From: <ha...@us...> - 2010-10-05 12:19:09
|
Revision: 14401 http://jmol.svn.sourceforge.net/jmol/?rev=14401&view=rev Author: hansonr Date: 2010-10-05 12:19:03 +0000 (Tue, 05 Oct 2010) Log Message: ----------- # new feature: calculate hbonds STRUCTURE (only those that define the DSSP "HGITEB" markings) 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 2010-10-05 12:18:20 UTC (rev 14400) +++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-10-05 12:19:03 UTC (rev 14401) @@ -11007,7 +11007,7 @@ return; } BitSet bs1 = null; - // calculate hbonds STRUCTURE -- only the structurally-defining H bonds + // calculate hbonds STRUCTURE -- only the DSSP structurally-defining H bonds asDSSP = (tokAt(++iToken) == Token.structure); if (asDSSP) bs1 = viewer.getSelectionSet(false); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-10-11 04:13:36
|
Revision: 14464 http://jmol.svn.sourceforge.net/jmol/?rev=14464&view=rev Author: hansonr Date: 2010-10-11 04:13:30 +0000 (Mon, 11 Oct 2010) Log Message: ----------- obitals 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 2010-10-11 04:12:42 UTC (rev 14463) +++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-10-11 04:13:30 UTC (rev 14464) @@ -8448,7 +8448,7 @@ continue; sb.append("\n") .append(((List<Map<String, Object>>) moData.get("mos")).size()) - .append(" molecular obitals in model ") + .append(" molecular orbitals in model ") .append(viewer.getModelNumberDotted(i)); } if (sb.length() > 0) This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-10-28 16:19:52
|
Revision: 14545 http://jmol.svn.sourceforge.net/jmol/?rev=14545&view=rev Author: hansonr Date: 2010-10-28 16:19:46 +0000 (Thu, 28 Oct 2010) Log Message: ----------- version=12.1.17_dev # new feature: load OFFSET {x y z} # --follows UNITCELL parameter, if present # --offsets the atoms in the file by a given amount # --may be fractional # --added to allow for shifts in origin for nonstandard CIF files # --applicable to ALL readers # --for example: # load quartz.cif {1 1 1} spacegroup "ignoreoperators" offset{0 0 2/3} # load caffeine.xyz offset {8.0 0 0} 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 2010-10-28 16:15:22 UTC (rev 14544) +++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-10-28 16:19:46 UTC (rev 14545) @@ -8276,7 +8276,10 @@ Point3f offset = getPoint3f(++i, true); if (coordinatesAreFractional) { offset.set(fractionalPoint); - htParams.put("unitCellOffsetFractional", (coordinatesAreFractional ? Boolean.TRUE : Boolean.FALSE)); + htParams.put("unitCellOffsetFractional", (coordinatesAreFractional ? Boolean.TRUE : Boolean.FALSE)); + sOptions += " offset {" + offset.x + " " + offset.y + " " + offset.z + "/1}"; + } else { + sOptions += " offset " + Escape.escape(offset); } htParams.put("unitCellOffset", offset); } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-12-21 12:28:13
|
Revision: 14854 http://jmol.svn.sourceforge.net/jmol/?rev=14854&view=rev Author: hansonr Date: 2010-12-21 12:28:07 +0000 (Tue, 21 Dec 2010) Log Message: ----------- version=12.1.27_dev # bug fix: space before [ not recognized as significant when following $xxx or {...} 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 2010-12-21 12:27:40 UTC (rev 14853) +++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-12-21 12:28:07 UTC (rev 14854) @@ -4071,7 +4071,7 @@ throws ScriptException { int tok = tokAt(i); if (tok == Token.spacebeforesquare) - tok = tokAt(i++); + tok = tokAt(++i); boolean haveBrace = (tok == Token.leftbrace); boolean haveSquare = (tok == Token.leftsquare); float[] fparams = null; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-01-27 12:55:02
|
Revision: 15057 http://jmol.svn.sourceforge.net/jmol/?rev=15057&view=rev Author: hansonr Date: 2011-01-27 12:54:56 +0000 (Thu, 27 Jan 2011) 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 2011-01-27 12:51:11 UTC (rev 15056) +++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2011-01-27 12:54:56 UTC (rev 15057) @@ -12875,7 +12875,7 @@ } if (isUserVariable) { - System.out.println("setvar " + key + " " + t); + //System.out.println("setvar " + key + " " + t); t.set(tv, false); return; } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-01-27 15:14:32
|
Revision: 15059 http://jmol.svn.sourceforge.net/jmol/?rev=15059&view=rev Author: hansonr Date: 2011-01-27 15:14:26 +0000 (Thu, 27 Jan 2011) Log Message: ----------- version=12.1.33_dev # bug fix: scriptLevelMax 20 too small -- changed to 100 # bug fix: for/while local variables improperly localized in iterative functions # bug fix: 12.1.32 should not have changed <string> + <array> to be <array> 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 2011-01-27 15:13:49 UTC (rev 15058) +++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2011-01-27 15:14:26 UTC (rev 15059) @@ -2323,21 +2323,23 @@ this.tQuiet = tQuiet; } - private ScriptContext thisContext = null; + protected ScriptContext thisContext = null; private void pushContext(ContextToken token) throws ScriptException { if (scriptLevel == scriptLevelMax) error(ERROR_tooManyScriptLevels); - scriptLevel++; thisContext = getScriptContext(); thisContext.token = token; - if (token != null) { + if (token == null) { + scriptLevel = ++thisContext.scriptLevel; + } else { + thisContext.scriptLevel = -1; contextVariables = new Hashtable<String, ScriptVariable>(); for (String key: token.contextVariables.keySet()) ScriptCompiler.addContextVariable(contextVariables, key); } if (Logger.debugging || isCmdLine_c_or_C_Option) - Logger.info("-->>-------------".substring(0, scriptLevel + 5) + Logger.info("-->>-------------".substring(0, Math.max(17, scriptLevel + 5)) + scriptLevel + " " + filename + " " + token + " " + thisContext); //System.out.println("scriptEval " + token + " " + scriptLevel + ": " + contextVariables); } @@ -2376,18 +2378,17 @@ } void popContext(boolean isFlowCommand, boolean statementOnly) { - if (scriptLevel == 0) - return; - scriptLevel--; if (thisContext == null) return; + if (thisContext.scriptLevel > 0) + scriptLevel = thisContext.scriptLevel - 1; // we must save (and thus NOT restore) the current statement // business when doing push/pop for commands like FOR and WHILE ScriptContext scTemp = (isFlowCommand ? getScriptContext() : null); restoreScriptContext(thisContext, true, isFlowCommand, statementOnly); restoreScriptContext(scTemp, true, false, true); if (Logger.debugging || isCmdLine_c_or_C_Option) - Logger.info("--<<-------------".substring(0, scriptLevel + 5) + Logger.info("--<<-------------".substring(0, Math.max(17, scriptLevel + 5)) + scriptLevel + " " + filename + " " + (thisContext == null ? "" : "" + thisContext.token) + " " + thisContext); @@ -2870,7 +2871,7 @@ return; } String s = getScriptContext().getContextTrace(null, true).toString(); - while (scriptLevel > 0) + while (thisContext != null) popContext(false, false); message += s; this.untranslated += s; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-01-27 16:59:30
|
Revision: 15060 http://jmol.svn.sourceforge.net/jmol/?rev=15060&view=rev Author: hansonr Date: 2011-01-27 16:59:24 +0000 (Thu, 27 Jan 2011) Log Message: ----------- version=12.1.33_dev # bug fix: scriptLevelMax 20 too small -- changed to 100 # bug fix: for/while local variables improperly localized in iterative functions # bug fix: 12.1.32 should not have changed <string> + <array> to be <array> 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 2011-01-27 15:14:26 UTC (rev 15059) +++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2011-01-27 16:59:24 UTC (rev 15060) @@ -2335,11 +2335,13 @@ } else { thisContext.scriptLevel = -1; contextVariables = new Hashtable<String, ScriptVariable>(); - for (String key: token.contextVariables.keySet()) - ScriptCompiler.addContextVariable(contextVariables, key); + if (token.contextVariables != null) + for (String key : token.contextVariables.keySet()) + ScriptCompiler.addContextVariable(contextVariables, key); } if (Logger.debugging || isCmdLine_c_or_C_Option) - Logger.info("-->>-------------".substring(0, Math.max(17, scriptLevel + 5)) + Logger.info("-->>-------------".substring(0, Math + .max(17, scriptLevel + 5)) + scriptLevel + " " + filename + " " + token + " " + thisContext); //System.out.println("scriptEval " + token + " " + scriptLevel + ": " + contextVariables); } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-02-12 15:42:37
|
Revision: 15154 http://jmol.svn.sourceforge.net/jmol/?rev=15154&view=rev Author: hansonr Date: 2011-02-12 15:42:31 +0000 (Sat, 12 Feb 2011) 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 2011-02-11 17:16:10 UTC (rev 15153) +++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2011-02-12 15:42:31 UTC (rev 15154) @@ -9242,7 +9242,7 @@ case Token.function: viewer.clearFunctions(); return; - case Token.reset: + case Token.structure: if (!isSyntaxCheck) { BitSet bsAllAtoms = new BitSet(); runScript(viewer.getDefaultStructure(null, bsAllAtoms)); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-02-12 19:40:44
|
Revision: 15155 http://jmol.svn.sourceforge.net/jmol/?rev=15155&view=rev Author: hansonr Date: 2011-02-12 19:40:37 +0000 (Sat, 12 Feb 2011) 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 2011-02-12 15:42:31 UTC (rev 15154) +++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2011-02-12 19:40:37 UTC (rev 15155) @@ -13971,7 +13971,7 @@ String type = ((len = statementLength) == 3 ? parameterAsString(2) : null); if (!isSyntaxCheck) { Object[] data = (type == null ? this.data : viewer.getData(type)); - msg = (data == null ? "no data" : "data " + msg = (data == null ? "no data" : "data \"" + data[0] + "\"\n" + (data[1] instanceof float[] ? Escape.escape((float[]) data[1], @@ -16576,11 +16576,13 @@ if (Float.isNaN(cutoff) && !Float.isNaN(sigma)) { Logger.error("sigma not supported"); } - s += " created with cutoff=" + cutoff; + s += " created"; + if (isIsosurface) + s += " with cutoff=" + cutoff; float[] minMax = (float[]) getShapeProperty(iShape, "minMaxInfo"); if (minMax[0] != Float.MAX_VALUE) s += " min=" + minMax[0] + " max=" + minMax[1]; - s += "; number of isosurfaces = " + getShapeProperty(iShape, "count"); + s += "; " + JmolConstants.shapeClassBases[iShape].toLowerCase() + " count: " + getShapeProperty(iShape, "count"); s += getIsosurfaceDataRange(iShape, "\n"); if (doCalcArea) s += "\nisosurfaceArea = " + Escape.escapeArray(area); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-03-25 14:09:15
|
Revision: 15352 http://jmol.svn.sourceforge.net/jmol/?rev=15352&view=rev Author: hansonr Date: 2011-03-25 14:09:08 +0000 (Fri, 25 Mar 2011) 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 2011-03-25 13:00:32 UTC (rev 15351) +++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2011-03-25 14:09:08 UTC (rev 15352) @@ -5794,7 +5794,7 @@ error(ERROR_invalidArgument); v = viewer.getOrSetNewVariable(key, false); } - if (v == null || v.tok != Token.bitset || v.intValue == Integer.MAX_VALUE) { + if (!isForCheck || v == null || v.tok != Token.bitset || v.intValue == Integer.MAX_VALUE) { if (v == null) { contextVariables.put(key.toLowerCase(), v = ScriptVariable.getVariable(bsIn)); v.intValue = 1; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-03-25 15:52:58
|
Revision: 15354 http://jmol.svn.sourceforge.net/jmol/?rev=15354&view=rev Author: hansonr Date: 2011-03-25 15:52:51 +0000 (Fri, 25 Mar 2011) Log Message: ----------- comment out - ready for release 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 2011-03-25 15:47:55 UTC (rev 15353) +++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2011-03-25 15:52:51 UTC (rev 15354) @@ -5739,7 +5739,6 @@ // for (var i = 1; i < 3; i = i + 1); // for (;;;); // for (var x in {...}) { xxxxx } - System.out.println("forcmd forcheck=" + isForCheck); Token token = theToken; int[] pts = new int[2]; int j = 0; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-06-12 18:55:00
|
Revision: 15573 http://jmol.svn.sourceforge.net/jmol/?rev=15573&view=rev Author: hansonr Date: 2011-06-12 18:54:53 +0000 (Sun, 12 Jun 2011) Log Message: ----------- version=12.1.50_dev #bug fix: throwing script parsing error on correct "isosurface slab within [4 elements # representing the slab box]" (was losing last "]"). 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 2011-06-12 17:59:52 UTC (rev 15572) +++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2011-06-12 18:54:53 UTC (rev 15573) @@ -4274,6 +4274,10 @@ i++; break; default: + if (nPoints >= 0 && n == nPoints) { + tok = Token.nada; + break; + } Point3f pt = getPoint3f(i, true); if (points == null) vp.add(pt); @@ -4283,7 +4287,7 @@ i = iToken + 1; } } - if (tok != Token.rightsquare || nPoints > 0 && n != nPoints) + if (tok != Token.rightsquare) error(ERROR_invalidArgument); if (points == null) { points = new Point3f[vp.size()]; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-06-18 21:36:24
|
Revision: 15623 http://jmol.svn.sourceforge.net/jmol/?rev=15623&view=rev Author: hansonr Date: 2011-06-18 21:36:17 +0000 (Sat, 18 Jun 2011) 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 2011-06-18 21:35:18 UTC (rev 15622) +++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2011-06-18 21:36:17 UTC (rev 15623) @@ -3748,6 +3748,8 @@ isBondSet = (expressionResult instanceof BondSet); if (!isBondSet) { viewer.excludeAtoms(bs, ignoreSubset); + if (bs.length() > viewer.getAtomCount()) + bs.clear(); } if (tempStatement != null) { statement = tempStatement; @@ -15794,7 +15796,10 @@ // isosurface intersection {A} {B} VDW.... // isosurface intersection {A} {B} function "a-b" VDW.... bsSelect = atomExpression(++i); - if (tokAt(iToken + 1) == Token.expressionBegin || tokAt(iToken + 1) == Token.bitset) { + if (isSyntaxCheck) { + bs = new BitSet(); + } else if (tokAt(iToken + 1) == Token.expressionBegin + || tokAt(iToken + 1) == Token.bitset) { bs = atomExpression(++iToken); bs.and(viewer.getAtomsWithin(5.0f, bsSelect, false)); } else { @@ -15803,19 +15808,21 @@ bs.andNot(viewer.getAtomBits(Token.molecule, bsSelect)); } bs.andNot(bsSelect); - sbCommand.append(" intersection ").append(Escape.escape(bsSelect)).append(" ").append(Escape.escape(bs)); + sbCommand.append(" intersection ").append(Escape.escape(bsSelect)) + .append(" ").append(Escape.escape(bs)); i = iToken; if (tokAt(i + 1) == Token.function) { i++; String f = (String) getToken(++i).value; sbCommand.append(" function ").append(Escape.escape(f)); if (!isSyntaxCheck) - addShapeProperty(propertyList, "func", createFunction("__iso__", "a,b", f)); + addShapeProperty(propertyList, "func", createFunction("__iso__", + "a,b", f)); } else { haveIntersection = true; } propertyName = "intersection"; - propertyValue = new BitSet[] { bsSelect, bs }; + propertyValue = new BitSet[] { bsSelect, bs }; break; case Token.display: case Token.within: @@ -16272,9 +16279,8 @@ propertyName = "nci"; sbCommand.append(" " + propertyName); int tok = tokAt(i + 1); - boolean isPromolecular = (tok != Token.file - && tok != Token.string && tok != Token.mrc); - propertyValue = Boolean.valueOf(isPromolecular); + boolean isPromolecular = (tok != Token.file && tok != Token.string && tok != Token.mrc); + propertyValue = Boolean.valueOf(isPromolecular); if (isPromolecular) surfaceObjectSeen = true; break; @@ -16514,7 +16520,8 @@ sbCommand.append(" ").append(Escape.escape(name)); vxy.add(name); if (!isSyntaxCheck) - addShapeProperty(propertyList, "func", createFunction("__iso__", "x,y,z", name)); + addShapeProperty(propertyList, "func", createFunction("__iso__", + "x,y,z", name)); break; } // override of function or data name when saved as a state @@ -16979,7 +16986,7 @@ } } - if (surfaceObjectSeen && !isLcaoCartoon && !isSyntaxCheck) { + if (surfaceObjectSeen && !isLcaoCartoon && !isSyntaxCheck) { propertyList.add(0, new Object[] { "newObject", null }); boolean needSelect = (bsSelect == null); if (needSelect) @@ -17001,7 +17008,7 @@ } } } - + // OK, now send them all if (haveIntersection && !haveSlab) { @@ -17012,8 +17019,9 @@ addShapeProperty(propertyList, "select", bs); addShapeProperty(propertyList, "sasurface", Float.valueOf(0)); } - addShapeProperty(propertyList, "slab", new Object[] {new Object[] { Float.valueOf(-100), - Float.valueOf(0) }, null, Boolean.FALSE }); + addShapeProperty(propertyList, "slab", new Object[] { + new Object[] { Float.valueOf(-100), Float.valueOf(0) }, null, + Boolean.FALSE }); } setShapeProperty(iShape, "setProperties", propertyList); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-06-28 14:28:16
|
Revision: 15655 http://jmol.svn.sourceforge.net/jmol/?rev=15655&view=rev Author: hansonr Date: 2011-06-28 14:28:10 +0000 (Tue, 28 Jun 2011) Log Message: ----------- version=12.1.51_dev # new feature: CONTACT {xxx} VDW # -- just maps a VDW isosurface with distances to another VDW 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 2011-06-28 13:50:58 UTC (rev 15654) +++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2011-06-28 14:28:10 UTC (rev 15655) @@ -15300,7 +15300,8 @@ // if INTRAMOLCULAR and no {B}, then this means "just {A} to {A}" // otherwise, {B} should be set to {!A}. - if (type != Token.nci && intramolecular == null) { + if (type != Token.nci && type != Token.vanderwaals + && intramolecular == null) { sbCommand.append(" intramolecular"); intramolecular = Boolean.valueOf(false); } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-06-28 14:30:28
|
Revision: 15656 http://jmol.svn.sourceforge.net/jmol/?rev=15656&view=rev Author: hansonr Date: 2011-06-28 14:30:21 +0000 (Tue, 28 Jun 2011) Log Message: ----------- version=12.1.51_dev # new feature: CONTACT {xxx} VDW # -- just maps a VDW isosurface with distances to another VDW 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 2011-06-28 14:28:10 UTC (rev 15655) +++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2011-06-28 14:30:21 UTC (rev 15656) @@ -15300,9 +15300,9 @@ // if INTRAMOLCULAR and no {B}, then this means "just {A} to {A}" // otherwise, {B} should be set to {!A}. - if (type != Token.nci && type != Token.vanderwaals + if (type != Token.nci && intramolecular == null) { - sbCommand.append(" intramolecular"); + sbCommand.append(" intermolecular"); intramolecular = Boolean.valueOf(false); } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-07-03 01:27:26
|
Revision: 15698 http://jmol.svn.sourceforge.net/jmol/?rev=15698&view=rev Author: hansonr Date: 2011-07-03 01:27:19 +0000 (Sun, 03 Jul 2011) 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 2011-07-03 01:19:00 UTC (rev 15697) +++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2011-07-03 01:27:19 UTC (rev 15698) @@ -15103,7 +15103,7 @@ // ID aaaa (if present, must be FIRST parameter, before {setA} // {setB} // DENSITY x.x - // DISTANCE x.x + // WITHIN x.x // PARAMETERS [....] // FULL|PLANAR|CONNECT|NCI (FULL not implemented yet) // HYDROPHOBIC|HBOND|MISCELLANEOUS @@ -15207,9 +15207,10 @@ .valueOf(resolution)); } break; + case Token.within: case Token.distance: distance = floatParameter(++i); - sbCommand.append(" distance ").append(distance); + sbCommand.append(" within ").append(distance); break; case Token.integer: rd = encodeRadiusParameter(i, false); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-07-03 01:28:45
|
Revision: 15699 http://jmol.svn.sourceforge.net/jmol/?rev=15699&view=rev Author: hansonr Date: 2011-07-03 01:28:38 +0000 (Sun, 03 Jul 2011) 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 2011-07-03 01:27:19 UTC (rev 15698) +++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2011-07-03 01:28:38 UTC (rev 15699) @@ -15331,7 +15331,6 @@ bs = viewer.getAtomsWithin(distance, bsA, true); // {B} always within some fixed distance of A bsB.and(bs); - } if (bsIgnore == null) bsIgnore = BitSetUtil.setAll(viewer.getAtomCount()); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-07-07 00:22:06
|
Revision: 15729 http://jmol.svn.sourceforge.net/jmol/?rev=15729&view=rev Author: hansonr Date: 2011-07-07 00:22:00 +0000 (Thu, 07 Jul 2011) 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 2011-07-06 23:34:17 UTC (rev 15728) +++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2011-07-07 00:22:00 UTC (rev 15729) @@ -16078,7 +16078,6 @@ boolean isFxy = false; boolean haveSlab = false; boolean haveIntersection = false; - boolean haveOrigin = false; float[] data = null; int thisSetNumber = -1; int nFiles = 0; @@ -16152,7 +16151,6 @@ case Token.origin: case Token.step: case Token.point: - haveOrigin = true; propertyName = theToken.value.toString(); sbCommand.append(" ").append(theToken.value); propertyValue = centerParameter(++i); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-07-07 02:41:33
|
Revision: 15731 http://jmol.svn.sourceforge.net/jmol/?rev=15731&view=rev Author: hansonr Date: 2011-07-07 02:41:26 +0000 (Thu, 07 Jul 2011) Log Message: ----------- version=12.1.51_dev # new feature: {atomset}.x? # -- creates an associative arraay of atom properties with names starting with "x" # -- print @1.? lists ALL atom properties # -- print {atomno < 3}.? creates an associative array of arrays # -- for example: # $ load caffeine.xyz;print @1.atom? # atomID : 0 # atomIndex : 0 # atomName : # H1 # # atomType : # H1 # # atomX : -3.380413 # atomY : -1.1272367 # atomZ : 0.5733036 # atomno : 1 # # $ show @{{atomno < 3}.atomn?} # { "atomName":["H1","N2"], "atomno":[1,2] } # 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 2011-07-07 02:32:13 UTC (rev 15730) +++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2011-07-07 02:41:26 UTC (rev 15731) @@ -1229,7 +1229,7 @@ Point3f zero = (minmaxtype == Token.allfloat ? new Point3f() : null); Point3f pt = (isPt || !isAtoms ? new Point3f() : null); - if (isExplicitlyAll || isString && minmaxtype != Token.allfloat) + if (isExplicitlyAll || isString && !haveIndex && minmaxtype != Token.allfloat) minmaxtype = Token.all; List<Object> vout = (minmaxtype == Token.all ? new ArrayList<Object>() : null); @@ -1466,6 +1466,8 @@ fout[i] = Parser.parseFloat(s); break; default: + if (vout == null) + return s; vout.add(s); } break; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-07-07 04:18:55
|
Revision: 15736 http://jmol.svn.sourceforge.net/jmol/?rev=15736&view=rev Author: hansonr Date: 2011-07-07 04:18:49 +0000 (Thu, 07 Jul 2011) 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 2011-07-07 04:08:42 UTC (rev 15735) +++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2011-07-07 04:18:49 UTC (rev 15736) @@ -8141,8 +8141,11 @@ // will evaluate the moment it is defined and then represent // that set of atoms forever. - + if (statementLength < 3 || !(getToken(1).value instanceof String)) + error(ERROR_invalidArgument); String setName = ((String) getToken(1).value).toLowerCase(); + if (Parser.parseInt(setName) != Integer.MIN_VALUE) + error(ERROR_invalidArgument); if (isSyntaxCheck) return; boolean isSite = setName.startsWith("site_"); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-07-07 04:54:41
|
Revision: 15737 http://jmol.svn.sourceforge.net/jmol/?rev=15737&view=rev Author: hansonr Date: 2011-07-07 04:54:35 +0000 (Thu, 07 Jul 2011) Log Message: ----------- resets picked variable whenever any "set picking" command is issued 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 2011-07-07 04:18:49 UTC (rev 15736) +++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2011-07-07 04:54:35 UTC (rev 15737) @@ -12284,12 +12284,12 @@ setIntProperty(key, intSetting(2, Integer.MAX_VALUE, 0, 1000)); break; case Token.picking: + if (!isSyntaxCheck) + viewer.setPicked(-1); if (statementLength > 2) { setPicking(); return; } - if (!isSyntaxCheck) - viewer.setPicked(-1); break; case Token.pickingstyle: if (statementLength > 2) { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-07-20 16:34:57
|
Revision: 15796 http://jmol.svn.sourceforge.net/jmol/?rev=15796&view=rev Author: hansonr Date: 2011-07-20 16:34:51 +0000 (Wed, 20 Jul 2011) Log Message: ----------- version=12.1.51 # bug fix: try {} does not pass VAR variables into its context. 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 2011-07-20 16:31:21 UTC (rev 15795) +++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2011-07-20 16:34:51 UTC (rev 15796) @@ -1996,8 +1996,8 @@ } if (function == null) return null; + pushContext(null); boolean isTry = (function.tok == Token.trycmd); - pushContext(null); thisContext.isFunction = !isTry; functionName = name; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-07-20 16:39:23
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Revision: 15798 http://jmol.svn.sourceforge.net/jmol/?rev=15798&view=rev Author: hansonr Date: 2011-07-20 16:39:16 +0000 (Wed, 20 Jul 2011) 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 2011-07-20 16:35:25 UTC (rev 15797) +++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2011-07-20 16:39:16 UTC (rev 15798) @@ -1943,7 +1943,6 @@ if (var.equals("expressionBegin")) return null; var = var.toLowerCase(); - System.out.println("var=" + var + " contextVariables "+(contextVariables == null ? 0 :contextVariables.hashCode())); if (contextVariables != null && contextVariables.containsKey(var)) return contextVariables.get(var); ScriptContext context = thisContext; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-09-22 11:21:39
|
Revision: 16096 http://jmol.svn.sourceforge.net/jmol/?rev=16096&view=rev Author: hansonr Date: 2011-09-22 11:21:33 +0000 (Thu, 22 Sep 2011) Log Message: ----------- removal of undocumented ancient select */2003 meaning "third model of file 2" 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 2011-09-22 11:17:54 UTC (rev 16095) +++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2011-09-22 11:21:33 UTC (rev 16096) @@ -2335,8 +2335,7 @@ fixed[j] = new Token(Token.integer, ((Integer) v).intValue(), v); } else if (v instanceof Float) { - fixed[j] = new Token(Token.decimal, ScriptEvaluator.getFloatEncodedInt("" + v), - v); + fixed[j] = new Token(Token.decimal, getFloatEncodedInt("" + v), v); } else if (v instanceof String) { if (!forceString) { if ((tok != Token.set || j > 1 && statement[1].tok != Token.echo) @@ -3557,10 +3556,8 @@ rpn.addX(getAtomBits(Token.spec_model, Integer.valueOf(iModel))); break; } - if (iModel < 1000) + if (iModel < 2147) // file number iModel = iModel * 1000000; - else - iModel = (iModel / 1000) * 1000000 + iModel % 1000; } rpn.addX(bitSetForModelFileNumber(iModel)); break; @@ -4169,7 +4166,7 @@ // model/frame number encoded break; case Token.string: - iFrame = ScriptEvaluator.getFloatEncodedInt(stringParameter(index)); + iFrame = getFloatEncodedInt(stringParameter(index)); break; default: error(ERROR_invalidArgument); @@ -6622,12 +6619,11 @@ error(ERROR_invalidArgument); break; default: - if ((order = ScriptEvaluator.getBondOrderFromString(parameterAsString(1))) == JmolEdge.BOND_ORDER_NULL) + if ((order = getBondOrderFromString(parameterAsString(1))) == JmolEdge.BOND_ORDER_NULL) error(ERROR_invalidArgument); // generic partial can be indicated by "partial n.m" if (order == JmolEdge.BOND_PARTIAL01 && tokAt(2) == Token.decimal) { - order = ScriptEvaluator - .getPartialBondOrderFromFloatEncodedInt(statement[2].intValue); + order = getPartialBondOrderFromFloatEncodedInt(statement[2].intValue); } } setShapeProperty(JmolConstants.SHAPE_STICKS, "bondOrder", Integer @@ -7228,7 +7224,7 @@ } } String cmd = parameterAsString(i); - if ((bo = ScriptEvaluator.getBondOrderFromString(cmd)) == JmolEdge.BOND_ORDER_NULL) { + if ((bo = getBondOrderFromString(cmd)) == JmolEdge.BOND_ORDER_NULL) { error(ERROR_invalidArgument); } // must be bond type @@ -7239,8 +7235,7 @@ case JmolEdge.BOND_PARTIAL01: switch (tokAt(i + 1)) { case Token.decimal: - bo = ScriptEvaluator - .getPartialBondOrderFromFloatEncodedInt(statement[++i].intValue); + bo = getPartialBondOrderFromFloatEncodedInt(statement[++i].intValue); break; case Token.integer: bo = (short) intParameter(++i); @@ -11946,8 +11941,7 @@ case Token.string: if (nFrames == 2) error(ERROR_invalidArgument); - int iFrame = (theTok == Token.string ? ScriptEvaluator - .getFloatEncodedInt((String) theToken.value) : theToken.intValue); + int iFrame = (theTok == Token.string ? getFloatEncodedInt((String) theToken.value) : theToken.intValue); if (iFrame == Integer.MAX_VALUE) iFrame = 0; // frame 0.0 if (iFrame == -1) { @@ -12335,7 +12329,7 @@ modelNumber = Parser.parseInt(modelDotted); useModelNumber = true; } else { - modelNumber = ScriptEvaluator.getFloatEncodedInt(modelDotted); + modelNumber = getFloatEncodedInt(modelDotted); } if (isSyntaxCheck) return; @@ -17941,11 +17935,12 @@ } /** - * encodes a string such as "2.10" as an integer instead of a float + * Encodes a string such as "2.10" as an integer instead of a float * so as to distinguish "2.1" from "2.10" * used for model numbers and partial bond orders. * 2147483647 is maxvalue, so this allows loading - * simultaneously up to 2147 files. + * simultaneously up to 2147 files, each with 999999 models (or trajectories) + * * @param strDecimal * @return float encoded as an integer */ @@ -17977,14 +17972,16 @@ } /** - * reads standard n.m float-as-integer n*1000000 + m - * and returns (n % 6) << 5 + (m % 0x1F) + * reads standard n.m float-as-integer n*1000000 + m and returns (n % 6) << 5 + * + (m % 0x1F) + * * @param bondOrderInteger * @return Bond order partial mask */ - public final static int getPartialBondOrderFromFloatEncodedInt(int bondOrderInteger) { - return ((((bondOrderInteger / 1000000) % 6) << 5) - + ((bondOrderInteger % 1000000) & 0x1F)); + public final static int getPartialBondOrderFromFloatEncodedInt( + int bondOrderInteger) { + return (((bondOrderInteger / 1000000) % 6) << 5) + + ((bondOrderInteger % 1000000) & 0x1F); } public final static int getBondOrderFromString(String s) { @@ -17994,8 +17991,7 @@ } public static int getPartialBondOrderFromString(String s) { - return ScriptEvaluator.getPartialBondOrderFromFloatEncodedInt(ScriptEvaluator - .getFloatEncodedInt(s)); + return getPartialBondOrderFromFloatEncodedInt(getFloatEncodedInt(s)); } } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2012-04-04 02:56:06
|
Revision: 16964 http://jmol.svn.sourceforge.net/jmol/?rev=16964&view=rev Author: hansonr Date: 2012-04-04 02:56:00 +0000 (Wed, 04 Apr 2012) 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 2012-04-04 02:55:25 UTC (rev 16963) +++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2012-04-04 02:56:00 UTC (rev 16964) @@ -10883,7 +10883,7 @@ default: error(ERROR_numberExpected); } - if (!isSyntaxCheck) + if (!isSyntaxCheck && !viewer.isHeadless()) delay(millis); } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |