Jmol Developers,
As a preliminary start to releasing Jmol 11.6 next week, I've created a
branch for it. No new features, I promise! Any bugs we find in the next week
(and for the forseeable future) should be entered into BOTH trunk and that
branch.
Next week I will change the version of the branch to "11.6.0" and the trunk
to "11.7.0", and then I'll continue adding bug fixes to both and new
features only for the 11.7 trunk.
That will signal the actual release of Jmol 11.6.
First up: the ability to apply coordinates from one file to another and a
molecular dynamics trajectory coordinate file reader. This will allow
visualization and analysis of molecular dynamics results within Jmol.
Bob
On Tue, Sep 23, 2008 at 8:29 AM, <[EMAIL PROTECTED]> wrote:
> Revision: 9927
> http://jmol.svn.sourceforge.net/jmol/?rev=9927&view=rev
> Author: hansonr
> Date: 2008-09-23 13:29:34 +0000 (Tue, 23 Sep 2008)
>
> Log Message:
> -----------
> version=11.6.RC17_dev
>
> # code: if (true...)/ if (false...) code cleanup
> # bug fix: select model=_modelNumber didn't differentiate between 2.10 and
> 2.1
>
> Modified Paths:
> --------------
> trunk/Jmol/src/org/jmol/adapter/readers/more/JaguarReader.java
> trunk/Jmol/src/org/jmol/export/_PovrayExporter.java
> trunk/Jmol/src/org/jmol/shapesurface/IsosurfaceRenderer.java
> trunk/Jmol/src/org/jmol/viewer/Eval.java
> trunk/Jmol/src/org/jmol/viewer/Jmol.properties
> trunk/Jmol/src/org/jmol/viewer/ScriptManager.java
> trunk/Jmol/src/org/jmol/viewer/TransformManager.java
>
> Modified: trunk/Jmol/src/org/jmol/adapter/readers/more/JaguarReader.java
> ===================================================================
> --- trunk/Jmol/src/org/jmol/adapter/readers/more/JaguarReader.java
> 2008-09-23 05:23:47 UTC (rev 9926)
> +++ trunk/Jmol/src/org/jmol/adapter/readers/more/JaguarReader.java
> 2008-09-23 13:29:34 UTC (rev 9927)
> @@ -247,8 +247,8 @@
> */
> void readBasisNormalized() throws Exception {
>
> - //don't know what this is about yet -- asking Jimmy Stewart
> -
> + //TODO don't know what this is about yet -- Bob Hanson
> +/*
> if (true)
> return;
> String lastAtom = "";
> @@ -271,6 +271,7 @@
> rCoef = parseFloat(tokens[5]);
> }
> }
> +*/
> }
>
> /*
>
> Modified: trunk/Jmol/src/org/jmol/export/_PovrayExporter.java
> ===================================================================
> --- trunk/Jmol/src/org/jmol/export/_PovrayExporter.java 2008-09-23 05:23:47
> UTC (rev 9926)
> +++ trunk/Jmol/src/org/jmol/export/_PovrayExporter.java 2008-09-23 13:29:34
> UTC (rev 9927)
> @@ -669,11 +669,12 @@
> String s = coef[0] + "," + coef[1] + "," + coef[2] + "," + coef[3] +
> ","
> + coef[4] + "," + coef[5] + "," + coef[6] + "," + coef[7] + ","
> + coef[8] + "," + coef[9] + "," + color4(colix);
> - if (true || selectedPoints == null) {
> + //if (true || selectedPoints == null) {
> output("q(" + s + ")\n");
> - return;
> - }
> + // return;
> + //}
> //TODO: The following does not work.
> + /*
> tempP1.set(ix, iy, iz);
> for (int i = 0; i < 3; i++) {
> tempP1.x += selectedPoints[i].x - ix;
> @@ -682,6 +683,7 @@
> }
> output("qf(" + s + "," + ix + "," + iy + "," + iz
> + "," + tempP1.x + "," + tempP1.y + "," + tempP1.z + ")\n");
> + */
> }
>
> public void renderBackground() {
>
> Modified: trunk/Jmol/src/org/jmol/shapesurface/IsosurfaceRenderer.java
> ===================================================================
> --- trunk/Jmol/src/org/jmol/shapesurface/IsosurfaceRenderer.java
> 2008-09-23 05:23:47 UTC (rev 9926)
> +++ trunk/Jmol/src/org/jmol/shapesurface/IsosurfaceRenderer.java
> 2008-09-23 13:29:34 UTC (rev 9927)
> @@ -174,7 +174,7 @@
> return;
> for (int i = vertexCount; --i >= 0;) {
> if (vertexValues != null && !Float.isNaN(vertexValues[i]))
> - if (true || (i % 3) == 0) { //investigate vertex normixes
> + //if ((i % 3) == 0) { //investigate vertex normixes
> ptTemp.set(mesh.vertices[i]);
> short n = mesh.normixes[i];
> // -n is an intensity2sided and does not correspond to a true
> normal index
> @@ -184,7 +184,7 @@
> g3d.fillCylinder(Graphics3D.ENDCAPS_SPHERICAL, 1,
> screens[i], ptTempi);
> }
> - }
> + //}
> }
> }
>
>
> Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
> ===================================================================
> --- trunk/Jmol/src/org/jmol/viewer/Eval.java 2008-09-23 05:23:47 UTC
> (rev 9926)
> +++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2008-09-23 13:29:34 UTC
> (rev 9927)
> @@ -159,6 +159,10 @@
> }
>
> private Object getNumericParameter(String var) {
> + if (var.equalsIgnoreCase("_modelNumber")) {
> + int modelIndex = viewer.getCurrentModelIndex();
> + return new Integer(modelIndex < 0 ? 0 :
> viewer.getModelFileNumber(modelIndex));
> + }
> Token token = getContextVariableAsToken(var);
> if (token == null) {
> Object val = viewer.getParameter(var);
> @@ -1375,7 +1379,8 @@
>
> private BitSet expression(Token[] code, int pcStart, int pcStop,
> boolean allowRefresh, boolean allowUnderflow,
> - boolean mustBeBitSet, boolean andNotDeleted)
> throws ScriptException {
> + boolean mustBeBitSet, boolean andNotDeleted)
> + throws ScriptException {
> //note that this is general -- NOT just statement[]
> //errors reported would improperly access statement/line context
> //there should be no errors anyway, because this is for
> @@ -1528,8 +1533,8 @@
> rpn.addX(getAtomBits(instruction.tok, (String) value));
> break;
> case Token.spec_model:
> - // from select */1002 or */1000002 or */1.2
> - // */1002 is equivalent to 1.2 when more than one file is present
> + // from select */1002 or */1000002 or */1.2
> + // */1002 is equivalent to 1.2 when more than one file is present
> case Token.spec_model2:
> // from just using the number 1.2
> int iModel = instruction.intValue;
> @@ -1549,14 +1554,17 @@
> break;
> case Token.spec_resid:
> case Token.spec_chain:
> - rpn.addX(getAtomBits(instruction.tok, new
> Integer(instruction.intValue)));
> + rpn
> + .addX(getAtomBits(instruction.tok,
> + new Integer(instruction.intValue)));
> break;
> case Token.spec_seqcode:
> if (isInMath) {
> rpn.addX(instruction.intValue);
> break;
> }
> - rpn.addX(getAtomBits(Token.spec_seqcode, new
> Integer(getSeqCode(instruction))));
> + rpn.addX(getAtomBits(Token.spec_seqcode, new Integer(
> + getSeqCode(instruction))));
> break;
> case Token.spec_seqcode_range:
> if (isInMath) {
> @@ -1565,8 +1573,9 @@
> rpn.addX(code[++pc].intValue);
> break;
> }
> - int chainID = (pc + 3 < code.length && code[pc + 2].tok ==
> Token.opAnd
> - && code[pc + 3].tok == Token.spec_chain ? code[pc +
> 3].intValue : '\t');
> + int chainID = (pc + 3 < code.length && code[pc + 2].tok ==
> Token.opAnd
> + && code[pc + 3].tok == Token.spec_chain ? code[pc +
> 3].intValue
> + : '\t');
> rpn.addX(getAtomBits(Token.spec_seqcode_range, new int[] {
> getSeqCode(instruction), getSeqCode(code[++pc]), chainID }));
> if (chainID != '\t')
> @@ -1622,15 +1631,15 @@
> .modelFileNumberFromFloat(((Float) val).floatValue());
> }
> if (val instanceof Integer || tokValue == Token.integer) {
> - comparisonValue *= (Compiler
> - .tokAttr(tokWhat, Token.comparefloatx100) ? 100 : 1);
> + comparisonValue *= (Compiler.tokAttr(tokWhat,
> Token.comparefloatx100) ? 100
> + : 1);
> comparisonFloat = comparisonValue;
> - if (isModel && viewer.haveFileSet()) {
> - if (comparisonValue >= 1000 && comparisonValue < 1000000) {
> + if (isModel) {
> + tokWhat = -Token.model;
> + if (viewer.haveFileSet() && comparisonValue >= 1000
> + && comparisonValue < 1000000)
> comparisonValue = (comparisonValue / 1000) * 1000000
> + comparisonValue % 1000;
> - tokWhat = -Token.model;
> - }
> }
> } else if (val instanceof Float) {
> if (isModel) {
> @@ -1689,10 +1698,11 @@
> error(ERROR_endOfStatementUnexpected);
> }
> expressionResult = ((Token) expressionResult).value;
> - if (expressionResult instanceof String &&
> - (mustBeBitSet || ((String) expressionResult).startsWith("({"))) {
> + if (expressionResult instanceof String
> + && (mustBeBitSet || ((String) expressionResult).startsWith("({")))
> {
> // allow for select @{x} where x is a string that can evaluate to a
> bitset
> - expressionResult = (isScriptCheck ? new BitSet() :
> getAtomBitSet(this, viewer, (String) expressionResult));
> + expressionResult = (isScriptCheck ? new BitSet() :
> getAtomBitSet(this,
> + viewer, (String) expressionResult));
> }
> if (!mustBeBitSet && !(expressionResult instanceof BitSet))
> return null; // because result is in expressionResult in that case
>
> Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
> ===================================================================
> --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-09-23 05:23:47
> UTC (rev 9926)
> +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-09-23 13:29:34
> UTC (rev 9927)
> @@ -3,7 +3,9 @@
>
> version=11.6.RC17_dev
>
> -# bug fix: select model=0.0 causes infinite loop
> +# code: if (true...)/ if (false...) code cleanup
> +# bug fix: select model=_modelNumber didn't differentiate between 2.10 and
> 2.1
> +# bug fix: select model=0.0 caused infinite loop
>
> #
> -----------------------------------------------------------------------------
>
>
> Modified: trunk/Jmol/src/org/jmol/viewer/ScriptManager.java
> ===================================================================
> --- trunk/Jmol/src/org/jmol/viewer/ScriptManager.java 2008-09-23 05:23:47
> UTC (rev 9926)
> +++ trunk/Jmol/src/org/jmol/viewer/ScriptManager.java 2008-09-23 13:29:34
> UTC (rev 9927)
> @@ -87,7 +87,7 @@
> scriptItem.addElement(isQuiet ? Boolean.TRUE : Boolean.FALSE);
> scriptItem.addElement(new Integer(useCommandThread ? -1 : 1));
> scriptQueue.addElement(scriptItem);
> - if (true || Logger.debugging)
> + if (Logger.debugging)
> Logger.info(scriptQueue.size() + " scripts; added: " + strScript);
> startScriptQueue(false);
> return "pending";
>
> Modified: trunk/Jmol/src/org/jmol/viewer/TransformManager.java
> ===================================================================
> --- trunk/Jmol/src/org/jmol/viewer/TransformManager.java 2008-09-23
> 05:23:47 UTC (rev 9926)
> +++ trunk/Jmol/src/org/jmol/viewer/TransformManager.java 2008-09-23
> 13:29:34 UTC (rev 9927)
> @@ -32,7 +32,6 @@
> import javax.vecmath.AxisAngle4f;
>
> import org.jmol.util.Escape;
> -import org.jmol.util.Logger;
> import org.jmol.util.Quaternion;
>
> import java.util.BitSet;
> @@ -1212,9 +1211,8 @@
>
> // note that the image is still centered at 0, 0 in the xy plane
>
> - if (false && Logger.debugging)
> - Logger.debug("modelCenterOffset + matrixTransform: " +
> modelCenterOffset
> - + matrixTransform);
> + // System.out.println("modelCenterOffset + matrixTransform: " +
> modelCenterOffset
> + // + matrixTransform);
>
> }
>
> @@ -1300,7 +1298,7 @@
>
> void transformPoint(Point3f pointAngstroms, Point3f screen) {
>
> - //used solely by RocketsRenderer
> + //used solely by RocketsRendr
>
> matrixTransform.transform(pointAngstroms, point3fScreenTemp);
> adjustTemporaryScreenPoint();
>
>
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>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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