From: <ha...@us...> - 2007-06-17 17:35:27
|
Revision: 7882 http://svn.sourceforge.net/jmol/?rev=7882&view=rev Author: hansonr Date: 2007-06-17 10:35:26 -0700 (Sun, 17 Jun 2007) Log Message: ----------- 11.2.0 -- perspectiveModel 11 default Modified Paths: -------------- branches/v11_2/Jmol/src/org/jmol/viewer/StateManager.java branches/v11_2/Jmol/src/org/jmol/viewer/TransformManager.java branches/v11_2/Jmol/src/org/jmol/viewer/TransformManager10.java Modified: branches/v11_2/Jmol/src/org/jmol/viewer/StateManager.java =================================================================== --- branches/v11_2/Jmol/src/org/jmol/viewer/StateManager.java 2007-06-17 17:35:11 UTC (rev 7881) +++ branches/v11_2/Jmol/src/org/jmol/viewer/StateManager.java 2007-06-17 17:35:26 UTC (rev 7882) @@ -634,7 +634,7 @@ //handle these specially for the CURRENT FILE, their current //settings won't be reflected in the load state, which is determined //earlier, when the file loads. - ";refreshing;defaults;backgroundmodel;stereo;" + ";refreshing;defaults;backgroundmodel;stereo;perspectivemodel;" + ";appendnew;bondsymmetryatoms;backgroundcolor;axescolor;axis1color;axis2color;axis3color;boundboxcolor;unitcellcolor;" + ";ambientpercent;diffusepercent;specular;specularexponent;specularpower;specularpercent;" + ";debugscript;showfrank;showaxes;showaxis1;showaxis2;showaxis3;showunitcell;showboundbox;" Modified: branches/v11_2/Jmol/src/org/jmol/viewer/TransformManager.java =================================================================== --- branches/v11_2/Jmol/src/org/jmol/viewer/TransformManager.java 2007-06-17 17:35:11 UTC (rev 7881) +++ branches/v11_2/Jmol/src/org/jmol/viewer/TransformManager.java 2007-06-17 17:35:26 UTC (rev 7882) @@ -45,6 +45,7 @@ final static float radiansPerDegree = (float) (2 * Math.PI / 360); final static float degreesPerRadian = (float) (360 / (2 * Math.PI)); + protected int perspectiveModel = 11; protected float cameraScaleFactor; protected float referencePlaneOffset; protected float modelCenterOffset; @@ -141,6 +142,7 @@ String getState() { StringBuffer commands = new StringBuffer( "# orientation/center/spin state;\nset refreshing false;\n"); + commands.append("perspectiveModel = "+ perspectiveModel +";\n"); if (!isWindowCentered()) commands.append("windowCentered = false;\n"); commands.append("cameraDepth = ").append(cameraDepth).append(";\n"); Modified: branches/v11_2/Jmol/src/org/jmol/viewer/TransformManager10.java =================================================================== --- branches/v11_2/Jmol/src/org/jmol/viewer/TransformManager10.java 2007-06-17 17:35:11 UTC (rev 7881) +++ branches/v11_2/Jmol/src/org/jmol/viewer/TransformManager10.java 2007-06-17 17:35:26 UTC (rev 7882) @@ -29,10 +29,12 @@ TransformManager10(Viewer viewer) { super(viewer); + perspectiveModel = 10; } TransformManager10(Viewer viewer, int width, int height) { super(viewer, width, height); + perspectiveModel = 10; } // older Jmol 10 method This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2007-06-21 03:19:54
|
Revision: 7892 http://svn.sourceforge.net/jmol/?rev=7892&view=rev Author: hansonr Date: 2007-06-20 20:19:37 -0700 (Wed, 20 Jun 2007) Log Message: ----------- 11.2.1 bug fix for spin save state wrong direction Modified Paths: -------------- branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties branches/v11_2/Jmol/src/org/jmol/viewer/TransformManager.java Modified: branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties 2007-06-20 15:12:43 UTC (rev 7891) +++ branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties 2007-06-21 03:19:37 UTC (rev 7892) @@ -1,9 +1,10 @@ -version=11.2.1_dev +version=11.2.1 # bug fix for 3D text echo staying in window # bug fix for draw text+translucency # bug fix for draw text not hovering for points # bug fix for multiple draw objects in show state +# bug fix for spin save reversed direction # ----------------------------------------------------------------------------- Modified: branches/v11_2/Jmol/src/org/jmol/viewer/TransformManager.java =================================================================== --- branches/v11_2/Jmol/src/org/jmol/viewer/TransformManager.java 2007-06-20 15:12:43 UTC (rev 7891) +++ branches/v11_2/Jmol/src/org/jmol/viewer/TransformManager.java 2007-06-21 03:19:37 UTC (rev 7892) @@ -193,15 +193,15 @@ s +="\nselect " + Escape.escape(viewer.getSelectionSet()) + ";\nrotateSelected "; if (isSpinInternal) { Point3f pt = new Point3f(internalRotationCenter); - pt.add(rotationAxis); - s += "spin " + rotationRate + " " + pt.sub(rotationAxis); + s += "\nspin " + rotationRate + " " + Escape.escape(internalRotationCenter) + " " + Escape.escape(pt); } else if (isSpinFixed) { - s += "spin axisangle " + Escape.escape(rotationAxis) + " " + s += "\nspin axisangle " + Escape.escape(rotationAxis) + " " + rotationRate; } else { - s += "spin on"; + s += "\nspin on"; } s += ";"; } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2007-06-28 03:08:06
|
Revision: 7911 http://svn.sourceforge.net/jmol/?rev=7911&view=rev Author: hansonr Date: 2007-06-27 20:08:01 -0700 (Wed, 27 Jun 2007) Log Message: ----------- 11.2.2 # bug fix: debugscript on;center 3-5; "-" missing # bug fix: zoomTo (5-7) read as "5 to -7" # bug fix: move with time < 0.03 seconds causes molecule to disappear Modified Paths: -------------- branches/v11_2/Jmol/src/org/jmol/viewer/Compiler.java branches/v11_2/Jmol/src/org/jmol/viewer/Eval.java branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties branches/v11_2/Jmol/src/org/jmol/viewer/TransformManager.java Modified: branches/v11_2/Jmol/src/org/jmol/viewer/Compiler.java =================================================================== --- branches/v11_2/Jmol/src/org/jmol/viewer/Compiler.java 2007-06-28 03:02:48 UTC (rev 7910) +++ branches/v11_2/Jmol/src/org/jmol/viewer/Compiler.java 2007-06-28 03:08:01 UTC (rev 7911) @@ -1724,8 +1724,14 @@ return false; int tok = tokPeek(); if (tok == Token.hyphen || tok == Token.integer && intPeek() < 0) { - if (tok == Token.hyphen) + if (tok == Token.hyphen) { tokenNext(); + } else if (tokPeek() == Token.integer && intPeek() < 0) { + // hyphen masquerading as neg int + int i = -intPeek(); + tokenNext().intValue = i; + returnToken(); + } seqToken.tok = Token.spec_seqcode_range; generateResidueSpecCode(seqToken); seqToken = getSequenceCode(true); @@ -1734,21 +1740,33 @@ return generateResidueSpecCode(seqToken); } - private Token getSequenceCode(boolean allowNull) { + private Token getSequenceCode(boolean isSecond) { + // problem is that some commands, like zoomTo allow negative numbers, + // while other, like center, do not. + // + // (25 [-] 35) ==> 25 - 35 + // (25 -35) ==> 25 - 35 + + // (25 [-] [-] 35) ==> 25 - -35 + // (25 [-] -35) ==> 25 - -35 + + // ([-] 25 [-] 35) ==> -25 - 35 + // (-25 -35) ==> -25 - 35 + boolean negative = false; int seqcode = Integer.MAX_VALUE; int seqvalue = Integer.MAX_VALUE; int tokPeek = tokPeek(); if (tokPeek == Token.hyphen) { tokenNext(); + tokPeek = tokPeek(); negative = true; - tokPeek = tokPeek(); } if (tokPeek == Token.seqcode) seqcode = tokenNext().intValue * (negative ? -1 : 1); else if (tokPeek == Token.integer) seqvalue = tokenNext().intValue * (negative ? -1 : 1); - else if (!allowNull){ + else if (!isSecond){ if (negative) returnToken(); return null; Modified: branches/v11_2/Jmol/src/org/jmol/viewer/Eval.java =================================================================== --- branches/v11_2/Jmol/src/org/jmol/viewer/Eval.java 2007-06-28 03:02:48 UTC (rev 7910) +++ branches/v11_2/Jmol/src/org/jmol/viewer/Eval.java 2007-06-28 03:08:01 UTC (rev 7911) @@ -1997,6 +1997,12 @@ switch (getToken(i).tok) { case Token.dollarsign: String id = objectNameParameter(++i); + // allow for $pt2.3 -- specific vertex + if (tokAt(i + 1) == Token.leftsquare) { + id += "." + intParameter(i + 2); + if (getToken(i + 3).tok != Token.rightsquare) + invalidArgument(); + } if (isSyntaxCheck) return new Point3f(); if ((center = getDrawObjectCenter(id)) == null) @@ -4150,6 +4156,20 @@ } break; case Token.dollarsign: + // $drawObject[n] + if (tokAt(i + 2) == Token.leftsquare) { + Point3f pt1 = centerParameter(i); + i = iToken; + if (isAxisAngle) { + if (axesOrientationRasmol) + pt1.y = -pt1.y; + rotAxis.set(pt1); + isAxisAngle = false; + } else { + points[nPoints++].set(pt1); + } + break; + } // $drawObject isInternal = true; axisID = objectNameParameter(++i); @@ -4157,6 +4177,9 @@ rotCenter = new Point3f(); rotAxis = new Vector3f(); } else { + //I was going to make this dependent upon type, but + //upon reflection, I think it is correct. + //bh rotCenter = getDrawObjectCenter(axisID); rotAxis = getDrawObjectAxis(axisID); if (rotCenter == null) @@ -4242,6 +4265,11 @@ "getSpinCenter:" + axisID); } + int getDrawObjectType(String axisID) { + return ((Integer) viewer.getShapeProperty(JmolConstants.SHAPE_DRAW, + "getType:" + axisID)).intValue(); + } + Vector3f getDrawObjectAxis(String axisID) { return (Vector3f) viewer.getShapeProperty(JmolConstants.SHAPE_DRAW, "getSpinAxis:" + axisID); @@ -4537,19 +4565,15 @@ } boolean isSameAtom = (center != null && currentCenter.distance(center) < 0.1); - - //zoom/zoomTo percent|-factor|+factor|*factor|/factor | 0 float factor = getZoomFactor(i, ptCenter, radius, zoom); - if (Float.isNaN(factor) && isZoomTo) { + if (isZoomTo) { // no factor -- check for no center (zoom out) or same center (zoom in) if (statementLength == 1 || isSameAtom) factor *= 2; else if (center == null) factor /= 2; - else - factor = zoom; } float xTrans = 0; float yTrans = 0; @@ -7721,7 +7745,17 @@ propertyName = "thisID"; break; case Token.dollarsign: + // $drawObject[m] + if (tokAt(i + 2) == Token.leftsquare) { + Point3f pt = centerParameter(i); + i = iToken; + propertyName = "coord"; + propertyValue = pt; + havePoints = true; + break; + } // $drawObject + propertyValue = objectNameParameter(++i); propertyName = "identifier"; havePoints = true; @@ -9115,7 +9149,7 @@ sb.append(Group.getSeqcodeString(getSeqCode(token))); token = statement[++i]; sb.append(' '); - if (token.intValue == Integer.MAX_VALUE) +// if (token.intValue == Integer.MAX_VALUE) sb.append("- "); //fall through case Token.spec_seqcode: Modified: branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties 2007-06-28 03:02:48 UTC (rev 7910) +++ branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties 2007-06-28 03:08:01 UTC (rev 7911) @@ -1,5 +1,9 @@ version=11.2.2_dev +# bug fix: debugscript on;center 3-5; "-" missing +# bug fix: zoomTo (5-7) read as "5 to -7" +# bug fix: move with time < 0.03 seconds causes molecule to disappear + # ----------------------------------------------------------------------------- #version=11.2.1 @@ -15,8 +19,31 @@ # version=11.2.0 +======= +# bug fix: debugscript on;center 3-5; "-" missing +# bug fix: zoomTo (5-7) read as "5 to -7" +# bug fix: move with time < 0.03 seconds causes molecule to disappear + +# ----------------------------------------------------------------------------- + +#version=11.3.0 + +>>>>>>> .merge-right.r7910 # perspectiveModel 11 default +# bug fix for 3D text echo staying in window +# bug fix for draw text+translucency +# bug fix for draw text not hovering for points +# bug fix for multiple draw objects in show state +# bug fix for spin save reversed direction +# bug fix for CdkAdapter not having auxiliaryInfo data +# +# adds the ability to find the coordinate of a specific +# draw object vertex using $objName[vertexId] as in +# draw p perp plane (atomno=1) (atomno=2) +# x = $p[3] +# draw pt1 $p[1] + # ----------------------------------------------------------------------------- #version=11.1.49 Modified: branches/v11_2/Jmol/src/org/jmol/viewer/TransformManager.java =================================================================== --- branches/v11_2/Jmol/src/org/jmol/viewer/TransformManager.java 2007-06-28 03:02:48 UTC (rev 7910) +++ branches/v11_2/Jmol/src/org/jmol/viewer/TransformManager.java 2007-06-28 03:08:01 UTC (rev 7911) @@ -1395,14 +1395,14 @@ long timeBegin = System.currentTimeMillis(); int timePerStep = 1000 / fps; int totalSteps = (int) (fps * floatSecondsTotal); + if (totalSteps == 0) + totalSteps = 1; // to catch a zero secondsTotal parameter float radiansPerDegreePerStep = (float) Math.PI / 180 / totalSteps; float radiansXStep = radiansPerDegreePerStep * dRot.x; float radiansYStep = radiansPerDegreePerStep * dRot.y; float radiansZStep = radiansPerDegreePerStep * dRot.z; viewer.setInMotion(true); float zoomPercent0 = zoomPercent; - if (totalSteps == 0) - totalSteps = 1; // to catch a zero secondsTotal parameter for (int i = 1; i <= totalSteps; ++i) { if (dRot.x != 0) rotateXRadians(radiansXStep); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2007-06-28 03:28:21
|
Revision: 7913 http://svn.sourceforge.net/jmol/?rev=7913&view=rev Author: hansonr Date: 2007-06-27 20:28:18 -0700 (Wed, 27 Jun 2007) Log Message: ----------- 11.2.2 bug fix: hover interruption Modified Paths: -------------- branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties branches/v11_2/Jmol/src/org/jmol/viewer/MouseManager.java Modified: branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties 2007-06-28 03:27:44 UTC (rev 7912) +++ branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties 2007-06-28 03:28:18 UTC (rev 7913) @@ -3,6 +3,7 @@ # bug fix: debugscript on;center 3-5; "-" missing # bug fix: zoomTo (5-7) read as "5 to -7" # bug fix: move with time < 0.03 seconds causes molecule to disappear +# bug fix: hover interruption # ----------------------------------------------------------------------------- Modified: branches/v11_2/Jmol/src/org/jmol/viewer/MouseManager.java =================================================================== --- branches/v11_2/Jmol/src/org/jmol/viewer/MouseManager.java 2007-06-28 03:27:44 UTC (rev 7912) +++ branches/v11_2/Jmol/src/org/jmol/viewer/MouseManager.java 2007-06-28 03:28:18 UTC (rev 7913) @@ -471,6 +471,8 @@ Logger.debug("mouseMoved("+x+","+y+","+modifiers"+)"); */ hoverOff(); + if (hoverWatcherThread == null) + startHoverWatcher(true); timeCurrent = mouseMovedTime = time; mouseMovedX = xCurrent = x; mouseMovedY = yCurrent = y; if (measurementMode || hoverActive) { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2007-06-28 17:49:09
|
Revision: 7917 http://svn.sourceforge.net/jmol/?rev=7917&view=rev Author: hansonr Date: 2007-06-28 10:49:05 -0700 (Thu, 28 Jun 2007) Log Message: ----------- 11.2.2 bug fix: image offsets in creating JPG image if model has been moved by CTRL-ALT-LEFT drag Modified Paths: -------------- branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties branches/v11_2/Jmol/src/org/jmol/viewer/TransformManager.java Modified: branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties 2007-06-28 17:48:13 UTC (rev 7916) +++ branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties 2007-06-28 17:49:05 UTC (rev 7917) @@ -4,6 +4,7 @@ # bug fix: zoomTo (5-7) read as "5 to -7" # bug fix: move with time < 0.03 seconds causes molecule to disappear # bug fix: hover interruption +# bug fix: image offsets in creating JPG image if model has been moved by CTRL-ALT-LEFT drag # ----------------------------------------------------------------------------- Modified: branches/v11_2/Jmol/src/org/jmol/viewer/TransformManager.java =================================================================== --- branches/v11_2/Jmol/src/org/jmol/viewer/TransformManager.java 2007-06-28 17:48:13 UTC (rev 7916) +++ branches/v11_2/Jmol/src/org/jmol/viewer/TransformManager.java 2007-06-28 17:49:05 UTC (rev 7917) @@ -1151,6 +1151,7 @@ // translate to the middle of the screen fixedTranslation.set(width * (andCenter ? 0.5f : xTranslationFraction), height * (andCenter ? 0.5f : yTranslationFraction), 0); + setTranslationFractions(); resetNavigationPoint(); // 2005 02 22 // switch to finding larger screen dimension This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2007-06-30 01:10:23
|
Revision: 7922 http://svn.sourceforge.net/jmol/?rev=7922&view=rev Author: hansonr Date: 2007-06-29 18:10:22 -0700 (Fri, 29 Jun 2007) Log Message: ----------- 11.2.3 bug fix: set picking label Modified Paths: -------------- branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties branches/v11_2/Jmol/src/org/jmol/viewer/PickingManager.java Modified: branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties 2007-06-30 01:09:44 UTC (rev 7921) +++ branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties 2007-06-30 01:10:22 UTC (rev 7922) @@ -1,5 +1,7 @@ version=11.2.3_dev +# bug fix: set picking label + # ----------------------------------------------------------------------------- #version=11.2.2 Modified: branches/v11_2/Jmol/src/org/jmol/viewer/PickingManager.java =================================================================== --- branches/v11_2/Jmol/src/org/jmol/viewer/PickingManager.java 2007-06-30 01:09:44 UTC (rev 7921) +++ branches/v11_2/Jmol/src/org/jmol/viewer/PickingManager.java 2007-06-30 01:10:22 UTC (rev 7922) @@ -123,7 +123,7 @@ toggleMeasurement(4); break; case JmolConstants.PICKING_LABEL: - viewer.script("toggleLabel = (atomindex="+atomIndex+")"); + viewer.script("toggleLabel = {atomindex="+atomIndex+"}"); break; case JmolConstants.PICKING_CENTER: viewer.script("zoomTo (atomindex=" + atomIndex+")"); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2007-06-30 16:22:59
|
Revision: 7926 http://svn.sourceforge.net/jmol/?rev=7926&view=rev Author: hansonr Date: 2007-06-30 09:22:57 -0700 (Sat, 30 Jun 2007) Log Message: ----------- 11.2.3 critical update bug fix # bug fix: set picking label # bug fix: minus-sign "fix" in 11.3.1 broke all {x -y z} notation # bug fix: state for phased atomic orbitals does not preserve red/blue color Modified Paths: -------------- branches/v11_2/Jmol/src/org/jmol/viewer/Eval.java branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v11_2/Jmol/src/org/jmol/viewer/Eval.java =================================================================== --- branches/v11_2/Jmol/src/org/jmol/viewer/Eval.java 2007-06-30 16:16:08 UTC (rev 7925) +++ branches/v11_2/Jmol/src/org/jmol/viewer/Eval.java 2007-06-30 16:22:57 UTC (rev 7926) @@ -2364,6 +2364,7 @@ return (Point4f) getToken(index).value; invalidArgument(); } + int multiplier = 1; out: for (int i = index; i < statement.length; i++) { switch (getToken(i).tok) { case Token.leftbrace: @@ -2373,12 +2374,18 @@ break; case Token.rightbrace: break out; + case Token.spec_seqcode_range: + if (n == 6) + invalidArgument(); + coord[n++] = theToken.intValue; + multiplier = -1; + break; case Token.integer: - case Token.spec_seqcode_range: case Token.spec_seqcode: if (n == 6) invalidArgument(); - coord[n++] = theToken.intValue; + coord[n++] = theToken.intValue * multiplier; + multiplier = 1; break; case Token.slash: getToken(++i); @@ -7123,7 +7130,7 @@ pt += 2; type = "VAR"; } else { - type = "image"; + type = "image"; } break; } @@ -9098,6 +9105,7 @@ int tok = statement[0].tok; boolean addParens = (Compiler.tokAttr(tok, Token.embeddedExpression)); boolean useBraces = (tok == Token.ifcmd || tok == Token.set); + boolean inBrace = false; for (int i = 0; i < statementLength; ++i) { if (iToken == i - 1) sb.append(" <<"); @@ -9122,6 +9130,10 @@ case Token.leftsquare: case Token.rightsquare: break; + case Token.leftbrace: + case Token.rightbrace: + inBrace = (token.tok == Token.leftbrace); + break; case Token.define: if (i > 0) sb.append("@"); @@ -9150,7 +9162,7 @@ token = statement[++i]; sb.append(' '); // if (token.intValue == Integer.MAX_VALUE) - sb.append("- "); + sb.append(inBrace ? "-" : "- "); //fall through case Token.spec_seqcode: if (token.intValue != Integer.MAX_VALUE) Modified: branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties 2007-06-30 16:16:08 UTC (rev 7925) +++ branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties 2007-06-30 16:22:57 UTC (rev 7926) @@ -1,7 +1,9 @@ -version=11.2.3_dev +version=11.2.3 # bug fix: set picking label - +# bug fix: minus-sign "fix" in 11.3.1 broke all {x -y z} notation +# bug fix: state for phased atomic orbitals does not preserve red/blue color + # ----------------------------------------------------------------------------- #version=11.2.2 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2007-07-23 10:19:25
|
Revision: 7981 http://svn.sourceforge.net/jmol/?rev=7981&view=rev Author: hansonr Date: 2007-07-23 03:19:21 -0700 (Mon, 23 Jul 2007) Log Message: ----------- 11.2.5 bug fix: set spin X was case-selective Modified Paths: -------------- branches/v11_2/Jmol/src/org/jmol/viewer/Eval.java branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v11_2/Jmol/src/org/jmol/viewer/Eval.java =================================================================== --- branches/v11_2/Jmol/src/org/jmol/viewer/Eval.java 2007-07-23 10:19:05 UTC (rev 7980) +++ branches/v11_2/Jmol/src/org/jmol/viewer/Eval.java 2007-07-23 10:19:21 UTC (rev 7981) @@ -6857,6 +6857,7 @@ } void setSpin(String key, int value) throws ScriptException { + key = key.toLowerCase(); if (Parser.isOneOf(key, "x;y;z;fps")) { if (isSyntaxCheck) return; Modified: branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties 2007-07-23 10:19:05 UTC (rev 7980) +++ branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties 2007-07-23 10:19:21 UTC (rev 7981) @@ -4,6 +4,7 @@ # note that xmlReader (SAX reader) is now set to ignore all DOCTYPE declarations # bug fix: odydata fix for files with \r\n for line ending # bug fix for PDB remediated T/DT difference of C5M/C7 +# bug fix: set spin X was case-selective # ----------------------------------------------------------------------------- This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2007-07-24 14:22:08
|
Revision: 8004 http://svn.sourceforge.net/jmol/?rev=8004&view=rev Author: hansonr Date: 2007-07-24 07:22:05 -0700 (Tue, 24 Jul 2007) Log Message: ----------- 11.2.6 # bug fix: nested ifs can cause last endif to throw error # bug fix: compiler bug working with very small real numbers Modified Paths: -------------- branches/v11_2/Jmol/src/org/jmol/viewer/Compiler.java branches/v11_2/Jmol/src/org/jmol/viewer/Eval.java branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v11_2/Jmol/src/org/jmol/viewer/Compiler.java =================================================================== --- branches/v11_2/Jmol/src/org/jmol/viewer/Compiler.java 2007-07-24 13:49:56 UTC (rev 8003) +++ branches/v11_2/Jmol/src/org/jmol/viewer/Compiler.java 2007-07-24 14:22:05 UTC (rev 8004) @@ -110,7 +110,11 @@ if (pt > 0 && (i = Integer.parseInt(strDecimal.substring(0, pt))) < 0) i = -i; if (pt < strDecimal.length() - 1) - j = Integer.parseInt(strDecimal.substring(pt + 1)); + try { + j = Integer.parseInt(strDecimal.substring(pt + 1)); + } catch(NumberFormatException e) { + // not a problem + } return i * 1000000 + j; } Modified: branches/v11_2/Jmol/src/org/jmol/viewer/Eval.java =================================================================== --- branches/v11_2/Jmol/src/org/jmol/viewer/Eval.java 2007-07-24 13:49:56 UTC (rev 8003) +++ branches/v11_2/Jmol/src/org/jmol/viewer/Eval.java 2007-07-24 14:22:05 UTC (rev 8004) @@ -758,13 +758,14 @@ switch (token.tok) { case Token.ifcmd: for (int i = 1; i <= ifLevel; i++) - if (ifs[ifLevel] == pc || ifs[ifLevel] == -1 - pc) { + if (ifs[i] == pc || ifs[i] == -1 - pc) { ifLevel = i - 1; break; } if (++ifLevel == MAX_IF_DEPTH) evalError(GT._("Too many nested {0} commands", "IF")); ifs[ifLevel] = (ifs[ifLevel - 1] >= 0 && ifCmd() ? pc : -1 - pc); + //System.out.println("if " + ifLevel + " = " + ifs[ifLevel]); break; case Token.elsecmd: if (ifLevel < 1) @@ -773,6 +774,7 @@ ifs[ifLevel] = -1 - ifs[ifLevel]; break; case Token.endifcmd: + //System.out.println("if " + pc +" " + ifLevel); if (--ifLevel < 0) evalError(GT._("Invalid {0} command", "ENDIF")); break; Modified: branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties 2007-07-24 13:49:56 UTC (rev 8003) +++ branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties 2007-07-24 14:22:05 UTC (rev 8004) @@ -5,6 +5,8 @@ # bug fix: dots not available in multimodel mode # bug fix: multiple isosurface cavities incorrect in a multimodel environment # bug fix: isosurface cavity not filled completely +# bug fix: nested ifs can cause last endif to throw error +# bug fix: compiler bug working with very small real numbers # ----------------------------------------------------------------------------- This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2007-08-23 03:31:16
|
Revision: 8134 http://jmol.svn.sourceforge.net/jmol/?rev=8134&view=rev Author: hansonr Date: 2007-08-22 20:31:15 -0700 (Wed, 22 Aug 2007) Log Message: ----------- 11.2.10 bug fix zoomTo (...) 100% doubling if given twice Modified Paths: -------------- branches/v11_2/Jmol/src/org/jmol/viewer/Eval.java branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v11_2/Jmol/src/org/jmol/viewer/Eval.java =================================================================== --- branches/v11_2/Jmol/src/org/jmol/viewer/Eval.java 2007-08-23 03:29:53 UTC (rev 8133) +++ branches/v11_2/Jmol/src/org/jmol/viewer/Eval.java 2007-08-23 03:31:15 UTC (rev 8134) @@ -2590,7 +2590,7 @@ //alternative (center) zoomFactor if (zoom == 0 || Float.isNaN(zoom)) { //alternative (atom expression) zoom - float factor = getZoomFactor(i, ptCenter, radius, zoom0); + float factor = Math.abs(getZoomFactor(i, ptCenter, radius, zoom0)); i = iToken + 1; if (Float.isNaN(factor)) invalidArgument(); @@ -4577,12 +4577,15 @@ //zoom/zoomTo percent|-factor|+factor|*factor|/factor | 0 float factor = getZoomFactor(i, ptCenter, radius, zoom); - if (isZoomTo) { + if (factor < 0) { + factor = -factor; + if (isZoomTo) { // no factor -- check for no center (zoom out) or same center (zoom in) if (statementLength == 1 || isSameAtom) factor *= 2; else if (center == null) factor /= 2; + } } float xTrans = 0; float yTrans = 0; @@ -4644,6 +4647,7 @@ invalidArgument(); } } else { + factor = -factor; --i; } } Modified: branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties 2007-08-23 03:29:53 UTC (rev 8133) +++ branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties 2007-08-23 03:31:15 UTC (rev 8134) @@ -1,5 +1,7 @@ version=11.2.10_dev +# bug fix: zoomTo 100% + # ----------------------------------------------------------------------------- #version=11.2.9 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2007-08-31 13:35:22
|
Revision: 8173 http://jmol.svn.sourceforge.net/jmol/?rev=8173&view=rev Author: hansonr Date: 2007-08-31 06:35:14 -0700 (Fri, 31 Aug 2007) Log Message: ----------- 11.2.11 # bug fix: HDO not recognized as "water" Modified Paths: -------------- branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties branches/v11_2/Jmol/src/org/jmol/viewer/JmolConstants.java Modified: branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties 2007-08-31 13:34:39 UTC (rev 8172) +++ branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties 2007-08-31 13:35:14 UTC (rev 8173) @@ -1,5 +1,7 @@ version=11.2.11_dev +# bug fix: HDO not recognized as "water" + # ----------------------------------------------------------------------------- #version=11.2.10 Modified: branches/v11_2/Jmol/src/org/jmol/viewer/JmolConstants.java =================================================================== --- branches/v11_2/Jmol/src/org/jmol/viewer/JmolConstants.java 2007-08-31 13:34:39 UTC (rev 8172) +++ branches/v11_2/Jmol/src/org/jmol/viewer/JmolConstants.java 2007-08-31 13:35:14 UTC (rev 8173) @@ -2381,7 +2381,7 @@ // these must be removed after various script commands so that they stay current public static String[] predefinedVariable = { - "@water _g>=70 & _g<=72, oxygen & connected(2, hydrogen or deuterium or tritium), (hydrogen or deuterium and tritium) & connected(oxygen & connected(2, hydrogen or deuterium or tritium))", + "@water _g>=70 & _g<=72, oxygen & connected(2, hydrogen or deuterium or tritium), (hydrogen or deuterium or tritium) & connected(oxygen & connected(2, hydrogen or deuterium or tritium))", "@turn structure=1", "@sheet structure=2", "@helix structure=3", This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2007-10-10 00:35:31
|
Revision: 8396 http://jmol.svn.sourceforge.net/jmol/?rev=8396&view=rev Author: hansonr Date: 2007-10-09 17:35:29 -0700 (Tue, 09 Oct 2007) Log Message: ----------- 11.2.14 # bug fix: semi missing in show orientation message, second part (zyz text) Modified Paths: -------------- branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties branches/v11_2/Jmol/src/org/jmol/viewer/TransformManager.java Modified: branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties 2007-10-10 00:33:00 UTC (rev 8395) +++ branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties 2007-10-10 00:35:29 UTC (rev 8396) @@ -2,6 +2,7 @@ # bug fix for application not accepting pastes into the # console consisting of multiple lines +# bug fix: semi missing in show orientation message, second part (zyz text) # ----------------------------------------------------------------------------- Modified: branches/v11_2/Jmol/src/org/jmol/viewer/TransformManager.java =================================================================== --- branches/v11_2/Jmol/src/org/jmol/viewer/TransformManager.java 2007-10-10 00:33:00 UTC (rev 8395) +++ branches/v11_2/Jmol/src/org/jmol/viewer/TransformManager.java 2007-10-10 00:35:29 UTC (rev 8396) @@ -1756,6 +1756,7 @@ sb.append("; rotate z"); truncate2(sb, rZ2); } + sb.append(";"); addZoomTranslationNavigationText(sb); return sb.toString(); } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2007-10-14 21:08:57
|
Revision: 8412 http://jmol.svn.sourceforge.net/jmol/?rev=8412&view=rev Author: hansonr Date: 2007-10-14 14:08:55 -0700 (Sun, 14 Oct 2007) Log Message: ----------- version=11.2.14 # bug fix: zoomto (atomExpression) 0 # zooms to 2x Modified Paths: -------------- branches/v11_2/Jmol/src/org/jmol/viewer/Eval.java branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v11_2/Jmol/src/org/jmol/viewer/Eval.java =================================================================== --- branches/v11_2/Jmol/src/org/jmol/viewer/Eval.java 2007-10-14 21:06:26 UTC (rev 8411) +++ branches/v11_2/Jmol/src/org/jmol/viewer/Eval.java 2007-10-14 21:08:55 UTC (rev 8412) @@ -4618,9 +4618,9 @@ } float getZoomFactor(int i, int ptCenter, float radius, float factor0) throws ScriptException { + BitSet bs = null; float factor = (isFloatParameter(i) ? floatParameter(i) : Float.NaN); if (factor == 0) { - BitSet bs = null; switch (statement[ptCenter].tok) { case Token.bitset: case Token.expressionBegin: @@ -4653,7 +4653,8 @@ invalidArgument(); } } else { - factor = -factor; + if (bs == null) + factor = -factor; --i; } } Modified: branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties 2007-10-14 21:06:26 UTC (rev 8411) +++ branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties 2007-10-14 21:08:55 UTC (rev 8412) @@ -1,5 +1,6 @@ version=11.2.14 +# bug fix: zoomto (atomExpression) 0 # zooms to 2x # bug fix: backbone not in state # bug fix for application not accepting pastes into the This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2007-10-14 21:33:31
|
Revision: 8414 http://jmol.svn.sourceforge.net/jmol/?rev=8414&view=rev Author: hansonr Date: 2007-10-14 14:33:30 -0700 (Sun, 14 Oct 2007) Log Message: ----------- version=11.2.14 # bug fix: zoomto cancels slabbing Modified Paths: -------------- branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties branches/v11_2/Jmol/src/org/jmol/viewer/TransformManager.java branches/v11_2/Jmol/src/org/jmol/viewer/TransformManager11.java Modified: branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties 2007-10-14 21:31:38 UTC (rev 8413) +++ branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties 2007-10-14 21:33:30 UTC (rev 8414) @@ -1,5 +1,6 @@ version=11.2.14 +# bug fix: zoomto cancels slabbing # bug fix: zoomto (atomExpression) 0 # zooms to 2x # bug fix: backbone not in state Modified: branches/v11_2/Jmol/src/org/jmol/viewer/TransformManager.java =================================================================== --- branches/v11_2/Jmol/src/org/jmol/viewer/TransformManager.java 2007-10-14 21:31:38 UTC (rev 8413) +++ branches/v11_2/Jmol/src/org/jmol/viewer/TransformManager.java 2007-10-14 21:33:30 UTC (rev 8414) @@ -136,7 +136,7 @@ navigating = false; slabPlane = null; depthPlane = null; - resetNavigationPoint(); + resetNavigationPoint(true); } String getState() { @@ -1063,7 +1063,7 @@ * @param percent */ void setCameraDepthPercent(float percent) { - resetNavigationPoint(); + resetNavigationPoint(true); float screenMultiples = (percent < 0 ? -percent / 100 : percent); if (screenMultiples == 0) return; @@ -1152,7 +1152,7 @@ fixedTranslation.set(width * (andCenter ? 0.5f : xTranslationFraction), height * (andCenter ? 0.5f : yTranslationFraction), 0); setTranslationFractions(); - resetNavigationPoint(); + resetNavigationPoint(true); // 2005 02 22 // switch to finding larger screen dimension // find smaller screen dimension @@ -1210,7 +1210,7 @@ void setNavigationMode(boolean TF) { isNavigationMode = (TF && canNavigate()); - resetNavigationPoint(); + resetNavigationPoint(true); } boolean getNavigating() { @@ -2071,7 +2071,7 @@ void setWindowCentered(boolean TF) { windowCentered = TF; - resetNavigationPoint(); + resetNavigationPoint(true); } void setDefaultRotation() { @@ -2097,7 +2097,7 @@ private void setRotationCenterAndRadiusXYZ(Point3f newCenterOfRotation, boolean andRadius) { - resetNavigationPoint(); + resetNavigationPoint(false); if (newCenterOfRotation == null) { setFixedRotationCenter(rotationCenterDefault); modelRadius = rotationRadiusDefault; @@ -2239,9 +2239,10 @@ } /** - * something has arisen that requires resetting of the navigation point. + * something has arisen that requires resetting of the navigation point. + * @param doResetSlab */ - protected void resetNavigationPoint() { + protected void resetNavigationPoint(boolean doResetSlab) { } /** Modified: branches/v11_2/Jmol/src/org/jmol/viewer/TransformManager11.java =================================================================== --- branches/v11_2/Jmol/src/org/jmol/viewer/TransformManager11.java 2007-10-14 21:31:38 UTC (rev 8413) +++ branches/v11_2/Jmol/src/org/jmol/viewer/TransformManager11.java 2007-10-14 21:33:30 UTC (rev 8414) @@ -329,7 +329,7 @@ private int navMode = NAV_MODE_RESET; - protected void resetNavigationPoint() { + protected void resetNavigationPoint(boolean doResetSlab) { //no release from navigation mode if too far zoomed in! @@ -341,10 +341,11 @@ navMode = NAV_MODE_RESET; slabPercentSetting = 0; perspectiveDepth = true; - } else { + } else if (doResetSlab) { slabPercentSetting = 100; } - slabEnabled = isNavigationMode; + if (doResetSlab) + slabEnabled = isNavigationMode; zoomFactor = Float.MAX_VALUE; zoomPercentSetting = zoomPercent; } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2007-10-15 19:08:00
|
Revision: 8430 http://jmol.svn.sourceforge.net/jmol/?rev=8430&view=rev Author: hansonr Date: 2007-10-15 12:07:57 -0700 (Mon, 15 Oct 2007) Log Message: ----------- version=11.2.15_dev # adds "OP1" and "OP2" as backbone designators (new PDB designation) Modified Paths: -------------- branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties branches/v11_2/Jmol/src/org/jmol/viewer/JmolConstants.java Modified: branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties 2007-10-15 19:07:31 UTC (rev 8429) +++ branches/v11_2/Jmol/src/org/jmol/viewer/Jmol.properties 2007-10-15 19:07:57 UTC (rev 8430) @@ -1,5 +1,6 @@ version=11.2.15_dev +# adds "OP1" and "OP2" as backbone designators (new PDB designation) # bug fix: rockets color incorrect for head groups # ----------------------------------------------------------------------------- Modified: branches/v11_2/Jmol/src/org/jmol/viewer/JmolConstants.java =================================================================== --- branches/v11_2/Jmol/src/org/jmol/viewer/JmolConstants.java 2007-10-15 19:07:31 UTC (rev 8429) +++ branches/v11_2/Jmol/src/org/jmol/viewer/JmolConstants.java 2007-10-15 19:07:57 UTC (rev 8430) @@ -2027,9 +2027,10 @@ "O", // 40 - carbonyl oxygen "O1", // 41 - carbonyl oxygen in some protein residues (4THN) null, // 42 - null, // 43 - null, // 44 + "OP1", // 43 - first equivalent oxygen on phosphorus of phosphate -- new designation + "OP2", // 44 - second equivalent oxygen on phosphorus of phosphate -- new designation + // Terminal nuclic acid "H5T", // 45 - 5' terminus hydrogen which replaces P + O1P + O2P "O5T", // 46 - 5' terminus oxygen which replaces P + O1P + O2P This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |