Revision: 18331
http://sourceforge.net/p/jmol/code/18331
Author: hansonr
Date: 2013-06-14 13:25:46 +0000 (Fri, 14 Jun 2013)
Log Message:
-----------
___JmolVersion="13.1.17_dev_2013.06.14"
bug fix: COMPARE could rotate to less-good fit with SMARTS search
Modified Paths:
--------------
branches/v13_0/Jmol/src/org/jmol/script/ScriptEvaluator.java
branches/v13_0/Jmol/src/org/jmol/script/ScriptMathProcessor.java
Modified: branches/v13_0/Jmol/src/org/jmol/script/ScriptEvaluator.java
===================================================================
--- branches/v13_0/Jmol/src/org/jmol/script/ScriptEvaluator.java
2013-06-14 12:44:40 UTC (rev 18330)
+++ branches/v13_0/Jmol/src/org/jmol/script/ScriptEvaluator.java
2013-06-14 13:25:46 UTC (rev 18331)
@@ -6814,9 +6814,12 @@
List<BitSet[]> vAtomSets = null;
List<Object[]> vQuatSets = null;
iToken = 0;
- float nSeconds = (isFloatParameter(1) ? floatParameter(++iToken) :
Float.NaN);
- BitSet bsFrom = (tokAt(++iToken) == Token.subset ? null :
atomExpression(iToken));
- BitSet bsTo = (tokAt(++iToken) == Token.subset ? null :
atomExpression(iToken));
+ float nSeconds = (isFloatParameter(1) ? floatParameter(++iToken)
+ : Float.NaN);
+ BitSet bsFrom = (tokAt(++iToken) == Token.subset ? null
+ : atomExpression(iToken));
+ BitSet bsTo = (tokAt(++iToken) == Token.subset ? null
+ : atomExpression(iToken));
if (bsFrom == null || bsTo == null)
error(ERROR_invalidArgument);
BitSet bsSubset = null;
@@ -6936,8 +6939,9 @@
if (isFrames) {
BitSet bsModels = viewer.getModelBitSet(bsFrom, false);
bsFrames = new BitSet[bsModels.cardinality()];
- for (int i = 0, iModel = bsModels.nextSetBit(0); iModel >= 0; iModel =
bsModels.nextSetBit(iModel + 1), i++)
- bsFrames[i] = viewer.getModelUndeletedAtomsBitSet(iModel);
+ for (int i = 0, iModel = bsModels.nextSetBit(0); iModel >= 0; iModel =
bsModels
+ .nextSetBit(iModel + 1), i++)
+ bsFrames[i] = viewer.getModelUndeletedAtomsBitSet(iModel);
} else {
bsFrames = new BitSet[] { bsFrom };
}
@@ -6956,6 +6960,8 @@
.add(bss = new BitSet[] { BitSetUtil.copy(bss[0]), bss[1] });
bss[0].and(bsFrom);
}
+ Point3f center = null;
+ Vector3f translation = null;
if (isAtoms) {
centerAndPoints = viewer.getCenterAndPoints(vAtomSets2, true);
q = Measure.calculateQuaternionRotation(centerAndPoints, retStddev,
@@ -6996,30 +7002,36 @@
*/
Matrix4f m4 = new Matrix4f();
+ center = new Point3f();
float stddev = getSmilesCorrelation(bsFrom, bsTo, strSmiles, null,
- null, m4, null, !isSmiles, false);
+ null, m4, null, !isSmiles, false, center);
if (Float.isNaN(stddev))
error(ERROR_invalidArgument);
- Vector3f translation = new Vector3f();
+ translation = new Vector3f();
m4.get(translation);
Matrix3f m3 = new Matrix3f();
m4.get(m3);
q = new Quaternion(m3);
}
- if (centerAndPoints == null)
+ if (centerAndPoints != null)
+ center = centerAndPoints[0][0];
+ if (center == null) {
centerAndPoints = viewer.getCenterAndPoints(vAtomSets2, true);
+ center = centerAndPoints[0][0];
+ }
Point3f pt1 = new Point3f();
float endDegrees = Float.NaN;
- Vector3f translation = null;
if (doTranslate) {
- translation = new Vector3f(centerAndPoints[1][0]);
- translation.sub(centerAndPoints[0][0]);
+ if (translation == null) {
+ translation = new Vector3f(centerAndPoints[1][0]);
+ translation.sub(centerAndPoints[0][0]);
+ }
endDegrees = 0;
}
if (doRotate) {
if (q == null)
evalError("option not implemented", null);
- pt1.set(centerAndPoints[0][0]);
+ pt1.set(center);
pt1.add(q.getNormal());
endDegrees = q.getTheta();
}
@@ -7030,9 +7042,9 @@
List<Point3f> ptsA = viewer.getAtomPointVector(bsFrom);
Matrix4f m4 = ScriptMathProcessor.getMatrix4f(q.getMatrix(),
translation);
- ptsB = Measure.transformPoints(ptsA, m4, centerAndPoints[0][0]);
+ ptsB = Measure.transformPoints(ptsA, m4, center);
}
- viewer.rotateAboutPointsInternal(centerAndPoints[0][0], pt1, endDegrees
+ viewer.rotateAboutPointsInternal(center, pt1, endDegrees
/ nSeconds, endDegrees, doAnimate, bsFrom, translation, ptsB);
}
}
@@ -7040,7 +7052,7 @@
float getSmilesCorrelation(BitSet bsA, BitSet bsB, String smiles,
List<Point3f> ptsA, List<Point3f> ptsB,
Matrix4f m4, List<BitSet> vReturn,
- boolean isSmarts, boolean asMap)
+ boolean isSmarts, boolean asMap, Point3f center)
throws ScriptException {
float tolerance = 0.1f; // TODO
try {
@@ -7049,6 +7061,7 @@
ptsB = new ArrayList<Point3f>();
}
Matrix4f m = new Matrix4f();
+ Point3f c = new Point3f();
Atom[] atoms = viewer.getModelSet().atoms;
int atomCount = viewer.getAtomCount();
@@ -7078,7 +7091,7 @@
ptsB.clear();
for (int j = 0; j < maps[i].length; j++)
ptsB.add(atoms[maps[i][j]]);
- float stddev = Measure.getTransformMatrix4(ptsA, ptsB, m, null);
+ float stddev = Measure.getTransformMatrix4(ptsA, ptsB, m, center);
Logger.info("getSmilesCorrelation stddev=" + stddev);
if (vReturn != null) {
if (stddev < tolerance) {
@@ -7090,7 +7103,10 @@
}
if (stddev < lowestStdDev) {
mapB = maps[i];
- m4.set(m);
+ if (m4 != null)
+ m4.set(m);
+ if (center != null)
+ center.set(c);
lowestStdDev = stddev;
}
}
@@ -7150,7 +7166,7 @@
List<BitSet> vReturn = new ArrayList<BitSet>();
float stddev = getSmilesCorrelation(bsMatch3D, bsSelected, pattern, null,
- null, null, vReturn, isSmarts, false);
+ null, null, vReturn, isSmarts, false, null);
if (Float.isNaN(stddev)) {
if (asOneBitset)
return new BitSet();
Modified: branches/v13_0/Jmol/src/org/jmol/script/ScriptMathProcessor.java
===================================================================
--- branches/v13_0/Jmol/src/org/jmol/script/ScriptMathProcessor.java
2013-06-14 12:44:40 UTC (rev 18330)
+++ branches/v13_0/Jmol/src/org/jmol/script/ScriptMathProcessor.java
2013-06-14 13:25:46 UTC (rev 18331)
@@ -842,7 +842,7 @@
if (bs1 == null || bs2 == null)
return addX("IDENTICAL");
stddev = eval.getSmilesCorrelation(bs1, bs2, smiles1, null, null, null,
- null, false, false);
+ null, false, false, null);
return addX(stddev < 0.2f ? "IDENTICAL"
: "IDENTICAL or CONFORMATIONAL ISOMERS (RMSD=" + stddev + ")");
} else if (isSmiles) {
@@ -857,7 +857,7 @@
if (sOpt == null)
return false;
stddev = eval.getSmilesCorrelation(bs1, bs2, sOpt, ptsA, ptsB, m, null,
- !isSmiles, isMap);
+ !isSmiles, isMap, null);
if (isMap) {
int nAtoms = ptsA.size();
if (nAtoms == 0)
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