Revision: 20290
http://sourceforge.net/p/jmol/code/20290
Author: hansonr
Date: 2015-02-14 19:42:33 +0000 (Sat, 14 Feb 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.3.12_2015.02.14"
bug fix: compare({atomA},{atomsB}) should return standard 4x4 matrix, not one
involving a rotation
about an atom center (follow-up ROTATESELECTED was broken in
14.3.11_2014.12.17)
Modified Paths:
--------------
trunk/Jmol/src/javajs/util/Measure.java
trunk/Jmol/src/org/jmol/scriptext/MathExt.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/javajs/util/Measure.java
===================================================================
--- trunk/Jmol/src/javajs/util/Measure.java 2015-02-12 12:51:26 UTC (rev
20289)
+++ trunk/Jmol/src/javajs/util/Measure.java 2015-02-14 19:42:33 UTC (rev
20290)
@@ -682,19 +682,34 @@
return q;
}
+ /**
+ * Fills a 4x4 matrix with rotation-translation of mapped points A to B.
+ * If centerA is null, this is a standard 4x4 rotation-translation matrix;
+ * otherwise, this 4x4 matrix is a rotation around a vector through the
center of ptsA,
+ * and centerA is filled with that center;
+ * Prior to Jmol 14.3.12_2014.02.14, when used from the JmolScript compare()
function,
+ * this method returned the second of these options instead of the first.
+ *
+ * @param ptsA
+ * @param ptsB
+ * @param m 4x4 matrix to be returned
+ * @param centerA return center of rotation; if null, then standard 4x4
matrix is returned
+ * @return stdDev
+ */
public static float getTransformMatrix4(Lst<P3> ptsA, Lst<P3> ptsB, M4 m,
P3 centerA) {
P3[] cptsA = getCenterAndPoints(ptsA);
P3[] cptsB = getCenterAndPoints(ptsB);
- //System.out.println("draw d1 " + cptsA[0]);
- //System.out.println("draw d2 " + cptsB[0]);
float[] retStddev = new float[2];
Quat q = calculateQuaternionRotation(new P3[][] { cptsA, cptsB },
- retStddev); // was false
- V3 v = V3.newVsub(cptsB[0], cptsA[0]);
- m.setMV(q.getMatrix(), v);
- if (centerA != null)
+ retStddev);
+ M3 r = q.getMatrix();
+ if (centerA == null)
+ r.rotate(cptsA[0]);
+ else
centerA.setT(cptsA[0]);
+ V3 t = V3.newVsub(cptsB[0], cptsA[0]);
+ m.setMV(r, t);
return retStddev[1];
}
Modified: trunk/Jmol/src/org/jmol/scriptext/MathExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2015-02-12 12:51:26 UTC
(rev 20289)
+++ trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2015-02-14 19:42:33 UTC
(rev 20290)
@@ -401,7 +401,8 @@
} catch (Exception ex) {
e.evalError(ex.getMessage(), null);
}
- float[] data = e.getSmilesExt().getFlexFitList(bs1, bs2, smiles1,
!isSmiles);
+ float[] data = e.getSmilesExt().getFlexFitList(bs1, bs2, smiles1,
+ !isSmiles);
return (data == null ? mp.addXStr("") : mp.addXAF(data));
}
try {
@@ -411,23 +412,24 @@
if (bs1 == null && bs2 == null)
return mp.addXStr(vwr.getSmilesMatcher()
.getRelationship(smiles1, smiles2).toUpperCase());
- String mf1 = (bs1 == null ? vwr.getSmilesMatcher()
- .getMolecularFormula(smiles1, false) : JmolMolecule
- .getMolecularFormula(vwr.ms.at, bs1, false, null, false));
- String mf2 = (bs2 == null ? vwr.getSmilesMatcher()
- .getMolecularFormula(smiles2, false) : JmolMolecule
- .getMolecularFormula(vwr.ms.at, bs2, false, null, false));
+ String mf1 = (bs1 == null ? vwr.getSmilesMatcher().getMolecularFormula(
+ smiles1, false) : JmolMolecule.getMolecularFormula(vwr.ms.at, bs1,
+ false, null, false));
+ String mf2 = (bs2 == null ? vwr.getSmilesMatcher().getMolecularFormula(
+ smiles2, false) : JmolMolecule.getMolecularFormula(vwr.ms.at, bs2,
+ false, null, false));
if (!mf1.equals(mf2))
return mp.addXStr("NONE");
if (bs1 != null)
- smiles1 = (String) e.getSmilesExt().getSmilesMatches("", null, bs1,
null, false, true);
+ smiles1 = (String) e.getSmilesExt().getSmilesMatches("", null, bs1,
+ null, false, true);
boolean check;
if (bs2 == null) {
// note: find smiles1 IN smiles2 here
check = (vwr.getSmilesMatcher().areEqual(smiles2, smiles1) > 0);
} else {
- check = (((BS) e.getSmilesExt().getSmilesMatches(smiles1, null, bs2,
null, false, true))
- .nextSetBit(0) >= 0);
+ check = (((BS) e.getSmilesExt().getSmilesMatches(smiles1, null, bs2,
+ null, false, true)).nextSetBit(0) >= 0);
}
if (!check) {
// MF matched, but didn't match SMILES
@@ -441,19 +443,19 @@
if (bs2 == null) {
check = (vwr.getSmilesMatcher().areEqual(smiles1, smiles2) >
0);
} else {
- check = (((BS) e.getSmilesExt().getSmilesMatches(smiles1,
null, bs2, null,
- false, true)).nextSetBit(0) >= 0);
+ check = (((BS) e.getSmilesExt().getSmilesMatches(smiles1, null,
+ bs2, null, false, true)).nextSetBit(0) >= 0);
}
if (check)
return mp.addXStr("ENANTIOMERS");
}
// remove all stereochemistry from SMILES string
if (bs2 == null) {
- check = (vwr.getSmilesMatcher().areEqual(
- "/nostereo/" + smiles2, smiles1) > 0);
+ check = (vwr.getSmilesMatcher().areEqual("/nostereo/" + smiles2,
+ smiles1) > 0);
} else {
- Object ret = e.getSmilesExt().getSmilesMatches("/nostereo/" +
smiles1, null, bs2,
- null, false, true);
+ Object ret = e.getSmilesExt().getSmilesMatches(
+ "/nostereo/" + smiles1, null, bs2, null, false, true);
check = (((BS) ret).nextSetBit(0) >= 0);
}
if (check)
@@ -465,8 +467,8 @@
//identical or conformational
if (bs1 == null || bs2 == null)
return mp.addXStr("IDENTICAL");
- stddev = e.getSmilesExt().getSmilesCorrelation(bs1, bs2, smiles1,
null, null, null,
- null, false, false, null, null, false, false);
+ stddev = e.getSmilesExt().getSmilesCorrelation(bs1, bs2, smiles1, null,
+ null, null, null, false, false, null, null, false, false);
return mp.addXStr(stddev < 0.2f ? "IDENTICAL"
: "IDENTICAL or CONFORMATIONAL ISOMERS (RMSD=" + stddev + ")");
} else if (isSmiles) {
@@ -484,19 +486,18 @@
boolean bestMap = (("best".equals(sOpt) || "bestH".equals(sOpt)));
if (sOpt == null || hMaps || allMaps || bestMap) {
// with explicitH we set to find only the first match.
- if (isMap || isSmiles) {
- sOpt = "/noaromatic"
- + (allMaps || bestMap ? "/" : " nostereo/")
- + e.getSmilesExt().getSmilesMatches((hMaps ? "H" : ""), null,
bs1, null, false,
- true);
- } else {
+ if (!isMap && !isSmiles)
return false;
- }
+ sOpt = "/noaromatic"
+ + (allMaps || bestMap ? "/" : " nostereo/")
+ + e.getSmilesExt().getSmilesMatches((hMaps ? "H" : ""), null,
+ bs1, null, false, true);
} else {
allMaps = true;
}
- stddev = e.getSmilesExt().getSmilesCorrelation(bs1, bs2, sOpt, ptsA,
ptsB, m, null,
- !isSmiles, isMap, null, null, !allMaps && !bestMap, bestMap);
+ stddev = e.getSmilesExt().getSmilesCorrelation(bs1, bs2, sOpt, ptsA,
+ ptsB, m, null, !isSmiles, isMap, null, null, !allMaps && !bestMap,
+ bestMap);
if (isMap) {
int nAtoms = ptsA.size();
if (nAtoms == 0)
@@ -510,9 +511,8 @@
a[j] = new int[] { ((Atom) ptsA.get(j)).i,
((Atom) ptsB.get(pt)).i };
}
- if (!allMaps)
- return (ret.size() > 0 ? mp.addXAII(ret.get(0)) : mp.addXStr(""));
- return mp.addXList(ret);
+ return (allMaps ? mp.addXList(ret) : ret.size() > 0 ? mp.addXAII(ret
+ .get(0)) : mp.addXStr(""));
}
} else {
ptsA = e.getPointVector(args[0], 0);
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-02-12 12:51:26 UTC
(rev 20289)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-02-14 19:42:33 UTC
(rev 20290)
@@ -15,8 +15,13 @@
TODO: remove HTML5 dependency on synchronous file loading (check SCRIPT
command for problems)
TODO: add 2D graphics panel for Ramachandran and NBO-style 2D graphics -- send
to browser as data uri?
-Jmol.___JmolVersion="14.3.12_2015.02.11"
+Jmol.___JmolVersion="14.3.12_2015.02.14"
+bug fix: compare({atomA},{atomsB}) should return standard 4x4 matrix, not one
involving a rotation
+ about an atom center (follow-up ROTATESELECTED was broken in
14.3.11_2014.12.17)
+
+JmolVersion="14.3.12_2015.02.11"
+
bug fix: 14.3.12_2015.02.09 breaks MODEL "someTitle" syntax
bug fix: MUTATE not properly saved in state
bug fix: "USER MOD" not accepted at beginning of PDB file (MolProbity
breaking PDB format here)
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