From: <ha...@us...> - 2010-03-27 21:35:14
|
Revision: 12721 http://jmol.svn.sourceforge.net/jmol/?rev=12721&view=rev Author: hansonr Date: 2010-03-27 21:35:08 +0000 (Sat, 27 Mar 2010) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java Modified: trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java =================================================================== --- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-03-27 21:16:37 UTC (rev 12720) +++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-03-27 21:35:08 UTC (rev 12721) @@ -5813,16 +5813,21 @@ // atoms if (bsAtoms1 == null) { bsAtoms1 = viewer.getAtomBitSet("spine"); - bsAtoms2 = BitSetUtil.copy(bsAtoms1); - bsAtoms1.and(bsFrom); - bsAtoms2.and(bsTo); + if (bsAtoms1.nextSetBit(0) < 0) { + bsAtoms1 = bsFrom; + bsAtoms2 = bsTo; + } else { + bsAtoms2 = BitSetUtil.copy(bsAtoms1); + bsAtoms1.and(bsFrom); + bsAtoms2.and(bsTo); + } vAtomSets = new Vector(); vAtomSets.add(new BitSet[] { bsAtoms1, bsAtoms2 }); } centerAndPoints = viewer.getCenterAndPoints(vAtomSets, true); q = ModelSet.calculateQuaternionRotation(centerAndPoints, retStddev); - float r0 = (int) (retStddev[0] * 100) / 100f; - float r1 = (int) (retStddev[1] * 100) / 100f; + float r0 = (Float.isNaN(retStddev[1]) ? Float.NaN : (int) (retStddev[0] * 100) / 100f); + float r1 = (Float.isNaN(retStddev[1]) ? Float.NaN : (int) (retStddev[1] * 100) / 100f); showString("RMSD " + r0 + " --> " + r1 + " Angstroms"); } Point3f pt1 = new Point3f(); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-03-28 01:46:06
|
Revision: 12724 http://jmol.svn.sourceforge.net/jmol/?rev=12724&view=rev Author: hansonr Date: 2010-03-28 01:46:00 +0000 (Sun, 28 Mar 2010) Log Message: ----------- 11.9.37 -- animated COMPARE and rotate COMPARE Modified Paths: -------------- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java Modified: trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java =================================================================== --- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-03-28 01:36:51 UTC (rev 12723) +++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-03-28 01:46:00 UTC (rev 12724) @@ -8004,6 +8004,7 @@ // System.out.println("# " + endDegrees + " " + theta + " ;draw " + // Escape.escape(points[0]) + Escape.escape(points[1])); } + m4 = ScriptMathProcessor.getMatrix4f(q.getMatrix(), translation); } nPoints = 1; } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-04-06 22:02:15
|
Revision: 12778 http://jmol.svn.sourceforge.net/jmol/?rev=12778&view=rev Author: hansonr Date: 2010-04-06 22:02:08 +0000 (Tue, 06 Apr 2010) Log Message: ----------- debug comments out Modified Paths: -------------- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java Modified: trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java =================================================================== --- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-04-06 21:57:10 UTC (rev 12777) +++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-04-06 22:02:08 UTC (rev 12778) @@ -2066,7 +2066,7 @@ if (scriptLevel == scriptLevelMax) error(ERROR_tooManyScriptLevels); stack[scriptLevel++] = getScriptContext(); - if (true || isCmdLine_c_or_C_Option) + if (isCmdLine_c_or_C_Option) Logger.info("-->>-------------".substring(0, scriptLevel + 5) + scriptLevel + " " + filename); if (token != null) { @@ -2074,6 +2074,17 @@ } } + private void popContext(boolean isPushPop) { + if (isCmdLine_c_or_C_Option) + Logger.info("--<<-------------".substring(0, scriptLevel + 5) + + scriptLevel + " " + filename); + if (scriptLevel == 0) + return; + ScriptContext context = stack[--scriptLevel]; + stack[scriptLevel] = null; + getScriptContext(context, true, isPushPop); + } + public ScriptContext getScriptContext() { ScriptContext context = new ScriptContext(); context.contextPath = contextPath; @@ -2143,17 +2154,6 @@ pcEnd = context.pcEnd; } - private void popContext(boolean isPushPop) { - if (true || isCmdLine_c_or_C_Option) - Logger.info("--<<-------------".substring(0, scriptLevel + 5) - + scriptLevel + " " + filename); - if (scriptLevel == 0) - return; - ScriptContext context = stack[--scriptLevel]; - stack[scriptLevel] = null; - getScriptContext(context, true, isPushPop); - } - private String getContext(boolean withVariables) { StringBuffer sb = new StringBuffer(); for (int i = 0; i < scriptLevel; i++) { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-04-13 16:03:21
|
Revision: 12847 http://jmol.svn.sourceforge.net/jmol/?rev=12847&view=rev Author: hansonr Date: 2010-04-13 16:03:15 +0000 (Tue, 13 Apr 2010) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java Modified: trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java =================================================================== --- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-04-13 16:00:48 UTC (rev 12846) +++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-04-13 16:03:15 UTC (rev 12847) @@ -7348,8 +7348,8 @@ if (filename.startsWith("@") && filename.length() > 1) { String s = getStringParameter(filename.substring(1), false); htParams.put("fileData", s); - loadScript = new StringBuffer("var " + filename.substring(1) + " = " - + Escape.escape(s) + ";\n " + loadScript); + loadScript = new StringBuffer("{\nvar " + filename.substring(1) + " = " + + Escape.escape(s) + ";\n " + loadScript + "\n}\n"); } else if (isInline) { htParams.put("fileData", filename); } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-04-16 11:51:06
|
Revision: 12868 http://jmol.svn.sourceforge.net/jmol/?rev=12868&view=rev Author: hansonr Date: 2010-04-16 11:50:59 +0000 (Fri, 16 Apr 2010) Log Message: ----------- version=12.0.RC6_dev # code: preliminary PARALLEL {.... PROCESS {....} ....} Modified Paths: -------------- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java Modified: trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java =================================================================== --- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-04-16 07:37:33 UTC (rev 12867) +++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-04-16 11:50:59 UTC (rev 12868) @@ -5133,6 +5133,7 @@ int ptNext = 0; switch (tok) { case Token.process: + pushContext((ContextToken) theToken); isDone = isOK = true; addProcess(pc, pt); break; @@ -5160,6 +5161,7 @@ } if (theTok == Token.process) { addProcess(pt, pc); + popContext(true); } isOK = (theTok == Token.process || theTok == Token.ifcmd); isForCheck = (theTok == Token.forcmd || theTok == Token.whilecmd); @@ -5267,6 +5269,7 @@ if (pc > 0) { vProcess = new Vector(); } else { + Token[][] statements = new Token[pt][]; for (int i = 0; i < vProcess.size(); i++) statements[i - pc] = (Token[]) vProcess.get(i); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-04-18 01:32:09
|
Revision: 12883 http://jmol.svn.sourceforge.net/jmol/?rev=12883&view=rev Author: hansonr Date: 2010-04-18 01:32:03 +0000 (Sun, 18 Apr 2010) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java Modified: trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java =================================================================== --- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-04-18 01:23:34 UTC (rev 12882) +++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-04-18 01:32:03 UTC (rev 12883) @@ -13435,12 +13435,12 @@ case Token.titleformat: if (i + 1 < statementLength && tokAt(i + 1) == Token.string) { propertyName = "titleFormat"; - propertyValue = parameterAsString(2); + propertyValue = parameterAsString(i + 1); } break; case Token.homo: case Token.lumo: - if ((offset = moOffset(1)) == Integer.MAX_VALUE) + if ((offset = moOffset(i)) == Integer.MAX_VALUE) error(ERROR_invalidArgument); moNumber = 0; break; @@ -13455,7 +13455,7 @@ return true; } if (propertyName != null) - addShapeProperty(propertyList, propertyName, propertyValue); + addShapeProperty(1propertyList, propertyName, propertyValue); if (moNumber != Integer.MAX_VALUE) { if (tokAt(i + 1) == Token.string) title = parameterAsString(i + 1); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-04-18 01:32:27
|
Revision: 12884 http://jmol.svn.sourceforge.net/jmol/?rev=12884&view=rev Author: hansonr Date: 2010-04-18 01:32:20 +0000 (Sun, 18 Apr 2010) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java Modified: trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java =================================================================== --- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-04-18 01:32:03 UTC (rev 12883) +++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-04-18 01:32:20 UTC (rev 12884) @@ -13455,7 +13455,7 @@ return true; } if (propertyName != null) - addShapeProperty(1propertyList, propertyName, propertyValue); + addShapeProperty(propertyList, propertyName, propertyValue); if (moNumber != Integer.MAX_VALUE) { if (tokAt(i + 1) == Token.string) title = parameterAsString(i + 1); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-04-18 11:13:30
|
Revision: 12888 http://jmol.svn.sourceforge.net/jmol/?rev=12888&view=rev Author: hansonr Date: 2010-04-18 11:13:23 +0000 (Sun, 18 Apr 2010) Log Message: ----------- version=12.0.RC7_dev # new feature: model numbers can be given as "2.1" in quotes # bug fix for parallel processing and isosurface Modified Paths: -------------- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java Modified: trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java =================================================================== --- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-04-18 11:03:57 UTC (rev 12887) +++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-04-18 11:13:23 UTC (rev 12888) @@ -3726,6 +3726,9 @@ iFrame = getToken(index).intValue; // decimal Token intValue is // model/frame number encoded break; + case Token.string: + iFrame = JmolConstants.modelValue(stringParameter(index)); + break; default: error(ERROR_invalidArgument); } @@ -10060,9 +10063,10 @@ isHyphen = true; // fall through case Token.integer: + case Token.string: if (nFrames == 2) error(ERROR_invalidArgument); - int iFrame = statement[i].intValue; + int iFrame = (theTok == Token.string ? JmolConstants.modelValue((String)theToken.value) : theToken.intValue); if (iFrame == -1) { checkLength(offset + 1); if (!isSyntaxCheck) This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-04-23 19:10:26
|
Revision: 12913 http://jmol.svn.sourceforge.net/jmol/?rev=12913&view=rev Author: hansonr Date: 2010-04-23 19:10:19 +0000 (Fri, 23 Apr 2010) Log Message: ----------- xyz reader made more flexible -- allows blank lines between models Modified Paths: -------------- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java Modified: trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java =================================================================== --- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-04-23 19:07:04 UTC (rev 12912) +++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-04-23 19:10:19 UTC (rev 12913) @@ -14577,6 +14577,7 @@ if (defaultMesh) { setShapeProperty(iShape, "token", new Integer(Token.mesh)); setShapeProperty(iShape, "token", new Integer(Token.nofill)); + setShapeProperty(iShape, "token", new Integer(Token.frontonly)); } if (iptDisplayProperty > 0) { if (!setMeshDisplayProperty(iShape, iptDisplayProperty, This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-05-26 17:49:32
|
Revision: 13219 http://jmol.svn.sourceforge.net/jmol/?rev=13219&view=rev Author: hansonr Date: 2010-05-26 17:49:26 +0000 (Wed, 26 May 2010) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java Modified: trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java =================================================================== --- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-05-26 17:46:59 UTC (rev 13218) +++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-05-26 17:49:26 UTC (rev 13219) @@ -10040,7 +10040,7 @@ bs = (statementLength == 2 ? null : expression(2)); checkLast(iToken); if (!isSyntaxCheck) - viewer.addHydrogens(bs, false); + viewer.addHydrogens(bs, false, false); return; case Token.pointgroup: pointGroup(); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-05-26 19:08:28
|
Revision: 13223 http://jmol.svn.sourceforge.net/jmol/?rev=13223&view=rev Author: hansonr Date: 2010-05-26 19:08:21 +0000 (Wed, 26 May 2010) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java Modified: trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java =================================================================== --- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-05-26 18:11:37 UTC (rev 13222) +++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-05-26 19:08:21 UTC (rev 13223) @@ -7047,11 +7047,22 @@ } if (isSyntaxCheck || shapeType < 0) return; - typeMask = (shapeType == JmolConstants.SHAPE_STRUTS ? JmolEdge.BOND_STRUT - : shapeType == JmolConstants.SHAPE_HSTICKS ? JmolEdge.BOND_HYDROGEN_MASK - : shapeType == JmolConstants.SHAPE_SSSTICKS ? JmolEdge.BOND_SULFUR_MASK - : shapeType == JmolConstants.SHAPE_STICKS ? JmolEdge.BOND_COVALENT_MASK - : 0); + switch (shapeType) { + case JmolConstants.SHAPE_STRUTS: + typeMask = JmolEdge.BOND_STRUT; + break; + case JmolConstants.SHAPE_HSTICKS: + typeMask = JmolEdge.BOND_HYDROGEN_MASK; + break; + case JmolConstants.SHAPE_SSSTICKS: + typeMask = JmolEdge.BOND_SULFUR_MASK; + break; + case JmolConstants.SHAPE_STICKS: + typeMask = JmolEdge.BOND_COVALENT_MASK; + break; + default: + typeMask = 0; + } if (typeMask == 0) { loadShape(shapeType); if (shapeType == JmolConstants.SHAPE_LABELS) This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-06-30 00:08:35
|
Revision: 13481 http://jmol.svn.sourceforge.net/jmol/?rev=13481&view=rev Author: hansonr Date: 2010-06-30 00:08:29 +0000 (Wed, 30 Jun 2010) Log Message: ----------- isosurface test for within(....) Modified Paths: -------------- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java Modified: trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java =================================================================== --- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-06-29 23:18:42 UTC (rev 13480) +++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-06-30 00:08:29 UTC (rev 13481) @@ -14196,12 +14196,31 @@ continue; case Token.within: ptWithin = i; - float distance = floatParameter(++i); - Point3f ptc = centerParameter(++i); - i = iToken; + float distance; + Point3f ptc; + bs = null; + boolean havePt = false; + if (tokAt(i + 1) == Token.expressionBegin) { + // within ( x.x , .... ) + distance = floatParameter(i + 3); + if (isPoint3f(i + 4)) { + ptc = centerParameter(i + 4); + havePt = true; + iToken = iToken + 2; + } else { + bs = expression(statement, i + 5, statementLength, true, false, false, true); + if (bs == null) + error(ERROR_invalidArgument); + ptc = viewer.getAtomSetCenter(bs); + } + } else { + distance = floatParameter(++i); + ptc = centerParameter(++i); + } + i = iToken; if (fullCommand.indexOf("# WITHIN=") >= 0) bs = Escape.unescapeBitset(extractCommandOption("# WITHIN")); - else + else if (!havePt) bs = (expressionResult instanceof BitSet ? (BitSet) expressionResult : null); if (!isSyntaxCheck) { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-06-30 21:56:44
|
Revision: 13493 http://jmol.svn.sourceforge.net/jmol/?rev=13493&view=rev Author: hansonr Date: 2010-06-30 21:56:33 +0000 (Wed, 30 Jun 2010) Log Message: ----------- quaternion frame state fix Modified Paths: -------------- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java Modified: trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java =================================================================== --- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-06-30 21:52:39 UTC (rev 13492) +++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-06-30 21:56:33 UTC (rev 13493) @@ -7996,13 +7996,14 @@ } int ptDataFrame = viewer.getJmolDataFrameIndex(modelIndex, type); if (ptDataFrame > 0) { + viewer.deleteAtoms(viewer.getModelUndeletedAtomsBitSet(ptDataFrame), true); // data frame can't be 0. - viewer.setCurrentModelIndex(ptDataFrame, true); + // viewer.setCurrentModelIndex(ptDataFrame, true); // BitSet bs2 = viewer.getModelAtomBitSet(ptDataFrame); // bs2.and(bs); // need to be able to set data directly as well. // viewer.display(BitSetUtil.setAll(viewer.getAtomCount()), bs2, tQuiet); - return; + // return; } String[] savedFileInfo = viewer.getFileInfo(); boolean oldAppendNew = viewer.getAppendNew(); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-07-09 13:54:52
|
Revision: 13530 http://jmol.svn.sourceforge.net/jmol/?rev=13530&view=rev Author: hansonr Date: 2010-07-09 13:54:44 +0000 (Fri, 09 Jul 2010) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java Modified: trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java =================================================================== --- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-07-09 13:33:44 UTC (rev 13529) +++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-07-09 13:54:44 UTC (rev 13530) @@ -5524,9 +5524,9 @@ private void help() throws ScriptException { if (isSyntaxCheck) return; - String what = optParameterAsString(1); + String what = optParameterAsString(1).toLowerCase(); int pt = 0; - if (what.toLowerCase().startsWith("mouse") && (pt = what.indexOf(" ")) >= 0 + if (what.startsWith("mouse") && (pt = what.indexOf(" ")) >= 0 && pt == what.lastIndexOf(" ")) { showString(viewer.getBindingInfo(what.substring(pt + 1))); return; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-07-15 04:24:52
|
Revision: 13585 http://jmol.svn.sourceforge.net/jmol/?rev=13585&view=rev Author: hansonr Date: 2010-07-15 04:24:45 +0000 (Thu, 15 Jul 2010) Log Message: ----------- version=12.0.RC25 # new feature: "load =xxxx AS ." "." means "into the default directory; same name" Modified Paths: -------------- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java Modified: trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java =================================================================== --- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-07-15 03:51:43 UTC (rev 13584) +++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-07-15 04:24:45 UTC (rev 13585) @@ -7751,10 +7751,8 @@ int filePt = i; String localName = null; - if (tokAt(filePt + 1) == Token.as) { - localName = stringParameter(i + 2); - i += 2; - } + if (tokAt(filePt + 1) == Token.as) + localName = stringParameter(i = i + 2); if (statementLength == i + 1) { if (i == 0 || (filename = parameterAsString(filePt)).length() == 0) filename = viewer.getFullPathName(); @@ -7970,6 +7968,9 @@ if (localName != null) { if (localName.equals(".")) localName = viewer.getFilePath(filename, true); + if (localName.length() == 0 + || viewer.getFilePath(localName, false).equalsIgnoreCase(viewer.getFilePath(filename, false))) + error(ERROR_invalidArgument); String[] fullPath = new String[] { localName }; os = viewer.getOutputStream(localName, fullPath); if (os == null) @@ -15403,7 +15404,7 @@ if (tokAt(i + 1) == Token.as) i += 2; // skip that } else if (tokAt(i + 1) == Token.as) { - localName = viewer.getFilePath(stringParameter(i = i + 2), false); + localName = viewer.getFilePath(stringParameter(iToken = (i = i + 2)), false); fullPathNameOrError = viewer.getFullPathNameOrError(localName); localName = fullPathNameOrError[0]; addShapeProperty(propertyList, "localName", localName); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-07-22 15:43:43
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Revision: 13641 http://jmol.svn.sourceforge.net/jmol/?rev=13641&view=rev Author: hansonr Date: 2010-07-22 15:43:37 +0000 (Thu, 22 Jul 2010) Log Message: ----------- color selectionhalos Modified Paths: -------------- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java Modified: trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java =================================================================== --- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-07-22 15:32:42 UTC (rev 13640) +++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-07-22 15:43:37 UTC (rev 13641) @@ -6995,7 +6995,8 @@ } else { int argb = 0; i = 2; - switch (getToken(1).tok) { + int tok = getToken(1).tok; + switch (tok) { case Token.dollarsign: setObjectProperty(); return; @@ -7073,7 +7074,7 @@ loadShape(JmolConstants.SHAPE_HALOS); setShapeProperty( JmolConstants.SHAPE_HALOS, - (theTok == Token.selectionhalos ? "argbSelection" : "argbHighlight"), + (tok == Token.selectionhalos ? "argbSelection" : "argbHighlight"), new Integer(argb)); return; case Token.axes: This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-07-22 16:26:25
|
Revision: 13643 http://jmol.svn.sourceforge.net/jmol/?rev=13643&view=rev Author: hansonr Date: 2010-07-22 16:26:19 +0000 (Thu, 22 Jul 2010) Log Message: ----------- version=12.0.RC27_dev # new feature: failed file loading with try/catch is caught # new feature: try/catch: # load quartz.cif # refresh # var x = 1 # print "outside, x = " + x # while(true) { # has its own local variables # print " inside while, x = " + x # x = 2 # print " setting x = " + x # try{ # has its own local variables # print " inside try, x = " + x # var x = 3 # print " setting x = " + x # print "TEST1" # load "adfkjd" # will be caught # } # catch(e) { # has its own local variables # print " inside catch, x = " + x # var x = 4 # print " setting x = " + x # prompt @e # break # from WHILE # } # print " after catch, x = " + x # x = 5 # print " setting x = " + x # print "out" # break; # } # print "way out" # print "outside, x = " + x Modified Paths: -------------- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java Modified: trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java =================================================================== --- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-07-22 16:03:54 UTC (rev 13642) +++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-07-22 16:26:19 UTC (rev 13643) @@ -1818,7 +1818,7 @@ if (isTry){ String err = (String) viewer.getParameter("_errorMessage"); if (err.length() > 0) { - contextVariables.put("_errorval", err); + contextVariables.put("_errorval", ScriptVariable.getVariable(err)); viewer.resetError(); } contextVariables.put("_tryret", contextVariables.get("_retval")); @@ -5416,6 +5416,7 @@ switch (tok) { case Token.catchcmd: pushContext((ContextToken) theToken); + isOK = !isDone; break; case Token.process: pushContext((ContextToken) theToken); @@ -5568,18 +5569,21 @@ returnCmd(ret); return false; } - String errMsg = (String)cv.get("_errorval"); + String errMsg = (String)((ScriptVariable)cv.get("_errorval")).value; if (errMsg.length() == 0) { int iBreak = ((ScriptVariable)cv.get("_breakval")).intValue; - if (iBreak != Integer.MAX_VALUE) + if (iBreak != Integer.MAX_VALUE) { breakCmd(pc - iBreak); - // normal return will skip the catch - } else if (pc + 1 < aatoken.length + return false; + } + } + // normal return will skip the catch + if (pc + 1 < aatoken.length && aatoken[pc + 1][0].tok == Token.catchcmd) { // set the intValue positive to indicate "not done" for the IF evaluation ContextToken ct = (ContextToken) aatoken[pc + 1][0]; ct.contextVariables.put(ct.name0, ScriptVariable.getVariable(errMsg)); - ct.intValue = Math.abs(ct.intValue); + ct.intValue = (errMsg.length() > 0 ? 1 : -1) * Math.abs(ct.intValue); } return false; case Token.catchcmd: This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-07-24 17:28:20
|
Revision: 13677 http://jmol.svn.sourceforge.net/jmol/?rev=13677&view=rev Author: hansonr Date: 2010-07-24 17:28:13 +0000 (Sat, 24 Jul 2010) Log Message: ----------- string parsing error after ! 56:A fix Modified Paths: -------------- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java Modified: trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java =================================================================== --- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-07-24 16:46:13 UTC (rev 13676) +++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-07-24 17:28:13 UTC (rev 13677) @@ -4606,8 +4606,8 @@ switch (getToken(i).tok) { case Token.leftbrace: case Token.comma: - // case Token.opOr: case Token.opAnd: + case Token.opAND: break; case Token.rightbrace: break out; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-07-24 17:38:01
|
Revision: 13678 http://jmol.svn.sourceforge.net/jmol/?rev=13678&view=rev Author: hansonr Date: 2010-07-24 17:37:54 +0000 (Sat, 24 Jul 2010) Log Message: ----------- string parsing error after ! 56:A fix Modified Paths: -------------- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java Modified: trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java =================================================================== --- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-07-24 17:28:13 UTC (rev 13677) +++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-07-24 17:37:54 UTC (rev 13678) @@ -3318,7 +3318,7 @@ rpn.addXNum(ScriptVariable.intVariable(code[++pc].intValue)); break; } - int chainID = (pc + 3 < code.length && code[pc + 2].tok == Token.opAnd + int chainID = (pc + 3 < code.length && code[pc + 2].tok == Token.opAND && code[pc + 3].tok == Token.spec_chain ? code[pc + 3].intValue : '\t'); rpn.addX(getAtomBits(Token.spec_seqcode_range, new int[] { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-08-06 13:01:59
|
Revision: 13845 http://jmol.svn.sourceforge.net/jmol/?rev=13845&view=rev Author: hansonr Date: 2010-08-06 13:01:52 +0000 (Fri, 06 Aug 2010) Log Message: ----------- code Modified Paths: -------------- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java Modified: trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java =================================================================== --- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-08-06 12:25:30 UTC (rev 13844) +++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-08-06 13:01:52 UTC (rev 13845) @@ -481,7 +481,7 @@ if (e.compileScript(null, EXPRESSION_KEY + " = " + expr, false)) { e.contextVariables = viewer.getContextVariables(); e.setStatement(0); - return e.parameterExpression(2, 0, "", false); + return e.parameterExpressionString(2, 0); } } else if (expr instanceof Token[]) { e.contextVariables = viewer.getContextVariables(); @@ -558,11 +558,21 @@ return V; } - private Object parameterExpression(int pt, int ptMax, String key, - boolean asVector) throws ScriptException { - return parameterExpression(pt, ptMax, key, true, asVector, -1, false, null, null); + @SuppressWarnings("unchecked") + private List<ScriptVariable> parameterExpressionList(int pt, int ptMax) throws ScriptException { + return (List<ScriptVariable>) parameterExpression(pt, ptMax, null, true, true, -1, false, null, null); } + private String parameterExpressionString(int pt, int ptMax) throws ScriptException { + return (String) parameterExpression(pt, ptMax, "", true, false, -1, false, null, null); + } + + private boolean parameterExpressionBoolean(int pt, int ptMax) + throws ScriptException { + return ((Boolean) parameterExpression(pt, ptMax, null, true, false, -1, + false, null, null)).booleanValue(); + } + /** * This is the primary driver of the RPN (reverse Polish notation) expression * processor. It handles all math outside of a "traditional" Jmol @@ -613,8 +623,8 @@ Object v, res; boolean isImplicitAtomProperty = (localVar != null); boolean isOneExpressionOnly = (pt < 0); - boolean returnBoolean = (key == null); - boolean returnString = (key != null && key.length() == 0); + boolean returnBoolean = (!asVector && key == null); + boolean returnString = (!asVector && key != null && key.length() == 0); int nSquare = 0; if (isOneExpressionOnly) pt = -pt; @@ -658,7 +668,7 @@ int iT = iToken; if (getToken(iT++).tok != Token.semicolon) error(ERROR_invalidArgument); - parameterExpression(iT, -1, null, false); + parameterExpressionBoolean(iT, -1); int iF = iToken; if (tokAt(iF++) != Token.semicolon) error(ERROR_invalidArgument); @@ -1103,6 +1113,7 @@ return data; } + @SuppressWarnings("unchecked") protected Object getBitsetProperty(BitSet bs, int tok, Point3f ptRef, Point4f planeRef, Object tokenValue, Object opValue, boolean useAtomMap, @@ -2097,11 +2108,11 @@ String var = parameterAsString(++i); boolean isClauseDefine = (tokAt(i) == Token.expressionBegin); if (isClauseDefine) { - List<Object> val = (List<Object>) parameterExpression(++i, 0, "_var", true); + List<ScriptVariable> val = parameterExpressionList(++i, 0); if (val == null || val.size() == 0) error(ERROR_invalidArgument); i = iToken; - ScriptVariable vt = (ScriptVariable) val.get(0); + ScriptVariable vt = val.get(0); v = (vt.tok == Token.list ? vt : ScriptVariable.oValue(vt)); } else { v = getParameter(var, false); @@ -2176,7 +2187,7 @@ fixed[j] = new Token(Token.matrix3f, v); } else if (v instanceof Matrix4f) { fixed[j] = new Token(Token.matrix4f, v); - } else if (v instanceof Hashtable) { + } else if (v instanceof Hashtable<?,?>) { fixed[j] = new Token(Token.hash, v); } else if (v instanceof String[]) { String[] sv = (String[]) v; @@ -2534,6 +2545,15 @@ final static int ERROR_writeWhat = 54; final static int ERROR_multipleModelsNotOK = 55; + /** + * @param iError + * @param value + * @param more + * @param more2 + * @param translated + * @return constructed error string + * + */ static String errorString(int iError, String value, String more, String more2, boolean translated) { boolean doTranslate = false; @@ -2997,9 +3017,8 @@ } private void addShapeProperty(List<Object[]> propertyList, String key, Object value) { - if (isSyntaxCheck) { - ; - } + if (isSyntaxCheck) + return; propertyList.add(new Object[] { key, value }); } @@ -3107,6 +3126,17 @@ return atomExpression(statement, index, 0, true, false, true, true); } + /** + * @param code + * @param pcStart + * @param pcStop + * @param allowRefresh + * @param allowUnderflow + * @param mustBeBitSet + * @param andNotDeleted IGNORED + * @return atom bitset + * @throws ScriptException + */ private BitSet atomExpression(Token[] code, int pcStart, int pcStop, boolean allowRefresh, boolean allowUnderflow, boolean mustBeBitSet, boolean andNotDeleted) @@ -4723,10 +4753,10 @@ private int intSetting(int pt) throws ScriptException { if (pt == statementLength) return Integer.MIN_VALUE; - List v = (List) parameterExpression(pt, -1, "XXX", true); + List<ScriptVariable> v = parameterExpressionList(pt, -1); if (v == null || v.size() == 0) error(ERROR_invalidArgument); - return ScriptVariable.iValue((ScriptVariable) v.get(0)); + return ScriptVariable.iValue(v.get(0)); } private float floatSetting(int pt, float min, float max) @@ -4740,27 +4770,27 @@ } private float floatSetting(int pt) throws ScriptException { - List v = (List) parameterExpression(pt, -1, "XXX", true); + List<ScriptVariable> v = parameterExpressionList(pt, -1); if (v == null || v.size() == 0) error(ERROR_invalidArgument); - return ScriptVariable.fValue((ScriptVariable) v.get(0)); + return ScriptVariable.fValue(v.get(0)); } private String stringSetting(int pt, boolean isJmolSet) throws ScriptException { if (isJmolSet && statementLength == pt + 1) return parameterAsString(pt); - List v = (List) parameterExpression(pt, -1, "XXX", true); + List<ScriptVariable> v = parameterExpressionList(pt, -1); if (v == null || v.size() == 0) error(ERROR_invalidArgument); - return ScriptVariable.sValue((ScriptVariable) v.get(0)); + return ScriptVariable.sValue(v.get(0)); } private ScriptVariable tokenSetting(int pt) throws ScriptException { - List v = (List) parameterExpression(pt, -1, "XXX", true); + List<ScriptVariable> v = parameterExpressionList(pt, -1); if (v == null || v.size() == 0) error(ERROR_invalidArgument); - return (ScriptVariable) v.get(0); + return v.get(0); } /* @@ -5576,8 +5606,7 @@ setVariable(j + 2, statementLength - 1, key, 0); } } - isOK = ((Boolean) parameterExpression(pts[0] + 1, pts[1], null, false)) - .booleanValue(); + isOK = parameterExpressionBoolean(pts[0] + 1, pts[1]); pt++; if (!isOK) popContext(true, false); @@ -5758,19 +5787,19 @@ if (tok == Token.defaultcmd) // never do the default one directly return -1; System.out.println("testing..."); - List<Object> v = (List<Object>) parameterExpression(1, 0, null, true); + List<ScriptVariable> v = parameterExpressionList(1, 0); if (tok == Token.casecmd) { - boolean isOK = ScriptVariable.areEqual(var, (ScriptVariable) v.get(0)); + boolean isOK = ScriptVariable.areEqual(var, v.get(0)); if (isOK) c.contextVariables.remove("_var"); return isOK ? 1 : -1; } - c.contextVariables.put("_var", (ScriptVariable) v.get(0)); + c.contextVariables.put("_var", v.get(0)); return 1; } private boolean ifCmd() throws ScriptException { - return ((Boolean) parameterExpression(1, 0, null, false)).booleanValue(); + return parameterExpressionBoolean(1, 0); } private void returnCmd(ScriptVariable tv) throws ScriptException { @@ -5780,8 +5809,8 @@ gotoCmd(null); return; } - List v = (tv != null || statementLength == 1 ? null : (List) parameterExpression(1, - 0, null, true)); + List<ScriptVariable> v = (tv != null || statementLength == 1 ? null : parameterExpressionList(1, + 0)); if (isSyntaxCheck) return; if (tv == null) @@ -7827,7 +7856,7 @@ error(ERROR_badArgumentCount); if (isSyntaxCheck) return; - String s = (String) parameterExpression(1, 0, "", false); + String s = parameterExpressionString(1, 0); if (tokAt(1) == Token.off) setStringProperty("logFile", ""); else @@ -8892,7 +8921,7 @@ private void print() throws ScriptException { if (statementLength == 1) error(ERROR_badArgumentCount); - showString((String) parameterExpression(1, 0, "", false), true); + showString(parameterExpressionString(1, 0), true); } private void prompt() throws ScriptException { @@ -8901,7 +8930,7 @@ if (!isSyntaxCheck) msg = getScriptContext().getContextTrace(null, true).toString(); } else { - msg = (String) parameterExpression(1, 0, "", false); + msg = parameterExpressionString(1, 0); } if (!isSyntaxCheck) viewer.prompt(msg, "OK", null, true); @@ -9434,7 +9463,7 @@ if (filename.equalsIgnoreCase("applet")) { // script APPLET x "....." String appID = parameterAsString(2); - theScript = parameterExpression(3, 0, "_script", false).toString(); + theScript = parameterExpressionString(3, 0); // had _script variable?? checkLast(iToken); if (isSyntaxCheck) return; @@ -9449,8 +9478,8 @@ tok = tokAt(statementLength - 1); doStep = (tok == Token.step); if (filename.equalsIgnoreCase("inline")) { - theScript = parameterExpression(2, - (doStep ? statementLength - 1 : 0), "_script", false).toString(); + theScript = parameterExpressionString(2, + (doStep ? statementLength - 1 : 0)); i = iToken + 1; } while (filename.equalsIgnoreCase("localPath") @@ -9547,9 +9576,9 @@ String name = (String) getToken(0).value; if (!viewer.isFunction(name)) error(ERROR_commandExpected); - List params = (statementLength == 1 || statementLength == 3 + List<ScriptVariable> params = (statementLength == 1 || statementLength == 3 && tokAt(1) == Token.leftparen && tokAt(2) == Token.rightparen ? null - : (List) parameterExpression(1, 0, null, true)); + : parameterExpressionList(1, 0)); if (isSyntaxCheck) return; runFunction(null, name, params, null, false); @@ -11543,7 +11572,7 @@ case Token.defaultlattice: if (statementLength > 2) { Point3f pt; - List<ScriptVariable> v = (List<ScriptVariable>) parameterExpression(2, 0, "XXX", true); + List<ScriptVariable> v = parameterExpressionList(2, 0); if (v == null || v.size() == 0) error(ERROR_invalidArgument); ScriptVariable var = v.get(0); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-08-06 23:50:16
|
Revision: 13888 http://jmol.svn.sourceforge.net/jmol/?rev=13888&view=rev Author: hansonr Date: 2010-08-06 23:50:10 +0000 (Fri, 06 Aug 2010) Log Message: ----------- version=12.1.2_dev # bug fix: struts not restored from state # bug fix: color STRUTS also colors hbonds Modified Paths: -------------- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java Modified: trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java =================================================================== --- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-08-06 23:48:48 UTC (rev 13887) +++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-08-06 23:50:10 UTC (rev 13888) @@ -6971,6 +6971,7 @@ setShapeProperty(JmolConstants.SHAPE_STICKS, "translucency", translucency, bsBonds); } + viewer.selectBonds(null); } if (!(tQuiet || scriptLevel > scriptReportingLevel)) scriptStatusOrBuffer(GT._("{0} new bonds; {1} modified", new Object[] { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-08-07 15:45:29
|
Revision: 13901 http://jmol.svn.sourceforge.net/jmol/?rev=13901&view=rev Author: hansonr Date: 2010-08-07 15:45:23 +0000 (Sat, 07 Aug 2010) Log Message: ----------- doList not continued to sub-script Modified Paths: -------------- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java Modified: trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java =================================================================== --- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-08-07 15:44:58 UTC (rev 13900) +++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-08-07 15:45:23 UTC (rev 13901) @@ -5120,7 +5120,7 @@ invertSelected(); break; case Token.javascript: - script(Token.javascript, null); + script(Token.javascript, null, false); break; case Token.load: load(); @@ -5192,7 +5192,7 @@ set(); break; case Token.script: - script(Token.script, null); + script(Token.script, null, doList); break; case Token.select: select(1); @@ -8304,7 +8304,7 @@ if (statementLength == 2) { if (errMsg.indexOf("NOTE: file recognized as a script file:") == 0) { filename = errMsg.substring(errMsg.indexOf("file:") + 5).trim(); - script(0, filename); + script(0, filename, false); return; } String surfaceType = (errMsg.indexOf("java.io.FileNotFound") >= 0 ? null : SurfaceFileTyper.determineSurfaceFileType(viewer @@ -9435,7 +9435,7 @@ : null); } - private void script(int tok, String filename) throws ScriptException { + private void script(int tok, String filename, boolean listCommands) throws ScriptException { boolean loadCheck = true; boolean isCheck = false; boolean doStep = false; @@ -9550,7 +9550,7 @@ boolean saveLoadCheck = isCmdLine_C_Option; isCmdLine_C_Option &= loadCheck; executionStepping |= doStep; - instructionDispatchLoop(isCheck); + instructionDispatchLoop(isCheck || listCommands); if (debugScript && viewer.getMessageStyleChime()) viewer.scriptStatus("script <exiting>"); isCmdLine_C_Option = saveLoadCheck; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-08-09 14:51:43
|
Revision: 13934 http://jmol.svn.sourceforge.net/jmol/?rev=13934&view=rev Author: hansonr Date: 2010-08-09 14:51:35 +0000 (Mon, 09 Aug 2010) Log Message: ----------- 12.1.3 VERSION # new feature: load "myfile.xxx" {1 1 1} unitcell [ax ay az bx by bz cx cy cz] # new feature: x = compare({atomset1}, {atomset2}, "ISOMER") # new feature: x = compare(smilesString1, smilesString2, "ISOMER") # bug fix: "CCCC".find("SMILES","CCCC") should return 1 (other returns 0 and -1) # bug fix: "CCCC".find("SMARTS","CCC") should return [1,5,8,11] (other returns [] and "?" # bug fix: SmilesGeneration stereochemistry error # bug fix: "smilesString".find("smarts","pattern") should return "?" upon parsing error # bug fix: proper "false AND"/"true OR" action where second operand is skipped Modified Paths: -------------- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java Modified: trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java =================================================================== --- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-08-09 14:18:05 UTC (rev 13933) +++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-08-09 14:51:35 UTC (rev 13934) @@ -4009,12 +4009,16 @@ if (haveBrace || haveSquare) i++; Point3f pt; - if (tokAt(i) == Token.string) { - String s = stringParameter(i); + String s = null; + switch (tokAt(i)) { + case Token.string: + case Token.list: + s = ScriptVariable.sValue(statement[i]); s = TextFormat.replaceAllCharacters(s, "{},[]\"'", ' '); fparams = Parser.parseFloatArray(s); n = fparams.length; - } else { + break; + default: while (n < nMax) { tok = tokAt(i); if (haveBrace && tok == Token.rightbrace || haveSquare @@ -4045,6 +4049,8 @@ default: v.add(new Float(floatParameter(i))); n++; + if (n == nMax && haveSquare && tokAt(i+1) == Token.rightbrace) + i++; } i++; } @@ -8141,7 +8147,9 @@ } if (tokAt(i) == Token.unitcell) { ++i; - fparams = floatParameterSet(i, 6, 9); // allow for specific vectors + fparams = floatParameterSet(i, 6, 9); + if (fparams.length != 6 && fparams.length != 9) + error(ERROR_invalidArgument); i = iToken; sOptions += " unitcell {"; for (int j = 0; j < 6; j++) This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-08-18 02:32:25
|
Revision: 14024 http://jmol.svn.sourceforge.net/jmol/?rev=14024&view=rev Author: hansonr Date: 2010-08-18 02:32:19 +0000 (Wed, 18 Aug 2010) Log Message: ----------- version=12.1.5_dev # bug fix: CURSOR_WAIT hourglass not turning off automatically after set picking JmolScript operation Modified Paths: -------------- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java Modified: trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java =================================================================== --- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-08-18 02:21:32 UTC (rev 14023) +++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-08-18 02:32:19 UTC (rev 14024) @@ -5270,7 +5270,8 @@ } private void setCursorWait(boolean TF) { - viewer.setCursor(TF ? Viewer.CURSOR_WAIT : Viewer.CURSOR_DEFAULT); + if (!isSyntaxCheck) + viewer.setCursor(TF ? Viewer.CURSOR_WAIT : Viewer.CURSOR_DEFAULT); } private void processShapeCommand(int tok) throws ScriptException { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-09-18 22:22:18
|
Revision: 14338 http://jmol.svn.sourceforge.net/jmol/?rev=14338&view=rev Author: hansonr Date: 2010-09-18 22:22:11 +0000 (Sat, 18 Sep 2010) Log Message: ----------- version=12.1.13_dev # new feature: hide/display bonds # new feature: hide/display [{bond set}] Modified Paths: -------------- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java Modified: trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java =================================================================== --- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-09-18 22:00:28 UTC (rev 14337) +++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-09-18 22:22:11 UTC (rev 14338) @@ -7324,12 +7324,15 @@ boolean isColor = false; boolean isIsosurface = (shapeType == JmolConstants.SHAPE_ISOSURFACE); int typeMask = 0; + boolean doClearBondSet = false; float translucentLevel = Float.MAX_VALUE; if (index < 0) { bs = atomExpression(-index); index = iToken + 1; - if (isBondSet) + if (isBondSet) { + doClearBondSet = true; shapeType = JmolConstants.SHAPE_STICKS; + } } if (isBackground) getToken(index); @@ -7541,6 +7544,8 @@ if (typeMask != 0) setShapeProperty(JmolConstants.SHAPE_STICKS, "type", Integer .valueOf(JmolEdge.BOND_COVALENT_MASK)); + if (doClearBondSet) + viewer.selectBonds(null); } private void colorShape(int shapeType, int typeMask, int argb, This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |