From: <ha...@us...> - 2010-05-16 15:12:42
|
Revision: 13107 http://jmol.svn.sourceforge.net/jmol/?rev=13107&view=rev Author: hansonr Date: 2010-05-16 15:12:36 +0000 (Sun, 16 May 2010) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2010-05-16 14:58:21 UTC (rev 13106) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2010-05-16 15:12:36 UTC (rev 13107) @@ -6881,11 +6881,12 @@ appConsole = null; } else if (appConsole == null && paramInfo != null && ((Boolean) paramInfo).booleanValue()) { - appConsole = (isApplet ? (JmolAppConsoleInterface) Interface - .getOptionInterface("applet.AppletConsole") - : (JmolAppConsoleInterface) Interface - .getApplicationInterface("jmolpanel.AppConsole")) - .getAppConsole(this, display); + for (int i = 0; i < 2 && appConsole == null; i++) + appConsole = (isApplet ? (JmolAppConsoleInterface) Interface + .getOptionInterface("applet.AppletConsole") + : (JmolAppConsoleInterface) Interface + .getApplicationInterface("jmolpanel.AppConsole")) + .getAppConsole(this, display); } scriptEditor = (appConsole == null ? null : appConsole .getScriptEditor()); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-05-17 02:10:41
|
Revision: 13109 http://jmol.svn.sourceforge.net/jmol/?rev=13109&view=rev Author: hansonr Date: 2010-05-17 02:10:34 +0000 (Mon, 17 May 2010) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2010-05-17 01:43:38 UTC (rev 13108) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2010-05-17 02:10:34 UTC (rev 13109) @@ -6881,12 +6881,19 @@ appConsole = null; } else if (appConsole == null && paramInfo != null && ((Boolean) paramInfo).booleanValue()) { - for (int i = 0; i < 2 && appConsole == null; i++) + for (int i = 0; i < 4 && appConsole == null; i++) { appConsole = (isApplet ? (JmolAppConsoleInterface) Interface .getOptionInterface("applet.AppletConsole") : (JmolAppConsoleInterface) Interface .getApplicationInterface("jmolpanel.AppConsole")) .getAppConsole(this, display); + if (appConsole == null) + try { + Thread.currentThread().wait(100); + } catch (InterruptedException e) { + // + } + } } scriptEditor = (appConsole == null ? null : appConsole .getScriptEditor()); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-05-21 13:33:42
|
Revision: 13168 http://jmol.svn.sourceforge.net/jmol/?rev=13168&view=rev Author: hansonr Date: 2010-05-21 13:33:36 +0000 (Fri, 21 May 2010) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2010-05-21 12:36:48 UTC (rev 13167) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2010-05-21 13:33:36 UTC (rev 13168) @@ -8226,7 +8226,7 @@ if (addHydrogen) bsSelected = addHydrogens(bsSelected, asScript); else if (bsSelected == null) { - //bsSelected = getModelAtomBitSet(getVisibleFramesBitSet().nextSetBit(0), true).nextSetBit(0); + bsSelected = getModelAtomBitSet(getVisibleFramesBitSet()); } try { getMinimizer(true).minimize(steps, crit, bsSelected, isSilent); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-05-28 13:31:16
|
Revision: 13246 http://jmol.svn.sourceforge.net/jmol/?rev=13246&view=rev Author: hansonr Date: 2010-05-28 13:31:09 +0000 (Fri, 28 May 2010) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2010-05-28 13:17:21 UTC (rev 13245) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2010-05-28 13:31:09 UTC (rev 13246) @@ -4213,6 +4213,7 @@ case '$': try { f = URLEncoder.encode(f, "US-ASCII"); + f = TextFormat.simpleReplace(f, "%2F", "/"); } catch (UnsupportedEncodingException e) { // } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ni...@us...> - 2010-06-19 09:36:38
|
Revision: 13432 http://jmol.svn.sourceforge.net/jmol/?rev=13432&view=rev Author: nicove Date: 2010-06-19 09:36:32 +0000 (Sat, 19 Jun 2010) Log Message: ----------- Warnings Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2010-06-18 22:24:22 UTC (rev 13431) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2010-06-19 09:36:32 UTC (rev 13432) @@ -95,7 +95,6 @@ import javax.vecmath.AxisAngle4f; import java.net.URL; -import java.net.URLEncoder; import java.io.BufferedInputStream; import java.io.BufferedOutputStream; import java.io.BufferedReader; @@ -106,7 +105,6 @@ import java.io.OutputStream; import java.io.Reader; import java.io.StringReader; -import java.io.UnsupportedEncodingException; /* * This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-06-19 16:48:23
|
Revision: 13435 http://jmol.svn.sourceforge.net/jmol/?rev=13435&view=rev Author: hansonr Date: 2010-06-19 16:48:17 +0000 (Sat, 19 Jun 2010) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2010-06-19 16:45:49 UTC (rev 13434) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2010-06-19 16:48:17 UTC (rev 13435) @@ -95,6 +95,7 @@ import javax.vecmath.AxisAngle4f; import java.net.URL; +import java.net.URLEncoder; import java.io.BufferedInputStream; import java.io.BufferedOutputStream; import java.io.BufferedReader; @@ -105,6 +106,7 @@ import java.io.OutputStream; import java.io.Reader; import java.io.StringReader; +import java.io.UnsupportedEncodingException; /* * @@ -4185,23 +4187,24 @@ public Object setLoadFormat(String name, char type, boolean withPrefix) { String f = name.substring(1); - switch(type) { + switch (type) { case '=': return TextFormat.formatString(global.loadFormat, "FILE", f); case '$': - /* + try { - f = URLEncoder.encode(f, "US-ASCII"); - f = TextFormat.simpleReplace(f, "%2F", "/"); - } catch (UnsupportedEncodingException e) { - // - } - */ - return (withPrefix ? "MOL::" : "") - + TextFormat.formatString(global.smilesUrlFormat, "FILE", f); + f = URLEncoder.encode(f, "US-ASCII"); + f = TextFormat.simpleReplace(f, "%2F", "/"); + } catch (UnsupportedEncodingException e) { + // + } + + return (withPrefix ? "MOL::" : "") + + TextFormat.formatString(global.smilesUrlFormat, "FILE", f); case '_': // isosurface "=...", but we code that type as '-' String server = FileManager.fixFileNameVariables(global.edsUrlFormat, f); - String strCutoff = FileManager.fixFileNameVariables(global.edsUrlCutoff, f); + String strCutoff = FileManager.fixFileNameVariables(global.edsUrlCutoff, + f); return new String[] { server, strCutoff }; } return name.substring(1); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-06-29 22:52:36
|
Revision: 13479 http://jmol.svn.sourceforge.net/jmol/?rev=13479&view=rev Author: hansonr Date: 2010-06-29 22:52:30 +0000 (Tue, 29 Jun 2010) Log Message: ----------- mol 2d reading bug? Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2010-06-29 21:25:07 UTC (rev 13478) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2010-06-29 22:52:30 UTC (rev 13479) @@ -2165,7 +2165,8 @@ .getModelSetAuxiliaryInfo("jmolscript"); minimize(Integer.MAX_VALUE, 0, bsNew, null, 0, true, true, true); // no longer necessary? -- this is the JME/SMILES data: - modelSet.getModelSetAuxiliaryInfo().put("jmolscript", jmolScript); + if (jmolScript != null) + modelSet.getModelSetAuxiliaryInfo().put("jmolscript", jmolScript); } if (!isAppend) initializeModel(); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-07-22 16:04:00
|
Revision: 13642 http://jmol.svn.sourceforge.net/jmol/?rev=13642&view=rev Author: hansonr Date: 2010-07-22 16:03:54 +0000 (Thu, 22 Jul 2010) Log Message: ----------- failure to load can cause improper file name stored Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2010-07-22 15:43:37 UTC (rev 13641) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2010-07-22 16:03:54 UTC (rev 13642) @@ -1853,7 +1853,7 @@ if (htParams == null) htParams = setLoadParameters(null); Object atomSetCollection; - + String[] saveInfo = fileManager.getFileInfo(); if (fileNames != null) { // 1) a set of file names @@ -1904,11 +1904,15 @@ // OK, the file has been read and is now closed. - if (tokType != 0) // all we are doing is reading atom data + if (tokType != 0) { // all we are doing is reading atom data + fileManager.setFileInfo(saveInfo); return loadAtomDataAndReturnError(atomSetCollection, tokType); + } - if (htParams.containsKey("isData")) + if (htParams.containsKey("isData")) { + fileManager.setFileInfo(saveInfo); return (String) atomSetCollection; + } // now we fix the load script (possibly) with the full path name if (loadScript != null) { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-07-29 17:24:24
|
Revision: 13731 http://jmol.svn.sourceforge.net/jmol/?rev=13731&view=rev Author: hansonr Date: 2010-07-29 17:24:17 +0000 (Thu, 29 Jul 2010) Log Message: ----------- debug comment out Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2010-07-29 12:41:50 UTC (rev 13730) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2010-07-29 17:24:17 UTC (rev 13731) @@ -2449,7 +2449,6 @@ public void zap(boolean notify, boolean resetUndo, boolean zapModelKit) { stopAnimationThreads("zap"); - System.out.println("zap notify resetundo zapmodelkit " + notify + " " + resetUndo + " " + zapModelKit); if (modelSet != null) { setBooleanProperty("appendNew", true); clearModelDependentObjects(); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-08-07 19:57:35
|
Revision: 13914 http://jmol.svn.sourceforge.net/jmol/?rev=13914&view=rev Author: hansonr Date: 2010-08-07 19:57:27 +0000 (Sat, 07 Aug 2010) Log Message: ----------- version=12.1.2_dev # bug fix: select within(branch,{},{}) exception Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2010-08-07 19:54:09 UTC (rev 13913) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2010-08-07 19:57:27 UTC (rev 13914) @@ -3067,7 +3067,7 @@ } public BitSet getBranchBitSet(int atomIndex, int atomIndexNot) { - if (atomIndex < 0) + if (atomIndex < 0 || atomIndex >= getAtomCount()) return new BitSet(); return JmolMolecule.getBranchBitSet(modelSet.atoms, getModelUndeletedAtomsBitSet(modelSet.atoms[atomIndex].modelIndex), This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-08-18 02:34:56
|
Revision: 14026 http://jmol.svn.sourceforge.net/jmol/?rev=14026&view=rev Author: hansonr Date: 2010-08-18 02:34:50 +0000 (Wed, 18 Aug 2010) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2010-08-18 02:33:12 UTC (rev 14025) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2010-08-18 02:34:50 UTC (rev 14026) @@ -4673,7 +4673,7 @@ } public void setCursor(int cursor) { - if (multiTouch || currentCursor == cursor || display == null) + if (currentCursor == cursor || multiTouch || display == null) return; int c; switch (currentCursor = cursor) { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-08-27 14:26:59
|
Revision: 14152 http://jmol.svn.sourceforge.net/jmol/?rev=14152&view=rev Author: hansonr Date: 2010-08-27 14:26:52 +0000 (Fri, 27 Aug 2010) Log Message: ----------- 12.1.8 VERSION # bug fix: isosurface planar mapping, contours, atomic orbital speed and scaling problems # bug fix: oops; isosurface atomicOrbital REALLY not scaling well Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2010-08-27 14:16:35 UTC (rev 14151) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2010-08-27 14:26:52 UTC (rev 14152) @@ -1807,6 +1807,8 @@ + Escape.escape(fileName) + "}"); return; } + } else if (type.equals("Jmol")) { + cmd = "load "; } else if (!type.equals("spt")) { evalString("zap; load " + Escape.escape(fileName) This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-09-05 03:27:41
|
Revision: 14242 http://jmol.svn.sourceforge.net/jmol/?rev=14242&view=rev Author: hansonr Date: 2010-09-05 03:27:35 +0000 (Sun, 05 Sep 2010) Log Message: ----------- version=12.1.10_dev # bug fix: reset should not reset spin (introduced in 11.7.47); new RESET SPIN includes reset spinning Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2010-09-05 03:26:33 UTC (rev 14241) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2010-09-05 03:27:35 UTC (rev 14242) @@ -541,7 +541,7 @@ @Override public void homePosition() { - evalString("reset"); + evalString("reset spin"); } /* This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-09-10 12:37:29
|
Revision: 14272 http://jmol.svn.sourceforge.net/jmol/?rev=14272&view=rev Author: hansonr Date: 2010-09-10 12:37:22 +0000 (Fri, 10 Sep 2010) Log Message: ----------- unnecessary Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2010-09-10 12:16:59 UTC (rev 14271) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2010-09-10 12:37:22 UTC (rev 14272) @@ -359,17 +359,6 @@ return viewer; } - /** - * - * @param display - * @param modelAdapter - * @return a viewer instance - */ - public static JmolViewer allocateViewer(Component display, - JmolAdapter modelAdapter) { - return allocateViewer(display, modelAdapter, null, null, null, null, null); - } - private boolean isSilent = false; private boolean isApplet = false; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-11-09 11:20:51
|
Revision: 14616 http://jmol.svn.sourceforge.net/jmol/?rev=14616&view=rev Author: hansonr Date: 2010-11-09 11:20:44 +0000 (Tue, 09 Nov 2010) Log Message: ----------- log $NOW$ Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2010-11-09 05:23:52 UTC (rev 14615) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2010-11-09 11:20:44 UTC (rev 14616) @@ -8895,8 +8895,8 @@ if (logFile == null || data == null) return; boolean doClear = (data.equals("$CLEAR$")); - if (data.startsWith("$NOW$")) - data = (new Date()).toString() + "\t" + data.substring(3); + if (data.indexOf("$NOW$") >= 0) + data = TextFormat.simpleReplace(data, "$NOW$", (new Date()).toString()); FileWriter fstream = new FileWriter(logFile, !doClear); BufferedWriter out = new BufferedWriter(fstream); if (!doClear) { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-12-18 05:25:40
|
Revision: 14822 http://jmol.svn.sourceforge.net/jmol/?rev=14822&view=rev Author: hansonr Date: 2010-12-18 05:25:31 +0000 (Sat, 18 Dec 2010) Log Message: ----------- g3d must have display set if it exists for -n option Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2010-12-18 04:45:53 UTC (rev 14821) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2010-12-18 05:25:31 UTC (rev 14822) @@ -260,6 +260,7 @@ if (Logger.debugging) { Logger.debug("Viewer constructor " + this); } + g3d = new Graphics3D(display); isDataOnly = (display == null); haveDisplay = (!isDataOnly && (commandOptions == null || commandOptions.indexOf("-n") < 0)); mustRender = haveDisplay; @@ -286,7 +287,6 @@ multiTouch = (commandOptions != null && commandOptions .indexOf("-multitouch") >= 0); stateManager = new StateManager(this); - g3d = new Graphics3D(display); colorManager = new ColorManager(this, g3d); statusManager = new StatusManager(this); scriptManager = new ScriptManager(this); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-01-02 22:11:50
|
Revision: 14934 http://jmol.svn.sourceforge.net/jmol/?rev=14934&view=rev Author: hansonr Date: 2011-01-02 22:11:43 +0000 (Sun, 02 Jan 2011) Log Message: ----------- prevents large state from stopping an image save. Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2011-01-02 21:29:41 UTC (rev 14933) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2011-01-02 22:11:43 UTC (rev 14934) @@ -3188,8 +3188,15 @@ if (isImage && !global.imageState || !global.preserveState) return ""; // we remove local file references in the embedded states for images - return JmolConstants.embedScript(FileManager.setScriptFileReferences( - getStateInfo(null), ".", null, null)); + String s = ""; + try { + s = JmolConstants.embedScript(FileManager.setScriptFileReferences( + getStateInfo(null), ".", null, null)); + } catch (Throwable e) { + // ignore if this uses too much memory + Logger.error("state could not be saved: " + e.getMessage()); + } + return s; } @Override This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-01-25 00:02:20
|
Revision: 15037 http://jmol.svn.sourceforge.net/jmol/?rev=15037&view=rev Author: hansonr Date: 2011-01-25 00:02:14 +0000 (Tue, 25 Jan 2011) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2011-01-24 23:58:22 UTC (rev 15036) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2011-01-25 00:02:14 UTC (rev 15037) @@ -4282,6 +4282,9 @@ @Override public Object scriptWaitStatus(String strScript, String statusList) { + // null statusList will return a String + // -- output from PRINT/MESSAGE/ECHO commands or an error message + // otherwise, specific status messages will be created as a Java object scriptManager.waitForQueue(); boolean doTranslateTemp = GT.getDoTranslate(); GT.setDoTranslate(false); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-05-30 15:08:29
|
Revision: 15514 http://jmol.svn.sourceforge.net/jmol/?rev=15514&view=rev Author: hansonr Date: 2011-05-30 15:08:23 +0000 (Mon, 30 May 2011) Log Message: ----------- version=12.1.48 # new feature: atomMovedCallback parameter: BitSet of atoms moved # new feature: appletReadyCallback parameters: htmlName, TRUE/FALSE # -- fired ONCE upon applet ready, once upon applet destroyed # new feature: load spacegroup "" loads data with current file's space group # new feature: load unitcell "" loads data with current file's unit cell and offset # set appendNew false # LOAD DATA "append" # 1 # testing # Na 0.5 0 0.5 # end "append" {1 1 1} spacegroup "P4/mmm" unitcell "" # new feature: draw ARROW [ATOM {aa} | BOND {bb} {cc}] [ATOM {aa} | BOND {bb} {cc}] # -- allows easy creation of curved mechanistic arrows from atoms to bonds, # bonds to atoms, atoms to atoms, or bonds to bonds. # -- when atoms are moved, these arrows follow the atoms. # new feature: isosurface CONNECT {xxx} # -- connects an isosurface to an atom (only the first in the set) so that # If that atom is moved, then entire isosurface is moved. # -- STATE ISSUE: From the state, all isosurfaces are created AFTER atoms are moved, # so an isosurface such as a molecular surface will not be recreated properly from the state # new feature: show state FILE "filename" --- show embedded state from file (for example, an image) # new feature: MO POINTS / AO POINTS mapping onto a plane # for (var i = -5;i < 5;i += 0.2) {isosurface color range -1.0 1.0 plane x= @i map atomicorbital 4 3 1 points 1000;refresh} # bug fix: set appendNew false; load =1q0y; load APPEND =1crn causes exception # bug fix: lcaoCartoon does not get hidden when atom deleted # bug fix: isosurface mesh incompatible with fullylit and frontonly # bug fix: isosurface SELECT should also set model index # bug fix: navigate broken # bug fix: modelKit dragMinimizeAtom broken in 12.0.43 # bug fix: dragMinimize should select all non-fixed atoms if there are fixed atoms # bug fix: write @{"xxxx"} fails # bug fix: xmlns designations for jvxl and cml added to JVXL file creation # bug fix: isosurface ... map VDW -- mapping not saved in state # bug fix: CRYSTAL reader does not read vibrations for atoms with two-character symbols # bug fix: cartoons with hermite level do not reposition for atom position changes or trajectories # bug fix: isosurface plane x=-1 (with no spaces) not accepted # bug fix: x = write("VRML") should give VRML contents and not write to disk # bug fix: third oxygen atom in 5'-terminal phosphate was not assigned to backbone (e.g. 4tna.pdb) Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2011-05-30 14:54:16 UTC (rev 15513) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2011-05-30 15:08:23 UTC (rev 15514) @@ -7675,8 +7675,6 @@ transformManager.rotateAxisAngleAtCenter(rotCenter, rotAxis, degreesPerSecond, endDegrees, isSpin, bsSelected); refresh(-1, "rotateAxisAngleAtCenter"); - if (bsSelected != null && !isSpin) - checkMinimization(); } public void rotateAboutPointsInternal(Point3f point1, Point3f point2, @@ -7696,8 +7694,6 @@ degreesPerSecond, endDegrees, false, isSpin, bsSelected, false, translation, finalPoints); refresh(-1, "rotateAxisAboutPointsInternal"); - if (bsSelected != null && !isSpin) - checkMinimization(); } int getPickingSpinRate() { @@ -7901,25 +7897,43 @@ // Eval modelSet.invertSelected(pt, null, -1, null, bs); checkMinimization(); + statusManager.setStatusAtomMoved(bs); } public void invertAtomCoord(Point4f plane, BitSet bs) { modelSet.invertSelected(null, plane, -1, null, bs); checkMinimization(); + statusManager.setStatusAtomMoved(bs); } public void invertSelected(Point3f pt, Point4f plane, int iAtom, BitSet invAtoms) { // Eval - modelSet.invertSelected(pt, plane, iAtom, invAtoms, getSelectionSet(false)); + BitSet bs = getSelectionSet(false); + if (bs.cardinality() == 0) + return; + modelSet.invertSelected(pt, plane, iAtom, invAtoms, bs); checkMinimization(); + statusManager.setStatusAtomMoved(bs); } + void moveAtoms(Matrix3f mNew, Matrix3f matrixRotate, Vector3f translation, + Point3f center, boolean isInternal, BitSet bsAtoms) { + // from TransformManager exclusively + if (bsAtoms.cardinality() == 0) + return; + modelSet.moveAtoms(mNew, matrixRotate, translation, bsAtoms, center, + isInternal); + checkMinimization(); + statusManager.setStatusAtomMoved(bsAtoms); + } + private boolean movingSelected; private boolean showSelected; public void moveSelected(int deltaX, int deltaY, int x, int y, - BitSet bsSelected, boolean isTranslation, boolean asAtoms) { + BitSet bsSelected, boolean isTranslation, + boolean asAtoms) { // cannot synchronize this -- it's from the mouse and the event queue if (x == Integer.MIN_VALUE) rotateBondIndex = -1; @@ -7947,27 +7961,24 @@ actionRotateBond(deltaX, deltaY, x, y); } else { bsSelected = setMovableBitSet(bsSelected, !asAtoms); - if (bsSelected.cardinality() == 0) - return; - if (isTranslation) { - Point3f ptCenter = getAtomSetCenter(bsSelected); - Point3i ptScreen = transformPoint(ptCenter); - Point3f ptScreenNew = new Point3f(ptScreen.x + deltaX + 0.5f, - ptScreen.y + deltaY + 0.5f, ptScreen.z); - Point3f ptNew = new Point3f(); - transformManager.finalizeTransformParameters(); - unTransformPoint(ptScreenNew, ptNew); - // script("draw ID 'pt" + Math.random() + "' " + Escape.escape(ptNew)); - ptNew.sub(ptCenter); - setAtomCoordRelative(ptNew, bsSelected); - refresh(2, ""); // should be syncing here - movingSelected = false; - return; - } - transformManager.rotateXYBy(deltaX, deltaY, bsSelected); + if (bsSelected.cardinality() != 0) { + if (isTranslation) { + Point3f ptCenter = getAtomSetCenter(bsSelected); + Point3i ptScreen = transformPoint(ptCenter); + Point3f ptScreenNew = new Point3f(ptScreen.x + deltaX + 0.5f, + ptScreen.y + deltaY + 0.5f, ptScreen.z); + Point3f ptNew = new Point3f(); + transformManager.finalizeTransformParameters(); + unTransformPoint(ptScreenNew, ptNew); + // script("draw ID 'pt" + Math.random() + "' " + Escape.escape(ptNew)); + ptNew.sub(ptCenter); + setAtomCoordRelative(ptNew, bsSelected); + } else { + transformManager.rotateXYBy(deltaX, deltaY, bsSelected); + } + } } refresh(2, ""); // should be syncing here - checkMinimization(); movingSelected = false; } @@ -8069,17 +8080,6 @@ null, null); } - void moveAtoms(Matrix3f mNew, Matrix3f matrixRotate, Vector3f translation, - Point3f center, boolean isInternal, BitSet bsAtoms) { - // from TransformManager exclusively - if (bsAtoms.cardinality() == 0) - return; - modelSet.moveAtoms(mNew, matrixRotate, translation, bsAtoms, center, - isInternal); - checkMinimization(); - statusManager.setStatusAtomMoved(bsAtoms); - } - public void refreshMeasures(boolean andStopMinimization) { setShapeProperty(JmolConstants.SHAPE_MEASURES, "refresh", null); if (andStopMinimization) This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-09-21 17:53:02
|
Revision: 16087 http://jmol.svn.sourceforge.net/jmol/?rev=16087&view=rev Author: hansonr Date: 2011-09-21 17:52:55 +0000 (Wed, 21 Sep 2011) Log Message: ----------- viewer.getBooleanValue("spinOn") Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2011-09-20 20:53:47 UTC (rev 16086) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2011-09-21 17:52:55 UTC (rev 16087) @@ -5575,6 +5575,8 @@ return colorManager.getDefaultColorRasmol(); if (key.equalsIgnoreCase("frank")) return getShowFrank(); + if (key.equalsIgnoreCase("spinOn")) + return getSpinOn(); if (key.equalsIgnoreCase("showSelections")) return modelSet.getSelectionHaloEnabled(); if (global.htUserVariables.containsKey(key)) { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-09-22 11:18:01
|
Revision: 16095 http://jmol.svn.sourceforge.net/jmol/?rev=16095&view=rev Author: hansonr Date: 2011-09-22 11:17:54 +0000 (Thu, 22 Sep 2011) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2011-09-22 10:35:48 UTC (rev 16094) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2011-09-22 11:17:54 UTC (rev 16095) @@ -3879,11 +3879,10 @@ if (!haveDisplay) return; repaintManager.requestRepaintAndWait(); - if (statusManager.doSync()) - statusManager.setSync(null); + setSync(); } - void setSync() { + private void setSync() { if (statusManager.doSync()) statusManager.setSync(null); } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-09-26 23:58:54
|
Revision: 16132 http://jmol.svn.sourceforge.net/jmol/?rev=16132&view=rev Author: hansonr Date: 2011-09-26 23:58:48 +0000 (Mon, 26 Sep 2011) Log Message: ----------- awt code refactoring part 2 Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2011-09-26 23:58:30 UTC (rev 16131) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2011-09-26 23:58:48 UTC (rev 16132) @@ -23,7 +23,7 @@ */ package org.jmol.viewer; -import org.jmol.popup.JmolPopup; +import org.jmol.awt.popup.JmolPopup; import org.jmol.script.ParallelProcessor; import org.jmol.script.ScriptCompiler; import org.jmol.script.ScriptContext; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-09-27 00:05:39
|
Revision: 16136 http://jmol.svn.sourceforge.net/jmol/?rev=16136&view=rev Author: hansonr Date: 2011-09-27 00:05:32 +0000 (Tue, 27 Sep 2011) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2011-09-27 00:03:11 UTC (rev 16135) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2011-09-27 00:05:32 UTC (rev 16136) @@ -4977,7 +4977,7 @@ case 'm': if (modelkit == null) { modelkit = (JmolModelKitInterface) Interface - .getOptionInterface("modelkit.ModelKit"); + .getOptionInterface("awt.modelkit.ModelKit"); if (modelkit == null) return; modelkit = modelkit.getModelKit(this, display); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-10-11 12:00:57
|
Revision: 16320 http://jmol.svn.sourceforge.net/jmol/?rev=16320&view=rev Author: hansonr Date: 2011-10-11 12:00:46 +0000 (Tue, 11 Oct 2011) Log Message: ----------- aHa! Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2011-10-11 11:04:45 UTC (rev 16319) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2011-10-11 12:00:46 UTC (rev 16320) @@ -282,7 +282,7 @@ } isDataOnly = (display == null); String platform = (commandOptions == null || !commandOptions.contains("platform=") - ? "org.jmol.awt.Platform" : commandOptions.substring(commandOptions.indexOf("platform=")) + 9); + ? "org.jmol.awt.Platform" : commandOptions.substring(commandOptions.indexOf("platform=") + 9)); apiPlatform = (ApiPlatform) Interface.getInterface(platform); g3d = new Graphics3D(apiPlatform, isDataOnly); haveDisplay = (!isDataOnly && (commandOptions == null || commandOptions.indexOf("-n") < 0)); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-10-12 12:22:13
|
Revision: 16336 http://jmol.svn.sourceforge.net/jmol/?rev=16336&view=rev Author: hansonr Date: 2011-10-12 12:22:04 +0000 (Wed, 12 Oct 2011) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2011-10-12 12:17:47 UTC (rev 16335) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2011-10-12 12:22:04 UTC (rev 16336) @@ -4975,23 +4975,25 @@ void popupMenu(int x, int y, char type) { if (!haveDisplay || !refreshing || isPreviewOnly || global.disablePopupMenu) return; - try { - switch (type) { - case 'j': + switch (type) { + case 'j': + try { getPopupMenu(); // can throw error if not present; that's ok jmolpopup.show(x, y); - break; - case 'a': - case 'b': - case 'm': - if (modelkit == null) - modelkit = apiPlatform.getModelKitMenu(this, display); + } catch (Throwable e) { + // no Swing -- tough luck! + global.disablePopupMenu = true; + } + break; + case 'a': + case 'b': + case 'm': + if (modelkit == null) + modelkit = apiPlatform.getModelKitMenu(this, display); + if (modelkit != null) modelkit.show(x, y, type); - } - } catch (Throwable e) { - // no Swing -- tough luck! - global.disablePopupMenu = true; + break; } } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |