Revision: 18332
http://sourceforge.net/p/jmol/code/18332
Author: hansonr
Date: 2013-06-14 13:26:24 +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:
--------------
trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java
trunk/Jmol/src/org/jmol/util/Measure.java
Modified: trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2013-06-14 13:25:46 UTC
(rev 18331)
+++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2013-06-14 13:26:24 UTC
(rev 18332)
@@ -7176,7 +7176,8 @@
JmolList<BS[]> vAtomSets = null;
JmolList<Object[]> vQuatSets = null;
iToken = 0;
- float nSeconds = (isFloatParameter(1) ? floatParameter(++iToken) :
Float.NaN);
+ 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)
@@ -7225,7 +7226,7 @@
}
bsAtoms2.and(bsTo);
if (vAtomSets == null)
- vAtomSets = new JmolList<BS[]>();
+ vAtomSets = new JmolList<BS[]>();
vAtomSets.addLast(new BS[] { bsAtoms1, bsAtoms2 });
i = iToken;
break;
@@ -7233,13 +7234,13 @@
if (vAtomSets != null)
error(ERROR_invalidArgument);
isQuaternion = true;
- data1 = ScriptMathProcessor
- .getQuaternionArray(((SV) theToken).getList(), T.list);
+ data1 = ScriptMathProcessor.getQuaternionArray(((SV) theToken)
+ .getList(), T.list);
getToken(++i);
- data2 = ScriptMathProcessor
- .getQuaternionArray(((SV) theToken).getList(), T.list);
+ data2 = ScriptMathProcessor.getQuaternionArray(((SV) theToken)
+ .getList(), T.list);
if (vQuatSets == null)
- vQuatSets = new JmolList<Object[]>();
+ vQuatSets = new JmolList<Object[]>();
vQuatSets.addLast(new Object[] { data1, data2 });
break;
case T.orientation:
@@ -7290,7 +7291,7 @@
bsAtoms1.and(bsFrom);
bsAtoms2.and(bsTo);
}
- vAtomSets = new JmolList<BS[]>();
+ vAtomSets = new JmolList<BS[]>();
vAtomSets.addLast(new BS[] { bsAtoms1, bsAtoms2 });
}
@@ -7298,8 +7299,9 @@
if (isFrames) {
BS bsModels = viewer.getModelBitSet(bsFrom, false);
bsFrames = new BS[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 BS[] { bsFrom };
}
@@ -7307,25 +7309,25 @@
bsFrom = bsFrames[iFrame];
float[] retStddev = new float[2]; // [0] final, [1] initial for atoms
Quaternion q = null;
- JmolList<Quaternion> vQ = new JmolList<Quaternion>();
+ JmolList<Quaternion> vQ = new JmolList<Quaternion>();
P3[][] centerAndPoints = null;
- JmolList<BS[]> vAtomSets2 = (isFrames ? new JmolList<BS[]>()
- : vAtomSets);
+ JmolList<BS[]> vAtomSets2 = (isFrames ? new JmolList<BS[]>() :
vAtomSets);
for (int i = 0; i < vAtomSets.size(); ++i) {
BS[] bss = vAtomSets.get(i);
if (isFrames)
- vAtomSets2
- .addLast(bss = new BS[] { BSUtil.copy(bss[0]), bss[1] });
+ vAtomSets2.addLast(bss = new BS[] { BSUtil.copy(bss[0]), bss[1] });
bss[0].and(bsFrom);
}
+ P3 center = null;
+ V3 translation = null;
if (isAtoms) {
centerAndPoints = viewer.getCenterAndPoints(vAtomSets2, true);
q = Measure.calculateQuaternionRotation(centerAndPoints, retStddev,
true);
- float r0 = (Float.isNaN(retStddev[1]) ? Float.NaN
- : Math.round(retStddev[0] * 100) / 100f);
- float r1 = (Float.isNaN(retStddev[1]) ? Float.NaN
- : Math.round(retStddev[1] * 100) / 100f);
+ float r0 = (Float.isNaN(retStddev[1]) ? Float.NaN : Math
+ .round(retStddev[0] * 100) / 100f);
+ float r1 = (Float.isNaN(retStddev[1]) ? Float.NaN : Math
+ .round(retStddev[1] * 100) / 100f);
showString("RMSD " + r0 + " --> " + r1 + " Angstroms");
} else if (isQuaternion) {
if (vQuatSets == null) {
@@ -7358,30 +7360,36 @@
*/
Matrix4f m4 = new Matrix4f();
+ center = new P3();
float stddev = getSmilesCorrelation(bsFrom, bsTo, strSmiles, null,
- null, m4, null, !isSmiles, false, null);
+ null, m4, null, !isSmiles, false, null, center);
if (Float.isNaN(stddev))
error(ERROR_invalidArgument);
- V3 translation = new V3();
+ translation = new V3();
m4.get(translation);
Matrix3f m3 = new Matrix3f();
m4.getRotationScale(m3);
q = Quaternion.newM(m3);
}
- if (centerAndPoints == null)
+ if (centerAndPoints != null)
+ center = centerAndPoints[0][0];
+ if (center == null) {
centerAndPoints = viewer.getCenterAndPoints(vAtomSets2, true);
+ center = centerAndPoints[0][0];
+ }
P3 pt1 = new P3();
float endDegrees = Float.NaN;
- V3 translation = null;
if (doTranslate) {
- translation = V3.newV(centerAndPoints[1][0]);
- translation.sub(centerAndPoints[0][0]);
+ if (translation == null) {
+ translation = V3.newV(centerAndPoints[1][0]);
+ translation.sub(center);
+ }
endDegrees = 0;
}
if (doRotate) {
if (q == null)
evalError("option not implemented", null);
- pt1.setT(centerAndPoints[0][0]);
+ pt1.setT(center);
pt1.add(q.getNormal());
endDegrees = q.getTheta();
}
@@ -7392,12 +7400,13 @@
JmolList<P3> 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);
}
if (!useThreads())
doAnimate = false;
- viewer.rotateAboutPointsInternal(this, centerAndPoints[0][0], pt1,
endDegrees
- / nSeconds, endDegrees, doAnimate, bsFrom, translation, ptsB, null);
+ viewer.rotateAboutPointsInternal(this, center, pt1,
+ endDegrees / nSeconds, endDegrees, doAnimate, bsFrom, translation,
+ ptsB, null);
if (doAnimate && isJS)
throw new ScriptInterruption(this, "compare", 1);
}
@@ -7406,7 +7415,7 @@
float getSmilesCorrelation(BS bsA, BS bsB, String smiles,
JmolList<P3> ptsA, JmolList<P3> ptsB,
Matrix4f m4, JmolList<BS> vReturn,
- boolean isSmarts, boolean asMap, int[][] mapSet)
+ boolean isSmarts, boolean asMap, int[][] mapSet,
P3 center)
throws ScriptException {
float tolerance = (mapSet == null ? 0.1f : Float.MAX_VALUE);
try {
@@ -7415,6 +7424,7 @@
ptsB = new JmolList<P3>();
}
Matrix4f m = new Matrix4f();
+ P3 c = new P3();
Atom[] atoms = viewer.modelSet.atoms;
int atomCount = viewer.getAtomCount();
@@ -7445,7 +7455,7 @@
ptsB.clear();
for (int j = 0; j < maps[i].length; j++)
ptsB.addLast(atoms[maps[i][j]]);
- float stddev = Measure.getTransformMatrix4(ptsA, ptsB, m, null);
+ float stddev = Measure.getTransformMatrix4(ptsA, ptsB, m, c);
Logger.info("getSmilesCorrelation stddev=" + stddev);
if (vReturn != null) {
if (stddev < tolerance) {
@@ -7459,6 +7469,8 @@
mapB = maps[i];
if (m4 != null)
m4.setM(m);
+ if (center != null)
+ center.setT(c);
lowestStdDev = stddev;
}
}
@@ -7523,7 +7535,7 @@
JmolList<BS> vReturn = new JmolList<BS>();
float stddev = getSmilesCorrelation(bsMatch3D, bsSelected, pattern, null,
- null, null, vReturn, isSmarts, false, null);
+ null, null, vReturn, isSmarts, false, null, null);
if (Float.isNaN(stddev)) {
if (asOneBitset)
return new BS();
Modified: trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java 2013-06-14
13:25:46 UTC (rev 18331)
+++ trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java 2013-06-14
13:26:24 UTC (rev 18332)
@@ -870,7 +870,7 @@
smiles1 = SV.sValue(args[2]);
int[][] mapSet = ArrayUtil.newInt2(2);
eval.getSmilesCorrelation(bs1, bs2, smiles1, null, null,
- null, null, true, false, mapSet);
+ null, null, true, false, mapSet, null);
int[][] bondMap1 = viewer.getDihedralMap(mapSet[0]);
int[][] bondMap2 = (bondMap1 == null ? null :
viewer.getDihedralMap(mapSet[1]));
if (bondMap2 == null || bondMap2.length != bondMap1.length)
@@ -952,7 +952,7 @@
if (bs1 == null || bs2 == null)
return addXStr("IDENTICAL");
stddev = eval.getSmilesCorrelation(bs1, bs2, smiles1, null, null, null,
- null, false, false, null);
+ null, false, false, null, null);
return addXStr(stddev < 0.2f ? "IDENTICAL"
: "IDENTICAL or CONFORMATIONAL ISOMERS (RMSD=" + stddev + ")");
} else if (isSmiles) {
@@ -967,7 +967,7 @@
if (sOpt == null)
return false;
stddev = eval.getSmilesCorrelation(bs1, bs2, sOpt, ptsA, ptsB, m, null,
- !isSmiles, isMap, null);
+ !isSmiles, isMap, null, null);
if (isMap) {
int nAtoms = ptsA.size();
if (nAtoms == 0)
Modified: trunk/Jmol/src/org/jmol/util/Measure.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Measure.java 2013-06-14 13:25:46 UTC (rev
18331)
+++ trunk/Jmol/src/org/jmol/util/Measure.java 2013-06-14 13:26:24 UTC (rev
18332)
@@ -456,6 +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] + "}");
float[] retStddev = new float[2];
Quaternion q = calculateQuaternionRotation(new P3[][] { cptsA,
cptsB }, retStddev, true); // was false
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