From: <ha...@us...> - 2016-08-29 16:26:51
|
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" This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2016-09-01 00:29:26
|
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" This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2016-09-01 19:52:08
|
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 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2016-09-21 12:39:05
|
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) This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2016-10-18 04:02:06
|
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 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2016-10-19 04:54:48
|
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" This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2016-10-26 17:26:05
|
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 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2016-11-03 03:06:42
|
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 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2017-06-20 04:06:24
|
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); } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2017-07-20 14:06:50
|
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 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2021-08-05 17:09:58
|
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) This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2021-11-25 14:48:09
|
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 '$': checkCIR(false); if (name.equals("$")) { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2021-11-28 01:02:53
|
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, This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2021-12-31 20:22:06
|
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(); } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2022-03-29 02:36:07
|
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; } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2022-08-10 16:58:35
|
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 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2022-09-28 12:00:38
|
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) This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |