (isCached || subFileList == null ? null : getPngjOrDroppedBytes(
         fullName, name));
     if (bytes == null) {
       Object t = getBufferedInputStreamOrErrorMessageFromName(name, fullName,
@@ -738,8 +732,8 @@
         bytes = (out != null || subFileList == null || subFileList.length <= 1
             || !Rdr.isZipS(bis) && !Rdr.isPngZipStream(bis) 
              && !Rdr.isTar(bis)
-            ? Rdr
-            .getStreamAsBytes(bis, out) : vwr.getJzt().getZipFileContentsAsBytes(bis, subFileList, 1));
+            ? Rdr.getStreamAsBytes(bis, out) 
+                : vwr.getJzt().getZipFileContentsAsBytes(bis, subFileList, 1));
 
         bis.close();
       } catch (Exception ioe) {

Modified: trunk/Jmol/src/org/jmol/viewer/OutputManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/OutputManager.java	2021-11-27 14:06:43 UTC (rev 22262)
+++ trunk/Jmol/src/org/jmol/viewer/OutputManager.java	2021-11-28 01:02:49 UTC (rev 22263)
@@ -982,9 +982,8 @@
           v.addLast(null); // data will be gotten from disk
         } else {
           // all remote files, and any file that was opened from a ZIP collection
-          boolean isCached = (name.indexOf("cache://") == 0);
           Object ret = (isSparDir ? fm.spardirCache.get(name)
-              : fm.getFileAsBytesW(name, null, isCached));
+              : fm.getFileAsBytes(name, null));
           if (!AU.isAB(ret))
             return "ERROR: " + (String) ret;
           newName = addPngFileBytes(name, (byte[]) ret, iFile, crcMap,

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[Jmol-commits] SF.net SVN: jmol:[22286] trunk/Jmol/src/org/jmol/viewer

[<ha...@us...>]

Revision: 22286
          http://sourceforge.net/p/jmol/code/22286
Author:   hansonr
Date:     2021-12-31 20:22:04 +0000 (Fri, 31 Dec 2021)
Log Message:
-----------
PDB menus not computed if menu does not exist before file is loaded.

Modified Paths:
--------------
    trunk/Jmol/src/org/jmol/viewer/StatusManager.java
    trunk/Jmol/src/org/jmol/viewer/Viewer.java

Modified: trunk/Jmol/src/org/jmol/viewer/StatusManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/StatusManager.java	2021-12-31 18:48:52 UTC (rev 22285)
+++ trunk/Jmol/src/org/jmol/viewer/StatusManager.java	2021-12-31 20:22:04 UTC (rev 22286)
@@ -443,6 +443,7 @@
   }
 
 
+  @SuppressWarnings("static-access")
   synchronized void setStatusFrameChanged(int fileNo, int modelNo, int firstNo,
                                           int lastNo, int currentFrame,
                                           float currentMorphModel, String entryName) {
@@ -459,7 +460,7 @@
               sJmol,
               new int[] { frameNo, fileNo, modelNo, firstNo, lastNo,
                   currentFrame }, entryName, Float.valueOf(currentMorphModel) });
-    if (!animating)
+    if (!animating && !vwr.isJSNoAWT)
       vwr.checkMenuUpdate();
   }
 

Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java	2021-12-31 18:48:52 UTC (rev 22285)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java	2021-12-31 20:22:04 UTC (rev 22286)
@@ -209,7 +209,8 @@
   public boolean autoExit = false;
   public boolean haveDisplay = false;
 
-  static public boolean isJS, isJSNoAWT, isSwingJS, isWebGL;
+  static public boolean isJS, isSwingJS, isWebGL;
+  public boolean isJSNoAWT;
   public boolean isSingleThreaded;
   public boolean queueOnHold = false;
 
@@ -1003,6 +1004,9 @@
         return null;
       }
     }
+
+    if (isJSNoAWT)
+      checkMenuUpdate();
     return jmolpopup.jpiGetMenuAsObject();
   }
 

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[Jmol-commits] SF.net SVN: jmol:[22384] trunk/Jmol/src/org/jmol/viewer

[<ha...@us...>]

Revision: 22384
          http://sourceforge.net/p/jmol/code/22384
Author:   hansonr
Date:     2022-03-29 02:36:04 +0000 (Tue, 29 Mar 2022)
Log Message:
-----------
bug fix: SET ECHO BOTTOM LEFT; ECHO "%SCALE" when perspective depth true
 -- should be for center of visible depth based on screen width
 

Modified Paths:
--------------
    trunk/Jmol/src/org/jmol/viewer/Jmol.properties
    trunk/Jmol/src/org/jmol/viewer/Viewer.java

Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2022-03-29 01:06:29 UTC (rev 22383)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2022-03-29 02:36:04 UTC (rev 22384)
@@ -85,6 +85,10 @@
 bug fix: POLYHEDRA COLLAPSED ... 
  -- initial COLLAPSED syntax without FaceOffset should be OK (to be compatible with older Jmol versions)
 
+bug fix: SET ECHO BOTTOM LEFT; ECHO "%SCALE" when perspective depth true
+ -- should be for center of visible depth based on screen width
+ 
+
 JmolVersion="14.32.43" //  also 15.2.43 (second upload)
 
 bug fix: duplicate atom number after delete/add
@@ -221,7 +225,6 @@
   
 new feature: SMILES generator will NOT remove [H] from nitrogens.
  
-
 JmolVersion="14.32.33" 
   also 15.2.33
 

Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java	2022-03-29 01:06:29 UTC (rev 22383)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java	2022-03-29 02:36:04 UTC (rev 22384)
@@ -10679,6 +10679,7 @@
             : g.measureDistanceUnits);
     float d = tm.modelRadius * tm.scaleDefaultPixelsPerAngstrom
         / tm.scalePixelsPerAngstrom / 4;
+    float f = (tm.perspectiveDepth ? 1f/tm.getPerspectiveFactor((tm.getCameraDepth() - 0.5f) * getScreenDim()) : 1);
     int m = 0, p = 0;
     float e = 0;
     int min = (g.antialiasDisplay ? 30 : 15);
@@ -10685,8 +10686,8 @@
     while (p < min) {
       e = Measurement.toUnits(d, u, false);
       m = (int) Math.floor(Math.log10(e));
-      e = (float) Math.pow(10, m) + 0.000001f;
-      p = (int) (Measurement.fromUnits(e, u) * tm.scalePixelsPerAngstrom);
+      e = Measurement.fromUnits((float) Math.pow(10, m) + 0.000001f, u);
+      p = (int) (e * tm.scalePixelsPerAngstrom * f);
       if (p < min) {
         d *= 10;
       }

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[Jmol-commits] SF.net SVN: jmol:[22452] trunk/Jmol/src/org/jmol/viewer

[<ha...@us...>]

Revision: 22452
          http://sourceforge.net/p/jmol/code/22452
Author:   hansonr
Date:     2022-08-10 16:58:32 +0000 (Wed, 10 Aug 2022)
Log Message:
-----------
Jmol.___JmolVersion="14.32.70" // P also 15.2.70

bug fix: reading of gzipped jvxl files from PNGJ fails in JavaScript
 - when caching and reading a file from a zip collection, as in JSmol, FileManager does not unzip the gzipped stream

Modified Paths:
--------------
    trunk/Jmol/src/org/jmol/viewer/FileManager.java
    trunk/Jmol/src/org/jmol/viewer/Jmol.properties

Modified: trunk/Jmol/src/org/jmol/viewer/FileManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/FileManager.java	2022-08-07 22:43:09 UTC (rev 22451)
+++ trunk/Jmol/src/org/jmol/viewer/FileManager.java	2022-08-10 16:58:32 UTC (rev 22452)
@@ -658,13 +658,7 @@
       // if we have a subFileList, we don't want to return the stream for the zip file itself
       else if (Rdr.isBZip2S(bis))
         bis = Rdr.getUnzippedInputStreamBZip2(vwr.getJzt(), bis);
-      // if we have a subFileList, we don't want to return the stream for the zip file itself
-      if (Rdr.isTar(bis)) {
-        Object o = vwr.getJzt().getZipFileDirectory(bis, subFileList, 1,
-            forceInputStream);
-        return (o instanceof String ? Rdr.getBR((String) o) : o);
-      }
-      
+      // if we have a subFileList, we don't want to return the stream for the zip file itself      
       if (forceInputStream && subFileList == null)
         return bis;
       if (Rdr.isCompoundDocumentS(bis)) {
@@ -679,12 +673,20 @@
       if (Rdr.isMessagePackS(bis) || Rdr.isPickleS(bis))
         return bis;
       bis = Rdr.getPngZipStream(bis, true);
+      Object o = null;
       if (Rdr.isZipS(bis)) {
         if (allowZipStream)
           return vwr.getJzt().newZipInputStream(bis);
-        Object o = vwr.getJzt().getZipFileDirectory(bis, subFileList, 1,
+        o = vwr.getJzt().getZipFileDirectory(bis, subFileList, 1,
             forceInputStream);
-        return (o instanceof String ? Rdr.getBR((String) o) : o);
+      } else if (Rdr.isTar(bis)) {
+         o = vwr.getJzt().getZipFileDirectory(bis, subFileList, 1,
+                  forceInputStream);
+      } 
+      if (o != null) {
+        if (!(o instanceof BufferedInputStream))
+          return (o instanceof String ? Rdr.getBR((String) o) : o);
+        bis = Rdr.getUnzippedInputStream(vwr.getJzt(), (BufferedInputStream) o);
       }
       return (forceInputStream ? bis : Rdr.getBufferedReader(bis, null));
     } catch (Exception ioe) {

Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2022-08-07 22:43:09 UTC (rev 22451)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2022-08-10 16:58:32 UTC (rev 22452)
@@ -67,8 +67,14 @@
 
 
 
-Jmol.___JmolVersion="14.32.69" // P also 15.2.69
+Jmol.___JmolVersion="14.32.70" // P also 15.2.70
 
+bug fix: reading of gzipped jvxl files from PNGJ fails in JavaScript
+ - when caching and reading a file from a zip collection, as in JSmol, FileManager does not unzip the gzipped stream
+
+
+JmolVersion="14.32.69" // P also 15.2.69
+
 bug fix: WRITE GIF with text background black creates speckled pattern.
   -- for transparent GIF, use background 0x040404
 

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[Jmol-commits] SF.net SVN: jmol:[22472] trunk/Jmol/src/org/jmol/viewer

[<ha...@us...>]

Revision: 22472
          http://sourceforge.net/p/jmol/code/22472
Author:   hansonr
Date:     2022-09-28 12:00:35 +0000 (Wed, 28 Sep 2022)
Log Message:
-----------
Jmol.___JmolVersion="14.32.76" // also 15.2.76

bug fix: SET PICKING DRAGMINIMIZE  should generally 
         move attached H atoms even if modelkit is not open as long as there is no unit cell.

bug fix: modelkit icons missing

Modified Paths:
--------------
    trunk/Jmol/src/org/jmol/viewer/Jmol.properties
    trunk/Jmol/src/org/jmol/viewer/Viewer.java

Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2022-09-16 01:35:33 UTC (rev 22471)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2022-09-28 12:00:35 UTC (rev 22472)
@@ -57,9 +57,15 @@
 # TODO: isosurface cavity delivers nonsense volume due to unclosed surface
 
 
+Jmol.___JmolVersion="14.32.76" // also 15.2.76
 
-Jmol.___JmolVersion="14.32.75" // also 15.2.75
+bug fix: SET PICKING DRAGMINIMIZE  should generally 
+         move attached H atoms even if modelkit is not open as long as there is no unit cell.
 
+bug fix: modelkit icons missing
+
+JmolVersion="14.32.75" // also 15.2.75
+
 bug fix: WRITE ISOSURFACE incorrect for COLOR DENSITY CUTOFF [min,max]
 
 JmolVersion="14.32.74" // also 15.2.74

Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java	2022-09-16 01:35:33 UTC (rev 22471)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java	2022-09-28 12:00:35 UTC (rev 22472)
@@ -9416,7 +9416,7 @@
     if (bsAtoms == null) {
       Atom atom = ms.at[atomIndex];
       bsAtoms = BSUtil.newAndSetBit(atomIndex);
-      Bond[] bonds = (isModelKitOpen()
+      Bond[] bonds = (this.getOperativeSymmetry() == null || isModelKitOpen()
           && !modelkit.hasConstraint(atomIndex, true, false) ? atom.bonds
               : null);
       if (bonds != null)

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