From: <ha...@us...> - 2012-07-14 21:03:49
|
Revision: 17350 http://jmol.svn.sourceforge.net/jmol/?rev=17350&view=rev Author: hansonr Date: 2012-07-14 21:03:42 +0000 (Sat, 14 Jul 2012) Log Message: ----------- version=12.2.33 # bug fix: select within(1.0, withinallmodels, 1.1) and 1.2 causes exception Modified Paths: -------------- branches/v12_2/Jmol/src/org/jmol/script/ScriptEvaluator.java branches/v12_2/Jmol/src/org/jmol/script/ScriptMathProcessor.java branches/v12_2/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v12_2/Jmol/src/org/jmol/script/ScriptEvaluator.java =================================================================== --- branches/v12_2/Jmol/src/org/jmol/script/ScriptEvaluator.java 2012-07-14 21:02:41 UTC (rev 17349) +++ branches/v12_2/Jmol/src/org/jmol/script/ScriptEvaluator.java 2012-07-14 21:03:42 UTC (rev 17350) @@ -3774,7 +3774,8 @@ break; default: if (Token.tokAttr(instruction.tok, Token.mathop)) { - rpn.addOp(instruction); + if (!rpn.addOp(instruction)) + error(ERROR_invalidArgument); break; } if (!(value instanceof String)) { Modified: branches/v12_2/Jmol/src/org/jmol/script/ScriptMathProcessor.java =================================================================== --- branches/v12_2/Jmol/src/org/jmol/script/ScriptMathProcessor.java 2012-07-14 21:02:41 UTC (rev 17349) +++ branches/v12_2/Jmol/src/org/jmol/script/ScriptMathProcessor.java 2012-07-14 21:03:42 UTC (rev 17350) @@ -556,6 +556,8 @@ break; case Token.opAnd: case Token.opOr: + if (!wasSyntaxCheck && xPt < 0) + return false; if (!wasSyntaxCheck && xStack[xPt].tok != Token.bitset && xStack[xPt].tok != Token.varray) { // check to see if we need to evaluate the second operand or not // if not, then set this to syntax check in order to skip :) Modified: branches/v12_2/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v12_2/Jmol/src/org/jmol/viewer/Jmol.properties 2012-07-14 21:02:41 UTC (rev 17349) +++ branches/v12_2/Jmol/src/org/jmol/viewer/Jmol.properties 2012-07-14 21:03:42 UTC (rev 17350) @@ -4,12 +4,10 @@ date=$Date$ -version=12.2.34_dev +version=12.2.33 -#version=12.2.33 +# bug fix: select within(1.0, withinallmodels, 1.1) and 1.2 causes exception -# no changes - # ------------------------------------------------------------------------------ #version=12.2.32 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2012-07-16 00:16:29
|
Revision: 17358 http://jmol.svn.sourceforge.net/jmol/?rev=17358&view=rev Author: hansonr Date: 2012-07-16 00:16:21 +0000 (Mon, 16 Jul 2012) Log Message: ----------- version=12.2.34_dev # bug fix: show $d1 where d1 is a DRAW object broken # bug fix: calculate hydrogens incorrect for proteins Modified Paths: -------------- branches/v12_2/Jmol/src/org/jmol/adapter/readers/molxyz/XyzReader.java branches/v12_2/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java branches/v12_2/Jmol/src/org/jmol/jvxl/data/JvxlCoder.java branches/v12_2/Jmol/src/org/jmol/jvxl/readers/IsoShapeReader.java branches/v12_2/Jmol/src/org/jmol/minimize/forcefield/Calculations.java branches/v12_2/Jmol/src/org/jmol/modelset/AtomCollection.java branches/v12_2/Jmol/src/org/jmol/modelset/Measurement.java branches/v12_2/Jmol/src/org/jmol/modelset/ModelSet.java branches/v12_2/Jmol/src/org/jmol/quantum/MOCalculation.java branches/v12_2/Jmol/src/org/jmol/script/ScriptCompilationTokenParser.java branches/v12_2/Jmol/src/org/jmol/script/ScriptCompiler.java branches/v12_2/Jmol/src/org/jmol/script/ScriptEvaluator.java branches/v12_2/Jmol/src/org/jmol/script/ScriptMathProcessor.java branches/v12_2/Jmol/src/org/jmol/shape/Text.java branches/v12_2/Jmol/src/org/jmol/shapespecial/Dots.java branches/v12_2/Jmol/src/org/jmol/shapesurface/IsosurfaceMesh.java branches/v12_2/Jmol/src/org/jmol/shapesurface/MolecularOrbital.java branches/v12_2/Jmol/src/org/jmol/smiles/SmilesParser.java branches/v12_2/Jmol/src/org/jmol/symmetry/HallInfo.java branches/v12_2/Jmol/src/org/jmol/symmetry/PointGroup.java branches/v12_2/Jmol/src/org/jmol/symmetry/UnitCell.java branches/v12_2/Jmol/src/org/jmol/util/SurfaceFileTyper.java branches/v12_2/Jmol/src/org/jmol/viewer/ActionManager.java branches/v12_2/Jmol/src/org/jmol/viewer/Jmol.properties branches/v12_2/Jmol/src/org/jmol/viewer/JmolConstants.java branches/v12_2/Jmol/src/org/jmol/viewer/Viewer.java Modified: branches/v12_2/Jmol/src/org/jmol/adapter/readers/molxyz/XyzReader.java =================================================================== --- branches/v12_2/Jmol/src/org/jmol/adapter/readers/molxyz/XyzReader.java 2012-07-14 22:28:54 UTC (rev 17357) +++ branches/v12_2/Jmol/src/org/jmol/adapter/readers/molxyz/XyzReader.java 2012-07-16 00:16:21 UTC (rev 17358) @@ -150,7 +150,7 @@ atom.atomSerial = parseInt(tokens[8]); } vpt++; - //fall through: + //$FALL-THROUGH$: default: // or sym x y z vx vy vz float vx = parseFloat(tokens[vpt++]); Modified: branches/v12_2/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java =================================================================== --- branches/v12_2/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java 2012-07-14 22:28:54 UTC (rev 17357) +++ branches/v12_2/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java 2012-07-16 00:16:21 UTC (rev 17358) @@ -922,12 +922,12 @@ // standard minXYZ.z--; maxXYZ.z++; - // fall through; + //$FALL-THROUGH$; case 2: // slab or standard minXYZ.y--; maxXYZ.y++; - // fall through; + //$FALL-THROUGH$; case 1: // slab, polymer, or standard minXYZ.x--; Modified: branches/v12_2/Jmol/src/org/jmol/jvxl/data/JvxlCoder.java =================================================================== --- branches/v12_2/Jmol/src/org/jmol/jvxl/data/JvxlCoder.java 2012-07-14 22:28:54 UTC (rev 17357) +++ branches/v12_2/Jmol/src/org/jmol/jvxl/data/JvxlCoder.java 2012-07-16 00:16:21 UTC (rev 17358) @@ -1168,7 +1168,7 @@ case '%': next[0]++; dataOut.append(chLast = ++ch); - //fall through + //$FALL-THROUGH$ case '1': case '2': case '3': Modified: branches/v12_2/Jmol/src/org/jmol/jvxl/readers/IsoShapeReader.java =================================================================== --- branches/v12_2/Jmol/src/org/jmol/jvxl/readers/IsoShapeReader.java 2012-07-14 22:28:54 UTC (rev 17357) +++ branches/v12_2/Jmol/src/org/jmol/jvxl/readers/IsoShapeReader.java 2012-07-16 00:16:21 UTC (rev 17358) @@ -120,7 +120,7 @@ break; case Parameters.SURFACE_ELLIPSOID2: type = "ellipsoid"; - // fall through + //$FALL-THROUGH$ case Parameters.SURFACE_SPHERE: default: radius = 1.2f * sphere_radiusAngstroms * eccentricityScale; Modified: branches/v12_2/Jmol/src/org/jmol/minimize/forcefield/Calculations.java =================================================================== --- branches/v12_2/Jmol/src/org/jmol/minimize/forcefield/Calculations.java 2012-07-14 22:28:54 UTC (rev 17357) +++ branches/v12_2/Jmol/src/org/jmol/minimize/forcefield/Calculations.java 2012-07-16 00:16:21 UTC (rev 17358) @@ -232,12 +232,12 @@ id = minList[3]; if (gradients) dd.set(atoms[id].coord); - //fall through + //$FALL-THROUGH$ case CALC_ANGLE: ic = minList[2]; if (gradients) dc.set(atoms[ic].coord); - //fall through + //$FALL-THROUGH$ case CALC_DISTANCE: ib = minList[1]; ia = minList[0]; @@ -288,10 +288,10 @@ switch(iType) { case CALC_TORSION: addForce(dd, id, dE); - //fall through + //$FALL-THROUGH$ case CALC_ANGLE: addForce(dc, ic, dE); - //fall through + //$FALL-THROUGH$ case CALC_DISTANCE: addForce(db, ib, dE); addForce(da, ia, dE); @@ -313,10 +313,10 @@ switch (iType) { case CALC_TORSION: id = minList[3]; - //fall through + //$FALL-THROUGH$ case CALC_ANGLE: ic = minList[2]; - //fall through + //$FALL-THROUGH$ case CALC_DISTANCE: ib = minList[1]; ia = minList[0]; Modified: branches/v12_2/Jmol/src/org/jmol/modelset/AtomCollection.java =================================================================== --- branches/v12_2/Jmol/src/org/jmol/modelset/AtomCollection.java 2012-07-14 22:28:54 UTC (rev 17357) +++ branches/v12_2/Jmol/src/org/jmol/modelset/AtomCollection.java 2012-07-16 00:16:21 UTC (rev 17358) @@ -1082,6 +1082,7 @@ if (v == null) v = new Vector3f(); s.append(v.x).append(" ").append(v.y).append(" ").append(v.z); + break; case TAINT_ELEMENT: s.append(atoms[i].getAtomicAndIsotopeNumber()); break; @@ -1302,7 +1303,7 @@ hAtoms[i][hPt++] = pt; if (vConnect != null) vConnect.add(atom); - // fall through + //$FALL-THROUGH$ case 3: z.set(-0.635f, -0.635f, 0.635f); pt = new Point3f(z); @@ -1310,7 +1311,7 @@ hAtoms[i][hPt++] = pt; if (vConnect != null) vConnect.add(atom); - // fall through + //$FALL-THROUGH$ case 2: z.set(-0.635f, 0.635f, -0.635f); pt = new Point3f(z); @@ -1318,7 +1319,7 @@ hAtoms[i][hPt++] = pt; if (vConnect != null) vConnect.add(atom); - // fall through + //$FALL-THROUGH$ case 1: z.set(0.635f, -0.635f, -0.635f); pt = new Point3f(z); @@ -1558,7 +1559,7 @@ break; } // C=C, no other atoms - // fall through + //$FALL-THROUGH$ case 2: hybridization = (isSp ? "sp" : "sp2"); break; @@ -1688,7 +1689,7 @@ break; } // C=C, no other atoms - // fall through + //$FALL-THROUGH$ case 2: // R-C=C* or C=C=C* // get third atom Modified: branches/v12_2/Jmol/src/org/jmol/modelset/Measurement.java =================================================================== --- branches/v12_2/Jmol/src/org/jmol/modelset/Measurement.java 2012-07-14 22:28:54 UTC (rev 17357) +++ branches/v12_2/Jmol/src/org/jmol/modelset/Measurement.java 2012-07-16 00:16:21 UTC (rev 17358) @@ -274,7 +274,7 @@ vectorBA.scale(0.5f); pointArc = new Point3f(vectorBA); } - // fall through + //$FALL-THROUGH$ case 4: strMeasurement = formatAngle(value); return; Modified: branches/v12_2/Jmol/src/org/jmol/modelset/ModelSet.java =================================================================== --- branches/v12_2/Jmol/src/org/jmol/modelset/ModelSet.java 2012-07-14 22:28:54 UTC (rev 17357) +++ branches/v12_2/Jmol/src/org/jmol/modelset/ModelSet.java 2012-07-16 00:16:21 UTC (rev 17358) @@ -769,7 +769,7 @@ case Token.trace: if (fValue > Shape.RADIUS_MAX) fValue = Shape.RADIUS_MAX; - // fall through + //$FALL-THROUGH$ case Token.halo: case Token.star: RadiusData rd = null; Modified: branches/v12_2/Jmol/src/org/jmol/quantum/MOCalculation.java =================================================================== --- branches/v12_2/Jmol/src/org/jmol/quantum/MOCalculation.java 2012-07-14 22:28:54 UTC (rev 17357) +++ branches/v12_2/Jmol/src/org/jmol/quantum/MOCalculation.java 2012-07-16 00:16:21 UTC (rev 17358) @@ -1097,7 +1097,7 @@ switch(d) { case 3: value *= r; - //fall through + //$FALL-THROUGH$ case 2: value *= r2; break; @@ -1130,7 +1130,7 @@ switch(d) { case 3: value *= r; - //fall through + //$FALL-THROUGH$ case 2: value *= r2; break; @@ -1150,7 +1150,7 @@ switch(a) { case 3: vdx *= X[ix]; - //fall through + //$FALL-THROUGH$ case 2: vdx *= dx2; break; @@ -1167,7 +1167,7 @@ switch(b) { case 3: vdy *= Y[iy]; - //fall through + //$FALL-THROUGH$ case 2: vdy *= dy2; break; @@ -1187,7 +1187,7 @@ switch(c) { case 3: value *= Z[iz]; - //fall through + //$FALL-THROUGH$ case 2: value *= dz2; break; @@ -1198,7 +1198,7 @@ switch(d) { case 3: value *= r; - //fall through + //$FALL-THROUGH$ case 2: value *= r2; break; Modified: branches/v12_2/Jmol/src/org/jmol/script/ScriptCompilationTokenParser.java =================================================================== --- branches/v12_2/Jmol/src/org/jmol/script/ScriptCompilationTokenParser.java 2012-07-14 22:28:54 UTC (rev 17357) +++ branches/v12_2/Jmol/src/org/jmol/script/ScriptCompilationTokenParser.java 2012-07-16 00:16:21 UTC (rev 17358) @@ -689,7 +689,7 @@ break; case Token.branch: allowComma = false; - // fall through + //$FALL-THROUGH$ case Token.atomtype: case Token.atomname: case Token.basepair: Modified: branches/v12_2/Jmol/src/org/jmol/script/ScriptCompiler.java =================================================================== --- branches/v12_2/Jmol/src/org/jmol/script/ScriptCompiler.java 2012-07-14 22:28:54 UTC (rev 17357) +++ branches/v12_2/Jmol/src/org/jmol/script/ScriptCompiler.java 2012-07-16 00:16:21 UTC (rev 17358) @@ -1250,7 +1250,7 @@ case Token.endifcmd: if (flowContext != null) flowContext.forceEndIf = false; - // fall through + //$FALL-THROUGH$ case Token.elsecmd: if (nTokens > 0) { isEndOfCommand = true; @@ -1261,7 +1261,7 @@ case Token.forcmd: if (bracketCount > 0) // ignore [FOR], as in 1C4D break; - // fall through + //$FALL-THROUGH$ case Token.casecmd: case Token.defaultcmd: case Token.elseif: @@ -1316,7 +1316,7 @@ flowContext.forceEndIf = false; return CONTINUE; } - // fall through + //$FALL-THROUGH$ case Token.leftparen: parenCount++; // the select() function uses dual semicolon notation @@ -1342,7 +1342,7 @@ } } braceCount--; - // fall through + //$FALL-THROUGH$ case Token.rightparen: parenCount--; if (parenCount < 0) @@ -1969,7 +1969,7 @@ case Token.catchcmd: pushCount++; vPush.add(ct); - // fall through + //$FALL-THROUGH$ case Token.ifcmd: case Token.switchcmd: default: @@ -2562,7 +2562,7 @@ default: if (!Character.isLetter(ch)) return false; - //fall through + //$FALL-THROUGH$ case '~': case '_': case '\'': Modified: branches/v12_2/Jmol/src/org/jmol/script/ScriptEvaluator.java =================================================================== --- branches/v12_2/Jmol/src/org/jmol/script/ScriptEvaluator.java 2012-07-14 22:28:54 UTC (rev 17357) +++ branches/v12_2/Jmol/src/org/jmol/script/ScriptEvaluator.java 2012-07-16 00:16:21 UTC (rev 17358) @@ -907,7 +907,7 @@ tok = Token.all; iToken += 2; } - // fall through + //$FALL-THROUGH$ case Token.all: if (tok == Token.all) v = viewer.getModelUndeletedAtomsBitSet(-1); @@ -952,7 +952,7 @@ if (tokAt(iToken + 3) == Token.per && tokAt(iToken + 4) == Token.bin) tok2 = Token.selectedfloat; - // fall through + //$FALL-THROUGH$ case Token.min: case Token.max: case Token.stddev: @@ -1407,7 +1407,7 @@ case Token.sum2: case Token.stddev: sum2 += ((double) fv) * fv; - // fall through + //$FALL-THROUGH$ case Token.sum: default: sum += fv; @@ -1479,7 +1479,7 @@ case Token.sum2: case Token.stddev: sum2 += ((double) iv) * iv; - // fall through + //$FALL-THROUGH$ case Token.sum: default: sum += iv; @@ -1542,7 +1542,7 @@ case Token.sum2: case Token.stddev: sum2 += (double) fv * fv; - // fall through + //$FALL-THROUGH$ case Token.sum: default: sum += fv; @@ -3162,7 +3162,7 @@ sb.append(' '); // if (token.intValue == Integer.MAX_VALUE) sb.append(inBrace ? "-" : "- "); - // fall through + //$FALL-THROUGH$ case Token.spec_seqcode: if (token.intValue != Integer.MAX_VALUE) sb.append(token.intValue); @@ -3180,7 +3180,7 @@ continue; case Token.spec_model: sb.append("*/"); - // fall through + //$FALL-THROUGH$ case Token.spec_model2: case Token.decimal: if (token.intValue < Integer.MAX_VALUE) { @@ -4180,7 +4180,7 @@ switch (tokAt(index)) { case Token.integer: useModelNumber = true; - // fall through + //$FALL-THROUGH$ case Token.decimal: iFrame = getToken(index).intValue; // decimal Token intValue is // model/frame number encoded @@ -4687,7 +4687,7 @@ plane = getPoint4f(i); break; } - // fall through + //$FALL-THROUGH$ case Token.bitset: case Token.expressionBegin: Point3f pt1 = atomCenterOrCoordinateParameter(i); @@ -4836,7 +4836,7 @@ default: if (!Token.tokAttr(theTok, Token.identifier)) break; - // fall through + //$FALL-THROUGH$ case Token.navy: case Token.string: return Graphics3D.getArgbFromString(parameterAsString(index)); @@ -6625,7 +6625,7 @@ viewer.navigate(timeSec, path, theta, 0, Integer.MAX_VALUE); continue; } - // fall through + //$FALL-THROUGH$ default: error(ERROR_invalidArgument); } @@ -6783,7 +6783,7 @@ switch (getToken(i).tok) { case Token.smiles: isSmiles = true; - // fall through + //$FALL-THROUGH$ case Token.search: strSmiles = stringParameter(++i); break; @@ -7254,7 +7254,7 @@ if (!haveOperation) operation = Token.modifyorcreate; haveOperation = true; - // fall through + //$FALL-THROUGH$ case Token.identifier: case Token.aromatic: case Token.hbond: @@ -7501,6 +7501,7 @@ else if (iShape == JmolConstants.SHAPE_PMESH && !isWild) return getIsosurfaceJvxl(true, JmolConstants.SHAPE_PMESH); s += (String) getShapeProperty(iShape, "command") + "\n"; + break; case Token.color: colorShape(iShape, iTok + 1, false); break; @@ -8136,7 +8137,7 @@ case 5: // parameters 3 and 4 are just for the ride: [end] and ["key"] dataString = parameterAsString(2); - // fall through + //$FALL-THROUGH$ case 4: case 2: dataLabel = parameterAsString(1); @@ -9259,6 +9260,7 @@ break; case Token.off: setShapeProperty(JmolConstants.SHAPE_MEASURES, "hide", countPlusIndexes); + break; default: setShapeProperty(JmolConstants.SHAPE_MEASURES, (strFormat == null ? "toggle" : "toggleOn"), countPlusIndexes); @@ -10940,7 +10942,7 @@ case Token.on: checkLength(2); TF = true; - // fall through + //$FALL-THROUGH$ case Token.off: checkLength(2); setBooleanProperty("slabEnabled", TF); @@ -11178,7 +11180,7 @@ break; case Token.decimal: isOnly = (floatParameter(1) < 0); - // fall through + //$FALL-THROUGH$ case Token.integer: default: rd = encodeRadiusParameter(1, isOnly, true); @@ -11471,7 +11473,7 @@ break; case Token.bitset: propertyName = "atomBitset"; - // fall through + //$FALL-THROUGH$ case Token.expressionBegin: if (propertyName == null) propertyName = (iHaveAtoms || iHaveCoord ? "endSet" : "startSet"); @@ -11727,7 +11729,7 @@ case Token.surface: isSurface = true; // deprecated - // fall through + //$FALL-THROUGH$ case Token.surfacedistance: /* * preferred: @@ -11896,7 +11898,7 @@ switch (getToken(1).tok) { case Token.on: animate = true; - // fall through + //$FALL-THROUGH$ case Token.off: if (!isSyntaxCheck) viewer.setAnimationOn(animate); @@ -12036,7 +12038,7 @@ useModelNumber = false; if ((fFrame = floatParameter(i)) < 0) error(ERROR_invalidArgument); - // fall through + //$FALL-THROUGH$ case Token.integer: case Token.string: if (nFrames == 2) @@ -12215,12 +12217,12 @@ if (scaleAngstromsPerPixel >= 5) // actually a zoom value scaleAngstromsPerPixel = viewer.getZoomSetting() / scaleAngstromsPerPixel / viewer.getScalePixelsPerAngstrom(false); - // fall through + //$FALL-THROUGH$ case 5: if (getToken(4).tok != Token.identifier) error(ERROR_invalidArgument); fontstyle = parameterAsString(4); - // fall through + //$FALL-THROUGH$ case 4: if (getToken(3).tok != Token.identifier) error(ERROR_invalidArgument); @@ -12458,7 +12460,7 @@ return; } newTok = Token.defaultvdw; - // fall through + //$FALL-THROUGH$ case Token.defaultvdw: // allows unquoted string for known vdw type if (statementLength > 2) { @@ -12771,7 +12773,7 @@ break; case Token.none: echoShapeActive = false; - // fall through + //$FALL-THROUGH$ case Token.all: // all and none get NO additional parameters; id = parameterAsString(2); @@ -13172,7 +13174,7 @@ case Token.measure: isMeasure = true; type = "MEASURE"; - // fall through + //$FALL-THROUGH$ case Token.select: if (checkLength34() == 4) i = 3; @@ -15446,7 +15448,7 @@ } if (tok == Token.nada) break; - // fall through to translucent + //$FALL-THROUGH$ to translucent case Token.translucent: case Token.opaque: okNoAtoms = true; @@ -15513,7 +15515,7 @@ case Token.nci: case Token.surface: localOnly = false; - // fall through + //$FALL-THROUGH$ case Token.trim: case Token.full: case Token.plane: @@ -15935,7 +15937,7 @@ v2 = new Vector3f(pts[2]); v2.sub(pts[0]); v2.scale(1000f); - // fall through + //$FALL-THROUGH$ case 2: // slab // "a b c" is really "z y x" v1 = new Vector3f(pts[1]); @@ -16032,7 +16034,7 @@ error(ERROR_invalidArgument); } isNegOffset = true; - // fall through + //$FALL-THROUGH$ case Token.homo: case Token.lumo: linearCombination = null; @@ -17856,7 +17858,7 @@ iToken++; else break; - // fall through + //$FALL-THROUGH$ case Token.opaque: case Token.translucent: if (!checkOnly) @@ -17892,7 +17894,7 @@ tok = Token.on; break; } - // fall through for on/off/display + //$FALL-THROUGH$ for on/off/display case Token.frontlit: case Token.backlit: case Token.fullylit: Modified: branches/v12_2/Jmol/src/org/jmol/script/ScriptMathProcessor.java =================================================================== --- branches/v12_2/Jmol/src/org/jmol/script/ScriptMathProcessor.java 2012-07-14 22:28:54 UTC (rev 17357) +++ branches/v12_2/Jmol/src/org/jmol/script/ScriptMathProcessor.java 2012-07-16 00:16:21 UTC (rev 17358) @@ -414,7 +414,7 @@ case Token.opNot: case Token.leftparen: isLeftOp = true; - // fall through + //$FALL-THROUGH$ default: if (isMathFunc) { if (!isDotSelector && wasX && !isArgument) @@ -615,7 +615,7 @@ switch (var.tok) { default: var = new ScriptVariable(Token.string, ScriptVariable.sValue(var)); - // fall through + //$FALL-THROUGH$ case Token.bitset: case Token.varray: case Token.string: @@ -1492,7 +1492,7 @@ return addX(""); return addX(Measure.getIntersection(pt2, null, plane, pt3, norm, vTemp)); } - // fall through + //$FALL-THROUGH$ case 3: case 4: switch (tok) { @@ -2547,7 +2547,7 @@ break; case Token.decimal: haveDecimal = true; - // fall through + //$FALL-THROUGH$ default: int n = ScriptVariable.iValue(var); float f = ScriptVariable.fValue(var); @@ -3459,7 +3459,7 @@ case Token.sum2: case Token.stddev: sum2 += ((double) v) * v; - // fall through + //$FALL-THROUGH$ case Token.sum: case Token.average: sum += v; Modified: branches/v12_2/Jmol/src/org/jmol/shape/Text.java =================================================================== --- branches/v12_2/Jmol/src/org/jmol/shape/Text.java 2012-07-14 22:28:54 UTC (rev 17357) +++ branches/v12_2/Jmol/src/org/jmol/shape/Text.java 2012-07-16 00:16:21 UTC (rev 17358) @@ -410,7 +410,7 @@ } else { strOff = "[" + movableXPercent + " " + movableYPercent + "%]"; } - //fall through + //$FALL-THROUGH$ case VALIGN_XYZ: if (strOff == null) strOff = Escape.escape(xyz); Modified: branches/v12_2/Jmol/src/org/jmol/shapespecial/Dots.java =================================================================== --- branches/v12_2/Jmol/src/org/jmol/shapespecial/Dots.java 2012-07-14 22:28:54 UTC (rev 17357) +++ branches/v12_2/Jmol/src/org/jmol/shapespecial/Dots.java 2012-07-16 00:16:21 UTC (rev 17358) @@ -198,7 +198,7 @@ if (rd.value == 0) isVisible = false; setRadius = rd.value; - // fall through + //$FALL-THROUGH$ default: rd.valueExtended = viewer.getCurrentSolventProbeRadius(); } Modified: branches/v12_2/Jmol/src/org/jmol/shapesurface/IsosurfaceMesh.java =================================================================== --- branches/v12_2/Jmol/src/org/jmol/shapesurface/IsosurfaceMesh.java 2012-07-14 22:28:54 UTC (rev 17357) +++ branches/v12_2/Jmol/src/org/jmol/shapesurface/IsosurfaceMesh.java 2012-07-16 00:16:21 UTC (rev 17358) @@ -326,7 +326,7 @@ case 1: if (f1 == 0) return; //because at A and not along BC, so only at A - // fall through + //$FALL-THROUGH$ case 2: // check CA only if v not found only at C already in testing BC f2 = (f2 == 1 ? Float.NaN : checkPt(vertexValues, iC, iA, value)); Modified: branches/v12_2/Jmol/src/org/jmol/shapesurface/MolecularOrbital.java =================================================================== --- branches/v12_2/Jmol/src/org/jmol/shapesurface/MolecularOrbital.java 2012-07-14 22:28:54 UTC (rev 17357) +++ branches/v12_2/Jmol/src/org/jmol/shapesurface/MolecularOrbital.java 2012-07-16 00:16:21 UTC (rev 17358) @@ -156,7 +156,7 @@ super.setProperty("color", value, bs); propertyName = "colorRGB"; myColorPt = 0; - //fall through + //$FALL-THROUGH$ } if ("colorRGB" == propertyName) { Modified: branches/v12_2/Jmol/src/org/jmol/smiles/SmilesParser.java =================================================================== --- branches/v12_2/Jmol/src/org/jmol/smiles/SmilesParser.java 2012-07-14 22:28:54 UTC (rev 17357) +++ branches/v12_2/Jmol/src/org/jmol/smiles/SmilesParser.java 2012-07-16 00:16:21 UTC (rev 17358) @@ -670,6 +670,7 @@ braceCount--; return true; } + break; default: return false; } Modified: branches/v12_2/Jmol/src/org/jmol/symmetry/HallInfo.java =================================================================== --- branches/v12_2/Jmol/src/org/jmol/symmetry/HallInfo.java 2012-07-14 22:28:54 UTC (rev 17357) +++ branches/v12_2/Jmol/src/org/jmol/symmetry/HallInfo.java 2012-07-16 00:16:21 UTC (rev 17358) @@ -247,7 +247,7 @@ c = code.charAt(2); ptr++; } - // fall through + //$FALL-THROUGH$ case '*': axisType = c; break; Modified: branches/v12_2/Jmol/src/org/jmol/symmetry/PointGroup.java =================================================================== --- branches/v12_2/Jmol/src/org/jmol/symmetry/PointGroup.java 2012-07-14 22:28:54 UTC (rev 17357) +++ branches/v12_2/Jmol/src/org/jmol/symmetry/PointGroup.java 2012-07-16 00:16:21 UTC (rev 17358) @@ -662,7 +662,7 @@ case c8: if (nAxes[c3] > 0) return false; - // fall through; + //$FALL-THROUGH$; case c6: case c4: if (nAxes[c5] > 0) Modified: branches/v12_2/Jmol/src/org/jmol/symmetry/UnitCell.java =================================================================== --- branches/v12_2/Jmol/src/org/jmol/symmetry/UnitCell.java 2012-07-14 22:28:54 UTC (rev 17357) +++ branches/v12_2/Jmol/src/org/jmol/symmetry/UnitCell.java 2012-07-16 00:16:21 UTC (rev 17358) @@ -84,10 +84,10 @@ switch (dimension) { case 3: pt.z = toFractional(pt.z); - // fall through + //$FALL-THROUGH$ case 2: pt.y = toFractional(pt.y); - // fall through + //$FALL-THROUGH$ case 1: pt.x = toFractional(pt.x); } @@ -98,10 +98,10 @@ switch (dimension) { case 3: pt.z = toFractional(pt.z); - // fall through + //$FALL-THROUGH$ case 2: pt.y = toFractional(pt.y); - // fall through + //$FALL-THROUGH$ case 1: pt.x = toFractional(pt.x); } @@ -170,7 +170,7 @@ case 1: // polymer minXYZ.y = 0; maxXYZ.y = 1; - // fall through + //$FALL-THROUGH$ case 2: // slab minXYZ.z = 0; maxXYZ.z = 1; Modified: branches/v12_2/Jmol/src/org/jmol/util/SurfaceFileTyper.java =================================================================== --- branches/v12_2/Jmol/src/org/jmol/util/SurfaceFileTyper.java 2012-07-14 22:28:54 UTC (rev 17357) +++ branches/v12_2/Jmol/src/org/jmol/util/SurfaceFileTyper.java 2012-07-16 00:16:21 UTC (rev 17358) @@ -68,6 +68,7 @@ case '@': if (line.indexOf("@text") == 0) return "Kinemage"; + break; case '#': if (line.indexOf(".obj") >= 0) return "Obj"; // #file: pymol.obj Modified: branches/v12_2/Jmol/src/org/jmol/viewer/ActionManager.java =================================================================== --- branches/v12_2/Jmol/src/org/jmol/viewer/ActionManager.java 2012-07-14 22:28:54 UTC (rev 17357) +++ branches/v12_2/Jmol/src/org/jmol/viewer/ActionManager.java 2012-07-16 00:16:21 UTC (rev 17358) @@ -1798,10 +1798,10 @@ return; case PICKING_MEASURE_TORSION: n++; - // fall through + //$FALL-THROUGH$ case PICKING_MEASURE_ANGLE: n++; - // fall through + //$FALL-THROUGH$ case PICKING_MEASURE: case PICKING_MEASURE_DISTANCE: case PICKING_MEASURE_SEQUENCE: Modified: branches/v12_2/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v12_2/Jmol/src/org/jmol/viewer/Jmol.properties 2012-07-14 22:28:54 UTC (rev 17357) +++ branches/v12_2/Jmol/src/org/jmol/viewer/Jmol.properties 2012-07-16 00:16:21 UTC (rev 17358) @@ -6,6 +6,9 @@ version=12.2.34_dev +# bug fix: show $d1 where d1 is a DRAW object broken +# bug fix: calculate hydrogens incorrect for proteins + # ------------------------------------------------------------------------------ #version=12.2.33 Modified: branches/v12_2/Jmol/src/org/jmol/viewer/JmolConstants.java =================================================================== --- branches/v12_2/Jmol/src/org/jmol/viewer/JmolConstants.java 2012-07-14 22:28:54 UTC (rev 17357) +++ branches/v12_2/Jmol/src/org/jmol/viewer/JmolConstants.java 2012-07-16 00:16:21 UTC (rev 17358) @@ -1100,6 +1100,7 @@ switch (group3.length()){ case 1: sb.append(" "); + break; case 2: sb.append(" "); } Modified: branches/v12_2/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- branches/v12_2/Jmol/src/org/jmol/viewer/Viewer.java 2012-07-14 22:28:54 UTC (rev 17357) +++ branches/v12_2/Jmol/src/org/jmol/viewer/Viewer.java 2012-07-16 00:16:21 UTC (rev 17358) @@ -3612,7 +3612,7 @@ switch (tok) { case Token.playrev: animationManager.reverseAnimation(); - // fall through + //$FALL-THROUGH$ case Token.play: case Token.resume: if (!animationManager.animationOn) @@ -9648,7 +9648,7 @@ break; case 0: n = Integer.MAX_VALUE; - // fall through + //$FALL-THROUGH$ default: if (n > MAX_ACTION_UNDO) n = (action == Token.undomove ? actionStates : actionStatesRedo).size(); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2012-07-16 15:40:20
|
Revision: 17362 http://jmol.svn.sourceforge.net/jmol/?rev=17362&view=rev Author: hansonr Date: 2012-07-16 15:40:08 +0000 (Mon, 16 Jul 2012) Log Message: ----------- version=12.2.34_dev # bug fix: isosurface MINSET or SET not compatible with SLAB Modified Paths: -------------- branches/v12_2/Jmol/src/org/jmol/util/MeshSurface.java branches/v12_2/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v12_2/Jmol/src/org/jmol/util/MeshSurface.java =================================================================== --- branches/v12_2/Jmol/src/org/jmol/util/MeshSurface.java 2012-07-16 15:39:43 UTC (rev 17361) +++ branches/v12_2/Jmol/src/org/jmol/util/MeshSurface.java 2012-07-16 15:40:08 UTC (rev 17362) @@ -409,7 +409,7 @@ } private int addIntersectionVertex(Point3f vertex, float value, int source, - Map<String, Integer> mapEdge, int i1, int i2) { + int set, Map<String, Integer> mapEdge, int i1, int i2) { String key = (i1 > i2 ? i2 + "_" + i1 : i1 + "_" + i2); if (i1 >= 0) { @@ -424,6 +424,12 @@ vertexSource = ArrayUtil.doubleLength(vertexSource); vertexSource[vertexCount] = source; } + if (vertexSets != null) { + if (vertexCount >= vertexSets.length) + vertexSets = ArrayUtil.doubleLength(vertexSets); + vertexSets[vertexCount] = set; + } + int i = addVertexCopy(vertex, value); mapEdge.put(key, Integer.valueOf(i)); return i; @@ -488,7 +494,7 @@ float[] fracs = new float[2]; double absD = Math.abs(distance); float d1, d2, d3, valA, valB, valC; - int sourceA = 0, sourceB = 0, sourceC = 0; + int sourceA = 0, sourceB = 0, sourceC = 0, setA = 0; List<int[]> iPts = (andCap ? new ArrayList<int[]>() : null); if (polygonCount == 0) { for (int i = mergeVertexCount0; i < vertexCount; i++) { @@ -517,6 +523,9 @@ sourceB = vertexSource[iB]; sourceC = vertexSource[iC]; } + if (vertexSets != null) + setA = vertexSets[iA]; + d1 = checkSlab(tokType, vA, valA, distance, plane, ptCenters); d2 = checkSlab(tokType, vB, valB, distance, plane, ptCenters); d3 = checkSlab(tokType, vC, valC, distance, plane, ptCenters); @@ -636,11 +645,11 @@ if (!getDE(fracs, 0, iA, iB, iC, tossBC)) break; if (iD < 0) - iD = addIntersectionVertex(pts[0], values[0], sourceA, mapEdge, - iA, iB); + iD = addIntersectionVertex(pts[0], values[0], sourceA, setA, + mapEdge, iA, iB); if (iE < 0) - iE = addIntersectionVertex(pts[1], values[1], sourceA, mapEdge, - iA, iC); + iE = addIntersectionVertex(pts[1], values[1], sourceA, setA, + mapEdge, iA, iC); bs = (tossBC ? bsSlab : bsSlabGhost); addPolygon(iA, iD, iE, check1 & 5 | 2, check2, 0, bs); if (!isGhost) @@ -651,13 +660,13 @@ break; bs = (tossBC ? bsSlabGhost : bsSlab); if (iE < 0) { - iE = addIntersectionVertex(pts[0], values[0], sourceB, mapEdge, iA, - iB); + iE = addIntersectionVertex(pts[0], values[0], sourceB, setA, mapEdge, + iA, iB); addPolygon(iE, iB, iC, check1 & 3, check2, 0, bs); } if (iD < 0) { - iD = addIntersectionVertex(pts[1], values[1], sourceC, mapEdge, iA, - iC); + iD = addIntersectionVertex(pts[1], values[1], sourceC, setA, mapEdge, + iA, iC); addPolygon(iD, iE, iC, check1 & 4 | 1, check2, 0, bs); } break; @@ -676,11 +685,11 @@ break; bs = (tossAC ? bsSlab : bsSlabGhost); if (iE < 0) - iE = addIntersectionVertex(pts[0], values[0], sourceB, mapEdge, - iB, iA); + iE = addIntersectionVertex(pts[0], values[0], sourceB, setA, + mapEdge, iB, iA); if (iD < 0) - iD = addIntersectionVertex(pts[1], values[1], sourceB, mapEdge, - iB, iC); + iD = addIntersectionVertex(pts[1], values[1], sourceB, setA, + mapEdge, iB, iC); addPolygon(iE, iB, iD, check1 & 3 | 4, check2, 0, bs); if (!isGhost) break; @@ -690,13 +699,13 @@ break; bs = (tossAC ? bsSlabGhost : bsSlab); if (iD < 0) { - iD = addIntersectionVertex(pts[0], values[0], sourceA, mapEdge, iB, - iA); + iD = addIntersectionVertex(pts[0], values[0], sourceA, setA, mapEdge, + iB, iA); addPolygon(iA, iD, iC, check1 & 5, check2, 0, bs); } if (iE < 0) { - iE = addIntersectionVertex(pts[1], values[1], sourceC, mapEdge, iB, - iC); + iE = addIntersectionVertex(pts[1], values[1], sourceC, setA, mapEdge, + iB, iC); addPolygon(iD, iE, iC, check1 & 2 | 1, check2, 0, bs); } break; @@ -713,11 +722,11 @@ if (!getDE(fracs, 0, iC, iA, iB, tossAB)) break; if (iD < 0) - iD = addIntersectionVertex(pts[0], values[0], sourceC, mapEdge, - iA, iC); //CA + iD = addIntersectionVertex(pts[0], values[0], sourceC, setA, + mapEdge, iA, iC); //CA if (iE < 0) - iE = addIntersectionVertex(pts[1], values[1], sourceC, mapEdge, - iB, iC); //CB + iE = addIntersectionVertex(pts[1], values[1], sourceC, setA, + mapEdge, iB, iC); //CB bs = (tossAB ? bsSlab : bsSlabGhost); addPolygon(iD, iE, iC, check1 & 6 | 1, check2, 0, bs); if (!isGhost) @@ -728,13 +737,13 @@ break; bs = (tossAB ? bsSlabGhost : bsSlab); if (iE < 0) { - iE = addIntersectionVertex(pts[0], values[0], sourceA, mapEdge, iA, - iC); //CA + iE = addIntersectionVertex(pts[0], values[0], sourceA, setA, mapEdge, + iA, iC); //CA addPolygon(iA, iB, iE, check1 & 5, check2, 0, bs); } if (iD < 0) { - iD = addIntersectionVertex(pts[1], values[1], sourceB, mapEdge, iB, - iC); //CB + iD = addIntersectionVertex(pts[1], values[1], sourceB, setA, mapEdge, + iB, iC); //CB addPolygon(iE, iB, iD, check1 & 2 | 4, check2, 0, bs); } break; @@ -759,7 +768,7 @@ center.add(vertices[ipts[1]]); } center.scale(0.5f / iPts.size()); - int v0 = addIntersectionVertex(center, 0, -1, mapEdge, -1, -1); + int v0 = addIntersectionVertex(center, 0, -1, setA, mapEdge, -1, -1); for (int i = iPts.size(); --i >= 0;) { int[] ipts = iPts.get(i); //int p = Modified: branches/v12_2/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v12_2/Jmol/src/org/jmol/viewer/Jmol.properties 2012-07-16 15:39:43 UTC (rev 17361) +++ branches/v12_2/Jmol/src/org/jmol/viewer/Jmol.properties 2012-07-16 15:40:08 UTC (rev 17362) @@ -6,6 +6,7 @@ version=12.2.34_dev +# bug fix: isosurface MINSET or SET not compatible with SLAB # bug fix: show $d1 where d1 is a DRAW object broken # bug fix: calculate hydrogens incorrect for proteins This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2012-07-18 02:50:56
|
Revision: 17367 http://jmol.svn.sourceforge.net/jmol/?rev=17367&view=rev Author: hansonr Date: 2012-07-18 02:50:49 +0000 (Wed, 18 Jul 2012) Log Message: ----------- version=12.2.34_dev # bug fix: isosurface SOLVENT producing cavity-like artifacts Modified Paths: -------------- branches/v12_2/Jmol/src/org/jmol/jvxl/readers/IsoSolventReader.java branches/v12_2/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v12_2/Jmol/src/org/jmol/jvxl/readers/IsoSolventReader.java =================================================================== --- branches/v12_2/Jmol/src/org/jmol/jvxl/readers/IsoSolventReader.java 2012-07-17 22:22:52 UTC (rev 17366) +++ branches/v12_2/Jmol/src/org/jmol/jvxl/readers/IsoSolventReader.java 2012-07-18 02:50:49 UTC (rev 17367) @@ -451,10 +451,37 @@ // created when the toroidal surfaces are split by faces. setVertexSource(); if (doCalculateTroughs && bsSurfacePoints != null) { + BitSet bsAll = new BitSet(); BitSet[] bsSurfaces = meshData.getSurfaceSet(); - for (int i = 0; i < meshData.nSets; i++) - if (!bsSurfaces[i].intersects(bsSurfacePoints)) - meshData.invalidateSurfaceSet(i); + BitSet[] bsSources = null; + double[] volumes = (double[]) (isPocket ? null : meshData + .calculateVolumeOrArea(-1, true, false)); + for (int i = 0; i < meshData.nSets; i++) { + BitSet bss = bsSurfaces[i]; + if (bss.intersects(bsSurfacePoints)) { + if (volumes == null || Math.abs(volumes[i]) > 1.7) // 1.2^3 + //doesn't allow for cavities, but doCalculateTroughs takes care of that + if (params.vertexSource != null) { + BitSet bs = new BitSet(); + if (bsSources == null) + bsSources = new BitSet[bsSurfaces.length]; + // don't allow two surfaces to involve the same atom. + for (int j = bss.nextSetBit(0); j >= 0; j = bss.nextSetBit(j + 1)) { + int iatom = params.vertexSource[j]; + if (iatom < 0) + continue; + if (bsAll.get(iatom)) { + meshData.invalidateSurfaceSet(i); + break; + } + bs.set(iatom); + } + bsAll.or(bs); + continue; + } + } + meshData.invalidateSurfaceSet(i); + } updateSurfaceData(); if (meshDataServer != null) { meshDataServer.fillMeshData(meshData, MeshData.MODE_PUT_SETS, null); Modified: branches/v12_2/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v12_2/Jmol/src/org/jmol/viewer/Jmol.properties 2012-07-17 22:22:52 UTC (rev 17366) +++ branches/v12_2/Jmol/src/org/jmol/viewer/Jmol.properties 2012-07-18 02:50:49 UTC (rev 17367) @@ -6,6 +6,7 @@ version=12.2.34_dev +# bug fix: isosurface SOLVENT producing cavity-like artifacts # bug fix: isosurface MINSET or SET not compatible with SLAB # bug fix: show $d1 where d1 is a DRAW object broken # bug fix: calculate hydrogens incorrect for proteins This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |