From: <ha...@us...> - 2011-06-15 22:45:52
|
Revision: 15592 http://jmol.svn.sourceforge.net/jmol/?rev=15592&view=rev Author: hansonr Date: 2011-06-15 22:45:43 +0000 (Wed, 15 Jun 2011) Log Message: ----------- version=12.0.46_dev # bug fix: UFF full listing (set loglevel 6;minimize steps 0;show minimization) missing n and cosNphi0 in torsions Modified Paths: -------------- branches/v12_0/Jmol/src/org/jmol/minimize/forcefield/CalculationsUFF.java branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v12_0/Jmol/src/org/jmol/minimize/forcefield/CalculationsUFF.java =================================================================== --- branches/v12_0/Jmol/src/org/jmol/minimize/forcefield/CalculationsUFF.java 2011-06-15 13:04:04 UTC (rev 15591) +++ branches/v12_0/Jmol/src/org/jmol/minimize/forcefield/CalculationsUFF.java 2011-06-15 22:45:43 UTC (rev 15592) @@ -985,9 +985,9 @@ case CALC_TORSION: return "\nT O R S I O N A L (" + torsions.length + " torsions)\n\n" - +" ATOMS ATOM TYPES FORCE TORSION\n" - +" I J K L I J K L CONSTANT ANGLE ENERGY\n" - +"----------------------------------------------------------------------------"; + +" ATOMS ATOM TYPES n COS FORCE TORSION\n" + +" I J K L I J K L (n phi0) CONSTANT ANGLE ENERGY\n" + +"---------------------------------------------------------------------------------------------"; case CALC_OOP: return "\nO U T - O F - P L A N E B E N D I N G\n\n" @@ -1030,14 +1030,14 @@ new int[] { atoms[c.ia].atom.getAtomNumber(), atoms[c.ib].atom.getAtomNumber(), atoms[c.ic].atom.getAtomNumber()} }); case CALC_TORSION: - return TextFormat.sprintf( - "%3d %3d %3d %3d %-5s %-5s %-5s %-5s %8.3f %8.3f %8.3f", - new Object[] { atoms[c.ia].type, atoms[c.ib].type, - atoms[c.ic].type, atoms[c.id].type, - new float[] { (float) c.dData[0]/*V*/, - (float) (c.theta * RAD_TO_DEG), (float) c.energy }, - new int[] { atoms[c.ia].atom.getAtomNumber(), atoms[c.ib].atom.getAtomNumber(), - atoms[c.ic].atom.getAtomNumber(), atoms[c.id].atom.getAtomNumber() } }); + return TextFormat.sprintf( + "%3d %3d %3d %3d %-5s %-5s %-5s %-5s %3d %8.3f %8.3f %8.3f %8.3f", + new Object[] { atoms[c.ia].type, atoms[c.ib].type, + atoms[c.ic].type, atoms[c.id].type, + new float[] { (float) c.dData[1]/*cosNphi0*/, (float) c.dData[0]/*V*/, + (float) (c.theta * RAD_TO_DEG), (float) c.energy }, + new int[] { atoms[c.ia].atom.getAtomNumber(), atoms[c.ib].atom.getAtomNumber(), + atoms[c.ic].atom.getAtomNumber(), atoms[c.id].atom.getAtomNumber(), c.iData[4] } }); case CALC_OOP: return TextFormat.sprintf("" + "%3d %3d %3d %3d %-5s %-5s %-5s %-5s %8.3f %8.3f %8.3f", Modified: branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties 2011-06-15 13:04:04 UTC (rev 15591) +++ branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties 2011-06-15 22:45:43 UTC (rev 15592) @@ -4,6 +4,7 @@ version=12.0.46_dev +# bug fix: UFF full listing (set loglevel 6;minimize steps 0;show minimization) missing n and cosNphi0 in torsions # bug fix: PQR reader mistaking " HD3" as deuterium # -------------------------------------------------------------- This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-06-20 11:10:45
|
Revision: 15631 http://jmol.svn.sourceforge.net/jmol/?rev=15631&view=rev Author: hansonr Date: 2011-06-20 11:10:38 +0000 (Mon, 20 Jun 2011) Log Message: ----------- version=12.0.46_dev # bug fix: throwing script parsing error on correct "isosurface slab within [4 elements # representing the slab box]" (was losing last "]"). Modified Paths: -------------- branches/v12_0/Jmol/src/org/jmol/script/ScriptEvaluator.java branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v12_0/Jmol/src/org/jmol/script/ScriptEvaluator.java =================================================================== --- branches/v12_0/Jmol/src/org/jmol/script/ScriptEvaluator.java 2011-06-19 21:36:09 UTC (rev 15630) +++ branches/v12_0/Jmol/src/org/jmol/script/ScriptEvaluator.java 2011-06-20 11:10:38 UTC (rev 15631) @@ -4198,15 +4198,18 @@ i++; break; default: + if (nPoints >= 0 && n == nPoints) { + tok = Token.nada; + break; + } Point3f pt = getPoint3f(i, true); - if (points == null) + if (points == null) vp.add(pt); else - points[n++] = pt; + points[n] = pt; + n++; i = iToken + 1; } - if (n == nPoints) - break; } if (tok != Token.rightsquare) error(ERROR_invalidArgument); Modified: branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties 2011-06-19 21:36:09 UTC (rev 15630) +++ branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties 2011-06-20 11:10:38 UTC (rev 15631) @@ -4,6 +4,8 @@ version=12.0.46_dev +# bug fix: throwing script parsing error on correct "isosurface slab within [4 elements +# representing the slab box]" (was losing last "]"). # bug fix: (application) Jmol console not receiving echo messages # bug fix: UFF full listing (set loglevel 6;minimize steps 0;show minimization) missing n and cosNphi0 in torsions # bug fix: PQR reader mistaking " HD3" as deuterium This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-06-22 14:46:05
|
Revision: 15635 http://jmol.svn.sourceforge.net/jmol/?rev=15635&view=rev Author: hansonr Date: 2011-06-22 14:45:54 +0000 (Wed, 22 Jun 2011) Log Message: ----------- version=12.0.46_dev # bug fix: WebMO reader fails to read HOMO/LUMO business. Modified Paths: -------------- branches/v12_0/Jmol/src/org/jmol/adapter/readers/quantum/WebMOReader.java branches/v12_0/Jmol/src/org/jmol/script/ScriptEvaluator.java branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v12_0/Jmol/src/org/jmol/adapter/readers/quantum/WebMOReader.java =================================================================== --- branches/v12_0/Jmol/src/org/jmol/adapter/readers/quantum/WebMOReader.java 2011-06-22 14:45:18 UTC (rev 15634) +++ branches/v12_0/Jmol/src/org/jmol/adapter/readers/quantum/WebMOReader.java 2011-06-22 14:45:54 UTC (rev 15635) @@ -342,5 +342,7 @@ mo.put("coefficients", coefs); orbitals.add(mo); nOrbitals++; + if (occupancy > 0) + moData.put("HOMO", Integer.valueOf(nOrbitals)); } } Modified: branches/v12_0/Jmol/src/org/jmol/script/ScriptEvaluator.java =================================================================== --- branches/v12_0/Jmol/src/org/jmol/script/ScriptEvaluator.java 2011-06-22 14:45:18 UTC (rev 15634) +++ branches/v12_0/Jmol/src/org/jmol/script/ScriptEvaluator.java 2011-06-22 14:45:54 UTC (rev 15635) @@ -15000,7 +15000,7 @@ if (f.floatValue() > 0) { // go for HOMO = highest non-negative moNumber = i; - break; + continue; } } if (moNumber < 0) Modified: branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties 2011-06-22 14:45:18 UTC (rev 15634) +++ branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties 2011-06-22 14:45:54 UTC (rev 15635) @@ -4,6 +4,7 @@ version=12.0.46_dev +# bug fix: WebMO reader fails to read HOMO/LUMO business. # bug fix: throwing script parsing error on correct "isosurface slab within [4 elements # representing the slab box]" (was losing last "]"). # bug fix: (application) Jmol console not receiving echo messages This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-07-03 17:18:50
|
Revision: 15710 http://jmol.svn.sourceforge.net/jmol/?rev=15710&view=rev Author: hansonr Date: 2011-07-03 17:18:43 +0000 (Sun, 03 Jul 2011) Log Message: ----------- version=12.0.47_dev # bug fix: draw pointgroup fixed to first model Modified Paths: -------------- branches/v12_0/Jmol/src/org/jmol/symmetry/PointGroup.java branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v12_0/Jmol/src/org/jmol/symmetry/PointGroup.java =================================================================== --- branches/v12_0/Jmol/src/org/jmol/symmetry/PointGroup.java 2011-07-03 16:46:40 UTC (rev 15709) +++ branches/v12_0/Jmol/src/org/jmol/symmetry/PointGroup.java 2011-07-03 17:18:43 UTC (rev 15710) @@ -163,7 +163,7 @@ return false; if (this.linearTolerance != pg.linearTolerance || this.distanceTolerance != pg.distanceTolerance - || this.nAtoms != pg.nAtoms || this.bsAtoms.equals(pg.bsAtoms)) + || this.nAtoms != pg.nAtoms || !this.bsAtoms.equals(pg.bsAtoms)) return false; for (int i = 0; i < nAtoms; i++) { // real floating == 0 here because they must be IDENTICAL POSITIONS Modified: branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties 2011-07-03 16:46:40 UTC (rev 15709) +++ branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties 2011-07-03 17:18:43 UTC (rev 15710) @@ -4,6 +4,8 @@ version=12.0.47_dev +# bug fix: draw pointgroup fixed to first model + # -------------------------------------------------------------- #version=12.0.46 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-07-09 00:55:21
|
Revision: 15753 http://jmol.svn.sourceforge.net/jmol/?rev=15753&view=rev Author: hansonr Date: 2011-07-09 00:55:15 +0000 (Sat, 09 Jul 2011) Log Message: ----------- version=12.0.48_dev # bug fix: set fontScaling does not scale offset with font Modified Paths: -------------- branches/v12_0/Jmol/src/org/jmol/shape/Text.java branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v12_0/Jmol/src/org/jmol/shape/Text.java =================================================================== --- branches/v12_0/Jmol/src/org/jmol/shape/Text.java 2011-07-09 00:50:08 UTC (rev 15752) +++ branches/v12_0/Jmol/src/org/jmol/shape/Text.java 2011-07-09 00:55:15 UTC (rev 15753) @@ -192,8 +192,8 @@ if (isLabelOrHover) { boxXY[0] = movableX; boxXY[1] = movableY; - setBoxXY(boxWidth, boxHeight, offsetX * imageFontScaling, offsetY - * imageFontScaling, boxXY, isExact); + setBoxXY(boxWidth, boxHeight, offsetX * imageFontScaling * fontScale, offsetY + * imageFontScaling * fontScale, boxXY, isExact); } else { setPosition(fontScale); } Modified: branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties 2011-07-09 00:50:08 UTC (rev 15752) +++ branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties 2011-07-09 00:55:15 UTC (rev 15753) @@ -4,6 +4,7 @@ version=12.0.48_dev +# bug fix: set fontScaling does not scale offset with font # bug fix: application Help menu item no long pushed right. # -------------------------------------------------------------- This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-07-13 18:39:50
|
Revision: 15764 http://jmol.svn.sourceforge.net/jmol/?rev=15764&view=rev Author: hansonr Date: 2011-07-13 18:39:43 +0000 (Wed, 13 Jul 2011) Log Message: ----------- version=12.0.48_dev # bug fix: CML files with atoms starting with both aNN and aNN_ will not bond correctly Modified Paths: -------------- branches/v12_0/Jmol/src/org/jmol/adapter/readers/xml/XmlCmlReader.java branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v12_0/Jmol/src/org/jmol/adapter/readers/xml/XmlCmlReader.java =================================================================== --- branches/v12_0/Jmol/src/org/jmol/adapter/readers/xml/XmlCmlReader.java 2011-07-12 11:38:20 UTC (rev 15763) +++ branches/v12_0/Jmol/src/org/jmol/adapter/readers/xml/XmlCmlReader.java 2011-07-13 18:39:43 UTC (rev 15764) @@ -236,6 +236,9 @@ break; case CRYSTAL: if (name.equals("scalar")) { + // we force this to be NOT serialized by number, because we might have a1 and a1_.... + checkedSerial = true; + isSerial = false; state = CRYSTAL_SCALAR; setKeepChars(true); scalarTitle = (String) atts.get("title"); Modified: branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties 2011-07-12 11:38:20 UTC (rev 15763) +++ branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties 2011-07-13 18:39:43 UTC (rev 15764) @@ -4,6 +4,7 @@ version=12.0.48_dev +# bug fix: CML files with atoms starting with both aNN and aNN_ will not bond correctly # bug fix: set fontScaling does not scale offset with font # bug fix: application Help menu item no long pushed right. This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-07-20 13:12:55
|
Revision: 15790 http://jmol.svn.sourceforge.net/jmol/?rev=15790&view=rev Author: hansonr Date: 2011-07-20 13:12:49 +0000 (Wed, 20 Jul 2011) Log Message: ----------- version=12.0.48_dev # bug fix: catch(err) not setting variable "err" Modified Paths: -------------- branches/v12_0/Jmol/src/org/jmol/script/ScriptEvaluator.java branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v12_0/Jmol/src/org/jmol/script/ScriptEvaluator.java =================================================================== --- branches/v12_0/Jmol/src/org/jmol/script/ScriptEvaluator.java 2011-07-19 03:26:18 UTC (rev 15789) +++ branches/v12_0/Jmol/src/org/jmol/script/ScriptEvaluator.java 2011-07-20 13:12:49 UTC (rev 15790) @@ -5567,9 +5567,13 @@ boolean isDone = (pt < 0 && !isSyntaxCheck); boolean isOK = true; int ptNext = 0; + ContextToken ct; switch (tok) { case Token.catchcmd: - pushContext((ContextToken) theToken); + ct = (ContextToken) theToken; + pushContext(ct); + if (!isDone && ct.name0 != null) + contextVariables.put(ct.name0, ct.contextVariables.get(ct.name0)); isOK = !isDone; break; case Token.process: @@ -5720,7 +5724,7 @@ // 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 = (ContextToken) aatoken[pc + 1][0]; if (ct.contextVariables != null) ct.contextVariables.put(ct.name0, ScriptVariable .getVariable(errMsg)); Modified: branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties 2011-07-19 03:26:18 UTC (rev 15789) +++ branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties 2011-07-20 13:12:49 UTC (rev 15790) @@ -4,6 +4,7 @@ version=12.0.48_dev +# bug fix: catch(err) not setting variable "err" # bug fix: CML files with atoms starting with both aNN and aNN_ will not bond correctly # bug fix: set fontScaling does not scale offset with font # bug fix: application Help menu item no long pushed right. This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-07-20 16:35:31
|
Revision: 15797 http://jmol.svn.sourceforge.net/jmol/?rev=15797&view=rev Author: hansonr Date: 2011-07-20 16:35:25 +0000 (Wed, 20 Jul 2011) Log Message: ----------- version=12.0.48 # bug fix: try {} does not pass VAR variables into its context. Modified Paths: -------------- branches/v12_0/Jmol/src/org/jmol/script/ScriptEvaluator.java branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v12_0/Jmol/src/org/jmol/script/ScriptEvaluator.java =================================================================== --- branches/v12_0/Jmol/src/org/jmol/script/ScriptEvaluator.java 2011-07-20 16:34:51 UTC (rev 15796) +++ branches/v12_0/Jmol/src/org/jmol/script/ScriptEvaluator.java 2011-07-20 16:35:25 UTC (rev 15797) @@ -1926,8 +1926,6 @@ ScriptVariable runFunction(ScriptFunction function, String name, List params, Token tokenAtom, boolean getReturn) throws ScriptException { - pushContext(null); - thisContext.isFunction = true; //System.out.println(contextPath); if (function == null) { function = viewer.getFunction(name); @@ -1937,7 +1935,10 @@ } if (function == null) return null; + pushContext(null); functionName = name; + boolean isTry = (function.tok == Token.trycmd); + thisContext.isFunction = !isTry; if (function instanceof ParallelProcessor) { synchronized (function) // can't do this -- too general @@ -1946,7 +1947,6 @@ vProcess = null; runFunction(function, params, tokenAtom); - boolean isTry = (function.tok == Token.trycmd); ScriptContext sc = getScriptContext(); if (isTry) { contextVariables.put("_breakval", ScriptVariable.intVariable(Integer.MAX_VALUE)); Modified: branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties 2011-07-20 16:34:51 UTC (rev 15796) +++ branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties 2011-07-20 16:35:25 UTC (rev 15797) @@ -4,6 +4,7 @@ version=12.0.48 +# bug fix: try {} does not pass VAR variables into its context. # bug fix: catch(err) not setting variable "err" # bug fix: CML files with atoms starting with both aNN and aNN_ will not bond correctly # bug fix: set fontScaling does not scale offset with font This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-07-21 21:02:15
|
Revision: 15812 http://jmol.svn.sourceforge.net/jmol/?rev=15812&view=rev Author: hansonr Date: 2011-07-21 21:02:08 +0000 (Thu, 21 Jul 2011) Log Message: ----------- version=12.0.49_dev # bug fix: isosurface slab -@xxxx... will negate variable xxxx if it is a plane Modified Paths: -------------- branches/v12_0/Jmol/src/org/jmol/script/ScriptEvaluator.java branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v12_0/Jmol/src/org/jmol/script/ScriptEvaluator.java =================================================================== --- branches/v12_0/Jmol/src/org/jmol/script/ScriptEvaluator.java 2011-07-21 15:41:23 UTC (rev 15811) +++ branches/v12_0/Jmol/src/org/jmol/script/ScriptEvaluator.java 2011-07-21 21:02:08 UTC (rev 15812) @@ -4440,7 +4440,7 @@ if (i < statementLength) switch (getToken(i).tok) { case Token.point4f: - plane = (Point4f) theToken.value; + plane = new Point4f((Point4f) theToken.value); break; case Token.dollarsign: String id = objectNameParameter(++i); Modified: branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties 2011-07-21 15:41:23 UTC (rev 15811) +++ branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties 2011-07-21 21:02:08 UTC (rev 15812) @@ -4,6 +4,8 @@ version=12.0.49_dev +# bug fix: isosurface slab -@xxxx... will negate variable xxxx if it is a plane + # -------------------------------------------------------------- #version=12.0.48 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-07-22 16:50:24
|
Revision: 15815 http://jmol.svn.sourceforge.net/jmol/?rev=15815&view=rev Author: hansonr Date: 2011-07-22 16:50:18 +0000 (Fri, 22 Jul 2011) Log Message: ----------- version=12.0.49_dev # bug fix: PDB reader may read bfactors off by 0.01 Modified Paths: -------------- branches/v12_0/Jmol/src/org/jmol/modelset/AtomCollection.java branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v12_0/Jmol/src/org/jmol/modelset/AtomCollection.java =================================================================== --- branches/v12_0/Jmol/src/org/jmol/modelset/AtomCollection.java 2011-07-22 16:23:12 UTC (rev 15814) +++ branches/v12_0/Jmol/src/org/jmol/modelset/AtomCollection.java 2011-07-22 16:50:18 UTC (rev 15815) @@ -752,7 +752,7 @@ bfactor100s = new short[atoms.length]; } bfactor100s[atomIndex] = (short) ((bfactor < -327.68f ? -327.68f - : bfactor > 327.67 ? 327.67 : bfactor) * 100); + : bfactor > 327.67 ? 327.67 : bfactor) * 100 + (bfactor < 0 ? -0.5 : 0.5)); return true; } Modified: branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties 2011-07-22 16:23:12 UTC (rev 15814) +++ branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties 2011-07-22 16:50:18 UTC (rev 15815) @@ -4,6 +4,7 @@ version=12.0.49_dev +# bug fix: PDB reader may read bfactors off by 0.01 # bug fix: isosurface slab -@xxxx... will negate variable xxxx if it is a plane # -------------------------------------------------------------- This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-07-27 14:04:54
|
Revision: 15862 http://jmol.svn.sourceforge.net/jmol/?rev=15862&view=rev Author: hansonr Date: 2011-07-27 14:04:48 +0000 (Wed, 27 Jul 2011) Log Message: ----------- version=12.0.49_dev # bug fix: zap of model with measurements causes exception Modified Paths: -------------- branches/v12_0/Jmol/src/org/jmol/modelset/Measurement.java branches/v12_0/Jmol/src/org/jmol/shape/Measures.java branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v12_0/Jmol/src/org/jmol/modelset/Measurement.java =================================================================== --- branches/v12_0/Jmol/src/org/jmol/modelset/Measurement.java 2011-07-27 14:04:21 UTC (rev 15861) +++ branches/v12_0/Jmol/src/org/jmol/modelset/Measurement.java 2011-07-27 14:04:48 UTC (rev 15862) @@ -379,10 +379,10 @@ return sameAs(countPlusIndices, pts, i, j); } - public List toVector() { + public List toVector(boolean asBitSet) { List V = new ArrayList(); for (int i = 1; i <= count; i++ ) - V.add(getLabel(i, false, false)); + V.add(getLabel(i, asBitSet, false)); V.add(strMeasurement); return V; } Modified: branches/v12_0/Jmol/src/org/jmol/shape/Measures.java =================================================================== --- branches/v12_0/Jmol/src/org/jmol/shape/Measures.java 2011-07-27 14:04:21 UTC (rev 15861) +++ branches/v12_0/Jmol/src/org/jmol/shape/Measures.java 2011-07-27 14:04:48 UTC (rev 15862) @@ -479,11 +479,11 @@ strFormat, measurementCount); measurements.add(measureNew); viewer.setStatusMeasuring("measureCompleted", measurementCount++, - measureNew.toVector().toString(), measureNew.getValue()); + measureNew.toVector(false).toString(), measureNew.getValue()); } private void deleteMeasurement(int i) { - String msg = ((Measurement) measurements.get(i)).toVector().toString(); + String msg = ((Measurement) measurements.get(i)).toVector(true).toString(); measurements.remove(i); measurementCount--; viewer.setStatusMeasuring("measureDeleted", i, msg, 0); @@ -495,7 +495,7 @@ return; if (measurementPending.getCount() > 1) viewer.setStatusMeasuring("measurePending", - measurementPending.getCount(), measurementPending.toVector().toString(), measurementPending.getValue()); + measurementPending.getCount(), measurementPending.toVector(false).toString(), measurementPending.getValue()); } private void reformatDistances() { Modified: branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties 2011-07-27 14:04:21 UTC (rev 15861) +++ branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties 2011-07-27 14:04:48 UTC (rev 15862) @@ -4,6 +4,7 @@ version=12.0.49_dev +# bug fix: zap of model with measurements causes exception # bug fix: PDB reader may read bfactors off by 0.01 # bug fix: isosurface slab -@xxxx... will negate variable xxxx if it is a plane This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-07-28 04:26:45
|
Revision: 15867 http://jmol.svn.sourceforge.net/jmol/?rev=15867&view=rev Author: hansonr Date: 2011-07-28 04:26:38 +0000 (Thu, 28 Jul 2011) Log Message: ----------- version=12.0.49_dev # bug fix: ++ipt; not working Modified Paths: -------------- branches/v12_0/Jmol/src/org/jmol/script/ScriptCompiler.java branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v12_0/Jmol/src/org/jmol/script/ScriptCompiler.java =================================================================== --- branches/v12_0/Jmol/src/org/jmol/script/ScriptCompiler.java 2011-07-28 01:07:51 UTC (rev 15866) +++ branches/v12_0/Jmol/src/org/jmol/script/ScriptCompiler.java 2011-07-28 04:26:38 UTC (rev 15867) @@ -323,6 +323,7 @@ tokCommand = Token.nada; lastFlowCommand = null; tokenAndEquals = null; + tokInitialPlusPlus = Token.nada; setBraceCount = 0; bracketCount = 0; forPoint3 = -1; @@ -619,6 +620,11 @@ } else if (setBraceCount > 0 && endOfLine && ichToken < cchScript) { return CONTINUE; } + if (tokInitialPlusPlus != Token.nada) { + if (!isNewSet) + checkNewSetCommand(); + tokenizePlusPlus(tokInitialPlusPlus, true); + } // end of command or comment iCommand = lltoken.size(); if (thisFunction != null && thisFunction.cmdpt0 < 0) { @@ -700,6 +706,7 @@ ltoken.clear(); nTokens = nSemiSkip = 0; tokenAndEquals = null; + tokInitialPlusPlus = Token.nada; ptSemi = -10; forPoint3 = -1; setEqualPt = Integer.MAX_VALUE; @@ -815,6 +822,7 @@ } private boolean isUserToken; + private int tokInitialPlusPlus; private String getPrefixToken() { String ident = script.substring(ichToken, ichToken + cchToken); @@ -1244,13 +1252,7 @@ if (!isNewSet && nTokens == 1) checkNewSetCommand(); if (isNewSet && parenCount == 0 && bracketCount == 0 && ichToken <= setEqualPt) { - nTokens = ltoken.size(); - addTokenToPrefix(Token.tokenEquals); - setEqualPt = 0; - for (int i = 1; i < nTokens; i++) - addTokenToPrefix((Token)ltoken.get(i)); - addTokenToPrefix(theTok == Token.minusMinus ? Token.tokenMinus : Token.tokenPlus); - addTokenToPrefix(Token.intToken(1)); + tokenizePlusPlus(theTok, false); return CONTINUE; } else if (nSemiSkip == forPoint3 && nTokens == ptSemi + 2) { token = lastToken; @@ -1335,6 +1337,22 @@ return OK; } + private void tokenizePlusPlus(int tok, boolean isPlusPlusX) { + // ++ipt; or ipt++ + if (isPlusPlusX) { + setCommand(Token.tokenSet); + ltoken.add(0, tokenCommand); + } + nTokens = ltoken.size(); + addTokenToPrefix(Token.tokenEquals); + setEqualPt = 0; + for (int i = 1; i < nTokens; i++) + addTokenToPrefix((Token) ltoken.get(i)); + addTokenToPrefix(tok == Token.minusMinus ? Token.tokenMinus + : Token.tokenPlus); + addTokenToPrefix(Token.intToken(1)); + } + private boolean checkNewSetCommand() { String name = ((Token) ltoken.get(0)).value.toString(); if (!isContextVariable(name.toLowerCase())) @@ -1421,6 +1439,9 @@ switch (theTok) { case Token.plusPlus: case Token.minusMinus: + tokInitialPlusPlus = theTok; + tokCommand = Token.nada; + return CONTINUE; case Token.identifier: case Token.var: case Token.define: @@ -1692,7 +1713,7 @@ bracketCount = 0; setEqualPt = Integer.MAX_VALUE; ptNewSetModifier = (isNewSet ? 1 : Integer.MAX_VALUE); - return (isSetBrace ? theToken : new Token(Token.identifier, ident)); + return ((isSetBrace || theToken.tok == Token.plusPlus || theToken.tok == Token.minusMinus)? theToken : new Token(Token.identifier, ident)); } private char nextChar() { Modified: branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties 2011-07-28 01:07:51 UTC (rev 15866) +++ branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties 2011-07-28 04:26:38 UTC (rev 15867) @@ -4,6 +4,7 @@ version=12.0.49_dev +# bug fix: ++ipt; not working # bug fix: zap of model with measurements causes exception # bug fix: PDB reader may read bfactors off by 0.01 # bug fix: isosurface slab -@xxxx... will negate variable xxxx if it is a plane This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-07-28 15:13:43
|
Revision: 15869 http://jmol.svn.sourceforge.net/jmol/?rev=15869&view=rev Author: hansonr Date: 2011-07-28 15:13:35 +0000 (Thu, 28 Jul 2011) Log Message: ----------- version=12.0.49_dev # bug fix: isosurface parameters @x does not work even when x is an array Modified Paths: -------------- branches/v12_0/Jmol/src/org/jmol/script/ScriptEvaluator.java branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v12_0/Jmol/src/org/jmol/script/ScriptEvaluator.java =================================================================== --- branches/v12_0/Jmol/src/org/jmol/script/ScriptEvaluator.java 2011-07-28 14:49:33 UTC (rev 15868) +++ branches/v12_0/Jmol/src/org/jmol/script/ScriptEvaluator.java 2011-07-28 15:13:35 UTC (rev 15869) @@ -4111,7 +4111,7 @@ n = fparams.length; break; case Token.varray: - fparams = ScriptVariable.flistValue(statement[i], 0); + fparams = ScriptVariable.flistValue(statement[i++], 0); n = fparams.length; break; default: Modified: branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties 2011-07-28 14:49:33 UTC (rev 15868) +++ branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties 2011-07-28 15:13:35 UTC (rev 15869) @@ -4,6 +4,7 @@ version=12.0.49_dev +# bug fix: isosurface parameters @x does not work even when x is an array # bug fix: ++ipt; not working # bug fix: zap of model with measurements causes exception # bug fix: PDB reader may read bfactors off by 0.01 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-07-30 12:12:03
|
Revision: 15884 http://jmol.svn.sourceforge.net/jmol/?rev=15884&view=rev Author: hansonr Date: 2011-07-30 12:11:56 +0000 (Sat, 30 Jul 2011) Log Message: ----------- version=12.0.49_dev # bug fix: select DEUTERIUM does not select deuterium Modified Paths: -------------- branches/v12_0/Jmol/src/org/jmol/modelset/Atom.java branches/v12_0/Jmol/src/org/jmol/script/ScriptEvaluator.java branches/v12_0/Jmol/src/org/jmol/script/Token.java branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v12_0/Jmol/src/org/jmol/modelset/Atom.java =================================================================== --- branches/v12_0/Jmol/src/org/jmol/modelset/Atom.java 2011-07-30 10:26:02 UTC (rev 15883) +++ branches/v12_0/Jmol/src/org/jmol/modelset/Atom.java 2011-07-30 12:11:56 UTC (rev 15884) @@ -1139,6 +1139,8 @@ case Token.element: case Token.elemno: return atom.getElementNumber(); + case Token.elemisono: + return atom.atomicAndIsotopeNumber; case Token.file: return atom.getModelFileIndex() + 1; case Token.formalcharge: Modified: branches/v12_0/Jmol/src/org/jmol/script/ScriptEvaluator.java =================================================================== --- branches/v12_0/Jmol/src/org/jmol/script/ScriptEvaluator.java 2011-07-30 10:26:02 UTC (rev 15883) +++ branches/v12_0/Jmol/src/org/jmol/script/ScriptEvaluator.java 2011-07-30 12:11:56 UTC (rev 15884) @@ -2035,7 +2035,7 @@ // _T ==> _isotope=iinn for each isotope // _3H ==> _isotope=iinn for each isotope for (int i = Elements.altElementMax; --i >= firstIsotope;) { - String def = " element=" + Elements.altElementNumberFromIndex(i); + String def = " _e=" + Elements.altElementNumberFromIndex(i); String definition = "@_" + Elements.altElementSymbolFromIndex(i); defineAtomSet(definition + def); definition = "@_" + Elements.altIsotopeSymbolFromIndex(i); Modified: branches/v12_0/Jmol/src/org/jmol/script/Token.java =================================================================== --- branches/v12_0/Jmol/src/org/jmol/script/Token.java 2011-07-30 10:26:02 UTC (rev 15883) +++ branches/v12_0/Jmol/src/org/jmol/script/Token.java 2011-07-30 12:11:56 UTC (rev 15884) @@ -566,6 +566,7 @@ public final static int cell = intproperty | 5; public final static int configuration = intproperty | 6 | scriptCommand; public final static int color = intproperty | 7 | scriptCommand | deprecatedparam | settable; + public final static int elemisono = intproperty | 8; // not advisable, but ok, since elemno is 'settable' public final static int elemno = intproperty | 8 | settable; //file: see xxx(a) public final static int formalcharge = intproperty | 9 | setparam | settable; @@ -1717,7 +1718,7 @@ "DSSP", new Token(dssp), "element", new Token(element), "elemno", new Token(elemno), - "_e", null, + "_e", new Token(elemisono), "error", new Token(error), "fill", new Token(fill), "find", new Token(find), Modified: branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties 2011-07-30 10:26:02 UTC (rev 15883) +++ branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties 2011-07-30 12:11:56 UTC (rev 15884) @@ -4,6 +4,7 @@ version=12.0.49_dev +# bug fix: select DEUTERIUM does not select deuterium # bug fix: isosurface parameters @x does not work even when x is an array # bug fix: ++ipt; not working # bug fix: zap of model with measurements causes exception This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-07-30 13:57:32
|
Revision: 15886 http://jmol.svn.sourceforge.net/jmol/?rev=15886&view=rev Author: hansonr Date: 2011-07-30 13:57:25 +0000 (Sat, 30 Jul 2011) Log Message: ----------- version=12.0.49_dev # bug fix: select deuterium, HOH, _1H, _H1 isotope business messed up Modified Paths: -------------- branches/v12_0/Jmol/src/org/jmol/modelset/Atom.java branches/v12_0/Jmol/src/org/jmol/popup/JmolPopup.java branches/v12_0/Jmol/src/org/jmol/script/ScriptEvaluator.java branches/v12_0/Jmol/src/org/jmol/util/Elements.java branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties branches/v12_0/Jmol/src/org/jmol/viewer/JmolConstants.java Modified: branches/v12_0/Jmol/src/org/jmol/modelset/Atom.java =================================================================== --- branches/v12_0/Jmol/src/org/jmol/modelset/Atom.java 2011-07-30 13:57:00 UTC (rev 15885) +++ branches/v12_0/Jmol/src/org/jmol/modelset/Atom.java 2011-07-30 13:57:25 UTC (rev 15886) @@ -307,11 +307,11 @@ } public short getElementNumber() { - return (short) (atomicAndIsotopeNumber % 128); + return Elements.getElementNumber(atomicAndIsotopeNumber); } public short getIsotopeNumber() { - return (short) (atomicAndIsotopeNumber >> 7); + return Elements.getIsotopeNumber(atomicAndIsotopeNumber); } public short getAtomicAndIsotopeNumber() { Modified: branches/v12_0/Jmol/src/org/jmol/popup/JmolPopup.java =================================================================== --- branches/v12_0/Jmol/src/org/jmol/popup/JmolPopup.java 2011-07-30 13:57:00 UTC (rev 15885) +++ branches/v12_0/Jmol/src/org/jmol/popup/JmolPopup.java 2011-07-30 13:57:25 UTC (rev 15886) @@ -169,7 +169,7 @@ String entryName = elementSymbol + " - " + elementName; addMenuItem(menu, entryName, "SELECT " + elementName, null); } - for (int i = JmolConstants.firstIsotope; i < Elements.altElementMax; ++i) { + for (int i = Elements.firstIsotope; i < Elements.altElementMax; ++i) { int n = Elements.elementNumberMax + i; if (elementsPresentBitSet.get(n)) { n = Elements.altElementNumberFromIndex(i); Modified: branches/v12_0/Jmol/src/org/jmol/script/ScriptEvaluator.java =================================================================== --- branches/v12_0/Jmol/src/org/jmol/script/ScriptEvaluator.java 2011-07-30 13:57:00 UTC (rev 15885) +++ branches/v12_0/Jmol/src/org/jmol/script/ScriptEvaluator.java 2011-07-30 13:57:25 UTC (rev 15886) @@ -2010,22 +2010,17 @@ for (int i = 0; i < JmolConstants.predefinedVariable.length; i++) defineAtomSet(JmolConstants.predefinedVariable[i]); // Now, define all the elements as predefined sets - // hydrogen is handled specially, so don't define it - int firstIsotope = JmolConstants.firstIsotope; - // name ==> e_=n for all standard elements + // name ==> elemno=n for all standard elements, isotope-blind + // _Xx ==> elemno=n for of all elements, isotope-blind for (int i = Elements.elementNumberMax; --i >= 0;) { - String definition = "@" + Elements.elementNameFromNumber(i) + " _e=" + i; - defineAtomSet(definition); + String definition = " elemno=" + i; + defineAtomSet("@" + Elements.elementNameFromNumber(i) + definition); + defineAtomSet("@_" + Elements.elementSymbolFromNumber(i) + definition); } - // _Xx ==> name for of all elements, isotope-blind - for (int i = Elements.elementNumberMax; --i >= 0;) { - String definition = "@_" + Elements.elementSymbolFromNumber(i) + " " - + Elements.elementNameFromNumber(i); - defineAtomSet(definition); - } + // name ==> _e=nn for each alternative element - for (int i = firstIsotope; --i >= 0;) { + for (int i = Elements.firstIsotope; --i >= 0;) { String definition = "@" + Elements.altElementNameFromIndex(i) + " _e=" + Elements.altElementNumberFromIndex(i); defineAtomSet(definition); @@ -2034,15 +2029,30 @@ // name ==> _isotope=iinn for each isotope // _T ==> _isotope=iinn for each isotope // _3H ==> _isotope=iinn for each isotope - for (int i = Elements.altElementMax; --i >= firstIsotope;) { - String def = " _e=" + Elements.altElementNumberFromIndex(i); + for (int i = Elements.altElementMax; --i >= Elements.firstIsotope;) { + short ei = Elements.altElementNumberFromIndex(i); + String def = " _e=" + ei; String definition = "@_" + Elements.altElementSymbolFromIndex(i); defineAtomSet(definition + def); + definition = "@_" + Elements.altIsotopeSymbolFromIndex(i); defineAtomSet(definition + def); + definition = "@_" + Elements.altIsotopeSymbolFromIndex2(i); + defineAtomSet(definition + def); + definition = "@" + Elements.altElementNameFromIndex(i); if (definition.length() > 1) defineAtomSet(definition + def); + + // @_12C _e=6 + // @_C12 _e=6 + short e = Elements.getElementNumber(ei); + ei = (short) Elements.getNaturalIsotope(e); + if (ei > 0) { + def = Elements.elementSymbolFromNumber(e); + defineAtomSet("@_" + def + ei + " _e=" + e); + defineAtomSet("@_" + ei + def + " _e=" + e); + } } defineAtomSet("# variable"); } @@ -7352,7 +7362,7 @@ return true; } } - for (int i = Elements.altElementMax; --i >= JmolConstants.firstIsotope;) { + for (int i = Elements.altElementMax; --i >= Elements.firstIsotope;) { if (str.equalsIgnoreCase("_" + Elements.altElementSymbolFromIndex(i))) { if (!isSyntaxCheck) viewer.setElementArgb(Elements.altElementNumberFromIndex(i), argb); Modified: branches/v12_0/Jmol/src/org/jmol/util/Elements.java =================================================================== --- branches/v12_0/Jmol/src/org/jmol/util/Elements.java 2011-07-30 13:57:00 UTC (rev 15885) +++ branches/v12_0/Jmol/src/org/jmol/util/Elements.java 2011-07-30 13:57:25 UTC (rev 15886) @@ -26,7 +26,6 @@ import java.util.Hashtable; -import org.jmol.viewer.JmolConstants; public class Elements { @@ -178,7 +177,7 @@ if (symbol.length() == 2) map.put(symbol.toUpperCase(), boxed); } - for (int i = Elements.altElementMax; --i >= JmolConstants.firstIsotope;) { + for (int i = Elements.altElementMax; --i >= Elements.firstIsotope;) { String symbol = Elements.altElementSymbols[i]; Integer boxed = new Integer(Elements.altElementNumbers[i]); map.put(symbol, boxed); @@ -376,6 +375,23 @@ return (code >> 7) + elementSymbolFromNumber(code & 127); } + /** + * @param i index into altElementSymbols + * @return H2 + */ + public final static String altIsotopeSymbolFromIndex2(int i) { + int code = Elements.altElementNumbers[i]; + return elementSymbolFromNumber(code & 127) + (code >> 7); + } + + public final static short getElementNumber(short atomicAndIsotopeNumber) { + return (short) (atomicAndIsotopeNumber % 128); + } + + public final static short getIsotopeNumber(short atomicAndIsotopeNumber) { + return (short) (atomicAndIsotopeNumber >> 7); + } + public final static short getAtomicAndIsotopeNumber(int n, int mass) { return (short) ((n < 0 ? 0 : n) + (mass <= 0 ? 0 : mass << 7)); } @@ -455,5 +471,11 @@ "", "", }; + + + /** + * first entry of an actual isotope int the altElementSymbols, altElementNames, altElementNumbers arrays + */ + public final static int firstIsotope = 4; } Modified: branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties 2011-07-30 13:57:00 UTC (rev 15885) +++ branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties 2011-07-30 13:57:25 UTC (rev 15886) @@ -4,7 +4,7 @@ version=12.0.49_dev -# bug fix: select DEUTERIUM does not select deuterium +# bug fix: select deuterium, HOH, _1H, _H1 isotope business messed up # bug fix: isosurface parameters @x does not work even when x is an array # bug fix: ++ipt; not working # bug fix: zap of model with measurements causes exception Modified: branches/v12_0/Jmol/src/org/jmol/viewer/JmolConstants.java =================================================================== --- branches/v12_0/Jmol/src/org/jmol/viewer/JmolConstants.java 2011-07-30 13:57:00 UTC (rev 15885) +++ branches/v12_0/Jmol/src/org/jmol/viewer/JmolConstants.java 2011-07-30 13:57:25 UTC (rev 15886) @@ -471,11 +471,6 @@ }; - /** - * first entry of an actual isotope int the altElementSymbols, altElementNames, altElementNumbers arrays - */ - public final static int firstIsotope = 4; - public final static int VDW_UNKNOWN = -1; public final static int VDW_JMOL = 0; // OpenBabel-1.0 public final static int VDW_BABEL = 1; // OpenBabel-2.2 @@ -2238,8 +2233,7 @@ // solvent // "@water _g>=" + GROUPID_WATER + " & _g<" + (GROUPID_SOLVENTS) - + ", oxygen & connected(2) & connected(2, hydrogen or deuterium or tritium), (hydrogen or deuterium or tritium) & connected(oxygen & connected(2) & connected(2, hydrogen or deuterium or tritium))", - "@hoh water", + + ", oxygen & connected(2) & connected(2, hydrogen), (hydrogen) & connected(oxygen & connected(2) & connected(2, hydrogen))", "@solvent water, (_g>=" + GROUPID_SOLVENTS + " & _g<=" + GROUPID_SULPHATE + ")", // water, other solvent or ions "@ligand hetero & !solvent", This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-08-11 16:36:29
|
Revision: 15963 http://jmol.svn.sourceforge.net/jmol/?rev=15963&view=rev Author: hansonr Date: 2011-08-11 16:36:23 +0000 (Thu, 11 Aug 2011) Log Message: ----------- version=12.0.49_dev # bug fix: CONTINUE in switch within for or while loops infinitely Modified Paths: -------------- branches/v12_0/Jmol/src/org/jmol/script/ScriptCompiler.java branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v12_0/Jmol/src/org/jmol/script/ScriptCompiler.java =================================================================== --- branches/v12_0/Jmol/src/org/jmol/script/ScriptCompiler.java 2011-08-11 16:35:43 UTC (rev 15962) +++ branches/v12_0/Jmol/src/org/jmol/script/ScriptCompiler.java 2011-08-11 16:36:23 UTC (rev 15963) @@ -1869,6 +1869,9 @@ case Token.continuecmd: isNew = false; ScriptFlowContext f = (flowContext == null ? null : flowContext.getBreakableContext(0)); + if (tokCommand == Token.continuecmd) + while (f != null && f.token.tok != Token.forcmd && f.token.tok != Token.whilecmd) + f = f.getParent(); if (f == null) return error(ERROR_badContext, ident); setCommand( new Token(tokCommand, f.pt0, ident)); //copy Modified: branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties 2011-08-11 16:35:43 UTC (rev 15962) +++ branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties 2011-08-11 16:36:23 UTC (rev 15963) @@ -4,6 +4,7 @@ version=12.0.49_dev +# bug fix: CONTINUE in switch within for or while loops infinitely # bug fix: select deuterium, HOH, _1H, _H1 isotope business messed up # bug fix: isosurface parameters @x does not work even when x is an array # bug fix: ++ipt; not working This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-08-17 14:30:10
|
Revision: 15976 http://jmol.svn.sourceforge.net/jmol/?rev=15976&view=rev Author: hansonr Date: 2011-08-17 14:30:01 +0000 (Wed, 17 Aug 2011) Log Message: ----------- version=12.0.49 # bug fix: show colorscheme "high" causes exception # bug fix: CONTINUE in switch within for or while loops infinitely # bug fix: select deuterium, HOH, _1H, _H1 isotope business messed up # bug fix: isosurface parameters @x does not work even when x is an array # bug fix: ++ipt; not working # bug fix: zap of model with measurements causes exception # bug fix: PDB reader may read bfactors off by 0.01 # bug fix: isosurface slab -@xxxx... will negate variable xxxx if it is a plane Modified Paths: -------------- branches/v12_0/Jmol/src/org/jmol/util/ColorEncoder.java branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v12_0/Jmol/src/org/jmol/util/ColorEncoder.java =================================================================== --- branches/v12_0/Jmol/src/org/jmol/util/ColorEncoder.java 2011-08-17 14:27:57 UTC (rev 15975) +++ branches/v12_0/Jmol/src/org/jmol/util/ColorEncoder.java 2011-08-17 14:30:01 UTC (rev 15976) @@ -332,12 +332,12 @@ case BGYOR: return ArrayUtil.arrayCopy(propertyColorEncoder.argbsRoygb, 0, -1, true); case LOW: - return ArrayUtil.arrayCopy(propertyColorEncoder.argbsRoygb, 0, ihalf, false); + return ArrayUtil.arrayCopy(propertyColorEncoder.argbsRoygb, 0, propertyColorEncoder.ihalf, false); case HIGH: - int[] a = ArrayUtil.arrayCopy(argbsRoygb, propertyColorEncoder.argbsRoygb.length - 2 * propertyColorEncoder.ihalf, -1, false); + int[] a = ArrayUtil.arrayCopy(propertyColorEncoder.argbsRoygb, propertyColorEncoder.argbsRoygb.length - 2 * propertyColorEncoder.ihalf, -1, false); b = new int[propertyColorEncoder.ihalf]; - for (int i = propertyColorEncoder.ihalf, j = propertyColorEncoder.argbsRoygb.length - 1; --i >= 0;j -= 2) - b[i] = a[j]; + for (int i = b.length, j = a.length; --i >= 0 && --j >= 0;) + b[i] = a[j--]; return b; case BW: return getPaletteBW(); Modified: branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties 2011-08-17 14:27:57 UTC (rev 15975) +++ branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties 2011-08-17 14:30:01 UTC (rev 15976) @@ -2,8 +2,9 @@ # NOTE: Generally only bug fixes should be entered here. # NOTE: New features should be introduced in the trunk version 12.1.x -version=12.0.49_dev +version=12.0.49 +# bug fix: show colorscheme "high" causes exception # bug fix: CONTINUE in switch within for or while loops infinitely # bug fix: select deuterium, HOH, _1H, _H1 isotope business messed up # bug fix: isosurface parameters @x does not work even when x is an array This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |