Revision: 20164
http://sourceforge.net/p/jmol/code/20164
Author: hansonr
Date: 2014-12-18 00:45:21 +0000 (Thu, 18 Dec 2014)
Log Message:
-----------
Jmol.___JmolVersion="14.3.11_2014.12.17"
bug fix: rotate selected <4x4 matrix> should not rotate about center of atoms
bug fix: use of a subset command will change value of a variable bitset if
"select x" is used
-- example:
x = {*}
subset {atomno < 10}
print x // just the first 9
select x // just the first 9
subset all
print x // but now x itself is truncated; this is not supposed to be the case
new feature: SYNC nnnn x
-- x is a math expression, possibly just a string, but also possibly an
associative array.
new feature: SYNC nnnn {type:"command", "command" : command, "var": vname,
"data":vdata}
-- script command request, with optional definition of a Jmol user variable
prior to execution)
-- for example:
x = {"type":"command","command":"background green; print y", "var":
"y", "data":['an array',2]}
sync 3000 x
-- allows simple transfer of data via JSON strings between applications
Modified Paths:
--------------
trunk/Jmol/src/javajs/util/Measure.java
trunk/Jmol/src/org/jmol/modelset/ModelSet.java
trunk/Jmol/src/org/jmol/script/ScriptEval.java
trunk/Jmol/src/org/jmol/script/ScriptExpr.java
trunk/Jmol/src/org/jmol/script/ScriptManager.java
trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
trunk/Jmol/src/org/jmol/scriptext/MathExt.java
trunk/Jmol/src/org/jmol/symmetry/SymmetryDesc.java
trunk/Jmol/src/org/jmol/thread/SpinThread.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/SelectionManager.java
trunk/Jmol/src/org/jmol/viewer/TransformManager.java
trunk/Jmol/src/org/jmol/viewer/Viewer.java
trunk/Jmol/src/org/openscience/jmol/app/jsonkiosk/JsonNioService.java
Modified: trunk/Jmol/src/javajs/util/Measure.java
===================================================================
--- trunk/Jmol/src/javajs/util/Measure.java 2014-12-16 03:52:45 UTC (rev
20163)
+++ trunk/Jmol/src/javajs/util/Measure.java 2014-12-18 00:45:21 UTC (rev
20164)
@@ -416,7 +416,7 @@
for (int i = 0; i < vPts.size(); i++) {
P3 pt = P3.newP(vPts.get(i));
pt.sub(center);
- m4.rotTrans2(pt, pt);
+ m4.rotTrans(pt);
pt.add(center);
v.addLast(pt);
}
Modified: trunk/Jmol/src/org/jmol/modelset/ModelSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2014-12-16 03:52:45 UTC
(rev 20163)
+++ trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2014-12-18 00:45:21 UTC
(rev 20164)
@@ -4059,20 +4059,27 @@
*/
}
-
- public void moveAtoms(M3 mNew, M3 rotation, V3 translation, BS bs,
+ public void moveAtoms(M4 m4, M3 mNew, M3 rotation, V3 translation, BS bs,
P3 center, boolean isInternal, boolean
translationOnly) {
- if (!translationOnly) {
+ if (m4 != null) {
+ for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1))
+ m4.rotTrans(at[i]);
+ mat4.setM4(m4);
+ translation = null;
+ } else if (!translationOnly) {
if (mNew == null) {
matTemp.setM3(rotation);
} else {
+ // screen frame?
+ // must do inv(currentRot) * mNew * currentRot
+ ptTemp.set(0, 0, 0);
matInv.setM3(rotation);
matInv.invert();
- ptTemp.set(0, 0, 0);
matTemp.mul2(mNew, rotation);
matTemp.mul2(matInv, matTemp);
}
if (isInternal) {
+ // adjust rotation to be around center of this set of atoms
vTemp.setT(center);
mat4.setIdentity();
mat4.setTranslation(vTemp);
@@ -4206,7 +4213,7 @@
pt = Measure.getCenterAndPoints(vNot)[0];
V3 v = V3.newVsub(thisAtom, pt);
Quat q = Quat.newVA(v, 180);
- moveAtoms(null, q.getMatrix(), null, bsAtoms, thisAtom, true, false);
+ moveAtoms(null, null, q.getMatrix(), null, bsAtoms, thisAtom, true,
false);
}
}
Modified: trunk/Jmol/src/org/jmol/script/ScriptEval.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEval.java 2014-12-16 03:52:45 UTC
(rev 20163)
+++ trunk/Jmol/src/org/jmol/script/ScriptEval.java 2014-12-18 00:45:21 UTC
(rev 20164)
@@ -5711,6 +5711,7 @@
V3 translation = null;
M4 m4 = null;
M3 m3 = null;
+ boolean is4x4 = false;
int direction = 1;
int tok;
Quat q = null;
@@ -5896,37 +5897,39 @@
isSelected = true;
continue;
case T.compare:
+ bsCompare = atomExpressionAt(++i);
+ ptsA = vwr.ms.getAtomPointVector(bsCompare);
+ if (ptsA == null) {
+ iToken = i;
+ invArg();
+ }
+ i = iToken;
+ ptsB = getPointVector(getToken(++i), i);
+ if (ptsB == null || ptsA.size() != ptsB.size()) {
+ iToken = i;
+ invArg();
+ }
+ m4 = new M4();
+ points[0] = new P3();
+ nPoints = 1;
+ Interface.getInterface("javajs.util.Eigen", vwr, "script");
+ float stddev = (chk ? 0 : Measure.getTransformMatrix4(ptsA, ptsB, m4,
+ points[0]));
+ // if the standard deviation is very small, we leave ptsB
+ // because it will be used to set the absolute final positions
+ if (stddev > 0.001)
+ ptsB = null;
+ //$FALL-THROUGH$
case T.matrix4f:
case T.matrix3f:
haveRotation = true;
- if (tok == T.compare) {
- bsCompare = atomExpressionAt(++i);
- ptsA = vwr.ms.getAtomPointVector(bsCompare);
- if (ptsA == null) {
- iToken = i;
- invArg();
- }
- i = iToken;
- ptsB = getPointVector(getToken(++i), i);
- if (ptsB == null || ptsA.size() != ptsB.size()) {
- iToken = i;
- invArg();
- }
- m4 = new M4();
- points[0] = new P3();
- nPoints = 1;
- Interface.getInterface("javajs.util.Eigen", vwr, "script");
- float stddev = (chk ? 0 : Measure.getTransformMatrix4(ptsA, ptsB, m4,
- points[0]));
- // if the standard deviation is very small, we leave ptsB
- // because it will be used to set the absolute final positions
- if (stddev > 0.001)
- ptsB = null;
- } else if (tok == T.matrix4f) {
+ m3 = new M3();
+ if (tok == T.matrix4f) {
+ is4x4 = true;
m4 = (M4) theToken.value;
}
- m3 = new M3();
if (m4 != null) {
+ // translation and rotation are calculated
translation = new V3();
m4.getTranslation(translation);
m4.getRotationScale(m3);
@@ -5977,9 +5980,9 @@
}
if (q != null) {
- // only when there is a translation (4x4 matrix or TRANSLATE)
+ // only when there is a translation but not a 4x4 matrix)
// do we set the rotation to be the center of the selected atoms or model
- if (nPoints == 0 && translation != null)
+ if (nPoints == 0 && translation != null && !is4x4)
points[0] = vwr.ms.getAtomSetCenter(bsAtoms != null ? bsAtoms
: isSelected ? vwr.bsA() : vwr.getAllAtoms());
if (helicalPath && translation != null) {
@@ -6080,6 +6083,7 @@
}
if (bsAtoms != null && isSpin && ptsB == null && m4 != null) {
ptsA = vwr.ms.getAtomPointVector(bsAtoms);
+ // note that this m4 is NOT through
ptsB = Measure.transformPoints(ptsA, m4, points[0]);
}
if (bsAtoms != null && !isSpin && ptsB != null) {
@@ -6088,7 +6092,7 @@
if (requiresThread && !useThreads())
return;
if (vwr.rotateAboutPointsInternal(this, points[0], points[1], rate,
- endDegrees, isSpin, bsAtoms, translation, ptsB, dihedralList)
+ endDegrees, isSpin, bsAtoms, translation, ptsB, dihedralList, is4x4
? m4 : null)
&& isJS
&& isSpin)
throw new ScriptInterruption(this, "rotate", 1);
@@ -7544,11 +7548,11 @@
private void cmdSync() throws ScriptException {
// new 11.3.9
- checkLength(-3);
String text = "";
String applet = "";
int port = PT.parseInt(optParameterAsString(1));
if (port == Integer.MIN_VALUE) {
+ checkLength(-3);
port = 0;
switch (slen) {
case 1:
@@ -7578,7 +7582,10 @@
break;
}
} else {
- text = (slen == 2 ? null : paramAsStr(2));
+ SV v = null;
+ if (slen > 2 && (v = setVariable(2, -1, "", false)) == null)
+ return;
+ text = (slen == 2 ? null : v.tok == T.hash ? v.toJSON() : v.asString());
applet = null;
}
if (chk)
Modified: trunk/Jmol/src/org/jmol/script/ScriptExpr.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptExpr.java 2014-12-16 03:52:45 UTC
(rev 20163)
+++ trunk/Jmol/src/org/jmol/script/ScriptExpr.java 2014-12-18 00:45:21 UTC
(rev 20164)
@@ -973,7 +973,7 @@
BS bs = (expressionResult instanceof BS ? (BS) expressionResult : new
BS());
isBondSet = (expressionResult instanceof BondSet);
if (!isBondSet
- && vwr.excludeAtoms(bs, ignoreSubset).length() > vwr.ms.ac)
+ && (bs = vwr.slm.excludeAtoms(bs, ignoreSubset)).length() > vwr.ms.ac)
bs.clearAll();
if (tempStatement != null) {
st = tempStatement;
Modified: trunk/Jmol/src/org/jmol/script/ScriptManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptManager.java 2014-12-16 03:52:45 UTC
(rev 20163)
+++ trunk/Jmol/src/org/jmol/script/ScriptManager.java 2014-12-18 00:45:21 UTC
(rev 20164)
@@ -497,7 +497,7 @@
if (eval == null)
eval = evalTemp = newScriptEvaluator();
}
- return vwr.excludeAtoms(eval.getAtomBitSet(atomExpression), false);
+ return vwr.slm.excludeAtoms(eval.getAtomBitSet(atomExpression), false);
}
@Override
Modified: trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2014-12-16 03:52:45 UTC
(rev 20163)
+++ trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2014-12-18 00:45:21 UTC
(rev 20164)
@@ -918,7 +918,7 @@
if (!eval.useThreads())
doAnimate = false;
if (vwr.rotateAboutPointsInternal(eval, center, pt1, endDegrees /
nSeconds,
- endDegrees, doAnimate, bsFrom, translation, ptsB, null)
+ endDegrees, doAnimate, bsFrom, translation, ptsB, null, null)
&& doAnimate
&& eval.isJS)
throw new ScriptInterruption(eval, "compare", 1);
Modified: trunk/Jmol/src/org/jmol/scriptext/MathExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2014-12-16 03:52:45 UTC
(rev 20163)
+++ trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2014-12-18 00:45:21 UTC
(rev 20164)
@@ -182,14 +182,14 @@
return evaluateRandom(mp, args);
case T.in:
return evaluateIn(mp, args);
+ case T.modulation:
+ return evaluateModulation(mp, args);
case T.replace:
return evaluateReplace(mp, args);
case T.search:
case T.smiles:
case T.substructure:
return evaluateSubstructure(mp, args, tok);
- case T.modulation:
- return evaluateModulation(mp, args);
case T.sort:
case T.count:
return evaluateSort(mp, args, tok);
Modified: trunk/Jmol/src/org/jmol/symmetry/SymmetryDesc.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/SymmetryDesc.java 2014-12-16 03:52:45 UTC
(rev 20163)
+++ trunk/Jmol/src/org/jmol/symmetry/SymmetryDesc.java 2014-12-18 00:45:21 UTC
(rev 20164)
@@ -797,7 +797,7 @@
P3 pt00, V3 vtrans) {
P3 p0 = P3.newP(pt00);
uc.toFractional(p0, false);
- op.rotTrans2(p0, p0);
+ op.rotTrans(p0);
p0.add(vtrans);
uc.toCartesian(p0, false);
return p0;
Modified: trunk/Jmol/src/org/jmol/thread/SpinThread.java
===================================================================
--- trunk/Jmol/src/org/jmol/thread/SpinThread.java 2014-12-16 03:52:45 UTC
(rev 20163)
+++ trunk/Jmol/src/org/jmol/thread/SpinThread.java 2014-12-18 00:45:21 UTC
(rev 20164)
@@ -29,6 +29,8 @@
import org.jmol.java.BS;
import org.jmol.script.T;
import javajs.util.Lst;
+import javajs.util.M4;
+
import org.jmol.util.Logger;
import javajs.util.P3;
import org.jmol.viewer.JC;
@@ -54,6 +56,7 @@
//private boolean navigatingSurface;
private BS[] bsBranches;
private boolean isDone = false;
+ private M4 m4;
/**
* @j2sIgnore
@@ -223,7 +226,7 @@
: transformManager.fixedRotationAxis).angle
/ myFps;
if (transformManager.isSpinInternal) {
- transformManager.rotateAxisAngleRadiansInternal(angle, bsAtoms);
+ transformManager.rotateAxisAngleRadiansInternal(angle, bsAtoms, m4);
} else {
transformManager.rotateAxisAngleRadiansFixed(angle, bsAtoms);
}
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2014-12-16 03:52:45 UTC
(rev 20163)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2014-12-18 00:45:21 UTC
(rev 20164)
@@ -15,8 +15,33 @@
TODO: design and implement sidechain mutation -- MUTATE command ?
TODO: remove HTML5 dependency on synchronous file loading (check SCRIPT
command for problems)
-Jmol.___JmolVersion="14.3.11_2014.12.15"
+Jmol.___JmolVersion="14.3.11_2014.12.17"
+
+bug fix: rotate selected <4x4 matrix> should not rotate about center of atoms
+bug fix: use of a subset command will change value of a variable bitset if
"select x" is used
+ -- example:
+ x = {*}
+ subset {atomno < 10}
+ print x // just the first 9
+ select x // just the first 9
+ subset all
+ print x // but now x itself is truncated; this is not supposed to be the
case
+
+
+new feature: SYNC nnnn x
+ -- x is a math expression, possibly just a string, but also possibly an
associative array.
+
+new feature: SYNC nnnn {type:"command", "command" : command, "var": vname,
"data":vdata}
+ -- script command request, with optional definition of a Jmol user variable
prior to execution)
+ -- for example:
+ x = {"type":"command","command":"background green; print y", "var":
"y", "data":['an array',2]}
+ sync 3000 x
+ -- allows simple transfer of data via JSON strings between applications
+
+
+JmolVersion="14.3.11_2014.12.15"
+
FEATURE CHANGE: JmolViewer interface streamlined
-- many esoteric methods removed
-- can be reinstated upon request
Modified: trunk/Jmol/src/org/jmol/viewer/SelectionManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/SelectionManager.java 2014-12-16
03:52:45 UTC (rev 20163)
+++ trunk/Jmol/src/org/jmol/viewer/SelectionManager.java 2014-12-18
00:45:21 UTC (rev 20164)
@@ -322,11 +322,12 @@
return BSUtil.copy(bsSelection);
}
- void excludeAtoms(BS bs, boolean ignoreSubset) {
+ public BS excludeAtoms(BS bs, boolean ignoreSubset) {
if (bsDeleted != null)
bs.andNot(bsDeleted);
if (!ignoreSubset && bsSubset != null)
- bs.and(bsSubset);
+ (bs = BSUtil.copy(bs)).and(bsSubset);
+ return bs;
}
void setMotionFixedAtoms(BS bs) {
Modified: trunk/Jmol/src/org/jmol/viewer/TransformManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/TransformManager.java 2014-12-16
03:52:45 UTC (rev 20163)
+++ trunk/Jmol/src/org/jmol/viewer/TransformManager.java 2014-12-18
00:45:21 UTC (rev 20164)
@@ -260,7 +260,7 @@
unTransformPoint(pt2, pt2);
vwr.setInMotion(false);
rotateAboutPointsInternal(null, pt2, pt1, 10 * speed, Float.NaN, false,
- true, null, true, null, null, null);
+ true, null, true, null, null, null, null);
}
// final V3 arcBall0 = new V3();
@@ -311,12 +311,12 @@
}
private void applyRotation(M3 mNew, boolean isInternal, BS bsAtoms,
- V3 translation, boolean translationOnly) {
+ V3 translation, boolean translationOnly, M4 m4) {
if (bsAtoms == null) {
matrixRotate.mul2(mNew, matrixRotate);
return;
}
- vwr.moveAtoms(mNew, matrixRotate, translation, internalRotationCenter,
+ vwr.moveAtoms(m4, mNew, matrixRotate, translation, internalRotationCenter,
isInternal, bsAtoms, translationOnly);
if (translation != null) {
internalRotationCenter.add(translation);
@@ -335,22 +335,22 @@
// the signs of both screen Y and screen Z in the end.
if (matrixTemp3.setAsBallRotation(JC.radiansPerDegree, -yDeg, -xDeg))
- applyRotation(matrixTemp3, false, bsAtoms, null, false);
+ applyRotation(matrixTemp3, false, bsAtoms, null, false, null);
}
public synchronized void rotateXRadians(float angleRadians, BS bsAtoms) {
applyRotation(matrixTemp3.setAsXRotation(angleRadians), false, bsAtoms,
- null, false);
+ null, false, null);
}
public synchronized void rotateYRadians(float angleRadians, BS bsAtoms) {
applyRotation(matrixTemp3.setAsYRotation(angleRadians), false, bsAtoms,
- null, false);
+ null, false, null);
}
public synchronized void rotateZRadians(float angleRadians) {
applyRotation(matrixTemp3.setAsZRotation(angleRadians), false, null, null,
- false);
+ false, null);
}
public void rotateAxisAngle(V3 rotAxis, float radians) {
@@ -359,7 +359,7 @@
}
private synchronized void rotateAxisAngle2(A4 axisAngle, BS bsAtoms) {
- applyRotation(matrixTemp3.setAA(axisAngle), false, bsAtoms, null, false);
+ applyRotation(matrixTemp3.setAA(axisAngle), false, bsAtoms, null, false,
null);
}
/*
@@ -436,6 +436,7 @@
* @param translation
* @param finalPoints
* @param dihedralList
+ * @param m4
* @return true if synchronous so that JavaScript can restart properly
*/
boolean rotateAboutPointsInternal(JmolScriptEvaluator eval, T3 point1,
@@ -443,7 +444,7 @@
float endDegrees, boolean isClockwise,
boolean isSpin, BS bsAtoms,
boolean isGesture, V3 translation,
- Lst<P3> finalPoints, float[] dihedralList)
{
+ Lst<P3> finalPoints, float[] dihedralList,
M4 m4) {
// *THE* Viewer INTERNAL frame rotation entry point
@@ -463,11 +464,7 @@
axis.scale(-1f);
internalRotationCenter.setT(point1);
rotationAxis.setT(axis);
- if (translation == null) {
- internalTranslation = null;
- } else {
- internalTranslation = V3.newV(translation);
- }
+ internalTranslation = (translation == null ? null :
V3.newV(translation));
}
boolean isSelected = (bsAtoms != null);
if (isSpin) {
@@ -498,12 +495,12 @@
}
float radians = endDegrees * JC.radiansPerDegree;
internalRotationAxis.setVA(axis, radians);
- rotateAxisAngleRadiansInternal(radians, bsAtoms);
+ rotateAxisAngleRadiansInternal(radians, bsAtoms, m4);
return false;
}
public synchronized void rotateAxisAngleRadiansInternal(float radians,
- BS bsAtoms) {
+ BS bsAtoms, M4 m4) {
// final matrix rotation when spinning or just rotating
@@ -518,7 +515,7 @@
// NOW apply that rotation
applyRotation(matrixTemp3.setAA(axisangleT), true, bsAtoms,
- internalTranslation, radians > 1e6f);
+ internalTranslation, radians > 1e6f, m4);
if (bsAtoms == null)
getNewFixedRotationCenter();
}
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2014-12-16 03:52:45 UTC (rev
20163)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2014-12-18 00:45:21 UTC (rev
20164)
@@ -110,6 +110,7 @@
import javajs.util.P4;
import org.jmol.util.Rectangle;
+import javajs.util.M4;
import javajs.util.Measure;
import javajs.util.Rdr;
import javajs.util.CU;
@@ -2581,18 +2582,13 @@
}
public BS getModelUndeletedAtomsBitSet(int modelIndex) {
- return excludeAtoms(ms.getModelAtomBitSetIncludingDeleted(modelIndex,
true), false);
+ return slm.excludeAtoms(ms.getModelAtomBitSetIncludingDeleted(modelIndex,
true), false);
}
public BS getModelUndeletedAtomsBitSetBs(BS bsModels) {
- return excludeAtoms(ms.getModelAtomBitSetIncludingDeletedBs(bsModels),
false);
+ return slm.excludeAtoms(ms.getModelAtomBitSetIncludingDeletedBs(bsModels),
false);
}
- public BS excludeAtoms(BS bs, boolean ignoreSubset) {
- slm.excludeAtoms(bs, ignoreSubset);
- return bs;
- }
-
@Override
public P3 getBoundBoxCenter() {
return ms.getBoundBoxCenter(am.cmi);
@@ -7134,7 +7130,7 @@
float endDegrees, boolean isSpin,
BS bsSelected, V3 translation,
Lst<P3> finalPoints,
- float[] dihedralList) {
+ float[] dihedralList, M4 m4) {
// Eval: rotate INTERNAL
if (headless) {
@@ -7145,7 +7141,7 @@
boolean isOK = tm.rotateAboutPointsInternal(eval, point1,
point2, degreesPerSecond, endDegrees, false, isSpin, bsSelected, false,
- translation, finalPoints, dihedralList);
+ translation, finalPoints, dihedralList, m4);
if (isOK)
setSync();
return isOK;
@@ -7161,7 +7157,7 @@
}
tm.rotateAboutPointsInternal(null, pt1, pt2,
g.pickingSpinRate, Float.MAX_VALUE, isClockwise, true, null,
- false, null, null, null);
+ false, null, null, null, null);
}
public V3 getModelDipole() {
@@ -7305,12 +7301,12 @@
sm.setStatusAtomMoved(bs);
}
- public void moveAtoms(M3 mNew, M3 rotation, V3 translation,
+ public void moveAtoms(M4 m4, M3 mNew, M3 rotation, V3 translation,
P3 center, boolean isInternal, BS bsAtoms, boolean
translationOnly) {
// from TransformManager exclusively
if (bsAtoms.cardinality() == 0)
return;
- ms.moveAtoms(mNew, rotation, translation, bsAtoms, center,
+ ms.moveAtoms(m4, mNew, rotation, translation, bsAtoms, center,
isInternal, translationOnly);
checkMinimization();
sm.setStatusAtomMoved(bsAtoms);
@@ -7474,7 +7470,7 @@
bs.andNot(slm.getMotionFixedAtoms());
rotateAboutPointsInternal(eval, atom1, atom2, 0, degrees, false, bs, null,
- null, null);
+ null, null, null);
}
public void refreshMeasures(boolean andStopMinimization) {
@@ -8916,7 +8912,7 @@
// used for set picking SELECT
if (atomExpression instanceof BS)
- return excludeAtoms((BS) atomExpression, false);
+ return slm.excludeAtoms((BS) atomExpression, false);
getScriptManager();
return getAtomBitSetEval(eval, atomExpression);
}
Modified: trunk/Jmol/src/org/openscience/jmol/app/jsonkiosk/JsonNioService.java
===================================================================
--- trunk/Jmol/src/org/openscience/jmol/app/jsonkiosk/JsonNioService.java
2014-12-16 03:52:45 UTC (rev 20163)
+++ trunk/Jmol/src/org/openscience/jmol/app/jsonkiosk/JsonNioService.java
2014-12-18 00:45:21 UTC (rev 20164)
@@ -93,7 +93,8 @@
*
* {"type" : "banner", "mode" : "ON" or "OFF" } (set banner for kiosk)
* {"type" : "banner", "text" : bannerText } (set banner for kiosk)
- * {"type" : "command", "command" : command } (script command request)
+ * {"type" : "command", "command" : command, "var": vname, "data":vdata}
+ * (script command request, with optional definition of a Jmol user
variable prior to execution)
* {"type" : "content", "id" : id } (load content request)
* {"type" : "move", "style" : (see below) } (mouse command request)
* {"type" : "quit" } (shut down request)
@@ -542,6 +543,8 @@
case 10: // command
if (contentDisabled)
break;
+ if (json.containsKey("var") && json.containsKey("data"))
+ vwr.g.setUserVariable(json.get("var").toString(),
SV.getVariable(json.get("data")));
sendScript(json.getString("command"));
break;
case 20: // content
@@ -771,7 +774,7 @@
public Object get(String key) {
Object o = super.get(key);
- return (o instanceof SV ? ((SV) o).value : o);
+ return (o instanceof SV ? SV.oValue((SV) o) : o);
}
public long getLong(String key) throws Exception {
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