From: <ha...@us...> - 2010-07-28 12:44:04
|
Revision: 13715 http://jmol.svn.sourceforge.net/jmol/?rev=13715&view=rev Author: hansonr Date: 2010-07-28 12:43:58 +0000 (Wed, 28 Jul 2010) Log Message: ----------- Added Paths: ----------- v12_00/ Removed Paths: ------------- v12_0/ This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2012-05-15 12:21:41
|
Revision: 17140 http://jmol.svn.sourceforge.net/jmol/?rev=17140&view=rev Author: hansonr Date: 2012-05-15 12:21:30 +0000 (Tue, 15 May 2012) Log Message: ----------- hold for fix of COMPARE command, please. Modified Paths: -------------- branches/v12_2/Jmol/src/org/jmol/viewer/Jmol.properties trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v12_2/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v12_2/Jmol/src/org/jmol/viewer/Jmol.properties 2012-05-15 05:24:07 UTC (rev 17139) +++ branches/v12_2/Jmol/src/org/jmol/viewer/Jmol.properties 2012-05-15 12:21:30 UTC (rev 17140) @@ -4,7 +4,7 @@ date=$Date$ -version=12.2.25 +version=12.2.25_HOLD # bug fix: isosurface molecular for certain flat models will fail to cap H atoms # bug fix: dipole command fails after model kit changes Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2012-05-15 05:24:07 UTC (rev 17139) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2012-05-15 12:21:30 UTC (rev 17140) @@ -3,7 +3,7 @@ date=$Date$ -version=12.3.25 +version=12.3.25_HOLD # new feature: MMFF94 single point energy calculation and minimization # set forcefield "MMFF" This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2012-05-15 12:22:43
|
Revision: 17141 http://jmol.svn.sourceforge.net/jmol/?rev=17141&view=rev Author: hansonr Date: 2012-05-15 12:22:31 +0000 (Tue, 15 May 2012) Log Message: ----------- hold for fix of COMPARE command, please. Modified Paths: -------------- branches/v12_2/Jmol/src/org/jmol/viewer/Jmol.properties trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v12_2/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v12_2/Jmol/src/org/jmol/viewer/Jmol.properties 2012-05-15 12:21:30 UTC (rev 17140) +++ branches/v12_2/Jmol/src/org/jmol/viewer/Jmol.properties 2012-05-15 12:22:31 UTC (rev 17141) @@ -6,6 +6,7 @@ version=12.2.25_HOLD +# TODO: fix COMPARE command # bug fix: isosurface molecular for certain flat models will fail to cap H atoms # bug fix: dipole command fails after model kit changes Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2012-05-15 12:21:30 UTC (rev 17140) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2012-05-15 12:22:31 UTC (rev 17141) @@ -5,6 +5,8 @@ version=12.3.25_HOLD +# TODO: fix COMPARE command + # new feature: MMFF94 single point energy calculation and minimization # set forcefield "MMFF" # checkmm.spt This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2013-07-28 17:10:26
|
Revision: 18505 http://sourceforge.net/p/jmol/code/18505 Author: hansonr Date: 2013-07-28 17:10:21 +0000 (Sun, 28 Jul 2013) Log Message: ----------- Modified Paths: -------------- branches/v13_2/Jmol/build.xml trunk/Jmol/build.xml Modified: branches/v13_2/Jmol/build.xml =================================================================== --- branches/v13_2/Jmol/build.xml 2013-07-28 16:37:17 UTC (rev 18504) +++ branches/v13_2/Jmol/build.xml 2013-07-28 17:10:21 UTC (rev 18505) @@ -59,6 +59,7 @@ <property name="tests.dir" value="build/unit.tests" /> <property name="javadoc.dir" value="build/javadoc" /> <property name="jmol.applet.build.dir" value="build" /> + <property name="jmol.applet.web.dir" value="appletweb" /> <property name="jmol.build.dir" value="build" /> <property name="docbook-xsl" value="docbook-xsl-1.76.1" /> <property name="docbook-xml" value="docbook-xml-4.4" /> @@ -1310,14 +1311,10 @@ <delete dir="build/dist/jmol-${version}"/> <mkdir dir="build/dist/jmol-${version}"/> <copy todir="build/dist/jmol-${version}" > - <fileset dir="${jmol.applet.build.dir}"> - <include name="JmolApplet*.jar" /> - </fileset> <fileset dir="${jmol.build.dir}"> <include name="Jmol.jar" /> - <include name="ChimeToJmol.jar" /> <include name="JmolData.jar" /> - <include name="JmolSmiles.jar" /> + <include name="JmolLib.jar" /> </fileset> <fileset dir="."> <include name="jmol" /> @@ -1339,9 +1336,7 @@ <copy todir="build/dist/jmol-${version}" > <fileset dir="./appletweb"> <include name="README*.txt" /> - <include name="Jmol*.js" /> - <include name="JSpecViewApplet.jar" /> - <include name="JSpecViewAppletSigned.jar" /> + <include name="jsmol.zip" /> </fileset> </copy> Modified: trunk/Jmol/build.xml =================================================================== --- trunk/Jmol/build.xml 2013-07-28 16:37:17 UTC (rev 18504) +++ trunk/Jmol/build.xml 2013-07-28 17:10:21 UTC (rev 18505) @@ -59,6 +59,7 @@ <property name="tests.dir" value="build/unit.tests" /> <property name="javadoc.dir" value="build/javadoc" /> <property name="jmol.applet.build.dir" value="build" /> + <property name="jmol.applet.web.dir" value="appletweb" /> <property name="jmol.build.dir" value="build" /> <property name="docbook-xsl" value="docbook-xsl-1.76.1" /> <property name="docbook-xml" value="docbook-xml-4.4" /> @@ -1310,14 +1311,10 @@ <delete dir="build/dist/jmol-${version}"/> <mkdir dir="build/dist/jmol-${version}"/> <copy todir="build/dist/jmol-${version}" > - <fileset dir="${jmol.applet.build.dir}"> - <include name="JmolApplet*.jar" /> - </fileset> <fileset dir="${jmol.build.dir}"> <include name="Jmol.jar" /> - <include name="ChimeToJmol.jar" /> <include name="JmolData.jar" /> - <include name="JmolSmiles.jar" /> + <include name="JmolLib.jar" /> </fileset> <fileset dir="."> <include name="jmol" /> @@ -1339,9 +1336,7 @@ <copy todir="build/dist/jmol-${version}" > <fileset dir="./appletweb"> <include name="README*.txt" /> - <include name="Jmol*.js" /> - <include name="JSpecViewApplet.jar" /> - <include name="JSpecViewAppletSigned.jar" /> + <include name="jsmol.zip" /> </fileset> </copy> This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2013-08-13 22:53:48
|
Revision: 18561 http://sourceforge.net/p/jmol/code/18561 Author: hansonr Date: 2013-08-13 22:53:44 +0000 (Tue, 13 Aug 2013) Log Message: ----------- Modified Paths: -------------- branches/v13_2/Jmol/src/org/jmol/viewer/Jmol.properties branches/v13_2/Jmol/src/org/jmol/viewer/Viewer.java trunk/Jmol/src/org/jmol/viewer/Jmol.properties trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: branches/v13_2/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v13_2/Jmol/src/org/jmol/viewer/Jmol.properties 2013-08-13 22:49:06 UTC (rev 18560) +++ branches/v13_2/Jmol/src/org/jmol/viewer/Jmol.properties 2013-08-13 22:53:44 UTC (rev 18561) @@ -20,18 +20,27 @@ via loadInline(List)* createModelSetAndReturnError - script LOAD - openDOM, openReader, openFile, openFiles* - via loadModelFromFile(*) + openDOM, openReader, openFile, openFiles + via loadModelFromFileRepaint* createModelSetAndReturnError - script CALCULATE HYDROGENS, PLOT, ZAP (modelkit) - loadInLine(String)* via loadInLineScript(*) + loadInLine(String) via loadInLineScriptRepaint* FileDropper (string drop) via openStringInline* - openStringInlineParamsAppend + via openStringInlineParamsAppend createModelSetAndReturnError + + external apps, applet only, via loadInline(String[])* + via openStringsInlineParamsAppend + createModelSetAndReturnError + + script LOAD + via loadModelFromFile + createModelSetAndReturnError + + script CALCULATE HYDROGENS, PLOT, ZAP (modelkit) + via openStringInlineParamsAppend + createModelSetAndReturnError - external apps, applet only, via loadInline(String[])* script LOAD DATA via loadFileFull and loadInlineScript openStringsInlineParamsAppend createModelSetAndReturnError Modified: branches/v13_2/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- branches/v13_2/Jmol/src/org/jmol/viewer/Viewer.java 2013-08-13 22:49:06 UTC (rev 18560) +++ branches/v13_2/Jmol/src/org/jmol/viewer/Viewer.java 2013-08-13 22:53:44 UTC (rev 18561) @@ -1927,22 +1927,32 @@ // //////////////// methods that open a file to create a model set /////////// // *indicates when a refresh is made (external apps and applets only) - // + // // external apps only // via loadInline(List)* // createModelSetAndReturnError - // - // script LOAD via loadModelFromFile - // openDOM, openReader, openFile, openFiles via loadModelFromFileRepaint* + // + // openDOM, openReader, openFile, openFiles + // via loadModelFromFileRepaint* // createModelSetAndReturnError - // - // script CALCULATE HYDROGENS, PLOT, ZAP (modelkit) + // // loadInLine(String) via loadInLineScriptRepaint* // FileDropper (string drop) via openStringInline* - // openStringInlineParamsAppend + // via openStringInlineParamsAppend // createModelSetAndReturnError // // external apps, applet only, via loadInline(String[])* + // via openStringsInlineParamsAppend + // createModelSetAndReturnError + // + // script LOAD + // via loadModelFromFile + // createModelSetAndReturnError + // + // script CALCULATE HYDROGENS, PLOT, ZAP (modelkit) + // via openStringInlineParamsAppend + // createModelSetAndReturnError + // // script LOAD DATA via loadFileFull and loadInlineScript // openStringsInlineParamsAppend // createModelSetAndReturnError Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-08-13 22:49:06 UTC (rev 18560) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-08-13 22:53:44 UTC (rev 18561) @@ -21,23 +21,31 @@ via loadInline(List)* createModelSetAndReturnError - script LOAD - openDOM, openReader, openFile, openFiles* - via loadModelFromFile(*) + openDOM, openReader, openFile, openFiles + via loadModelFromFileRepaint* createModelSetAndReturnError - script CALCULATE HYDROGENS, PLOT, ZAP (modelkit) - loadInLine(String)* via loadInLineScript(*) + loadInLine(String) via loadInLineScriptRepaint* FileDropper (string drop) via openStringInline* - openStringInlineParamsAppend + via openStringInlineParamsAppend createModelSetAndReturnError + + external apps, applet only, via loadInline(String[])* + via openStringsInlineParamsAppend + createModelSetAndReturnError + + script LOAD + via loadModelFromFile + createModelSetAndReturnError + + script CALCULATE HYDROGENS, PLOT, ZAP (modelkit) + via openStringInlineParamsAppend + createModelSetAndReturnError - external apps, applet only, via loadInline(String[])* script LOAD DATA via loadFileFull and loadInlineScript openStringsInlineParamsAppend createModelSetAndReturnError - new feature: incommensurate modulation of ADPs. new feature: Jana2006 M40/M50 file reading Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2013-08-13 22:49:06 UTC (rev 18560) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2013-08-13 22:53:44 UTC (rev 18561) @@ -1929,22 +1929,32 @@ // *indicates when a refresh is made (external apps and applets only) - // + // // external apps only // via loadInline(List)* // createModelSetAndReturnError - // - // script LOAD via loadModelFromFile - // openDOM, openReader, openFile, openFiles via loadModelFromFileRepaint* + // + // openDOM, openReader, openFile, openFiles + // via loadModelFromFileRepaint* // createModelSetAndReturnError - // - // script CALCULATE HYDROGENS, PLOT, ZAP (modelkit) + // // loadInLine(String) via loadInLineScriptRepaint* // FileDropper (string drop) via openStringInline* - // openStringInlineParamsAppend + // via openStringInlineParamsAppend // createModelSetAndReturnError // // external apps, applet only, via loadInline(String[])* + // via openStringsInlineParamsAppend + // createModelSetAndReturnError + // + // script LOAD + // via loadModelFromFile + // createModelSetAndReturnError + // + // script CALCULATE HYDROGENS, PLOT, ZAP (modelkit) + // via openStringInlineParamsAppend + // createModelSetAndReturnError + // // script LOAD DATA via loadFileFull and loadInlineScript // openStringsInlineParamsAppend // createModelSetAndReturnError This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2013-10-02 01:46:51
|
Revision: 18761 http://sourceforge.net/p/jmol/code/18761 Author: hansonr Date: 2013-10-02 01:46:45 +0000 (Wed, 02 Oct 2013) Log Message: ----------- Modified Paths: -------------- branches/v13_2/Jmol/tools/jmol-release.stable.xml trunk/Jmol/tools/jmol-release.xml Modified: branches/v13_2/Jmol/tools/jmol-release.stable.xml =================================================================== --- branches/v13_2/Jmol/tools/jmol-release.stable.xml 2013-10-02 01:35:01 UTC (rev 18760) +++ branches/v13_2/Jmol/tools/jmol-release.stable.xml 2013-10-02 01:46:45 UTC (rev 18761) @@ -38,6 +38,7 @@ <input message="Do you really want to copy files to ${path.release}/${prefix.release}${version} (y/n) ?" validargs="y,n" + defaultvalue="y" addproperty="do.scp" /> <condition property="do.abort"> Modified: trunk/Jmol/tools/jmol-release.xml =================================================================== --- trunk/Jmol/tools/jmol-release.xml 2013-10-02 01:35:01 UTC (rev 18760) +++ trunk/Jmol/tools/jmol-release.xml 2013-10-02 01:46:45 UTC (rev 18761) @@ -38,6 +38,7 @@ <input message="Do you really want to copy files to ${path.release}/${prefix.release}${version} (y/n) ?" validargs="y,n" + defaultvalue="y" addproperty="do.scp" /> <condition property="do.abort"> This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2013-12-05 00:31:12
|
Revision: 19068 http://sourceforge.net/p/jmol/code/19068 Author: hansonr Date: 2013-12-05 00:31:04 +0000 (Thu, 05 Dec 2013) Log Message: ----------- coding error in JSpecView file manager reading MOL files causes NPE in Jmol Tools...JSpecView Modified Paths: -------------- branches/v14_0/Jmol/jars/JSpecView.jar trunk/Jmol/jars/JSpecView.jar Modified: branches/v14_0/Jmol/jars/JSpecView.jar =================================================================== (Binary files differ) Modified: trunk/Jmol/jars/JSpecView.jar =================================================================== (Binary files differ) This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2013-12-05 16:04:21
|
Revision: 19069 http://sourceforge.net/p/jmol/code/19069 Author: hansonr Date: 2013-12-05 16:04:17 +0000 (Thu, 05 Dec 2013) Log Message: ----------- Modified Paths: -------------- branches/v14_0/Jmol/srcjs/js/package.js trunk/Jmol/srcjs/js/package.js Modified: branches/v14_0/Jmol/srcjs/js/package.js =================================================================== --- branches/v14_0/Jmol/srcjs/js/package.js 2013-12-05 00:31:04 UTC (rev 19068) +++ branches/v14_0/Jmol/srcjs/js/package.js 2013-12-05 16:04:17 UTC (rev 19069) @@ -123,6 +123,7 @@ "J.thread.MinimizationThread" ]); +/* ClazzLoader.jarClasspath (base + "corezip.z.js", [ "JZ.Checksum", "$.CRC32", @@ -156,7 +157,7 @@ "J.io2.ZipUtil", "$.JmolZipInputStream" ]); - + */ ClazzLoader.jarClasspath (base + "corebio.z.js", [ "J.adapter.readers.pdb.PdbReader", "J.adapter.smarter.Structure", @@ -254,5 +255,25 @@ "$.SmilesParser" ]); +// note - we don't need to list ALL the classes -- only the ones that are entry points. +// several moe classe are in each fo these files -- see build_03_tojs.xml + + ClazzLoader.jarClasspath (base + "corejsvmenu.z.js", [ + "JSV.js2d.JsPopup" + ]); + + ClazzLoader.jarClasspath (base + "corejsvexport.z.js", [ + "JSV.export.Exporter" + ]); + + ClazzLoader.jarClasspath (base + "corejsvdialog.z.js", [ + "JSV.dialog.IntegrationDialog", + "$.PeakListDialog", + "$.MeasurementsDialog", + "$.OverlayLegendDialog", + "$.ViewsDialog" + ]); + + }) (); window["java.registered"] = true; Modified: trunk/Jmol/srcjs/js/package.js =================================================================== --- trunk/Jmol/srcjs/js/package.js 2013-12-05 00:31:04 UTC (rev 19068) +++ trunk/Jmol/srcjs/js/package.js 2013-12-05 16:04:17 UTC (rev 19069) @@ -123,6 +123,7 @@ "J.thread.MinimizationThread" ]); +/* ClazzLoader.jarClasspath (base + "corezip.z.js", [ "JZ.Checksum", "$.CRC32", @@ -156,7 +157,7 @@ "J.io2.ZipUtil", "$.JmolZipInputStream" ]); - + */ ClazzLoader.jarClasspath (base + "corebio.z.js", [ "J.adapter.readers.pdb.PdbReader", "J.adapter.smarter.Structure", @@ -254,5 +255,25 @@ "$.SmilesParser" ]); +// note - we don't need to list ALL the classes -- only the ones that are entry points. +// several moe classe are in each fo these files -- see build_03_tojs.xml + + ClazzLoader.jarClasspath (base + "corejsvmenu.z.js", [ + "JSV.js2d.JsPopup" + ]); + + ClazzLoader.jarClasspath (base + "corejsvexport.z.js", [ + "JSV.export.Exporter" + ]); + + ClazzLoader.jarClasspath (base + "corejsvdialog.z.js", [ + "JSV.dialog.IntegrationDialog", + "$.PeakListDialog", + "$.MeasurementsDialog", + "$.OverlayLegendDialog", + "$.ViewsDialog" + ]); + + }) (); window["java.registered"] = true; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2013-12-05 23:01:12
|
Revision: 19071 http://sourceforge.net/p/jmol/code/19071 Author: hansonr Date: 2013-12-05 23:01:07 +0000 (Thu, 05 Dec 2013) Log Message: ----------- Modified Paths: -------------- branches/v14_0/Jmol/srcjs/js/package.js trunk/Jmol/srcjs/js/package.js Modified: branches/v14_0/Jmol/srcjs/js/package.js =================================================================== --- branches/v14_0/Jmol/srcjs/js/package.js 2013-12-05 16:27:43 UTC (rev 19070) +++ branches/v14_0/Jmol/srcjs/js/package.js 2013-12-05 23:01:07 UTC (rev 19071) @@ -19,6 +19,9 @@ if (Jmol._debugCode) return; +// note - we don't need to list ALL the classes -- only the ones that are entry points. +// several more classe are in each of these files -- see build_03_tojs.xml + ClazzLoader.jarClasspath (base + "coretext.z.js", [ "J.modelset.Object2d", "$.Text", @@ -26,11 +29,7 @@ "$.TextShape", "$.Labels", "$.Echo", - "$.Hover", - "J.render.TextRenderer", - "$.LabelsRenderer", - "$.EchoRenderer", - "$.HoverRenderer" + "$.Hover" ]); ClazzLoader.jarClasspath (base + "corescript.z.js", [ @@ -39,11 +38,6 @@ "$.JmolScriptFunction", "J.script.ScriptEvaluator", "$.ScriptCompiler", - "$.ScriptCompilationTokenParser", - "$.ScriptFlowContext", - "$.ScriptFunction", - "$.ScriptInterruption", - "$.ScriptMathProcessor", "$.CommandWatcherThread", "$.ScriptQueueThread", "$.ScriptDelayThread", @@ -123,83 +117,20 @@ "J.thread.MinimizationThread" ]); -/* ClazzLoader.jarClasspath (base + "corezip.z.js", [ - "JZ.Checksum", - "$.CRC32", - "$.InflaterInputStream", - "$.ZStream", - "$.Inflater", - "$.Adler32", - "$.Tree", - "$.GZIPHeader", - "$.StaticTree", - "$.Inflate", - "$.InfTree", - "$.InfBlocks", - "$.InfCodes", - "$.Inflater", - "$.InflaterInputStream", - "$.GZIPInputStream", - "$.PushbackInputStream", - "java.util.zip.CRC32", - "$.CheckedInputStream", - "$.GZIPInputStream", - "$.Inflater", - "$.InflaterInputStream", - "$.ZipException", - "$.ZipConstants", - "$.ZipEntry", - "$.ZipConstants64", - "$.ZipInputStream", "J.api.JmolZipUtility", "$.ZInputStream", "J.io2.ZipUtil", "$.JmolZipInputStream" ]); - */ + ClazzLoader.jarClasspath (base + "corebio.z.js", [ "J.adapter.readers.pdb.PdbReader", "J.adapter.smarter.Structure", - "J.dssx.Bridge", - "J.dssx.DSSP", "J.api.JmolBioResolver", "J.modelsetbio.Resolver", - "$.Monomer", - "$.AlphaMonomer", - "$.ProteinStructure", - "$.Helix", - "$.Sheet", - "$.Turn", - "$.BioPolymer", - "$.AlphaPolymer", - "$.AminoMonomer", - "$.AminoPolymer", - "$.BioModel", - "$.CarbohydrateMonomer", - "$.CarbohydratePolymer", - "$.PhosphorusMonomer", - "$.NucleicMonomer", - "$.NucleicPolymer", - "$.PhosphorusPolymer", - "J.shapebio.BioShape", - "$.BioShapeCollection", - "$.Ribbons", - "$.MeshRibbons", - "$.Strands", - "$.Rockets", - "$.Cartoon", - "$.Backbone", - "$.Trace", - "J.renderbio.BioShapeRenderer", - "$.StrandsRenderer", - "$.RibbonsRenderer", - "$.MeshRibbonsRenderer", - "$.RocketsRenderer", - "$.CartoonRenderer", - "$.BackboneRenderer", - "$.TraceRenderer" - ]); + "$.BioModel" + ]); ClazzLoader.jarClasspath (base + "coresurface.z.js", [ @@ -255,9 +186,6 @@ "$.SmilesParser" ]); -// note - we don't need to list ALL the classes -- only the ones that are entry points. -// several moe classe are in each fo these files -- see build_03_tojs.xml - ClazzLoader.jarClasspath (base + "corejsvmenu.z.js", [ "JSV.js2d.JsPopup" ]); @@ -275,5 +203,6 @@ ]); + }) (); window["java.registered"] = true; Modified: trunk/Jmol/srcjs/js/package.js =================================================================== --- trunk/Jmol/srcjs/js/package.js 2013-12-05 16:27:43 UTC (rev 19070) +++ trunk/Jmol/srcjs/js/package.js 2013-12-05 23:01:07 UTC (rev 19071) @@ -19,6 +19,9 @@ if (Jmol._debugCode) return; +// note - we don't need to list ALL the classes -- only the ones that are entry points. +// several more classe are in each of these files -- see build_03_tojs.xml + ClazzLoader.jarClasspath (base + "coretext.z.js", [ "J.modelset.Object2d", "$.Text", @@ -26,11 +29,7 @@ "$.TextShape", "$.Labels", "$.Echo", - "$.Hover", - "J.render.TextRenderer", - "$.LabelsRenderer", - "$.EchoRenderer", - "$.HoverRenderer" + "$.Hover" ]); ClazzLoader.jarClasspath (base + "corescript.z.js", [ @@ -39,11 +38,6 @@ "$.JmolScriptFunction", "J.script.ScriptEvaluator", "$.ScriptCompiler", - "$.ScriptCompilationTokenParser", - "$.ScriptFlowContext", - "$.ScriptFunction", - "$.ScriptInterruption", - "$.ScriptMathProcessor", "$.CommandWatcherThread", "$.ScriptQueueThread", "$.ScriptDelayThread", @@ -123,83 +117,20 @@ "J.thread.MinimizationThread" ]); -/* ClazzLoader.jarClasspath (base + "corezip.z.js", [ - "JZ.Checksum", - "$.CRC32", - "$.InflaterInputStream", - "$.ZStream", - "$.Inflater", - "$.Adler32", - "$.Tree", - "$.GZIPHeader", - "$.StaticTree", - "$.Inflate", - "$.InfTree", - "$.InfBlocks", - "$.InfCodes", - "$.Inflater", - "$.InflaterInputStream", - "$.GZIPInputStream", - "$.PushbackInputStream", - "java.util.zip.CRC32", - "$.CheckedInputStream", - "$.GZIPInputStream", - "$.Inflater", - "$.InflaterInputStream", - "$.ZipException", - "$.ZipConstants", - "$.ZipEntry", - "$.ZipConstants64", - "$.ZipInputStream", "J.api.JmolZipUtility", "$.ZInputStream", "J.io2.ZipUtil", "$.JmolZipInputStream" ]); - */ + ClazzLoader.jarClasspath (base + "corebio.z.js", [ "J.adapter.readers.pdb.PdbReader", "J.adapter.smarter.Structure", - "J.dssx.Bridge", - "J.dssx.DSSP", "J.api.JmolBioResolver", "J.modelsetbio.Resolver", - "$.Monomer", - "$.AlphaMonomer", - "$.ProteinStructure", - "$.Helix", - "$.Sheet", - "$.Turn", - "$.BioPolymer", - "$.AlphaPolymer", - "$.AminoMonomer", - "$.AminoPolymer", - "$.BioModel", - "$.CarbohydrateMonomer", - "$.CarbohydratePolymer", - "$.PhosphorusMonomer", - "$.NucleicMonomer", - "$.NucleicPolymer", - "$.PhosphorusPolymer", - "J.shapebio.BioShape", - "$.BioShapeCollection", - "$.Ribbons", - "$.MeshRibbons", - "$.Strands", - "$.Rockets", - "$.Cartoon", - "$.Backbone", - "$.Trace", - "J.renderbio.BioShapeRenderer", - "$.StrandsRenderer", - "$.RibbonsRenderer", - "$.MeshRibbonsRenderer", - "$.RocketsRenderer", - "$.CartoonRenderer", - "$.BackboneRenderer", - "$.TraceRenderer" - ]); + "$.BioModel" + ]); ClazzLoader.jarClasspath (base + "coresurface.z.js", [ @@ -255,9 +186,6 @@ "$.SmilesParser" ]); -// note - we don't need to list ALL the classes -- only the ones that are entry points. -// several moe classe are in each fo these files -- see build_03_tojs.xml - ClazzLoader.jarClasspath (base + "corejsvmenu.z.js", [ "JSV.js2d.JsPopup" ]); @@ -275,5 +203,6 @@ ]); + }) (); window["java.registered"] = true; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2013-12-15 13:53:59
|
Revision: 19109 http://sourceforge.net/p/jmol/code/19109 Author: hansonr Date: 2013-12-15 13:53:51 +0000 (Sun, 15 Dec 2013) Log Message: ----------- allowing DOS ".SPT" instead of ".spt" for drag/drop Modified Paths: -------------- branches/v14_0/Jmol/src/org/jmol/script/ScriptManager.java trunk/Jmol/src/org/jmol/script/ScriptManager.java Modified: branches/v14_0/Jmol/src/org/jmol/script/ScriptManager.java =================================================================== --- branches/v14_0/Jmol/src/org/jmol/script/ScriptManager.java 2013-12-14 22:31:12 UTC (rev 19108) +++ branches/v14_0/Jmol/src/org/jmol/script/ScriptManager.java 2013-12-15 13:53:51 UTC (rev 19109) @@ -541,7 +541,7 @@ cmd = "isosurface "; return; } - if (!fileName.endsWith(".spt")) { + if (!fileName.toLowerCase().endsWith(".spt")) { String type = getFileTypeName(fileName); if (type == null) { type = JmolBinary.determineSurfaceTypeIs(viewer Modified: trunk/Jmol/src/org/jmol/script/ScriptManager.java =================================================================== --- trunk/Jmol/src/org/jmol/script/ScriptManager.java 2013-12-14 22:31:12 UTC (rev 19108) +++ trunk/Jmol/src/org/jmol/script/ScriptManager.java 2013-12-15 13:53:51 UTC (rev 19109) @@ -541,7 +541,7 @@ cmd = "isosurface "; return; } - if (!fileName.endsWith(".spt")) { + if (!fileName.toLowerCase().endsWith(".spt")) { String type = getFileTypeName(fileName); if (type == null) { type = JmolBinary.determineSurfaceTypeIs(viewer This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2014-02-20 23:02:15
|
Revision: 19369 http://sourceforge.net/p/jmol/code/19369 Author: hansonr Date: 2014-02-20 23:02:09 +0000 (Thu, 20 Feb 2014) Log Message: ----------- ___JmolVersion="14.0.11_2014.02.20a" bug fix:modelkitmode broken for Java in 14.0.10 Modified Paths: -------------- branches/v14_0/Jmol/src/org/jmol/modelset/ModelCollection.java branches/v14_0/Jmol/src/org/jmol/scriptext/ScriptExt.java branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v14_0/Jmol/src/org/jmol/modelset/ModelCollection.java =================================================================== --- branches/v14_0/Jmol/src/org/jmol/modelset/ModelCollection.java 2014-02-20 22:33:46 UTC (rev 19368) +++ branches/v14_0/Jmol/src/org/jmol/modelset/ModelCollection.java 2014-02-20 23:02:09 UTC (rev 19369) @@ -358,7 +358,6 @@ } public float calcRotationRadius(int modelIndex, P3 center) { - System.out.println("modelcoll center=" + center); if (isJmolDataFrameForModel(modelIndex)) { float r = models[modelIndex].defaultRotationRadius; return (r == 0 ? 10 : r); Modified: branches/v14_0/Jmol/src/org/jmol/scriptext/ScriptExt.java =================================================================== --- branches/v14_0/Jmol/src/org/jmol/scriptext/ScriptExt.java 2014-02-20 22:33:46 UTC (rev 19368) +++ branches/v14_0/Jmol/src/org/jmol/scriptext/ScriptExt.java 2014-02-20 23:02:09 UTC (rev 19369) @@ -5007,7 +5007,7 @@ if (msg != null) { if (!msg.startsWith("OK")) eval.evalError(msg, null); - eval.scriptStatusOrBuffer(data); + eval.report(data); } return ""; } else if (data == "MENU") { @@ -5124,7 +5124,7 @@ */ { } - eval.scriptStatusOrBuffer((String) bytes); + eval.report((String) bytes); return (String) bytes; } if (type.equals("SCENE")) @@ -5170,7 +5170,7 @@ { } } - eval.scriptStatusOrBuffer(msg + eval.report(msg + (isImage ? "; width=" + width + "; height=" + height : "")); return msg; } @@ -5433,6 +5433,7 @@ if (!chk) msg = viewer.getSpecularState(); break; + case T.saved: case T.save: if (!chk) msg = viewer.listSavedStates(); @@ -5741,9 +5742,9 @@ ScriptContext context = eval.thisContext; while (context != null) { if (withVariables) { - if (context.contextVariables != null) { + if (context.vars != null) { sb.append(getScriptID(context)); - sb.append(StateManager.getVariableList(context.contextVariables, 80, + sb.append(StateManager.getVariableList(context.vars, 80, true, false)); } } else { @@ -5820,23 +5821,23 @@ private void assignAtom(int atomIndex, P3 pt, String type) { if (type.equals("X")) viewer.setRotateBondIndex(-1); - ModelSet modelSet = viewer.modelSet; - if (modelSet.atoms[atomIndex].modelIndex != modelSet.modelCount - 1) + if (viewer.modelSet.atoms[atomIndex].modelIndex != viewer.modelSet.modelCount - 1) return; viewer.clearModelDependentObjects(); - int atomCount = modelSet.getAtomCount(); + int atomCount = viewer.modelSet.getAtomCount(); if (pt == null) { viewer.statusManager.modifySend(atomIndex, - modelSet.atoms[atomIndex].modelIndex, 1, eval.fullCommand); - modelSet.assignAtom(atomIndex, type, true); + viewer.modelSet.atoms[atomIndex].modelIndex, 1, eval.fullCommand); + // After this next command, viewer.modelSet will be a different instance + viewer.modelSet.assignAtom(atomIndex, type, true); if (!PT.isOneOf(type, ";Mi;Pl;X;")) - modelSet.setAtomNamesAndNumbers(atomIndex, -atomCount, null); + viewer.modelSet.setAtomNamesAndNumbers(atomIndex, -atomCount, null); viewer.statusManager.modifySend(atomIndex, - modelSet.atoms[atomIndex].modelIndex, -1, "OK"); + viewer.modelSet.atoms[atomIndex].modelIndex, -1, "OK"); viewer.refresh(3, "assignAtom"); return; } - Atom atom = modelSet.atoms[atomIndex]; + Atom atom = viewer.modelSet.atoms[atomIndex]; BS bs = BSUtil.newAndSetBit(atomIndex); P3[] pts = new P3[] { pt }; List<Atom> vConnections = new List<Atom>(); @@ -5845,12 +5846,13 @@ viewer.statusManager.modifySend(atomIndex, modelIndex, 3, eval.fullCommand); try { bs = viewer.addHydrogensInline(bs, vConnections, pts); + // new ModelSet here atomIndex = bs.nextSetBit(0); - modelSet.assignAtom(atomIndex, type, false); + viewer.modelSet.assignAtom(atomIndex, type, false); } catch (Exception e) { // } - modelSet.setAtomNamesAndNumbers(atomIndex, -atomCount, null); + viewer.modelSet.setAtomNamesAndNumbers(atomIndex, -atomCount, null); viewer.statusManager.modifySend(atomIndex, modelIndex, -3, "OK"); } @@ -5927,7 +5929,7 @@ return; n = viewer.autoHbond(bs1, bs2, false); if (n != Integer.MIN_VALUE) - eval.scriptStatusOrBuffer(GT.i(GT._("{0} hydrogen bonds"), + eval.report(GT.i(GT._("{0} hydrogen bonds"), Math.abs(n))); return; case T.hydrogen: @@ -10163,7 +10165,7 @@ boolean report = eval.doReport(); if (isDelete) { if (report) - eval.scriptStatusOrBuffer(GT.i(GT._("{0} connections deleted"), nModified)); + eval.report(GT.i(GT._("{0} connections deleted"), nModified)); return; } if (isColorOrRadius) { @@ -10175,7 +10177,7 @@ viewer.selectBonds(null); } if (report) - eval.scriptStatusOrBuffer(GT.o(GT._("{0} new bonds; {1} modified"), + eval.report(GT.o(GT._("{0} new bonds; {1} modified"), new Object[] { Integer.valueOf(nNew), Integer.valueOf(nModified) })); } Modified: branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties 2014-02-20 22:33:46 UTC (rev 19368) +++ branches/v14_0/Jmol/src/org/jmol/viewer/Jmol.properties 2014-02-20 23:02:09 UTC (rev 19369) @@ -9,8 +9,12 @@ # The quotes above look odd for a parameter file, but they are # important for the JavaScript version of Jmol. -___JmolVersion="14.0.10_2014.02.19" +___JmolVersion="14.0.11_2014.02.20a" +bug fix:modelkitmode broken for Java in 14.0.10 + +JmolVersion="14.0.10_2014.02.19" + bug fix: color atoms formalcharge not saved in state bug fix: averageAtomPosition never updated. bug fix: load of model with one atom does not set center to that atom Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2014-02-20 22:33:46 UTC (rev 19368) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2014-02-20 23:02:09 UTC (rev 19369) @@ -44,7 +44,7 @@ throw "testing here" print "continuing" } catch(e) { - print "thown_value=" + thrown_value; + print "thrown_value=" + thrown_value; } results in: This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2014-06-13 16:40:20
|
Revision: 19834 http://sourceforge.net/p/jmol/code/19834 Author: hansonr Date: 2014-06-13 16:40:09 +0000 (Fri, 13 Jun 2014) Log Message: ----------- Modified Paths: -------------- branches/v14_2/Jmol/src/org/jmol/modelset/ModelSet.java trunk/Jmol/src/org/jmol/modelset/ModelSet.java Modified: branches/v14_2/Jmol/src/org/jmol/modelset/ModelSet.java =================================================================== --- branches/v14_2/Jmol/src/org/jmol/modelset/ModelSet.java 2014-06-13 15:56:54 UTC (rev 19833) +++ branches/v14_2/Jmol/src/org/jmol/modelset/ModelSet.java 2014-06-13 16:40:09 UTC (rev 19834) @@ -2350,9 +2350,9 @@ int ia = ((BS) specInfo).nextSetBit(0); if (ia < 0) return new BS(); - if (at[ia].getGroup3(true) != null) + if (at[ia].group.isProtein) return at[ia].group.getBSSideChain(); - // treat as molecule if not PDB residue; + // treat as molecule if not PDB protein; //$FALL-THROUGH$ case T.molecule: return getMoleculeBitSet((BS) specInfo); Modified: trunk/Jmol/src/org/jmol/modelset/ModelSet.java =================================================================== --- trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2014-06-13 15:56:54 UTC (rev 19833) +++ trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2014-06-13 16:40:09 UTC (rev 19834) @@ -2350,9 +2350,9 @@ int ia = ((BS) specInfo).nextSetBit(0); if (ia < 0) return new BS(); - if (at[ia].getGroup3(true) != null) + if (at[ia].group.isProtein) return at[ia].group.getBSSideChain(); - // treat as molecule if not PDB residue; + // treat as molecule if not PDB protein; //$FALL-THROUGH$ case T.molecule: return getMoleculeBitSet((BS) specInfo); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2014-06-28 23:45:40
|
Revision: 19854 http://sourceforge.net/p/jmol/code/19854 Author: hansonr Date: 2014-06-28 23:45:37 +0000 (Sat, 28 Jun 2014) Log Message: ----------- cannot reach return for HTML5 (Google Closure Compiler found this) Modified Paths: -------------- branches/v14_2/Jmol/src/org/jmol/io/JmolUtil.java trunk/Jmol/src/org/jmol/io/JmolUtil.java Modified: branches/v14_2/Jmol/src/org/jmol/io/JmolUtil.java =================================================================== --- branches/v14_2/Jmol/src/org/jmol/io/JmolUtil.java 2014-06-28 23:17:32 UTC (rev 19853) +++ branches/v14_2/Jmol/src/org/jmol/io/JmolUtil.java 2014-06-28 23:45:37 UTC (rev 19854) @@ -736,13 +736,11 @@ * return null; */ { - if (apiPlatform.getImageWidth(image) < 1) - return "invalid or missing image " + fullPathName; + return (apiPlatform.getImageWidth(image) < 1 ? "invalid or missing image " + fullPathName : image); } } catch (Exception e) { return e.toString() + " opening " + fullPathName; } - return image; } } Modified: trunk/Jmol/src/org/jmol/io/JmolUtil.java =================================================================== --- trunk/Jmol/src/org/jmol/io/JmolUtil.java 2014-06-28 23:17:32 UTC (rev 19853) +++ trunk/Jmol/src/org/jmol/io/JmolUtil.java 2014-06-28 23:45:37 UTC (rev 19854) @@ -736,13 +736,11 @@ * return null; */ { - if (apiPlatform.getImageWidth(image) < 1) - return "invalid or missing image " + fullPathName; + return (apiPlatform.getImageWidth(image) < 1 ? "invalid or missing image " + fullPathName : image); } } catch (Exception e) { return e.toString() + " opening " + fullPathName; } - return image; } } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2014-10-13 01:06:02
|
Revision: 20063 http://sourceforge.net/p/jmol/code/20063 Author: hansonr Date: 2014-10-13 01:05:53 +0000 (Mon, 13 Oct 2014) Log Message: ----------- Modified Paths: -------------- branches/v14_2/Jmol/src/org/jmol/jvxl/readers/IsoSolventReader.java trunk/Jmol/src/org/jmol/jvxl/readers/IsoSolventReader.java Modified: branches/v14_2/Jmol/src/org/jmol/jvxl/readers/IsoSolventReader.java =================================================================== --- branches/v14_2/Jmol/src/org/jmol/jvxl/readers/IsoSolventReader.java 2014-10-13 00:48:37 UTC (rev 20062) +++ branches/v14_2/Jmol/src/org/jmol/jvxl/readers/IsoSolventReader.java 2014-10-13 01:05:53 UTC (rev 20063) @@ -379,8 +379,9 @@ isSurfacePoint = (bsSurfaceVoxels != null && (bsSurfaceVoxels.get(vA) || bsSurfaceVoxels .get(vB))); if (voxelSource != null) { - int vs = Math.abs(valueA < valueB ? voxelSource[vA] : voxelSource[vB]); - iAtomSurface = atomIndex[vs - 1]; + int vs = Math.abs(Float.isNaN(valueB)||valueA < valueB ? voxelSource[vA] : voxelSource[vB]); + if (vs > 0) + iAtomSurface = atomIndex[vs - 1]; } if (testLinear || voxelSource == null || voxelSource[vA] == 0 || voxelSource[vA] != voxelSource[vB]) Modified: trunk/Jmol/src/org/jmol/jvxl/readers/IsoSolventReader.java =================================================================== --- trunk/Jmol/src/org/jmol/jvxl/readers/IsoSolventReader.java 2014-10-13 00:48:37 UTC (rev 20062) +++ trunk/Jmol/src/org/jmol/jvxl/readers/IsoSolventReader.java 2014-10-13 01:05:53 UTC (rev 20063) @@ -379,8 +379,9 @@ isSurfacePoint = (bsSurfaceVoxels != null && (bsSurfaceVoxels.get(vA) || bsSurfaceVoxels .get(vB))); if (voxelSource != null) { - int vs = Math.abs(valueA < valueB ? voxelSource[vA] : voxelSource[vB]); - iAtomSurface = atomIndex[vs - 1]; + int vs = Math.abs(Float.isNaN(valueB)||valueA < valueB ? voxelSource[vA] : voxelSource[vB]); + if (vs > 0) + iAtomSurface = atomIndex[vs - 1]; } if (testLinear || voxelSource == null || voxelSource[vA] == 0 || voxelSource[vA] != voxelSource[vB]) This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2014-10-14 00:53:19
|
Revision: 20070 http://sourceforge.net/p/jmol/code/20070 Author: hansonr Date: 2014-10-14 00:53:12 +0000 (Tue, 14 Oct 2014) Log Message: ----------- {*}.modo.all reports current modulation Modified Paths: -------------- branches/v14_2/Jmol/src/org/jmol/util/ModulationSet.java trunk/Jmol/src/org/jmol/util/ModulationSet.java Modified: branches/v14_2/Jmol/src/org/jmol/util/ModulationSet.java =================================================================== --- branches/v14_2/Jmol/src/org/jmol/util/ModulationSet.java 2014-10-14 00:33:47 UTC (rev 20069) +++ branches/v14_2/Jmol/src/org/jmol/util/ModulationSet.java 2014-10-14 00:53:12 UTC (rev 20070) @@ -428,8 +428,8 @@ return P3.new3((float) ta[0][0], (modDim > 1 ? (float) ta[1][0] : 0), (modDim > 2 ? (float) ta[2][0] : 0)); case 'O': - // return vOcc - return Float.valueOf(modTemp.calculate(tuv, false).vOcc * 100); + // return vOcc current or calculated + return Float.valueOf((tuv == null ? vOcc : modTemp.calculate(tuv, false).vOcc) * 100); } return null; } Modified: trunk/Jmol/src/org/jmol/util/ModulationSet.java =================================================================== --- trunk/Jmol/src/org/jmol/util/ModulationSet.java 2014-10-14 00:33:47 UTC (rev 20069) +++ trunk/Jmol/src/org/jmol/util/ModulationSet.java 2014-10-14 00:53:12 UTC (rev 20070) @@ -428,8 +428,8 @@ return P3.new3((float) ta[0][0], (modDim > 1 ? (float) ta[1][0] : 0), (modDim > 2 ? (float) ta[2][0] : 0)); case 'O': - // return vOcc - return Float.valueOf(modTemp.calculate(tuv, false).vOcc * 100); + // return vOcc current or calculated + return Float.valueOf((tuv == null ? vOcc : modTemp.calculate(tuv, false).vOcc) * 100); } return null; } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2014-11-21 13:18:12
|
Revision: 20118 http://sourceforge.net/p/jmol/code/20118 Author: hansonr Date: 2014-11-21 13:17:58 +0000 (Fri, 21 Nov 2014) Log Message: ----------- Jmol.___JmolVersion="14.3.9_2014.11.21" bug fix: PNGJ writing broken bug fix: VASP CHGCAR reader not recognized for primitive cell bug fix: Euler ZYZ and ZXZ for quaternion({0 0 1},theta) where theta < 0 in error Modified Paths: -------------- branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties branches/v14_2/Jmol/src/org/jmol/viewer/OutputManager.java trunk/Jmol/src/org/jmol/viewer/Jmol.properties trunk/Jmol/src/org/jmol/viewer/OutputManager.java Modified: branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties 2014-11-21 12:44:49 UTC (rev 20117) +++ branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties 2014-11-21 13:17:58 UTC (rev 20118) @@ -7,6 +7,7 @@ Jmol.___JmolVersion="14.2.9_2014.11.21" +bug fix: PNGJ writing broken bug fix: VASP CHGCAR reader not recognized for primitive cell bug fix: Euler ZYZ and ZXZ for quaternion({0 0 1},theta) where theta < 0 in error Modified: branches/v14_2/Jmol/src/org/jmol/viewer/OutputManager.java =================================================================== --- branches/v14_2/Jmol/src/org/jmol/viewer/OutputManager.java 2014-11-21 12:44:49 UTC (rev 20117) +++ branches/v14_2/Jmol/src/org/jmol/viewer/OutputManager.java 2014-11-21 13:17:58 UTC (rev 20118) @@ -107,7 +107,7 @@ /** * * Creates an image of params.type form -- PNG, PNGJ, PNGT, JPG, JPG64, PDF, - * PPM. + * PPM, GIF, GIFT * * From createImage and getImageAsBytes * @@ -177,11 +177,11 @@ params.put("pngAppPrefix", "Jmol Type"); } } - if (type.equals("PNGT") || type.equals("GIFT")) { + if (type.equals("PNGT") || type.equals("GIFT")) params.put("transparentColor", Integer.valueOf(vwr.getBackgroundArgb())); - type = type.substring(0, 3); - } + if (type.length() == 4) // PNGT PNGJ GIFT + type = type.substring(0, 3); if (comment != null) params.put("comment", comment.length() == 0 ? Viewer.getJmolVersion() : comment); Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2014-11-21 12:44:49 UTC (rev 20117) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2014-11-21 13:17:58 UTC (rev 20118) @@ -17,6 +17,7 @@ Jmol.___JmolVersion="14.3.9_2014.11.21" +bug fix: PNGJ writing broken bug fix: VASP CHGCAR reader not recognized for primitive cell bug fix: Euler ZYZ and ZXZ for quaternion({0 0 1},theta) where theta < 0 in error Modified: trunk/Jmol/src/org/jmol/viewer/OutputManager.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/OutputManager.java 2014-11-21 12:44:49 UTC (rev 20117) +++ trunk/Jmol/src/org/jmol/viewer/OutputManager.java 2014-11-21 13:17:58 UTC (rev 20118) @@ -107,7 +107,7 @@ /** * * Creates an image of params.type form -- PNG, PNGJ, PNGT, JPG, JPG64, PDF, - * PPM. + * PPM, GIF, GIFT. * * From createImage and getImageAsBytes * @@ -177,11 +177,11 @@ params.put("pngAppPrefix", "Jmol Type"); } } - if (type.equals("PNGT") || type.equals("GIFT")) { + if (type.equals("PNGT") || type.equals("GIFT")) params.put("transparentColor", Integer.valueOf(vwr.getBackgroundArgb())); - type = type.substring(0, 3); - } + if (type.length() == 4) // PNGT PNGJ GIFT + type = type.substring(0, 3); if (comment != null) params.put("comment", comment.length() == 0 ? Viewer.getJmolVersion() : comment); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2015-12-15 00:52:31
|
Revision: 20890 http://sourceforge.net/p/jmol/code/20890 Author: hansonr Date: 2015-12-15 00:52:28 +0000 (Tue, 15 Dec 2015) Log Message: ----------- Jmol.___JmolVersion="14.5.1_2015.12.14" bug fix: JSmol (JSmolCore.js) check for MS Edge browser, which does not support dataURI Modified Paths: -------------- branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2015-12-13 18:31:29 UTC (rev 20889) +++ branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2015-12-15 00:52:28 UTC (rev 20890) @@ -7,8 +7,13 @@ # see also http://chemapps.stolaf.edu/jmol/zip for daily updates -Jmol.___JmolVersion="14.4.1_2015.12.13" +Jmol.___JmolVersion="14.4.1_2015.12.14" +bug fix: JSmol (JSmolCore.js) check for MS Edge browser, which does not support dataURI + +JmolVersion="14.4.1_2015.12.13" +released + bug fix: JavaScript Chrome/Edge fix for slow response due to setTimeout issues; uses requestAnimationFrame instead in JSmol.js bug fix: zoomTo not setting time to 0 in the case of scriptWait bug fix: set selectAllModels should restrict action of display/hide as well Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-12-13 18:31:29 UTC (rev 20889) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-12-15 00:52:28 UTC (rev 20890) @@ -62,8 +62,12 @@ TODO: consider if models with no atoms will cause issues in relation to model.firstAtomIndex -Jmol.___JmolVersion="14.5.0_2015.12.13" +Jmol.___JmolVersion="14.5.1_2015.12.14" +bug fix: JSmol (JSmolCore.js) check for MS Edge browser, which does not support dataURI + +JmolVersion="14.5.0_2015.12.13" + new feature: "#_DOCACHE_" suffix for file name loading tells Jmol to insert full structure into any state -- allows SPT files to preserve the original file (as in all PNGJ files) -- for example: This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2015-12-17 19:09:17
|
Revision: 20893 http://sourceforge.net/p/jmol/code/20893 Author: hansonr Date: 2015-12-17 19:09:15 +0000 (Thu, 17 Dec 2015) Log Message: ----------- public static String nonArrayString(Object x) { /** * @j2sNative * * return (x.constructor == Array ? null : x.toString()); * */ Modified Paths: -------------- branches/v14_4/Jmol/src/javajs/util/PT.java trunk/Jmol/src/javajs/util/PT.java Modified: branches/v14_4/Jmol/src/javajs/util/PT.java =================================================================== --- branches/v14_4/Jmol/src/javajs/util/PT.java 2015-12-17 18:58:19 UTC (rev 20892) +++ branches/v14_4/Jmol/src/javajs/util/PT.java 2015-12-17 19:09:15 UTC (rev 20893) @@ -873,9 +873,7 @@ /** * @j2sNative * - * var s = x.constructor.toString(); - * var pt = s.indexOf("Array("); - * return (pt <= 0 || pt >= s.indexOf("{") ? x.toString() : null); + * return (x.constructor == Array ? null : x.toString()); * */ { Modified: trunk/Jmol/src/javajs/util/PT.java =================================================================== --- trunk/Jmol/src/javajs/util/PT.java 2015-12-17 18:58:19 UTC (rev 20892) +++ trunk/Jmol/src/javajs/util/PT.java 2015-12-17 19:09:15 UTC (rev 20893) @@ -873,9 +873,7 @@ /** * @j2sNative * - * var s = x.constructor.toString(); - * var pt = s.indexOf("Array("); - * return (pt <= 0 || pt >= s.indexOf("{") ? x.toString() : null); + * return (x.constructor == Array ? null : x.toString()); * */ { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2015-12-30 16:49:37
|
Revision: 20905 http://sourceforge.net/p/jmol/code/20905 Author: hansonr Date: 2015-12-30 16:49:34 +0000 (Wed, 30 Dec 2015) Log Message: ----------- T3/P4 order in Escape.e(x) Modified Paths: -------------- branches/v14_4/Jmol/src/org/jmol/util/Escape.java trunk/Jmol/src/org/jmol/util/Escape.java Modified: branches/v14_4/Jmol/src/org/jmol/util/Escape.java =================================================================== --- branches/v14_4/Jmol/src/org/jmol/util/Escape.java 2015-12-23 21:59:40 UTC (rev 20904) +++ branches/v14_4/Jmol/src/org/jmol/util/Escape.java 2015-12-30 16:49:34 UTC (rev 20905) @@ -114,10 +114,10 @@ return escapeMap((Map<String, Object>) x); if (x instanceof BS) return eBS((BS) x); + if (x instanceof P4) + return eP4((P4) x); if (x instanceof T3) return eP((T3) x); - if (x instanceof P4) - return eP4((P4) x); if (AU.isAP(x)) return eAP((T3[]) x); if (AU.isAS(x)) Modified: trunk/Jmol/src/org/jmol/util/Escape.java =================================================================== --- trunk/Jmol/src/org/jmol/util/Escape.java 2015-12-23 21:59:40 UTC (rev 20904) +++ trunk/Jmol/src/org/jmol/util/Escape.java 2015-12-30 16:49:34 UTC (rev 20905) @@ -114,10 +114,10 @@ return escapeMap((Map<String, Object>) x); if (x instanceof BS) return eBS((BS) x); + if (x instanceof P4) + return eP4((P4) x); if (x instanceof T3) return eP((T3) x); - if (x instanceof P4) - return eP4((P4) x); if (AU.isAP(x)) return eAP((T3[]) x); if (AU.isAS(x)) This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2016-01-01 17:03:38
|
Revision: 20912 http://sourceforge.net/p/jmol/code/20912 Author: hansonr Date: 2016-01-01 17:03:36 +0000 (Fri, 01 Jan 2016) Log Message: ----------- code fix for recent PyMOL reader changes Modified Paths: -------------- branches/v14_4/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java Modified: branches/v14_4/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java =================================================================== --- branches/v14_4/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java 2016-01-01 15:32:36 UTC (rev 20911) +++ branches/v14_4/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java 2016-01-01 17:03:36 UTC (rev 20912) @@ -982,7 +982,7 @@ setting = stateSettings.get(Integer.valueOf(i)); if (setting == null && objectSettings != null) setting = objectSettings.get(Integer.valueOf(i)); - if (setting == null) + if (setting == null && i < settings.size()) setting = (Lst<Object>) settings.get(i); return setting; } Modified: trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java 2016-01-01 15:32:36 UTC (rev 20911) +++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java 2016-01-01 17:03:36 UTC (rev 20912) @@ -982,7 +982,7 @@ setting = stateSettings.get(Integer.valueOf(i)); if (setting == null && objectSettings != null) setting = objectSettings.get(Integer.valueOf(i)); - if (setting == null) + if (setting == null && i < settings.size()) setting = (Lst<Object>) settings.get(i); return setting; } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2016-01-09 06:06:18
|
Revision: 20928 http://sourceforge.net/p/jmol/code/20928 Author: hansonr Date: 2016-01-09 06:06:15 +0000 (Sat, 09 Jan 2016) Log Message: ----------- Jmol.___JmolVersion="14.4.1_2016.01.08" bug fix: labels, echos, and measurements improperly shaded when z-shaded with nonblack background bug fix: rendering error when set zshade followed by set antialiasdisplay code: (JavaScript) refactoring to reduce extraneous file download Modified Paths: -------------- branches/v14_4/Jmol/src/org/jmol/g3d/Graphics3D.java branches/v14_4/Jmol/src/org/jmol/g3d/Pixelator.java branches/v14_4/Jmol/src/org/jmol/g3d/PixelatorShaded.java branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties trunk/Jmol/src/org/jmol/g3d/Graphics3D.java trunk/Jmol/src/org/jmol/g3d/Pixelator.java trunk/Jmol/src/org/jmol/g3d/PixelatorShaded.java Modified: branches/v14_4/Jmol/src/org/jmol/g3d/Graphics3D.java =================================================================== --- branches/v14_4/Jmol/src/org/jmol/g3d/Graphics3D.java 2016-01-07 13:27:50 UTC (rev 20927) +++ branches/v14_4/Jmol/src/org/jmol/g3d/Graphics3D.java 2016-01-09 06:06:15 UTC (rev 20928) @@ -235,7 +235,9 @@ public void destroy() { releaseBuffers(); platform = null; - pixel = pixel0 = pixelScreened = pixelShaded = null; + pixel = pixel0 = pixelShaded = null; + pixelT0 = null; + pixelScreened = null; graphicsForMetrics = null; } @@ -256,8 +258,8 @@ Pixelator pixel; Pixelator pixel0; - private Pixelator pixelT0; - private Pixelator pixelScreened; + private PixelatorT pixelT0; + private PixelatorScreened pixelScreened; private PixelatorShaded pixelShaded; protected int zMargin; @@ -363,6 +365,7 @@ colixCurrent = 0; haveTranslucentObjects = wasScreened = false; pixel = pixel0; + pixel.bgcolor = bgcolor; translucentCoverOnly = !translucentMode; if (pbuf == null) { platform.allocateBuffers(windowWidth, windowHeight, antialiasThisFrame, @@ -373,6 +376,8 @@ pixel0.setBuf(); if (pixelT0 != null) pixelT0.setBuf(); + if (pixelShaded != null) + pixelShaded.setBuf(); } setWidthHeight(antialiasThisFrame); if (pixelScreened != null) Modified: branches/v14_4/Jmol/src/org/jmol/g3d/Pixelator.java =================================================================== --- branches/v14_4/Jmol/src/org/jmol/g3d/Pixelator.java 2016-01-07 13:27:50 UTC (rev 20927) +++ branches/v14_4/Jmol/src/org/jmol/g3d/Pixelator.java 2016-01-09 06:06:15 UTC (rev 20928) @@ -33,6 +33,7 @@ Pixelator p0; protected int[] zb, pb; int width; + int bgcolor; /** @@ -40,6 +41,7 @@ */ Pixelator(Graphics3D graphics3d) { g = graphics3d; + bgcolor = g.bgcolor; setBuf(); } @@ -62,6 +64,8 @@ public void addImagePixel(byte shade, int tLog, int offset, int z, int argb, int bgargb) { + if (zb != g.zbuf) + System.out.println("OH"); if (z < zb[offset]) { switch (shade) { case 0: @@ -78,7 +82,7 @@ if (bgargb != 0) p = Graphics3D.mergeBufferPixel(p, bgargb, bgargb); p = Graphics3D.mergeBufferPixel(p, (argb & 0xFFFFFF) - | (shade << 24), bgargb); + | (shade << 24), bgcolor); addPixel(offset, z, p); } } Modified: branches/v14_4/Jmol/src/org/jmol/g3d/PixelatorShaded.java =================================================================== --- branches/v14_4/Jmol/src/org/jmol/g3d/PixelatorShaded.java 2016-01-07 13:27:50 UTC (rev 20927) +++ branches/v14_4/Jmol/src/org/jmol/g3d/PixelatorShaded.java 2016-01-09 06:06:15 UTC (rev 20928) @@ -45,12 +45,13 @@ } Pixelator set(int zSlab, int zDepth, int zShadePower) { - bgRGB = new int[] { g.bgcolor & 0xFF, (g.bgcolor >> 8) & 0xFF, + bgcolor = g.bgcolor; + bgRGB = new int[] { bgcolor & 0xFF, (bgcolor >> 8) & 0xFF, (g.bgcolor >> 16) & 0xFF }; this.zSlab = zSlab < 0 ? 0 : zSlab; this.zDepth = zDepth < 0 ? 0 : zDepth; this.zShadePower = zShadePower; - this.p0 = g.pixel0; + p0 = g.pixel0; return this; } Modified: branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2016-01-07 13:27:50 UTC (rev 20927) +++ branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2016-01-09 06:06:15 UTC (rev 20928) @@ -7,8 +7,11 @@ # see also http://chemapps.stolaf.edu/jmol/zip for daily updates -Jmol.___JmolVersion="14.4.1_2016.01.07" +Jmol.___JmolVersion="14.4.1_2016.01.08" +bug fix: labels, echos, and measurements improperly shaded when z-shaded with nonblack background +bug fix: rendering error when set zshade followed by set antialiasdisplay + code: (JavaScript) refactoring to reduce extraneous file download JmolVersion="14.4.1_2016.01.06" Modified: trunk/Jmol/src/org/jmol/g3d/Graphics3D.java =================================================================== --- trunk/Jmol/src/org/jmol/g3d/Graphics3D.java 2016-01-07 13:27:50 UTC (rev 20927) +++ trunk/Jmol/src/org/jmol/g3d/Graphics3D.java 2016-01-09 06:06:15 UTC (rev 20928) @@ -235,7 +235,9 @@ public void destroy() { releaseBuffers(); platform = null; - pixel = pixel0 = pixelScreened = pixelShaded = null; + pixel = pixel0 = pixelShaded = null; + pixelT0 = null; + pixelScreened = null; graphicsForMetrics = null; } @@ -256,8 +258,8 @@ Pixelator pixel; Pixelator pixel0; - private Pixelator pixelT0; - private Pixelator pixelScreened; + private PixelatorT pixelT0; + private PixelatorScreened pixelScreened; private PixelatorShaded pixelShaded; protected int zMargin; @@ -363,6 +365,7 @@ colixCurrent = 0; haveTranslucentObjects = wasScreened = false; pixel = pixel0; + pixel.bgcolor = bgcolor; translucentCoverOnly = !translucentMode; if (pbuf == null) { platform.allocateBuffers(windowWidth, windowHeight, antialiasThisFrame, @@ -373,6 +376,8 @@ pixel0.setBuf(); if (pixelT0 != null) pixelT0.setBuf(); + if (pixelShaded != null) + pixelShaded.setBuf(); } setWidthHeight(antialiasThisFrame); if (pixelScreened != null) Modified: trunk/Jmol/src/org/jmol/g3d/Pixelator.java =================================================================== --- trunk/Jmol/src/org/jmol/g3d/Pixelator.java 2016-01-07 13:27:50 UTC (rev 20927) +++ trunk/Jmol/src/org/jmol/g3d/Pixelator.java 2016-01-09 06:06:15 UTC (rev 20928) @@ -33,6 +33,7 @@ Pixelator p0; protected int[] zb, pb; int width; + int bgcolor; /** @@ -40,6 +41,7 @@ */ Pixelator(Graphics3D graphics3d) { g = graphics3d; + bgcolor = g.bgcolor; setBuf(); } @@ -62,6 +64,8 @@ public void addImagePixel(byte shade, int tLog, int offset, int z, int argb, int bgargb) { + if (zb != g.zbuf) + System.out.println("OH"); if (z < zb[offset]) { switch (shade) { case 0: @@ -78,7 +82,7 @@ if (bgargb != 0) p = Graphics3D.mergeBufferPixel(p, bgargb, bgargb); p = Graphics3D.mergeBufferPixel(p, (argb & 0xFFFFFF) - | (shade << 24), bgargb); + | (shade << 24), bgcolor); addPixel(offset, z, p); } } Modified: trunk/Jmol/src/org/jmol/g3d/PixelatorShaded.java =================================================================== --- trunk/Jmol/src/org/jmol/g3d/PixelatorShaded.java 2016-01-07 13:27:50 UTC (rev 20927) +++ trunk/Jmol/src/org/jmol/g3d/PixelatorShaded.java 2016-01-09 06:06:15 UTC (rev 20928) @@ -45,12 +45,13 @@ } Pixelator set(int zSlab, int zDepth, int zShadePower) { - bgRGB = new int[] { g.bgcolor & 0xFF, (g.bgcolor >> 8) & 0xFF, + bgcolor = g.bgcolor; + bgRGB = new int[] { bgcolor & 0xFF, (bgcolor >> 8) & 0xFF, (g.bgcolor >> 16) & 0xFF }; this.zSlab = zSlab < 0 ? 0 : zSlab; this.zDepth = zDepth < 0 ? 0 : zDepth; this.zShadePower = zShadePower; - this.p0 = g.pixel0; + p0 = g.pixel0; return this; } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2016-02-06 17:04:24
|
Revision: 20953 http://sourceforge.net/p/jmol/code/20953 Author: hansonr Date: 2016-02-06 17:04:21 +0000 (Sat, 06 Feb 2016) Log Message: ----------- Jmol.___JmolVersion="14.5.2_2016.02.06" Modified Paths: -------------- branches/v14_4/Jmol/src/org/jmol/render/MeshRenderer.java trunk/Jmol/src/org/jmol/render/MeshRenderer.java Modified: branches/v14_4/Jmol/src/org/jmol/render/MeshRenderer.java =================================================================== --- branches/v14_4/Jmol/src/org/jmol/render/MeshRenderer.java 2016-02-06 16:33:26 UTC (rev 20952) +++ branches/v14_4/Jmol/src/org/jmol/render/MeshRenderer.java 2016-02-06 17:04:21 UTC (rev 20953) @@ -217,10 +217,9 @@ : selectedPolyOnly ? mesh.bsSlabDisplay : null); renderLow = (!isExport && !vwr.checkMotionRendering(T.mesh)); - boolean allowFrontOnly = (!tm.slabEnabled - && !mesh.isTwoSided && !selectedPolyOnly + boolean allowFrontOnly = (!mesh.isTwoSided && !selectedPolyOnly && (meshSlabValue == Integer.MIN_VALUE || meshSlabValue >= 100)); - frontOnly = renderLow || mesh.frontOnly && allowFrontOnly; + frontOnly = renderLow || mesh.frontOnly && !tm.slabEnabled && allowFrontOnly; isShell = mesh.isShell && allowFrontOnly; screens = vwr.allocTempScreens(vertexCount); if (isPrecision) Modified: trunk/Jmol/src/org/jmol/render/MeshRenderer.java =================================================================== --- trunk/Jmol/src/org/jmol/render/MeshRenderer.java 2016-02-06 16:33:26 UTC (rev 20952) +++ trunk/Jmol/src/org/jmol/render/MeshRenderer.java 2016-02-06 17:04:21 UTC (rev 20953) @@ -217,10 +217,9 @@ : selectedPolyOnly ? mesh.bsSlabDisplay : null); renderLow = (!isExport && !vwr.checkMotionRendering(T.mesh)); - boolean allowFrontOnly = (!tm.slabEnabled - && !mesh.isTwoSided && !selectedPolyOnly + boolean allowFrontOnly = (!mesh.isTwoSided && !selectedPolyOnly && (meshSlabValue == Integer.MIN_VALUE || meshSlabValue >= 100)); - frontOnly = renderLow || mesh.frontOnly && allowFrontOnly; + frontOnly = renderLow || mesh.frontOnly && !tm.slabEnabled && allowFrontOnly; isShell = mesh.isShell && allowFrontOnly; screens = vwr.allocTempScreens(vertexCount); if (isPrecision) This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2016-02-06 21:26:22
|
Revision: 20956 http://sourceforge.net/p/jmol/code/20956 Author: hansonr Date: 2016-02-06 21:26:19 +0000 (Sat, 06 Feb 2016) Log Message: ----------- delphi issue Modified Paths: -------------- branches/v14_4/Jmol/src/org/jmol/viewer/FileManager.java trunk/Jmol/src/org/jmol/viewer/FileManager.java Modified: branches/v14_4/Jmol/src/org/jmol/viewer/FileManager.java =================================================================== --- branches/v14_4/Jmol/src/org/jmol/viewer/FileManager.java 2016-02-06 18:16:31 UTC (rev 20955) +++ branches/v14_4/Jmol/src/org/jmol/viewer/FileManager.java 2016-02-06 21:26:19 UTC (rev 20956) @@ -1206,10 +1206,10 @@ if (pt0 >= 0) { if (line.indexOf(FileManager.PMESH_BINARY_MAGIC_NUMBER) == 0) return "Pmesh"; + if (line.indexOf("MAP ") == 208) + return "Mrc"; if (line.indexOf(DELPHI_BINARY_MAGIC_NUMBER) == 0) return "DelPhi"; - if (line.indexOf("MAP ") == 208) - return "Mrc"; if (line.length() > 37 && (line.charAt(36) == 0 && line.charAt(37) == 100 || line.charAt(36) == 0 && line.charAt(37) == 100)) { // header19 (short)100 Modified: trunk/Jmol/src/org/jmol/viewer/FileManager.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/FileManager.java 2016-02-06 18:16:31 UTC (rev 20955) +++ trunk/Jmol/src/org/jmol/viewer/FileManager.java 2016-02-06 21:26:19 UTC (rev 20956) @@ -1206,10 +1206,10 @@ if (pt0 >= 0) { if (line.indexOf(FileManager.PMESH_BINARY_MAGIC_NUMBER) == 0) return "Pmesh"; + if (line.indexOf("MAP ") == 208) + return "Mrc"; if (line.indexOf(DELPHI_BINARY_MAGIC_NUMBER) == 0) return "DelPhi"; - if (line.indexOf("MAP ") == 208) - return "Mrc"; if (line.length() > 37 && (line.charAt(36) == 0 && line.charAt(37) == 100 || line.charAt(36) == 0 && line.charAt(37) == 100)) { // header19 (short)100 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2016-02-10 02:28:35
|
Revision: 20958 http://sourceforge.net/p/jmol/code/20958 Author: hansonr Date: 2016-02-10 02:28:32 +0000 (Wed, 10 Feb 2016) Log Message: ----------- Jmol.___JmolVersion="14.5.2_2016.02.09" new feature: invertselected ATOMS {ring atoms to invert} -- inverts ring stereochemistry -- requires prior selection of all atoms to be involved in the inversion bug fix: SMARTS pattern [ALA.*] not working without biological polymer type indication bug fix: SMARTS pattern [r500] not working outside of MINIMIZE Revision Links: -------------- http://sourceforge.net/p/jmol/code/500 Modified Paths: -------------- branches/v14_4/Jmol/src/org/jmol/viewer/ActionManager.java trunk/Jmol/src/org/jmol/viewer/ActionManager.java Modified: branches/v14_4/Jmol/src/org/jmol/viewer/ActionManager.java =================================================================== --- branches/v14_4/Jmol/src/org/jmol/viewer/ActionManager.java 2016-02-10 02:22:20 UTC (rev 20957) +++ branches/v14_4/Jmol/src/org/jmol/viewer/ActionManager.java 2016-02-10 02:28:32 UTC (rev 20958) @@ -1824,7 +1824,7 @@ return; case PICKING_INVERT_STEREO: if (bnd(clickAction, ACTION_assignNew)) - vwr.invertRingAt(atomIndex), true); + vwr.invertRingAt(atomIndex, true); return; case PICKING_DELETE_ATOM: if (bnd(clickAction, ACTION_deleteAtom)) { Modified: trunk/Jmol/src/org/jmol/viewer/ActionManager.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/ActionManager.java 2016-02-10 02:22:20 UTC (rev 20957) +++ trunk/Jmol/src/org/jmol/viewer/ActionManager.java 2016-02-10 02:28:32 UTC (rev 20958) @@ -1824,7 +1824,7 @@ return; case PICKING_INVERT_STEREO: if (bnd(clickAction, ACTION_assignNew)) - vwr.invertRingAt(atomIndex), true); + vwr.invertRingAt(atomIndex, true); return; case PICKING_DELETE_ATOM: if (bnd(clickAction, ACTION_deleteAtom)) { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2016-02-27 19:28:51
|
Revision: 20966 http://sourceforge.net/p/jmol/code/20966 Author: hansonr Date: 2016-02-27 19:28:48 +0000 (Sat, 27 Feb 2016) Log Message: ----------- Jmol.___JmolVersion="14.4.3_2016.02.27" bug fix: [function:"yyy",Function:"zzz"] fails to retain key capitalization after first entry for special names bug fix: (JavaScript only) polyhedra not saved in state bug fix: (Applet) broken image in coverImage bug fix: polyhedra DELETE can crash Jmol if polyhedra are not colored Modified Paths: -------------- branches/v14_4/Jmol/src/org/jmol/shapespecial/Polyhedron.java trunk/Jmol/src/org/jmol/shapespecial/Polyhedron.java Modified: branches/v14_4/Jmol/src/org/jmol/shapespecial/Polyhedron.java =================================================================== --- branches/v14_4/Jmol/src/org/jmol/shapespecial/Polyhedron.java 2016-02-27 18:59:52 UTC (rev 20965) +++ branches/v14_4/Jmol/src/org/jmol/shapespecial/Polyhedron.java 2016-02-27 19:28:48 UTC (rev 20966) @@ -108,6 +108,7 @@ id = (info.containsKey("id") ? info.get("id").asString() : null); if (id == null) { centralAtom = at[info.get("atomIndex").intValue]; + modelIndex = centralAtom.mi; } else { center = P3.newP(SV.ptValue(info.get("center"))); modelIndex = info.get("modelIndex").intValue; Modified: trunk/Jmol/src/org/jmol/shapespecial/Polyhedron.java =================================================================== --- trunk/Jmol/src/org/jmol/shapespecial/Polyhedron.java 2016-02-27 18:59:52 UTC (rev 20965) +++ trunk/Jmol/src/org/jmol/shapespecial/Polyhedron.java 2016-02-27 19:28:48 UTC (rev 20966) @@ -108,6 +108,7 @@ id = (info.containsKey("id") ? info.get("id").asString() : null); if (id == null) { centralAtom = at[info.get("atomIndex").intValue]; + modelIndex = centralAtom.mi; } else { center = P3.newP(SV.ptValue(info.get("center"))); modelIndex = info.get("modelIndex").intValue; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |