Revision: 18337
http://sourceforge.net/p/jmol/code/18337
Author: hansonr
Date: 2013-06-16 16:46:21 +0000 (Sun, 16 Jun 2013)
Log Message:
-----------
___JmolVersion="13.1.17_dev_2013.06.16"
new feature: {atomset1}.distance.min({atomset2})
-- returns an array
-- minimum distance of each atom in atomset1 to any atom in atomset2
new feature: {atomset1}.distance.max({atomset2})
-- returns an array
-- maximum distance of each atom in atomset1 to any atom in atomset2
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/script/SV.java
trunk/Jmol/src/org/jmol/script/ScriptCompiler.java
trunk/Jmol/src/org/jmol/script/ScriptContext.java
trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java
trunk/Jmol/src/org/jmol/thread/SpinThread.java
trunk/Jmol/src/org/jmol/util/Measure.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/TransformManager.java
Modified: trunk/Jmol/src/org/jmol/script/SV.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/SV.java 2013-06-15 15:33:57 UTC (rev
18336)
+++ trunk/Jmol/src/org/jmol/script/SV.java 2013-06-16 16:46:21 UTC (rev
18337)
@@ -1266,15 +1266,11 @@
JmolList<Object> o = new JmolList<Object>();
for (int j = 0; j < l2.size(); j++) {
v = l2.get(j);
- System.out.println(v);
-
}
list.addLast(o);
}
- System.out.println(v);
}
- return list;
-
+ return list;
}
static float[] flistValue(T x, int nMin) {
if (x.tok != varray)
Modified: trunk/Jmol/src/org/jmol/script/ScriptCompiler.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptCompiler.java 2013-06-15 15:33:57 UTC
(rev 18336)
+++ trunk/Jmol/src/org/jmol/script/ScriptCompiler.java 2013-06-16 16:46:21 UTC
(rev 18337)
@@ -2667,7 +2667,7 @@
: errorLine)
+ " <<<<";
errorMessage = GT._("script compiler ERROR: ") + errorMessage
- + ScriptEvaluator.setErrorLineMessage(null, filename, lineCurrent,
iCommand, lineInfo);
+ + ScriptEvaluator.getErrorLineMessage(null, filename, lineCurrent,
iCommand, lineInfo);
if (!isSilent) {
ichToken = Math.max(ichEnd, ichToken);
while (!lookingAtEndOfLine() && !lookingAtTerminator())
Modified: trunk/Jmol/src/org/jmol/script/ScriptContext.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptContext.java 2013-06-15 15:33:57 UTC
(rev 18336)
+++ trunk/Jmol/src/org/jmol/script/ScriptContext.java 2013-06-16 16:46:21 UTC
(rev 18337)
@@ -31,45 +31,49 @@
import org.jmol.util.SB;
public class ScriptContext {
- /**
- *
- */
- public String fullpath = "";
- public String scriptFileName;
- public JmolParallelProcessor parallelProcessor;
- public String functionName;
- public String script;
- public short[] lineNumbers;
- public int[][] lineIndices;
+
+ private static int contextCount = 0;
+
public T[][] aatoken;
- public T[] statement;
- public int statementLength;
- public int pc;
- public int pcEnd = Integer.MAX_VALUE;
- public int lineEnd = Integer.MAX_VALUE;
- public int iToken;
- public SB outputBuffer;
- public Map<String, SV> contextVariables;
- public boolean isFunction;
- public boolean isStateScript;
- public boolean isTryCatch;
+ public boolean allowJSThreads;
+ boolean chk;
+ public String contextPath = " >> ";
+ Map<String, SV> contextVariables;
+ boolean displayLoadErrorsSave;
public String errorMessage;
- public String errorMessageUntranslated;
- public int iCommandError = -1;
+ String errorMessageUntranslated;
public String errorType;
- public int scriptLevel;
- public boolean chk;
+ public boolean executionPaused;
public boolean executionStepping;
- public boolean executionPaused;
- public String scriptExtensions;
- public String contextPath = " >> ";
+ public String functionName;
+ public int iCommandError = -1;
+ int id;
+ public boolean isComplete = true;
+ boolean isFunction;
+ public boolean isJSThread;
+ boolean isStateScript;
+ boolean isTryCatch;
+ int iToken;
+ int lineEnd = Integer.MAX_VALUE;
+ public int[][] lineIndices;
+ short[] lineNumbers;
+ public boolean mustResumeEval;
+ public SB outputBuffer;
+ JmolParallelProcessor parallelProcessor;
public ScriptContext parentContext;
- public ContextToken token;
- public boolean mustResumeEval;
- public boolean isJSThread;
- public boolean allowJSThreads;
- public boolean displayLoadErrorsSave;
- public int tryPt;
- public boolean isComplete = true;
+ public int pc;
+ public int pcEnd = Integer.MAX_VALUE;
+ public String script;
+ String scriptExtensions;
+ public String scriptFileName;
+ int scriptLevel;
+ T[] statement;
+ int statementLength;
+ ContextToken token;
+ int tryPt;
+
+ ScriptContext() {
+ id = ++contextCount;
+ }
}
\ No newline at end of file
Modified: trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2013-06-15 15:33:57 UTC
(rev 18336)
+++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2013-06-16 16:46:21 UTC
(rev 18337)
@@ -463,7 +463,7 @@
static SB getContextTrace(ScriptContext sc, SB sb, boolean isTop) {
if (sb == null)
sb = new SB();
- sb.append(setErrorLineMessage(sc.functionName, sc.scriptFileName,
+ sb.append(getErrorLineMessage(sc.functionName, sc.scriptFileName,
sc.lineNumbers[sc.pc], sc.pc,
ScriptEvaluator.statementAsString(sc.statement, (isTop ? sc.iToken : 9999),
false)));
if (sc.parentContext != null)
getContextTrace(sc.parentContext, sb, false);
@@ -548,7 +548,7 @@
* @return a string indicating the statement
*/
public String getNextStatement() {
- return (pc < aatoken.length ? setErrorLineMessage(functionName,
scriptFileName,
+ return (pc < aatoken.length ? getErrorLineMessage(functionName,
scriptFileName,
getLinenumber(null), pc, statementAsString(aatoken[pc], -9999,
logMessages)) : "");
}
@@ -1124,7 +1124,7 @@
case T.sum:
case T.sum2:
case T.average:
- allowMathFunc = (isUserFunction || tok2 == T.minmaxmask || tok2 ==
T.selectedfloat);
+ allowMathFunc = (isUserFunction || token.intValue == T.distance ||
tok2 == T.minmaxmask || tok2 == T.selectedfloat);
token.intValue |= tok2;
getToken(iToken + 2);
}
@@ -2730,11 +2730,13 @@
if (debugScript || isCmdLine_c_or_C_Option)
Logger.info("-->>-------------".substring(0, Math
.max(17, scriptLevel + 5))
- + scriptLevel + " " + scriptFileName + " " + token + " " +
thisContext);
+ + scriptLevel + " " + scriptFileName + " " + token + " " +
thisContext.id);
}
public ScriptContext getScriptContext() {
ScriptContext context = new ScriptContext();
+ if (debugScript)
+ Logger.info("creating context " + context.id);
context.scriptLevel = scriptLevel;
context.parentContext = thisContext;
context.contextPath = contextPath;
@@ -2787,9 +2789,7 @@
+ " "
+ scriptFileName
+ " "
- + (thisContext == null ? "" : "" + thisContext.token)
- + " "
- + thisContext);
+ + (thisContext == null ? "" : "" + thisContext.id));
}
private void restoreScriptContext(ScriptContext context,
@@ -2798,6 +2798,10 @@
if (context == null)
return;
+ if (debugScript || isCmdLine_c_or_C_Option)
+ Logger.info("--<<-------------".substring(0, Math
+ .max(17, scriptLevel + 5))
+ + scriptLevel + " " + scriptFileName + " isPop " + isPopContext + "
" + context.id);
if (!isFlowCommand) {
st = context.statement;
slen = context.statementLength;
@@ -2846,7 +2850,7 @@
true, false));
}
} else {
- sb.append(setErrorLineMessage(context.functionName,
context.scriptFileName,
+ sb.append(getErrorLineMessage(context.functionName,
context.scriptFileName,
getLinenumber(context), context.pc, statementAsString(
context.statement, -9999, logMessages)));
}
@@ -2859,7 +2863,7 @@
false));
}
} else {
- sb.append(setErrorLineMessage(functionName, scriptFileName,
+ sb.append(getErrorLineMessage(functionName, scriptFileName,
getLinenumber(null), pc, statementAsString(st, -9999,
logMessages)));
}
@@ -2875,7 +2879,7 @@
String fuName = (context == null ? functionName : "function "
+ context.functionName);
String fiName = (context == null ? scriptFileName :
context.scriptFileName);
- return "\n# " + fuName + " (file " + fiName + ")\n";
+ return "\n# " + fuName + " (file " + fiName + (context == null ? "" : "
context " + context.id)+")\n";
}
// /////////////// error message support /////////////////
@@ -3269,7 +3273,7 @@
return msg;
}
- static String setErrorLineMessage(String functionName, String filename,
+ static String getErrorLineMessage(String functionName, String filename,
int lineCurrent, int pcCurrent,
String lineInfo) {
String err = "\n----";
@@ -3756,11 +3760,13 @@
case T.selected:
rpn.addXBs(BSUtil.copy(viewer.getSelectionSet(false)));
break;
- case T.subset:
- BS bsSubset = viewer.getSelectionSubset();
- rpn.addXBs(bsSubset == null ? viewer.getModelUndeletedAtomsBitSet(-1)
- : BSUtil.copy(bsSubset));
- break;
+ //removed in 13.1.17. Undocumented; unneccessary (same as "all")
+
+ //case T.subset:
+ //BS bsSubset = viewer.getSelectionSubset();
+ //rpn.addXBs(bsSubset == null ? viewer.getModelUndeletedAtomsBitSet(-1)
+ // : BSUtil.copy(bsSubset));
+ //break;
case T.hidden:
rpn.addXBs(BSUtil.copy(viewer.getHiddenSet()));
break;
@@ -5520,6 +5526,8 @@
break;
if (lineNumbers[pc] > lineEnd)
break;
+ if (debugScript && !chk)
+ Logger.info("Command " + pc);
theToken = (aatoken[pc].length == 0 ? null : aatoken[pc][0]);
// when checking scripts, we can't check statments
// containing @{...}
@@ -7175,10 +7183,12 @@
iToken = 0;
float nSeconds = (isFloatParameter(1) ? floatParameter(++iToken)
: Float.NaN);
- BS bsFrom = (tokAt(++iToken) == T.subset ? null :
atomExpressionAt(iToken));
- BS bsTo = (tokAt(++iToken) == T.subset ? null : atomExpressionAt(iToken));
- if (bsFrom == null || bsTo == null)
- error(ERROR_invalidArgument);
+ ///BS bsFrom = (tokAt(++iToken) == T.subset ? null :
atomExpressionAt(iToken));
+ //BS bsTo = (tokAt(++iToken) == T.subset ? null :
atomExpressionAt(iToken));
+ //if (bsFrom == null || bsTo == null)
+ ///error(ERROR_invalidArgument);
+ BS bsFrom = atomExpressionAt(++iToken);
+ BS bsTo = atomExpressionAt(++iToken);
BS bsSubset = null;
boolean isSmiles = false;
String strSmiles = null;
@@ -7406,10 +7416,9 @@
}
if (!useThreads())
doAnimate = false;
- viewer.rotateAboutPointsInternal(this, center, pt1,
+ if (viewer.rotateAboutPointsInternal(this, center, pt1,
endDegrees / nSeconds, endDegrees, doAnimate, bsFrom, translation,
- ptsB, null);
- if (doAnimate && isJS)
+ ptsB, null) && doAnimate && isJS)
throw new ScriptInterruption(this, "compare", 1);
}
}
Modified: trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java 2013-06-15
15:33:57 UTC (rev 18336)
+++ trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java 2013-06-16
16:46:21 UTC (rev 18337)
@@ -766,13 +766,13 @@
return evaluateCross(args);
case T.data:
return evaluateData(args);
- case T.angle:
case T.distance:
case T.dot:
+ if (op.tok == T.propselector)
+ return evaluateDot(args, tok, op.intValue);
+ //$FALL-THROUGH$
+ case T.angle:
case T.measure:
- if ((tok == T.distance || tok == T.dot)
- && op.tok == T.propselector)
- return evaluateDot(args, tok);
return evaluateMeasure(args, op.tok);
case T.file:
case T.load:
@@ -1224,37 +1224,72 @@
return false;
}
- private boolean evaluateDot(SV[] args, int tok)
+ /**
+ * distance, dot
+ *
+ * @param args
+ * @param tok
+ * @param intValue
+ * @return variable
+ * @throws ScriptException
+ */
+ private boolean evaluateDot(SV[] args, int tok, int intValue)
throws ScriptException {
if (args.length != 1)
return false;
SV x1 = getX();
SV x2 = args[0];
- P3 pt2 = ptValue(x2, true);
+ P3 pt2 = (x2.tok == T.varray ? null : ptValue(x2, false));
P4 plane2 = planeValue(x2);
- if (x1.tok == T.bitset && tok != T.dot)
- return addXObj(eval.getBitsetProperty(SV.bsSelectVar(x1),
- T.distance, pt2, plane2, x1.value, null, false, x1.index, false));
+ if (tok == T.distance) {
+ int minMax = intValue & T.minmaxmask;
+ switch (x1.tok) {
+ case T.bitset:
+ switch (x2.tok) {
+ case T.bitset:
+ BS bs = SV.bsSelectVar(x1);
+ if (minMax == T.min || minMax == T.max) {
+ BS bs2 = SV.bsSelectVar(x2);
+ float[] data = new float[bs.cardinality()];
+ Atom[] atoms = viewer.modelSet.atoms;
+ for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
+ pt2 = atoms[i];
+ data[i] = ((Float) eval.getBitsetProperty(bs2, intValue, pt2,
+ plane2, x1.value, null, false, x1.index,
false)).floatValue();
+ }
+ return addXAF(data);
+ }
+ return addXObj(eval.getBitsetProperty(bs, intValue, pt2, plane2,
+ x1.value, null, false, x1.index, false));
+ }
+ }
+ }
+ return addXFloat(getDistance(x1, x2, tok));
+ }
+
+ private float getDistance(SV x1, SV x2, int tok) throws ScriptException {
P3 pt1 = ptValue(x1, true);
P4 plane1 = planeValue(x1);
+ P3 pt2 = ptValue(x2, true);
+ P4 plane2 = planeValue(x2);
if (tok == T.dot) {
if (plane1 != null && plane2 != null)
// q1.dot(q2) assume quaternions
- return addXFloat(plane1.x * plane2.x + plane1.y * plane2.y + plane1.z
- * plane2.z + plane1.w * plane2.w);
+ return plane1.x * plane2.x + plane1.y * plane2.y + plane1.z
+ * plane2.z + plane1.w * plane2.w;
// plane.dot(point) =
if (plane1 != null)
pt1 = P3.new3(plane1.x, plane1.y, plane1.z);
// point.dot(plane)
if (plane2 != null)
pt2 = P3.new3(plane2.x, plane2.y, plane2.z);
- return addXFloat(pt1.x * pt2.x + pt1.y * pt2.y + pt1.z * pt2.z);
+ return pt1.x * pt2.x + pt1.y * pt2.y + pt1.z * pt2.z;
}
if (plane1 == null)
- return addXFloat(plane2 == null ? pt2.distance(pt1) :
Measure.distanceToPlane(
+ return (plane2 == null ? pt2.distance(pt1) : Measure.distanceToPlane(
plane2, pt1));
- return addXFloat(Measure.distanceToPlane(plane1, pt2));
+ return Measure.distanceToPlane(plane1, pt2);
}
public P3 ptValue(SV x, boolean allowFloat)
Modified: trunk/Jmol/src/org/jmol/thread/SpinThread.java
===================================================================
--- trunk/Jmol/src/org/jmol/thread/SpinThread.java 2013-06-15 15:33:57 UTC
(rev 18336)
+++ trunk/Jmol/src/org/jmol/thread/SpinThread.java 2013-06-16 16:46:21 UTC
(rev 18337)
@@ -53,9 +53,8 @@
private int index;
//private boolean navigatingSurface;
private BS[] bsBranches;
+ boolean isDone = false;
- private int nmove = 0;
-
public boolean isGesture() {
return isGesture;
}
@@ -165,8 +164,10 @@
else
viewer.requestRepaintAndWait();
//System.out.println(angle * degreesPerRadian + " " + count + " " +
nDegrees + " " + endDegrees);
- if (!isNav && nDegrees >= endDegrees - 0.001)
+ if (!isNav && nDegrees >= endDegrees - 0.001) {
+ isDone = true;
transformManager.setSpinOff();
+ }
if (!runSleep(sleepTime, MAIN))
return;
mode = MAIN;
@@ -185,7 +186,9 @@
transformManager.setSpinOff();
viewer.startHoverWatcher(true);
}
+ stopped = !isDone;
resumeEval();
+ stopped = true;
return;
}
}
Modified: trunk/Jmol/src/org/jmol/util/Measure.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Measure.java 2013-06-15 15:33:57 UTC (rev
18336)
+++ trunk/Jmol/src/org/jmol/util/Measure.java 2013-06-16 16:46:21 UTC (rev
18337)
@@ -456,8 +456,8 @@
public static float getTransformMatrix4(JmolList<P3> ptsA, JmolList<P3>
ptsB, Matrix4f m, P3 centerA) {
P3[] cptsA = getCenterAndPoints(ptsA);
P3[] cptsB = getCenterAndPoints(ptsB);
- System.out.println("draw d1 @{point" + cptsA[0] + "}");
- System.out.println("draw d2 @{point" + cptsB[0] + "}");
+ //System.out.println("draw d1 @{point" + cptsA[0] + "}");
+ //System.out.println("draw d2 @{point" + cptsB[0] + "}");
float[] retStddev = new float[2];
Quaternion q = calculateQuaternionRotation(new P3[][] { cptsA,
cptsB }, retStddev, true); // was false
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-06-15 15:33:57 UTC
(rev 18336)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-06-16 16:46:21 UTC
(rev 18337)
@@ -9,8 +9,15 @@
# The quotes above look odd for a parameter file, but they are
# important for the JavaScript version of Jmol.
-___JmolVersion="13.1.17_dev_2013.06.15"
+___JmolVersion="13.1.17_dev_2013.06.16"
+new feature: {atomset1}.distance.min({atomset2})
+ -- returns an array
+ -- minimum distance of each atom in atomset1 to any atom in atomset2
+new feature: {atomset1}.distance.max({atomset2})
+ -- returns an array
+ -- maximum distance of each atom in atomset1 to any atom in atomset2
+
bug fix: JavaScript not returning arrays properly from Jmol.getPropertyXXXX()
-- very important to have {} after j2sNative directive!
bug fix: COMPARE could rotate to less-good fit with SMARTS search
Modified: trunk/Jmol/src/org/jmol/viewer/TransformManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/TransformManager.java 2013-06-15
15:33:57 UTC (rev 18336)
+++ trunk/Jmol/src/org/jmol/viewer/TransformManager.java 2013-06-16
16:46:21 UTC (rev 18337)
@@ -383,12 +383,29 @@
* ROTATIONS**************************************************************
*/
+ /**
+ *
+ * @param eval
+ * @param point1
+ * @param point2
+ * @param degreesPerSecond
+ * @param endDegrees
+ * @param isClockwise
+ * @param isSpin
+ * @param bsAtoms
+ * @param isGesture
+ * @param translation
+ * @param finalPoints
+ * @param dihedralList
+ * @return true if synchronous so that JavaScript can restart properly
+ */
boolean rotateAboutPointsInternal(JmolScriptEvaluator eval, P3 point1,
P3 point2, float degreesPerSecond,
float endDegrees, boolean isClockwise,
boolean isSpin, BS bsAtoms,
boolean isGesture, V3 translation,
- JmolList<P3> finalPoints, float[]
dihedralList) {
+ JmolList<P3> finalPoints,
+ float[] dihedralList) {
// *THE* Viewer INTERNAL frame rotation entry point
@@ -401,7 +418,8 @@
isSpin = false;
}
- if (dihedralList == null && (translation == null || translation.length() <
0.001)
+ if (dihedralList == null
+ && (translation == null || translation.length() < 0.001)
&& (!isSpin || endDegrees == 0 || Float.isNaN(degreesPerSecond) ||
degreesPerSecond == 0)
&& (isSpin || endDegrees == 0))
return false;
@@ -421,29 +439,30 @@
if (isSpin) {
// we need to adjust the degreesPerSecond to match a multiple of the
frame rate
if (dihedralList == null) {
- int nFrames = (int) (Math.abs(endDegrees) / Math.abs(degreesPerSecond)
- * spinFps + 0.5);
- if (Float.isNaN(endDegrees)) {
- rotationRate = degreesPerSecond;
+ int nFrames = (int) (Math.abs(endDegrees) / Math.abs(degreesPerSecond)
+ * spinFps + 0.5);
+ if (Float.isNaN(endDegrees)) {
+ rotationRate = degreesPerSecond;
+ } else {
+ rotationRate = degreesPerSecond = endDegrees / nFrames * spinFps;
+ if (translation != null)
+ internalTranslation.scale(1f / (nFrames));
+ }
+ internalRotationAxis.setVA(axis, rotationRate * JC.radiansPerDegree);
+ isSpinInternal = true;
+ isSpinFixed = false;
+ isSpinSelected = isSelected;
} else {
- rotationRate = degreesPerSecond = endDegrees / nFrames * spinFps;
- if (translation != null)
- internalTranslation.scale(1f / (nFrames));
- }
- internalRotationAxis.setVA(axis, rotationRate * JC.radiansPerDegree);
- isSpinInternal = true;
- isSpinFixed = false;
- isSpinSelected = isSelected;
- } else {
endDegrees = degreesPerSecond;
}
- setSpin(eval, true, endDegrees, finalPoints, dihedralList, bsAtoms,
isGesture);
- return false;
+ setSpin(eval, true, endDegrees, finalPoints, dihedralList, bsAtoms,
+ isGesture);
+ return (dihedralList != null || bsAtoms != null);
}
float radians = endDegrees * JC.radiansPerDegree;
internalRotationAxis.setVA(axis, radians);
rotateAxisAngleRadiansInternal(radians, bsAtoms);
- return true;
+ return false;
}
public synchronized void rotateAxisAngleRadiansInternal(float radians,
@@ -1981,16 +2000,18 @@
boolean isGesture) {
if (navOn && spinOn)
setNavOn(false);
+ if (this.spinOn == spinOn)
+ return;
this.spinOn = spinOn;
viewer.getGlobalSettings().setB("_spinning", spinOn);
if (spinOn) {
if (spinThread == null) {
spinThread = new SpinThread(this, viewer, endDegrees, endPositions,
dihedralList,
bsAtoms, false, isGesture);
- spinThread.setEval(eval);
- if (bsAtoms == null) {
+ if (bsAtoms == null && dihedralList == null) {
spinThread.start();
} else {
+ spinThread.setEval(eval);
spinThread.run();
}
}
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