Revision: 20869
http://sourceforge.net/p/jmol/code/20869
Author: hansonr
Date: 2015-11-27 11:57:16 +0000 (Fri, 27 Nov 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.5.0_2015.11.27"
bug fix: {atomset}.split() [split atomset by model] returns array of strings,
not array of atoms
code: BSUtil.cardinalityOf cleanup.
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/modelset/ModelSet.java
trunk/Jmol/src/org/jmol/script/SV.java
trunk/Jmol/src/org/jmol/script/ScriptExpr.java
trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
trunk/Jmol/src/org/jmol/scriptext/MathExt.java
trunk/Jmol/src/org/jmol/shape/Measures.java
trunk/Jmol/src/org/jmol/shapespecial/Dipoles.java
trunk/Jmol/src/org/jmol/shapespecial/Draw.java
trunk/Jmol/src/org/jmol/symmetry/PointGroup.java
trunk/Jmol/src/org/jmol/util/TriangleData.java
trunk/Jmol/src/org/jmol/viewer/AnimationManager.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/PropertyManager.java
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/org/jmol/modelset/ModelSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2015-11-26 16:34:25 UTC
(rev 20868)
+++ trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2015-11-27 11:57:16 UTC
(rev 20869)
@@ -667,7 +667,7 @@
// full models are deleted for any model containing the specified atoms
includeAllRelatedFrames(bsModels);
- int nModelsDeleted = BSUtil.cardinalityOf(bsModels);
+ int nModelsDeleted = bsModels.cardinality();
if (nModelsDeleted == 0)
return null;
@@ -1309,14 +1309,14 @@
ptCenter.add(at[i]);
}
}
- if (nPoints > 0)
+ if (nPoints > 1)
ptCenter.scale(1.0f / nPoints);
return ptCenter;
}
public P3 getAverageAtomPoint() {
if (averageAtomPoint == null)
- (averageAtomPoint = new P3()).setT(getAtomSetCenter(vwr.getAllAtoms()));
+ averageAtomPoint = getAtomSetCenter(vwr.getAllAtoms());
return averageAtomPoint;
}
@@ -2709,7 +2709,7 @@
+ " pseudo-hbond calculation");
calcRasmolHydrogenBonds(bsA, bsB, null, false, Integer.MAX_VALUE, false,
bsHBonds);
- return -BSUtil.cardinalityOf(bsHBonds);
+ return -bsHBonds.cardinality();
}
Logger.info(haveHAtoms ? "Standard Hbond calculation"
: "Jmol pseudo-hbond calculation");
Modified: trunk/Jmol/src/org/jmol/script/SV.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/SV.java 2015-11-26 16:34:25 UTC (rev
20868)
+++ trunk/Jmol/src/org/jmol/script/SV.java 2015-11-27 11:57:16 UTC (rev
20869)
@@ -122,7 +122,7 @@
static int sizeOf(T x) {
switch (x == null ? nada : x.tok) {
case bitset:
- return BSUtil.cardinalityOf(bsSelectToken(x));
+ return bsSelectToken(x).cardinality();
case on:
case off:
return -1;
@@ -549,7 +549,7 @@
// case matrix4f:
return (int) fValue(x);
case bitset:
- return BSUtil.cardinalityOf(bsSelectToken(x));
+ return bsSelectToken(x).cardinality();
case barray:
return ((BArray) x.value).data.length;
default:
@@ -881,10 +881,10 @@
if (tokenIn.value instanceof BondSet) {
bs = BondSet.newBS((BS) tokenIn.value,
((BondSet) tokenIn.value).associatedAtoms);
- len = BSUtil.cardinalityOf(bs);
+ len = bs.cardinality();
} else {
bs = BSUtil.copy((BS) tokenIn.value);
- len = (isInputSelected ? 1 : BSUtil.cardinalityOf(bs));
+ len = (isInputSelected ? 1 : bs.cardinality());
}
break;
case barray:
Modified: trunk/Jmol/src/org/jmol/script/ScriptExpr.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptExpr.java 2015-11-26 16:34:25 UTC
(rev 20868)
+++ trunk/Jmol/src/org/jmol/script/ScriptExpr.java 2015-11-27 11:57:16 UTC
(rev 20869)
@@ -298,7 +298,7 @@
// are there for now that require it; could go, though.
BS bsSelect = new BS();
BS bsX = new BS();
- String[] sout = (isFor ? new String[BSUtil.cardinalityOf(bsAtoms)]
+ String[] sout = (isFor ? new String[bsAtoms.cardinality()]
: null);
if (localVars == null)
localVars = new Hashtable<String, SV>();
@@ -2248,7 +2248,7 @@
private void setBitsetProperty(BS bs, int tok, int iValue, float fValue,
T tokenValue) throws ScriptException {
- if (chk || BSUtil.cardinalityOf(bs) == 0)
+ if (chk || bs.cardinality() == 0)
return;
String[] list = null;
String sValue = null;
Modified: trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-11-26 16:34:25 UTC
(rev 20868)
+++ trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-11-27 11:57:16 UTC
(rev 20869)
@@ -276,7 +276,7 @@
LabelToken[] tokens = (asIdentity ? null : isAtoms ? labeler.compile(
vwr, label, '\0', null) : labeler.compile(vwr, label, '\1',
htValues));
- int nmax = (haveIndex ? 1 : BSUtil.cardinalityOf(bs));
+ int nmax = (haveIndex ? 1 : bs.cardinality());
String[] sout = new String[nmax];
P3 ptTemp = new P3();
for (int j = (haveIndex ? index : bs.nextSetBit(0)); j >= 0; j = bs
@@ -4790,7 +4790,7 @@
switch (tokAt(++i)) {
case T.bitset:
case T.expressionBegin:
- pt = P3.newP(vwr.ms.getAtomSetCenter(atomExpressionAt(i)));
+ pt = vwr.ms.getAtomSetCenter(atomExpressionAt(i));
vwr.toFractional(pt, true);
i = eval.iToken;
break;
Modified: trunk/Jmol/src/org/jmol/scriptext/MathExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2015-11-26 16:34:25 UTC
(rev 20868)
+++ trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2015-11-27 11:57:16 UTC
(rev 20869)
@@ -2883,15 +2883,14 @@
case T.split:
if (x.tok == T.bitset) {
BS bsSelected = SV.bsSelectVar(x);
- sArg = "\n";
int modelCount = vwr.ms.mc;
- s = "";
+ Lst<SV> lst = new Lst<SV>();
for (int i = 0; i < modelCount; i++) {
- s += (i == 0 ? "" : "\n");
BS bs = vwr.getModelUndeletedAtomsBitSet(i);
bs.and(bsSelected);
- s += Escape.eBS(bs);
+ lst.addLast(SV.getVariable(bs));
}
+ return mp.addXList(lst);
}
return mp.addXAS(PT.split(s, sArg));
case T.join:
@@ -3372,7 +3371,7 @@
private BS getAtomsNearPts(float distance, T3[] points, BS bsInclude) {
BS bsResult = new BS();
- if (points.length == 0 || bsInclude != null && bsInclude.cardinality() ==
0)
+ if (points.length == 0 || bsInclude != null && bsInclude.isEmpty())
return bsResult;
if (bsInclude == null)
bsInclude = BSUtil.setAll(points.length);
Modified: trunk/Jmol/src/org/jmol/shape/Measures.java
===================================================================
--- trunk/Jmol/src/org/jmol/shape/Measures.java 2015-11-26 16:34:25 UTC (rev
20868)
+++ trunk/Jmol/src/org/jmol/shape/Measures.java 2015-11-27 11:57:16 UTC (rev
20869)
@@ -140,7 +140,7 @@
if ("select" == propertyName) {
BS bs = (BS) value;
- if (bs == null || BSUtil.cardinalityOf(bs) == 0) {
+ if (BSUtil.cardinalityOf(bs) == 0) {
bsSelected = null;
} else {
bsSelected = new BS();
Modified: trunk/Jmol/src/org/jmol/shapespecial/Dipoles.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapespecial/Dipoles.java 2015-11-26 16:34:25 UTC
(rev 20868)
+++ trunk/Jmol/src/org/jmol/shapespecial/Dipoles.java 2015-11-27 11:57:16 UTC
(rev 20869)
@@ -227,7 +227,7 @@
endCoord = null;
startCoord = ms.getAtomSetCenter(bsAtoms);
tempDipole.set2Value(startCoord, P3.new3(0, 0, 0), dipoleValue);
- if (BSUtil.cardinalityOf(bsAtoms) == 1)
+ if (bsAtoms.cardinality() == 1)
atomIndex1 = bsAtoms.nextSetBit(0);
return;
}
@@ -248,7 +248,7 @@
if ("endSet" == propertyName) {
iHaveTwoEnds = true;
BS atomset = (BS) value;
- if (atomIndex1 >= 0 && BSUtil.cardinalityOf(atomset) == 1) {
+ if (atomIndex1 >= 0 && atomset.cardinality() == 1) {
atomIndex2 = atomset.nextSetBit(0);
tempDipole.set2AtomValue(ms.at[atomIndex1], ms.at[atomIndex2], 1);
currentDipole = findDipoleFor(tempDipole.thisID,
tempDipole.dipoleInfo);
Modified: trunk/Jmol/src/org/jmol/shapespecial/Draw.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapespecial/Draw.java 2015-11-26 16:34:25 UTC
(rev 20868)
+++ trunk/Jmol/src/org/jmol/shapespecial/Draw.java 2015-11-27 11:57:16 UTC
(rev 20869)
@@ -358,13 +358,6 @@
return;
}
- if ("coords" == propertyName) {
- Lst<SV> pts = (Lst<SV>) value;
- for (int i = 0, n = pts.size(); i < n; i++)
- vData.addLast(new Object[] { Integer.valueOf(PT_COORD),
SV.ptValue(pts.get(i)) });
- return;
- }
-
if ("offset" == propertyName) {
offset = V3.newV((P3) value);
if (thisMesh != null)
@@ -373,9 +366,9 @@
}
if ("atomSet" == propertyName) {
- if (BSUtil.cardinalityOf((BS) value) == 0)
+ BS bsAtoms = (BS) value;
+ if (bsAtoms.isEmpty())
return;
- BS bsAtoms = (BS) value;
vData.addLast(new Object[] { Integer.valueOf(PT_BITSET), bsAtoms });
//nbitsets++;
if (isCircle && diameter == 0 && width == 0)
@@ -383,9 +376,13 @@
return;
}
+ if ("coords" == propertyName) {
+ addPoints(PT_COORD, value, false);
+ return;
+ }
+
if ("modelBasedPoints" == propertyName) {
- vData.addLast(new Object[] { Integer.valueOf(PT_MODEL_BASED_POINTS),
- value });
+ addPoints(PT_MODEL_BASED_POINTS, value, true);
return;
}
@@ -419,7 +416,27 @@
setPropertySuper(propertyName, value, bs);
}
- private void deleteModels(int modelIndex) {
+ private void addPoints(int type, Object value, boolean allowNull) {
+ @SuppressWarnings("unchecked")
+ Lst<SV> pts = (Lst<SV>) value;
+ Integer key = Integer.valueOf(type);
+ for (int i = 0, n = pts.size(); i < n; i++) {
+ SV v = pts.get(i);
+ P3 pt;
+ switch (v.tok) {
+ case T.bitset:
+ if (!allowNull && ((BS) v.value).isEmpty())
+ continue;
+ pt = vwr.ms.getAtomSetCenter((BS) v.value);
+ break;
+ default:
+ pt = SV.ptValue(v);
+ }
+ vData.addLast(new Object[] { key, pt });
+ }
+ }
+
+private void deleteModels(int modelIndex) {
//int firstAtomDeleted = ((int[])((Object[])value)[2])[1];
//int nAtomsDeleted = ((int[])((Object[])value)[2])[2];
for (int i = meshCount; --i >= 0;) {
@@ -1034,7 +1051,7 @@
return;
}
- protected void scale(Mesh mesh, float newScale) {
+ private void scale(Mesh mesh, float newScale) {
DrawMesh dmesh = (DrawMesh) mesh;
/*
* allows for Draw to scale object
@@ -1149,7 +1166,7 @@
T3 v = pickedMesh.vs[pickedMesh.pis[pickedModel][pickedVertex]];
int modelIndex = pickedMesh.modelIndex;
BS bs = ((DrawMesh) pickedMesh).modelFlags;
- if (modelIndex < 0 && bs != null && BSUtil.cardinalityOf(bs) == 1)
+ if (modelIndex < 0 && BSUtil.cardinalityOf(bs) == 1)
modelIndex = bs.nextSetBit(0);
Map<String, Object> map = null;
if (action != 0)
@@ -1323,7 +1340,7 @@
return (pickedMesh != null);
}
- protected String getCommand(Mesh mesh) {
+ private String getCommand(Mesh mesh) {
if (mesh != null)
return getCommand2(mesh, mesh.modelIndex);
@@ -1339,7 +1356,7 @@
return sb.toString();
}
- protected String getCommand2(Mesh mesh, int iModel) {
+ private String getCommand2(Mesh mesh, int iModel) {
DrawMesh dmesh = (DrawMesh) mesh;
if (!dmesh.isValid ||
dmesh.drawType == EnumDrawType.NONE
Modified: trunk/Jmol/src/org/jmol/symmetry/PointGroup.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/PointGroup.java 2015-11-26 16:34:25 UTC
(rev 20868)
+++ trunk/Jmol/src/org/jmol/symmetry/PointGroup.java 2015-11-27 11:57:16 UTC
(rev 20869)
@@ -393,7 +393,7 @@
private final static int ATOM_COUNT_MAX = 100;
private boolean getPointsAndElements(T3[] atomset) {
- int ac = BSUtil.cardinalityOf(bsAtoms);
+ int ac = bsAtoms.cardinality();
if (isAtoms && ac > ATOM_COUNT_MAX)
return false;
points = new P3[ac];
Modified: trunk/Jmol/src/org/jmol/util/TriangleData.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/TriangleData.java 2015-11-26 16:34:25 UTC
(rev 20868)
+++ trunk/Jmol/src/org/jmol/util/TriangleData.java 2015-11-27 11:57:16 UTC
(rev 20869)
@@ -357,7 +357,7 @@
i++;
}
//System.out.println();
- int nPoints = BSUtil.cardinalityOf(bsPoints);
+ int nPoints = bsPoints.cardinality();
P3[] pts = new P3[nPoints];
v.addLast(pts);
int[]list = new int[12];
Modified: trunk/Jmol/src/org/jmol/viewer/AnimationManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/AnimationManager.java 2015-11-26
16:34:25 UTC (rev 20868)
+++ trunk/Jmol/src/org/jmol/viewer/AnimationManager.java 2015-11-27
11:57:16 UTC (rev 20869)
@@ -173,7 +173,7 @@
}
void setDisplay(BS bs) {
- bsDisplay = (bs == null || bs.cardinality() == 0? null : BSUtil.copy(bs));
+ bsDisplay = (bs == null || bs.isEmpty() ? null : BSUtil.copy(bs));
}
public void setMorphCount(int n) {
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-11-26 16:34:25 UTC
(rev 20868)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-11-27 11:57:16 UTC
(rev 20869)
@@ -62,8 +62,13 @@
TODO: consider if models with no atoms will cause issues in relation to
model.firstAtomIndex
-Jmol.___JmolVersion="14.5.0_2015.11.26"
+Jmol.___JmolVersion="14.5.0_2015.11.27"
+bug fix: {atomset}.split() [split atomset by model] returns array of strings,
not array of atoms
+code: BSUtil.cardinalityOf cleanup.
+
+JmolVersion="14.5.0_2015.11.26"
+
bug fix: getproperty SHAPEINFO fails if CGO is present
bug fix: CGO from state deletes DRAW objects
bug fix: CGO not properly isolated to current model; "fixed" not implemented
Modified: trunk/Jmol/src/org/jmol/viewer/PropertyManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/PropertyManager.java 2015-11-26 16:34:25 UTC
(rev 20868)
+++ trunk/Jmol/src/org/jmol/viewer/PropertyManager.java 2015-11-27 11:57:16 UTC
(rev 20869)
@@ -976,8 +976,7 @@
if (m.modelSetProperties != null) {
info.put("modelSetProperties", m.modelSetProperties);
}
- info.put("modelCountSelected", Integer.valueOf(BSUtil
- .cardinalityOf(bsModels)));
+ info.put("modelCountSelected", Integer.valueOf(bsModels.cardinality()));
info.put("modelsSelected", bsModels);
Lst<Map<String, Object>> vModels = new Lst<Map<String, Object>>();
m.getMolecules();
@@ -1186,7 +1185,7 @@
if (doTransform && atoms[i].isDeleted())
bsAtoms.clear(i);
BS bsBonds = getCovalentBondsForAtoms(ms.bo, ms.bondCount, bsAtoms);
- if (!asXYZVIB && bsAtoms.cardinality() == 0)
+ if (!asXYZVIB && bsAtoms.isEmpty())
return "";
boolean isOK = true;
BS bsModels = vwr.ms.getModelBS(bsAtoms, true);
@@ -1217,7 +1216,7 @@
.nextSetBit(i + 1)) {
BS bsTemp = BSUtil.copy(bsAtoms);
bsTemp.and(ms.getModelAtomBitSetIncludingDeleted(i, false));
- if (bsTemp.cardinality() == 0)
+ if (bsTemp.isEmpty())
continue;
mol.appendI(bsTemp.cardinality()).appendC('\n');
Properties props = ms.am[i].properties;
@@ -2290,7 +2289,7 @@
public String getModelCml(BS bs, int atomsMax, boolean addBonds, boolean
doTransform, boolean allTrajectories) {
// not allowing full trajectory business here.
SB sb = new SB();
- int nAtoms = BSUtil.cardinalityOf(bs);
+ int nAtoms = bs.cardinality();
if (nAtoms == 0)
return "";
// creating an instance prevents pre-loading by JavaScript
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-11-26 16:34:25 UTC (rev
20868)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-11-27 11:57:16 UTC (rev
20869)
@@ -7381,7 +7381,7 @@
}
public void setAtomCoords(BS bs, int tokType, Object xyzValues) {
- if (bs.cardinality() == 0)
+ if (bs.isEmpty())
return;
ms.setAtomCoords(bs, tokType, xyzValues);
checkMinimization();
@@ -7392,7 +7392,7 @@
// Eval
if (bs == null)
bs = bsA();
- if (bs.cardinality() == 0)
+ if (bs.isEmpty())
return;
ms.setAtomCoordsRelative(offset, bs);
checkMinimization();
@@ -7415,7 +7415,7 @@
public void invertSelected(P3 pt, P4 plane, int iAtom, BS invAtoms) {
// Eval
BS bs = bsA();
- if (bs.cardinality() == 0)
+ if (bs.isEmpty())
return;
ms.invertSelected(pt, plane, iAtom, invAtoms, bs);
checkMinimization();
@@ -7425,7 +7425,7 @@
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)
+ if (bsAtoms.isEmpty())
return;
ms.moveAtoms(m4, mNew, rotation, translation, bsAtoms, center, isInternal,
translationOnly);
@@ -7470,7 +7470,7 @@
actionRotateBond(deltaX, deltaY, x, y);
} else {
bsSelected = setMovableBitSet(bsSelected, !asAtoms);
- if (bsSelected.cardinality() != 0) {
+ if (!bsSelected.isEmpty()) {
if (isTranslation) {
P3 ptCenter = ms.getAtomSetCenter(bsSelected);
tm.finalizeTransformParameters();
@@ -8872,7 +8872,7 @@
}
public void calculatePartialCharges(BS bsSelected) throws JmolAsyncException
{
- if (bsSelected == null || bsSelected.cardinality() == 0)
+ if (bsSelected == null || bsSelected.isEmpty())
bsSelected = getModelUndeletedAtomsBitSetBs(getVisibleFramesBitSet());
int pt = bsSelected.nextSetBit(0);
if (pt < 0)
@@ -9009,7 +9009,7 @@
if (bsAtoms == null)
bsAtoms = getModelUndeletedAtomsBitSet(getVisibleFramesBitSet().length()
- 1);
BS bsB = new BS();
- if (bsAtoms.cardinality() == 0)
+ if (bsAtoms.isEmpty())
return bsB;
int modelIndex = ms.at[bsAtoms.nextSetBit(0)].mi;
if (modelIndex != ms.mc - 1)
@@ -9324,7 +9324,7 @@
void dragMinimizeAtom(int iAtom) {
stopMinimization();
- BS bs = (getMotionFixedAtoms().cardinality() == 0 ? ms.getAtoms(
+ BS bs = (getMotionFixedAtoms().isEmpty() ? ms.getAtoms(
(ms.isAtomPDB(iAtom) ? T.group : T.molecule),
BSUtil.newAndSetBit(iAtom)) : BSUtil.setAll(ms.ac));
try {
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