Revision: 20860
http://sourceforge.net/p/jmol/code/20860
Author: hansonr
Date: 2015-11-07 00:19:29 +0000 (Sat, 07 Nov 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.5.0_2015.11.06"
bug fix: restoring bonds to a model having fewer bonds than the model for which
they were saved throws an exception
bug fix: mCIF does not read incommensurately modulated mCIF files
bug fix: WRITE xxx.ZIP crashes Jmol
bug fix: POLYHEDRA ... {xxx} TO {yyy} not working
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
trunk/Jmol/src/org/jmol/modelset/ModelSet.java
trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
trunk/Jmol/src/org/jmol/scriptext/MathExt.java
trunk/Jmol/src/org/jmol/symmetry/PointGroup.java
trunk/Jmol/src/org/jmol/util/Modulation.java
trunk/Jmol/src/org/jmol/util/ModulationSet.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/StateManager.java
Modified: trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2015-11-06
04:48:47 UTC (rev 20859)
+++ trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2015-11-07
00:19:29 UTC (rev 20860)
@@ -224,8 +224,9 @@
public Lst<P3> getAtomPointVector(BS bs) {
Lst<P3> v = new Lst<P3>();
+ int n = ac;
if (bs != null) {
- for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i+1)) {
+ for (int i = bs.nextSetBit(0); i >= 0 && i < n; i = bs.nextSetBit(i+1)) {
v.addLast(at[i]);
}
}
Modified: trunk/Jmol/src/org/jmol/modelset/ModelSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2015-11-06 04:48:47 UTC
(rev 20859)
+++ trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2015-11-07 00:19:29 UTC
(rev 20860)
@@ -530,7 +530,6 @@
SymmetryInterface pointGroup = this.pointGroup;
boolean isPolyhedron = (type != null &&
type.toUpperCase().indexOf(":POLY") >= 0);
if (isPolyhedron) {
-
Object[] data = new Object[] { Integer.valueOf(iAtom), null };
vwr.shm.getShapePropertyData(JC.SHAPE_POLYHEDRA, "points", data);
pts = (T3[]) data[1];
Modified: trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-11-06 04:48:47 UTC
(rev 20859)
+++ trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-11-07 00:19:29 UTC
(rev 20860)
@@ -3294,10 +3294,10 @@
case T.to:
if (nAtomSets > 1 || id != null && !haveCenter)
invPO();
- if ((tokAt(++i) == T.bitset || tokAt(i) == T.expressionBegin)
- && !needsGenerating) {
+ nAtomSets = 3; // don't allow two of these
+ if (tokAt(++i) == T.bitset || tokAt(i) == T.expressionBegin) {
// select... polyhedron .... to ....
- propertyName = "toBitSet";
+ propertyName = (needsGenerating ? "to" : "toBitSet");
propertyValue = atomExpressionAt(i);
} else if (eval.isArrayParameter(i)) {
// select... polyhedron .... to [...]
@@ -3329,8 +3329,7 @@
}
propertyValue = atomExpressionAt(i);
i = eval.iToken;
- if (i + 1 == slen)
- needsGenerating = true;
+ needsGenerating |= (i + 1 == slen);
break;
case T.color:
case T.translucent:
@@ -3408,7 +3407,7 @@
} else if (!edgeParameterSeen && offset == null && Float.isNaN(scale)) {//
&& lighting == T.nada)
error(ScriptError.ERROR_insufficientArguments);
}
- if (offset != null)
+ if (offset != null)
setShapeProperty(JC.SHAPE_POLYHEDRA, "offset", offset);
if (!Float.isNaN(scale))
setShapeProperty(JC.SHAPE_POLYHEDRA, "scale", Float.valueOf(scale));
@@ -3914,7 +3913,8 @@
} else if (data == "ZIP" || data == "ZIPALL") {
if (fileName != null) {
params = new Hashtable<String, Object>();
- params.put("data", scripts);
+ if (scripts != null)
+ params.put("data", scripts);
if ((bytes = data = (String) vwr.createZip(fileName, type, params))
== null)
eval.evalError("#CANCELED#", null);
}
Modified: trunk/Jmol/src/org/jmol/scriptext/MathExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2015-11-06 04:48:47 UTC
(rev 20859)
+++ trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2015-11-07 00:19:29 UTC
(rev 20860)
@@ -227,25 +227,69 @@
private boolean evaluatePointGroup(ScriptMathProcessor mp, SV[] args) {
// pointGroup(points)
// pointGroup(points, center)
+ // pointGroup(points, center, distanceTolerance (def. 0.2 A),
linearTolerance (def. 8 deg.)
+ // center can be non-point to ignore, such as 0 or ""
+ T3[] pts;
P3 center = null;
- T3[] pts;
+ float distanceTolerance = Float.NaN;
+ float linearTolerance = Float.NaN;
+ BS bsAtoms;
switch (args.length) {
+ case 4:
+ linearTolerance = args[3].asFloat();
+ //$FALL-THROUGH$
+ case 3:
+ distanceTolerance = args[2].asFloat();
+ //$FALL-THROUGH$
case 2:
- center = SV.ptValue(args[1]);
+ switch (args[1].tok) {
+ case T.point3f:
+ center = SV.ptValue(args[1]);
+ break;
+ case T.bitset:
+ bsAtoms = SV.getBitSet(args[0], false);
+ int iatom = bsAtoms.nextSetBit(0);
+ if (iatom < 0 || iatom >= vwr.ms.ac || bsAtoms.cardinality() != 1)
+ return false;
+ center = vwr.ms.at[iatom];
+ break;
+ }
//$FALL-THROUGH$
case 1:
+ switch (args[0].tok) {
+ case T.list:
Lst<SV> points = args[0].getList();
pts = new T3[points.size()];
for (int i = pts.length; --i >= 0;)
pts[i] = SV.ptValue(points.get(i));
break;
+ case T.bitset:
+ bsAtoms = SV.getBitSet(args[0], false);
+ Lst<P3> atoms = vwr.ms.getAtomPointVector(bsAtoms);
+ pts = new T3[atoms.size()];
+ for (int i = pts.length; --i >= 0;)
+ pts[i] = atoms.get(i);
+ break;
+ default:
+ return false;
+ }
+ break;
default:
- return false;
+ return false;
}
- SymmetryInterface pointGroup = vwr.ms.getSymTemp(true).setPointGroup(null,
center, pts,
- null, false,
- vwr.getFloat(T.pointgroupdistancetolerance),
vwr.getFloat(T.pointgrouplineartolerance), true);
- return mp.addXMap((Map<String, ?>) pointGroup.getPointGroupInfo(-1, false,
true, null, 0, 1));
+ SymmetryInterface pointGroup = vwr.ms.getSymTemp(true).setPointGroup(
+ null,
+ center,
+ pts,
+ null,
+ false,
+ Float.isNaN(distanceTolerance) ? vwr
+ .getFloat(T.pointgroupdistancetolerance) : distanceTolerance,
+ Float.isNaN(linearTolerance) ? vwr
+ .getFloat(T.pointgrouplineartolerance)
+ : linearTolerance, true);
+ return mp.addXMap((Map<String, ?>) pointGroup.getPointGroupInfo(-1, false,
+ true, null, 0, 1));
}
private boolean evaluateUnitCell(ScriptMathProcessor mp, SV[] args) {
Modified: trunk/Jmol/src/org/jmol/symmetry/PointGroup.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/PointGroup.java 2015-11-06 04:48:47 UTC
(rev 20859)
+++ trunk/Jmol/src/org/jmol/symmetry/PointGroup.java 2015-11-07 00:19:29 UTC
(rev 20860)
@@ -41,6 +41,7 @@
import org.jmol.util.Escape;
import org.jmol.util.Logger;
import org.jmol.util.Node;
+import org.jmol.util.Point3fi;
import javajs.util.P3;
import javajs.util.V3;
@@ -410,6 +411,8 @@
int bondIndex = (localEnvOnly ? 1 : 1 + Math.max(3,
((Node) p).getCovalentBondCount()));
elements[nAtoms] = ((Node) p).getElementNumber() * bondIndex;
+ } else if (p instanceof Point3fi) {
+ elements[nAtoms] = ((Point3fi) p).sD;
}
if (needCenter)
center.add(points[nAtoms]);
@@ -418,7 +421,7 @@
center.scale(1f / nAtoms);
for (int i = nAtoms; --i >= 0;) {
float r = center.distance(points[i]);
- if (r < distanceTolerance)
+ if (isAtoms && r < distanceTolerance)
centerAtomIndex = i;
radius = Math.max(radius, r);
}
Modified: trunk/Jmol/src/org/jmol/util/Modulation.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Modulation.java 2015-11-06 04:48:47 UTC
(rev 20859)
+++ trunk/Jmol/src/org/jmol/util/Modulation.java 2015-11-07 00:19:29 UTC
(rev 20860)
@@ -270,6 +270,8 @@
if (isSpin) {
float[] f = ms.axesLengths;
+ if (f == null)
+ System.out.println("Modulation.java axis error");
switch (axis) {
case 'x':
ms.mxyz.x += v / f[0];
Modified: trunk/Jmol/src/org/jmol/util/ModulationSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/ModulationSet.java 2015-11-06 04:48:47 UTC
(rev 20859)
+++ trunk/Jmol/src/org/jmol/util/ModulationSet.java 2015-11-07 00:19:29 UTC
(rev 20860)
@@ -359,6 +359,9 @@
vib.modScale = 1;
mxyz = new V3(); // modulations of spin
axesLengths = symmetry.getUnitCellParams(); // required for calculating
mxyz
+ if (axesLengths == null)
+ axesLengths = symmetry.getUnitCellParams(); // required for
calculating mxyz
+
}
Matrix vR00 = Matrix.newT(r00, true);
Matrix vR0 = Matrix.newT(r0, true);
@@ -575,24 +578,25 @@
private ModulationSet getModCalc() {
if (modCalc == null) {
modCalc = new ModulationSet();
+ modCalc.axesLengths = axesLengths;
+ modCalc.enabled = true;
+ modCalc.fileOcc = fileOcc;
+ modCalc.gammaE = gammaE;
+ modCalc.gammaIinv = gammaIinv;
modCalc.id = id;
- modCalc.tau = tau;
- modCalc.spinOp = spinOp;
+ modCalc.modDim = modDim;
modCalc.mods = mods;
- modCalc.gammaE = gammaE;
- modCalc.modDim = modDim;
- modCalc.gammaIinv = gammaIinv;
+ modCalc.nOps = nOps;
+ modCalc.occParams = occParams;
+ modCalc.occSiteMultiplicity = occSiteMultiplicity;
+ modCalc.r0 = r0;
+ modCalc.rI = rI;
modCalc.sigma = sigma;
- modCalc.r0 = r0;
+ modCalc.spinOp = spinOp;
+ modCalc.symmetry = symmetry;
+ modCalc.tau = tau;
modCalc.v0 = v0;
modCalc.vib = vib;
- modCalc.symmetry = symmetry;
- modCalc.rI = rI;
- modCalc.fileOcc = fileOcc;
- modCalc.occParams = occParams;
- modCalc.occSiteMultiplicity = occSiteMultiplicity;
- modCalc.nOps = nOps;
- modCalc.enabled = true;
if (mxyz != null)
modCalc.mxyz = new V3();
}
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-11-06 04:48:47 UTC
(rev 20859)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-11-07 00:19:29 UTC
(rev 20860)
@@ -62,8 +62,15 @@
TODO: consider if models with no atoms will cause issues in relation to
model.firstAtomIndex
-Jmol.___JmolVersion="14.5.0_2015.11.03"
+Jmol.___JmolVersion="14.5.0_2015.11.06"
+bug fix: restoring bonds to a model having fewer bonds than the model for
which they were saved throws an exception
+bug fix: mCIF does not read incommensurately modulated mCIF files
+bug fix: WRITE xxx.ZIP crashes Jmol
+bug fix: POLYHEDRA ... {xxx} TO {yyy} not working
+
+JmolVersion="14.5.0_2015.11.03"
+
new feature: x = pointgroup([array of points],center)
-- center is optional, defaulting to average of the points
-- returns a map:
Modified: trunk/Jmol/src/org/jmol/viewer/StateManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/StateManager.java 2015-11-06 04:48:47 UTC
(rev 20859)
+++ trunk/Jmol/src/org/jmol/viewer/StateManager.java 2015-11-07 00:19:29 UTC
(rev 20860)
@@ -458,8 +458,8 @@
b.colix = c.colix;
b.shapeVisibilityFlags = c.shapeVisibilityFlags;
}
- for (int i = bondCount; --i >= 0;)
- modelSet.bo[i].index = i;
+ for (int i = modelSet.bondCount; --i >= 0;)
+ modelSet.bo[i].index = i;
vwr.setShapeProperty(JC.SHAPE_STICKS, "reportAll", null);
return true;
}
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