Revision: 18330
http://sourceforge.net/p/jmol/code/18330
Author: hansonr
Date: 2013-06-14 12:44:40 +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
bug fix: draw ARROW ATOM/BOND broken
new feature: compare({atomset1} {atomset2} "ccCCN" "bonds")
new feature: {1.1}.find("ccCCN", "BONDS")
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
trunk/Jmol/src/org/jmol/modelset/ModelSet.java
trunk/Jmol/src/org/jmol/script/SV.java
trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java
trunk/Jmol/src/org/jmol/smiles/SmilesMatcher.java
trunk/Jmol/src/org/jmol/thread/SpinThread.java
trunk/Jmol/src/org/jmol/util/Measure.java
trunk/Jmol/src/org/jmol/viewer/ActionManager.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/TransformManager.java
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2013-06-14
12:43:25 UTC (rev 18329)
+++ trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2013-06-14
12:44:40 UTC (rev 18330)
@@ -2537,6 +2537,7 @@
info.put("info", getAtomInfo(i, null));
info.put("sym", getElementSymbol(i));
}
-
+
+
}
Modified: trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2013-06-14
12:43:25 UTC (rev 18329)
+++ trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2013-06-14
12:44:40 UTC (rev 18330)
@@ -3381,4 +3381,30 @@
return info;
}
+ public int[][] getDihedralMap(int[] alist) {
+ JmolList<int[]> list = new JmolList<int[]>();
+ int n = alist.length;
+ Atom ai = null, aj = null, ak = null, al = null;
+ for (int i = n - 1; --i >= 0;)
+ for (int j = n; --j > i;) {
+ ai = atoms[alist[i]];
+ aj = atoms[alist[j]];
+ if (ai.isBonded(aj)) {
+ for (int k = n; --k >= 0;)
+ if (k != i && k != j && (ak = atoms[alist[k]]).isBonded(ai))
+ for (int l = n; --l >= 0;)
+ if (l != i && l != j && l != k
+ && (al = atoms[alist[l]]).isBonded(aj))
+ list.addLast(new int[] { ak.index, ai.index, aj.index,
+ al.index });
+ }
+ }
+ n = list.size();
+ int[][] ilist = new int[n][];
+ for (int i = n; --i >= 0;)
+ ilist[n - i - 1] = list.get(i);
+ return ilist;
+ }
+
+
}
Modified: trunk/Jmol/src/org/jmol/modelset/ModelSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2013-06-14 12:43:25 UTC
(rev 18329)
+++ trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2013-06-14 12:44:40 UTC
(rev 18330)
@@ -25,6 +25,7 @@
package org.jmol.modelset;
+import org.jmol.util.AxisAngle4f;
import org.jmol.util.BS;
import org.jmol.util.BSUtil;
import org.jmol.util.JmolEdge;
@@ -40,6 +41,7 @@
import org.jmol.util.V3;
import org.jmol.viewer.JC;
+import org.jmol.viewer.TransformManager;
import org.jmol.viewer.Viewer;
import org.jmol.script.T;
import org.jmol.api.Interface;
@@ -50,6 +52,7 @@
import org.jmol.util.JmolList;
+import java.util.Hashtable;
import java.util.Map;
@@ -831,6 +834,29 @@
private final Matrix4f mat4t = new Matrix4f();
private final V3 vTemp = new V3();
+ public void setDihedrals(float[] dihedralList, BS[] bsBranches, float f) {
+ int n = dihedralList.length / 6;
+ for (int j = 0, pt = 0; j < n; j++, pt += 6) {
+ BS bs = bsBranches[j];
+ if (bs == null || bs.isEmpty())
+ continue;
+ Atom a1 = atoms[(int) dihedralList[pt + 1]];
+ Atom a2 = atoms[(int) dihedralList[pt + 2]];
+ V3 v = V3.newV(a2);
+ v.sub(a1);
+ float angle = (dihedralList[pt + 5] - dihedralList[pt + 4]) * f;
+ AxisAngle4f aa = AxisAngle4f.newVA(v, (float)(-angle /
TransformManager.degreesPerRadian));
+ matTemp.setAA(aa);
+ ptTemp.setT(a1);
+ for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
+ atoms[i].sub(ptTemp);
+ matTemp.transform(atoms[i]);
+ atoms[i].add(ptTemp);
+ taintAtom(i, TAINT_COORD);
+ }
+ }
+ }
+
public void moveAtoms(Matrix3f mNew, Matrix3f matrixRotate,
V3 translation, BS bs, P3 center,
boolean isInternal) {
@@ -882,7 +908,6 @@
recalculatePositionDependentQuantities(bs, mat4);
}
-
public void recalculatePositionDependentQuantities(BS bs, Matrix4f mat) {
if (getHaveStraightness())
calculateStraightness();
@@ -901,5 +926,38 @@
*/
}
+ public BS[] getBsBranches(float[] dihedralList) {
+ int n = dihedralList.length / 6;
+ BS[] bsBranches = new BS[n];
+ Map<String, Boolean> map = new Hashtable<String, Boolean>();
+ for (int i = 0, pt = 0; i < n; i++, pt += 6) {
+ float dv = dihedralList[pt + 5] - dihedralList[pt + 4];
+ if (Math.abs(dv) < 1f)
+ continue;
+ int i0 = (int) dihedralList[pt + 1];
+ int i1 = (int) dihedralList[pt + 2];
+ String s = "" + i0 + "_" + i1;
+ if (map.containsKey(s))
+ continue;
+ map.put(s, Boolean.TRUE);
+ BS bs = viewer.getBranchBitSet(i1, i0, true);
+ Bond[] bonds = atoms[i0].bonds;
+ Atom a0 = atoms[i0];
+ for (int j = 0; j < bonds.length; j++) {
+ Bond b = bonds[j];
+ if (!b.isCovalent())
+ continue;
+ int i2 = b.getOtherAtom(a0).index;
+ if (i2 == i1)
+ continue;
+ if (bs.get(i2)) {
+ bs = null;
+ break;
+ }
+ }
+ bsBranches[i] = bs;
+ }
+ return bsBranches;
+ }
}
Modified: trunk/Jmol/src/org/jmol/script/SV.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/SV.java 2013-06-14 12:43:25 UTC (rev
18329)
+++ trunk/Jmol/src/org/jmol/script/SV.java 2013-06-14 12:44:40 UTC (rev
18330)
@@ -329,7 +329,7 @@
static SV getVariableAI(int[] ix) {
JmolList<SV> objects = new JmolList<SV>();
for (int i = 0; i < ix.length; i++)
- objects.addLast(newVariable(integer, Integer.valueOf(ix[i])));
+ objects.addLast(newScriptVariableInt(ix[i]));
return newVariable(varray, objects);
}
@@ -1254,6 +1254,28 @@
return list;
}
+ static JmolList<Object> listAny(SV x) {
+ JmolList<Object> list = new JmolList<Object>();
+ JmolList<SV> l = x.getList();
+ for (int i = 0; i < l.size(); i++) {
+ SV v = l.get(i);
+ JmolList<SV> l2 = v.getList();
+ if (l2 == null) {
+ list.addLast(v.value);
+ } else {
+ JmolList<Object> o = new JmolList<Object>();
+ for (int j = 0; j < l2.size(); j++) {
+ v = l2.get(j);
+ System.out.println(v);
+
+ }
+ list.addLast(o);
+ }
+ System.out.println(v);
+ }
+ return list;
+
+ }
static float[] flistValue(T x, int nMin) {
if (x.tok != varray)
return new float[] { fValue(x) };
Modified: trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2013-06-14 12:43:25 UTC
(rev 18329)
+++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2013-06-14 12:44:40 UTC
(rev 18330)
@@ -4591,6 +4591,7 @@
float[] fparams = null;
int n = 0;
String s = null;
+ iToken = i;
switch (tokAt(i)) {
case T.string:
s = SV.sValue(st[i]);
@@ -7358,7 +7359,7 @@
Matrix4f m4 = new Matrix4f();
float stddev = getSmilesCorrelation(bsFrom, bsTo, strSmiles, null,
- null, m4, null, !isSmiles, false);
+ null, m4, null, !isSmiles, false, null);
if (Float.isNaN(stddev))
error(ERROR_invalidArgument);
V3 translation = new V3();
@@ -7396,7 +7397,7 @@
if (!useThreads())
doAnimate = false;
viewer.rotateAboutPointsInternal(this, centerAndPoints[0][0], pt1,
endDegrees
- / nSeconds, endDegrees, doAnimate, bsFrom, translation, ptsB);
+ / nSeconds, endDegrees, doAnimate, bsFrom, translation, ptsB, null);
if (doAnimate && isJS)
throw new ScriptInterruption(this, "compare", 1);
}
@@ -7404,17 +7405,16 @@
float getSmilesCorrelation(BS bsA, BS bsB, String smiles,
JmolList<P3> ptsA, JmolList<P3> ptsB,
- Matrix4f m, JmolList<BS> vReturn,
- boolean isSmarts, boolean asMap)
+ Matrix4f m4, JmolList<BS> vReturn,
+ boolean isSmarts, boolean asMap, int[][] mapSet)
throws ScriptException {
- float tolerance = 0.1f; // TODO
+ float tolerance = (mapSet == null ? 0.1f : Float.MAX_VALUE);
try {
if (ptsA == null) {
ptsA = new JmolList<P3>();
ptsB = new JmolList<P3>();
}
- if (m == null)
- m = new Matrix4f();
+ Matrix4f m = new Matrix4f();
Atom[] atoms = viewer.modelSet.atoms;
int atomCount = viewer.getAtomCount();
@@ -7424,8 +7424,9 @@
evalError(viewer.getSmilesMatcher().getLastException(), null);
if (maps.length == 0)
return Float.NaN;
- for (int i = 0; i < maps[0].length; i++)
- ptsA.addLast(atoms[maps[0][i]]);
+ int[] mapA = maps[0];
+ for (int i = 0; i < mapA.length; i++)
+ ptsA.addLast(atoms[mapA[i]]);
maps = viewer.getSmilesMatcher().getCorrelationMaps(smiles, atoms,
atomCount, bsB, isSmarts, false);
if (maps == null)
@@ -7456,9 +7457,16 @@
}
if (stddev < lowestStdDev) {
mapB = maps[i];
+ if (m4 != null)
+ m4.setM(m);
lowestStdDev = stddev;
}
}
+ if (mapSet != null) {
+ mapSet[0] = mapA;
+ mapSet[1] = mapB;
+ }
+ ptsB.clear();
for (int i = 0; i < mapB.length; i++)
ptsB.addLast(atoms[mapB[i]]);
return lowestStdDev;
@@ -7515,7 +7523,7 @@
JmolList<BS> vReturn = new JmolList<BS>();
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 BS();
@@ -10357,6 +10365,7 @@
float endDegrees = Float.MAX_VALUE;
boolean isMolecular = false;
boolean haveRotation = false;
+ float[] dihedralList = null;
JmolList<P3> ptsA = null;
P3[] points = new P3[2];
V3 rotAxis = V3.new3(0, 1, 0);
@@ -10393,8 +10402,7 @@
// {X, Y, Z}
// $drawObject[n]
P3 pt1 = centerParameterForModel(i, viewer.getCurrentModelIndex());
- if (!chk && tok == T.dollarsign
- && tokAt(i + 2) != T.leftsquare) {
+ if (!chk && tok == T.dollarsign && tokAt(i + 2) != T.leftsquare) {
// rotation about an axis such as $line1
isMolecular = true;
rotAxis = getDrawObjectAxis(objectNameParameter(++i), viewer
@@ -10419,6 +10427,7 @@
if (isSpin) {
// rotate spin ... [degreesPerSecond]
// rotate spin ... [endDegrees] [degreesPerSecond]
+ // rotate spin BRANCH <DihedralList> [seconds]
if (degreesPerSecond == Float.MIN_VALUE) {
degreesPerSecond = floatParameter(i);
continue;
@@ -10481,17 +10490,23 @@
q = Quaternion.newVA(rotAxis, endDegrees);
break;
case T.branch:
- haveRotation = true;
- int iAtom1 = atomExpressionAt(++i).nextSetBit(0);
- int iAtom2 = atomExpressionAt(++iToken).nextSetBit(0);
- if (iAtom1 < 0 || iAtom2 < 0)
- return;
- bsAtoms = viewer.getBranchBitSet(iAtom2, iAtom1);
isSelected = true;
isMolecular = true;
- points[0] = viewer.getAtomPoint3f(iAtom1);
- points[1] = viewer.getAtomPoint3f(iAtom2);
- nPoints = 2;
+ haveRotation = true;
+ if (isArrayParameter(++i)) {
+ dihedralList = floatParameterSet(i, 6, Integer.MAX_VALUE);
+ i = iToken;
+ isSpin = true;
+ } else {
+ int iAtom1 = atomExpressionAt(i).nextSetBit(0);
+ int iAtom2 = atomExpressionAt(++iToken).nextSetBit(0);
+ if (iAtom1 < 0 || iAtom2 < 0)
+ return;
+ bsAtoms = viewer.getBranchBitSet(iAtom2, iAtom1, true);
+ points[0] = viewer.getAtomPoint3f(iAtom1);
+ points[1] = viewer.getAtomPoint3f(iAtom2);
+ nPoints = 2;
+ }
break;
// 12.0 options
@@ -10527,8 +10542,7 @@
if (endDegrees == 0 && points[0] != null) {
// glide plane
rotAxis.normalize();
- Measure.getPlaneThroughPoint(points[0], rotAxis,
- invPlane = new P4());
+ Measure.getPlaneThroughPoint(points[0], rotAxis, invPlane = new
P4());
}
q = Quaternion.newVA(rotAxis, endDegrees);
nPoints = (points[0] == null ? 0 : 1);
@@ -10552,8 +10566,8 @@
m4 = new Matrix4f();
points[0] = new P3();
nPoints = 1;
- float stddev = (chk ? 0 : Measure.getTransformMatrix4(ptsA,
- ptsB, m4, points[0]));
+ float stddev = (chk ? 0 : Measure.getTransformMatrix4(ptsA, ptsB, m4,
+ points[0]));
// if the standard deviation is very small, we leave ptsB
// because it will be used to set the absolute final positions
if (stddev > 0.001)
@@ -10589,11 +10603,11 @@
bsAtoms = bsCompare;
}
float rate = (degreesPerSecond == Float.MIN_VALUE ? 10
- : endDegrees == Float.MAX_VALUE ? degreesPerSecond
- : (degreesPerSecond < 0) == (endDegrees > 0) ?
- // -n means number of seconds, not degreesPerSecond
- -endDegrees / degreesPerSecond
- : degreesPerSecond);
+ : endDegrees == Float.MAX_VALUE ? degreesPerSecond
+ : (degreesPerSecond < 0) == (endDegrees > 0) ?
+ // -n means number of seconds, not degreesPerSecond
+ -endDegrees / degreesPerSecond
+ : degreesPerSecond);
if (q != null) {
// only when there is a translation (4x4 matrix or TRANSLATE)
// do we set the rotation to be the center of the selected atoms or model
@@ -10631,7 +10645,7 @@
if (rotAxis == null)
return;
}
- if (nPoints < 2) {
+ if (nPoints < 2 && dihedralList == null) {
if (!isMolecular) {
// fixed-frame rotation
// rotate x 10 # Chime-like
@@ -10640,8 +10654,9 @@
// rotate x 10 $object # point-centered
if (isSpin && bsAtoms == null && !useThreads())
return;
- if (viewer.rotateAxisAngleAtCenter(this, points[0], rotAxis, rate,
endDegrees,
- isSpin, bsAtoms) && isJS && isSpin && bsAtoms == null)
+ if (viewer.rotateAxisAngleAtCenter(this, points[0], rotAxis, rate,
+ endDegrees, isSpin, bsAtoms)
+ && isJS && isSpin && bsAtoms == null)
throw new ScriptInterruption(this, "rotate", 1);
return;
}
@@ -10685,8 +10700,9 @@
} else {
if (!useThreads())
return;
- if (viewer.rotateAboutPointsInternal(this, points[0], points[1], rate,
endDegrees,
- isSpin, bsAtoms, translation, ptsB) && isJS && isSpin)
+ if (viewer.rotateAboutPointsInternal(this, points[0], points[1], rate,
+ endDegrees, isSpin, bsAtoms, translation, ptsB, dihedralList)
+ && isJS && isSpin)
throw new ScriptInterruption(this, "rotate", 1);
}
}
Modified: trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java 2013-06-14
12:43:25 UTC (rev 18329)
+++ trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java 2013-06-14
12:44:40 UTC (rev 18330)
@@ -77,7 +77,7 @@
*
*/
- private boolean isSyntaxCheck;
+ private boolean chk;
private boolean wasSyntaxCheck;
private boolean logMessages;
private ScriptEvaluator eval;
@@ -105,7 +105,7 @@
this.eval = eval;
this.viewer = eval.viewer;
this.logMessages = eval.logMessages;
- this.isSyntaxCheck = wasSyntaxCheck = eval.chk;
+ this.chk = wasSyntaxCheck = eval.chk;
this.isArrayItem = isArrayItem;
this.asVector = asVector || isArrayItem;
this.asBitSet = asBitSet;
@@ -453,7 +453,7 @@
case T.plusPlus:
incrementX = (op.tok == T.plusPlus ? 1 : -1);
if (ptid == ptx) {
- if (isSyntaxCheck)
+ if (chk)
return true;
SV x = xStack[xPt];
xStack[xPt] = SV.newVariable(T.string, "").setv(x, false);
@@ -625,7 +625,7 @@
boolean tf = getX().asBoolean();
addXVar(SV.getBoolean(tf));
if (tf == (op.tok == T.opOr)) { // TRUE or.. FALSE and...
- isSyntaxCheck = true;
+ chk = true;
op = (op.tok == T.opOr ? T.tokenOrTRUE : T.tokenAndFALSE);
}
}
@@ -730,7 +730,7 @@
// we cannot know what variables are real
// if this is a property selector, as in x.func(), then we
// just exit; otherwise we add a new TRUE to xStack
- if (isSyntaxCheck)
+ if (chk)
return (op.tok == T.propselector ? true : addXBool(true));
switch (tok) {
case T.abs:
@@ -842,6 +842,7 @@
// compare({bitset},{bitset}[,"SMARTS"|"SMILES"],smilesString [,"stddev"])
// returns matrix4f for rotation/translation or stddev
// compare({bitset},{bitset},"ISOMER") 12.1.5
+ // compare({bitset},{bitset},"BONDS",smilesString) 13.1.17
if (args.length < 2 || args.length > 5)
return false;
@@ -849,7 +850,9 @@
String sOpt = SV.sValue(args[args.length - 1]);
boolean isStdDev = sOpt.equalsIgnoreCase("stddev");
boolean isIsomer = sOpt.equalsIgnoreCase("ISOMER");
- boolean isSmiles = (!isIsomer && args.length > (isStdDev ? 3 : 2));
+ boolean isBonds = sOpt.equalsIgnoreCase("BONDS");
+ boolean isSmiles = (isBonds || !isIsomer
+ && args.length > (isStdDev ? 3 : 2));
BS bs1 = (args[0].tok == T.bitset ? (BS) args[0].value : null);
BS bs2 = (args[1].tok == T.bitset ? (BS) args[1].value : null);
String smiles1 = (bs1 == null ? SV.sValue(args[0]) : "");
@@ -861,51 +864,82 @@
if (bs1 == null || bs2 == null)
return false;
}
+ if (isBonds) {
+ if (args.length != 4)
+ return false;
+ smiles1 = SV.sValue(args[2]);
+ int[][] mapSet = ArrayUtil.newInt2(2);
+ eval.getSmilesCorrelation(bs1, bs2, smiles1, null, null,
+ null, null, true, false, mapSet);
+ int[][] bondMap1 = viewer.getDihedralMap(mapSet[0]);
+ int[][] bondMap2 = (bondMap1 == null ? null :
viewer.getDihedralMap(mapSet[1]));
+ if (bondMap2 == null || bondMap2.length != bondMap1.length)
+ return addXStr("");
+ float[][] angles = new float[bondMap1.length][3];
+ Atom[] atoms = viewer.modelSet.atoms;
+ getTorsions(atoms, bondMap2, angles, 0);
+ getTorsions(atoms, bondMap1, angles, 1);
+ float[] data = new float[bondMap1.length * 6];
+ for (int i = 0, pt = 0; i < bondMap1.length; i++) {
+ int[] map = bondMap1[i];
+ data[pt++] = map[0];
+ data[pt++] = map[1];
+ data[pt++] = map[2];
+ data[pt++] = map[3];
+ data[pt++] = angles[i][0];
+ data[pt++] = angles[i][1];
+ }
+ return addXAF(data);
+ }
if (isIsomer) {
if (args.length != 3)
return false;
- if (bs1 == null && bs2 == null)
- return addXStr(viewer.getSmilesMatcher().getRelationship(smiles1,
smiles2).toUpperCase());
+ if (bs1 == null && bs2 == null)
+ return addXStr(viewer.getSmilesMatcher().getRelationship(smiles1,
+ smiles2).toUpperCase());
String mf1 = (bs1 == null ? viewer.getSmilesMatcher()
- .getMolecularFormula(smiles1, false) :
JmolMolecule.getMolecularFormula(
- viewer.getModelSet().atoms, bs1, false));
+ .getMolecularFormula(smiles1, false) : JmolMolecule
+ .getMolecularFormula(viewer.getModelSet().atoms, bs1, false));
String mf2 = (bs2 == null ? viewer.getSmilesMatcher()
- .getMolecularFormula(smiles2, false) :
JmolMolecule.getMolecularFormula(
- viewer.getModelSet().atoms, bs2, false));
+ .getMolecularFormula(smiles2, false) : JmolMolecule
+ .getMolecularFormula(viewer.getModelSet().atoms, bs2, false));
if (!mf1.equals(mf2))
return addXStr("NONE");
if (bs1 != null)
- smiles1 = (String) eval.getSmilesMatches("", null, bs1, null, false,
true);
+ smiles1 = (String) eval.getSmilesMatches("", null, bs1, null, false,
+ true);
boolean check;
if (bs2 == null) {
// note: find smiles1 IN smiles2 here
check = (viewer.getSmilesMatcher().areEqual(smiles2, smiles1) > 0);
} else {
- check = (((BS) eval.getSmilesMatches(smiles1, null, bs2, null,
- false, true)).nextSetBit(0) >= 0);
+ check = (((BS) eval.getSmilesMatches(smiles1, null, bs2, null, false,
+ true)).nextSetBit(0) >= 0);
}
if (!check) {
// MF matched, but didn't match SMILES
String s = smiles1 + smiles2;
if (s.indexOf("/") >= 0 || s.indexOf("\\") >= 0 || s.indexOf("@") >=
0) {
- if (smiles1.indexOf("@") >= 0 && (bs2 != null ||
smiles2.indexOf("@") >= 0)) {
+ if (smiles1.indexOf("@") >= 0
+ && (bs2 != null || smiles2.indexOf("@") >= 0)) {
// reverse chirality centers
smiles1 = viewer.getSmilesMatcher().reverseChirality(smiles1);
if (bs2 == null) {
check = (viewer.getSmilesMatcher().areEqual(smiles1, smiles2) >
0);
} else {
- check = (((BS) eval.getSmilesMatches(smiles1, null, bs2,
- null, false, true)).nextSetBit(0) >= 0);
+ check = (((BS) eval.getSmilesMatches(smiles1, null, bs2, null,
+ false, true)).nextSetBit(0) >= 0);
}
if (check)
return addXStr("ENANTIOMERS");
}
// remove all stereochemistry from SMILES string
if (bs2 == null) {
- check = (viewer.getSmilesMatcher().areEqual("/nostereo/" +
smiles2, smiles1) > 0);
+ check = (viewer.getSmilesMatcher().areEqual("/nostereo/" + smiles2,
+ smiles1) > 0);
} else {
- Object ret = eval.getSmilesMatches("/nostereo/" + smiles1, null,
bs2, null,
- false, true);
+ Object ret = eval.getSmilesMatches("/nostereo/" + smiles1, null,
+ bs2, null, false, true);
check = (((BS) ret).nextSetBit(0) >= 0);
}
if (check)
@@ -918,12 +952,12 @@
if (bs1 == null || bs2 == null)
return addXStr("IDENTICAL");
stddev = eval.getSmilesCorrelation(bs1, bs2, smiles1, null, null, null,
- null, false, false);
+ null, false, false, null);
return addXStr(stddev < 0.2f ? "IDENTICAL"
: "IDENTICAL or CONFORMATIONAL ISOMERS (RMSD=" + stddev + ")");
} else if (isSmiles) {
- ptsA = new JmolList<P3>();
- ptsB = new JmolList<P3>();
+ ptsA = new JmolList<P3>();
+ ptsB = new JmolList<P3>();
sOpt = SV.sValue(args[2]);
boolean isMap = sOpt.equalsIgnoreCase("MAP");
isSmiles = (sOpt.equalsIgnoreCase("SMILES"));
@@ -933,18 +967,19 @@
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)
return addXStr("");
int nMatch = ptsB.size() / nAtoms;
- JmolList<int[][]> ret = new JmolList<int[][]>();
+ JmolList<int[][]> ret = new JmolList<int[][]>();
for (int i = 0, pt = 0; i < nMatch; i++) {
int[][] a = ArrayUtil.newInt2(nAtoms);
ret.addLast(a);
for (int j = 0; j < nAtoms; j++, pt++)
- a[j] = new int[] { ((Atom)ptsA.get(j)).index,
((Atom)ptsB.get(pt)).index};
+ a[j] = new int[] { ((Atom) ptsA.get(j)).index,
+ ((Atom) ptsB.get(pt)).index };
}
return addXList(ret);
}
@@ -957,6 +992,22 @@
return (isStdDev || Float.isNaN(stddev) ? addXFloat(stddev) : addXM4(m));
}
+ private static void getTorsions(Atom[] atoms, int[][] bondMap,
+ float[][] diff, int pt) {
+ for (int i = bondMap.length; --i >= 0;) {
+ int[] map = bondMap[i];
+ float v = Measure.computeTorsion(atoms[map[0]], atoms[map[1]],
+ atoms[map[2]], atoms[map[3]], true);
+ if (pt == 1) {
+ if (v - diff[i][0] > 180)
+ v -= 360;
+ else if (v - diff[i][0] <= -180)
+ v += 360;
+ }
+ diff[i][pt] = v;
+ }
+ }
+
// private boolean evaluateVolume(ScriptVariable[] args) throws
ScriptException {
// ScriptVariable x1 = getX();
// if (x1.tok != Token.bitset)
@@ -1209,7 +1260,7 @@
public P3 ptValue(SV x, boolean allowFloat)
throws ScriptException {
Object pt;
- if (isSyntaxCheck)
+ if (chk)
return new P3();
switch (x.tok) {
case T.point3f:
@@ -1236,7 +1287,7 @@
}
private P4 planeValue(T x) {
- if (isSyntaxCheck)
+ if (chk)
return new P4();
switch (x.tok) {
case T.point4f:
@@ -1386,6 +1437,7 @@
// "CCCC".find("SMARTS", "CC")
// "CCCC".find("SMILES", "MF")
// {2.1}.find("CCCC",{1.1}) // find pattern "CCCC" in {2.1} with
conformation given by {1.1}
+ // {*}.find("ccCCN","BONDS")
SV x1 = getX();
String sFind = SV.sValue(args[0]);
@@ -1399,7 +1451,9 @@
int iPt = (isSmiles || isSearch ? 2 : 1);
BS bs2 = (iPt < args.length && args[iPt].tok == T.bitset ? (BS)
args[iPt++].value
: null);
- boolean isAll = (args[args.length - 1].tok == T.on);
+ boolean asBonds = ("bonds".equalsIgnoreCase(SV
+ .sValue(args[args.length - 1])));
+ boolean isAll = (asBonds || args[args.length - 1].tok == T.on);
Object ret = null;
switch (x1.tok) {
case T.string:
@@ -1407,12 +1461,12 @@
if (bs2 != null)
return false;
if (flags.equalsIgnoreCase("mf")) {
- ret = viewer.getSmilesMatcher()
- .getMolecularFormula(smiles, isSearch);
+ ret = viewer.getSmilesMatcher().getMolecularFormula(smiles,
isSearch);
if (ret == null)
eval.evalError(viewer.getSmilesMatcher().getLastException(), null);
} else {
- ret = eval.getSmilesMatches(flags, smiles, null, null, isSearch,
!isAll);
+ ret = eval.getSmilesMatches(flags, smiles, null, null, isSearch,
+ !isAll);
}
break;
case T.bitset:
@@ -1420,16 +1474,24 @@
return addXStr(JmolMolecule.getMolecularFormula(
viewer.getModelSet().atoms, (BS) x1.value, false));
if (isSequence)
- return addXStr(viewer.getSmiles(-1, -1, (BS) x1.value, true, isAll,
isAll, false));
+ return addXStr(viewer.getSmiles(-1, -1, (BS) x1.value, true, isAll,
+ isAll, false));
if (isSmiles || isSearch)
sFind = flags;
BS bsMatch3D = bs2;
- ret = eval.getSmilesMatches(sFind, null, (BS) x1.value, bsMatch3D,
!isSmiles,
- !isAll);
+ if (asBonds) {
+ int[][] map = viewer.getSmilesMatcher().getCorrelationMaps(sFind,
+ viewer.modelSet.atoms, viewer.getAtomCount(), (BS) x1.value,
+ !isSmiles, true);
+ ret = (map.length > 0 ? viewer.getDihedralMap(map[0]) : new int[0]);
+ } else {
+ ret = eval.getSmilesMatches(sFind, null, (BS) x1.value, bsMatch3D,
+ !isSmiles, !isAll);
+ }
break;
}
if (ret == null)
- eval.error(ScriptEvaluator.ERROR_invalidArgument);
+ eval.error(ScriptEvaluator.ERROR_invalidArgument);
return addXObj(ret);
}
boolean isReverse = (flags.indexOf("v") >= 0);
@@ -1452,7 +1514,7 @@
int ipt = 0;
int n = 0;
Matcher matcher = null;
- JmolList<String> v = (asMatch ? new JmolList<String>() : null);
+ JmolList<String> v = (asMatch ? new JmolList<String>() : null);
for (int i = 0; i < list.length; i++) {
String what = list[i];
matcher = pattern.matcher(what);
@@ -1468,8 +1530,8 @@
}
if (!isList) {
return (asMatch ? addXStr(v.size() == 1 ? (String) v.get(0) : "")
- : isReverse ? addXBool(n == 1) : asMatch ? addXStr(n == 0 ? "" :
matcher
- .group()) : addXInt(n == 0 ? 0 : matcher.start() + 1));
+ : isReverse ? addXBool(n == 1) : asMatch ? addXStr(n == 0 ? ""
+ : matcher.group()) : addXInt(n == 0 ? 0 : matcher.start() +
1));
}
if (n == 1)
return addXStr(asMatch ? (String) v.get(0) : list[ipt]);
@@ -2341,7 +2403,7 @@
return false;
return addXBs(viewer.getBranchBitSet(
((BS) args[2].value).nextSetBit(0), ((BS) args[1].value)
- .nextSetBit(0)));
+ .nextSetBit(0), true));
case T.smiles:
case T.substructure: // same as "SMILES"
case T.search:
@@ -2506,7 +2568,7 @@
if (i == args.length || !(args[i].value instanceof BS))
return false;
BS bsA = BSUtil.copy(SV.bsSelectVar(args[i++]));
- if (isSyntaxCheck)
+ if (chk)
return addXBs(new BS());
BS bsB = (i < args.length ? BSUtil.copy(SV
.bsSelectVar(args[i])) : null);
@@ -2719,14 +2781,14 @@
x2 = SV.selectItemVar(x2);
if (op.tok == T.minusMinus || op.tok == T.plusPlus) {
- if (!isSyntaxCheck && !x2.increment(incrementX))
+ if (!chk && !x2.increment(incrementX))
return false;
wasX = true;
putX(x2); // reverse getX()
return true;
}
if (op.tok == T.opNot) {
- if (isSyntaxCheck)
+ if (chk)
return addXBool(true);
switch (x2.tok) {
case T.point4f: // quaternion
@@ -2802,9 +2864,9 @@
}
break;
case T.boundbox:
- return (isSyntaxCheck ? addXStr("x") : getBoundBox(x2));
+ return (chk ? addXStr("x") : getBoundBox(x2));
}
- if (isSyntaxCheck)
+ if (chk)
return addXStr(SV.sValue(x2));
if (x2.tok == T.string) {
Object v = SV
@@ -2820,9 +2882,9 @@
// binary:
SV x1 = getX();
- if (isSyntaxCheck) {
+ if (chk) {
if (op == T.tokenAndFALSE || op == T.tokenOrTRUE)
- isSyntaxCheck = false;
+ chk = false;
return addXVar(SV.newScriptVariableToken(x1));
}
switch (op.tok) {
@@ -3362,7 +3424,7 @@
throws ScriptException {
if (x2.tok != T.bitset)
return false;
- if (isSyntaxCheck)
+ if (chk)
return addXStr("");
BS bs = SV.bsSelectVar(x2);
JmolList<T> tokens;
@@ -3397,7 +3459,7 @@
private boolean getBoundBox(SV x2) {
if (x2.tok != T.bitset)
return false;
- if (isSyntaxCheck)
+ if (chk)
return addXStr("");
BoxInfo b = viewer.getBoxInfo(SV.bsSelectVar(x2), 1);
P3[] pts = b.getBoundBoxPoints(true);
Modified: trunk/Jmol/src/org/jmol/smiles/SmilesMatcher.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmilesMatcher.java 2013-06-14 12:43:25 UTC
(rev 18329)
+++ trunk/Jmol/src/org/jmol/smiles/SmilesMatcher.java 2013-06-14 12:44:40 UTC
(rev 18330)
@@ -365,8 +365,7 @@
@SuppressWarnings({ "unchecked" })
private Object match(String pattern, JmolNode[] atoms, int atomCount,
BS bsSelected, BS bsAromatic, boolean isSmarts,
- boolean matchAllAtoms, boolean firstMatchOnly,
- int mode) {
+ boolean matchAllAtoms, boolean firstMatchOnly, int
mode) {
InvalidSmilesException.setLastError(null);
try {
SmilesSearch search = SmilesParser.getMolecule(pattern, isSmarts);
Modified: trunk/Jmol/src/org/jmol/thread/SpinThread.java
===================================================================
--- trunk/Jmol/src/org/jmol/thread/SpinThread.java 2013-06-14 12:43:25 UTC
(rev 18329)
+++ trunk/Jmol/src/org/jmol/thread/SpinThread.java 2013-06-14 12:44:40 UTC
(rev 18330)
@@ -42,6 +42,7 @@
private final TransformManager transformManager;
private float endDegrees;
private JmolList<P3> endPositions;
+ private float[] dihedralList;
private float nDegrees;
private BS bsAtoms;
private boolean isNav;
@@ -51,16 +52,24 @@
private boolean haveNotified;
private int index;
//private boolean navigatingSurface;
+ private BS[] bsBranches;
+ private int nmove = 0;
+
public boolean isGesture() {
return isGesture;
}
- public SpinThread(TransformManager transformManager, Viewer viewer, float
endDegrees, JmolList<P3> endPositions, BS bsAtoms, boolean isNav, boolean
isGesture) {
+ public SpinThread(TransformManager transformManager, Viewer viewer,
+ float endDegrees, JmolList<P3> endPositions, float[] dihedralList, BS
bsAtoms, boolean isNav,
+ boolean isGesture) {
super();
setViewer(viewer, "SpinThread");
this.transformManager = transformManager;
- this.endDegrees = Math.abs(endDegrees);
+ this.endDegrees = endDegrees;
+ this.dihedralList = dihedralList;
+ if (dihedralList != null)
+ bsBranches = viewer.getBsBranches(dihedralList);
this.endPositions = endPositions;
this.bsAtoms = bsAtoms;
this.isNav = isNav;
@@ -163,7 +172,9 @@
mode = MAIN;
break;
case FINISH:
- if (bsAtoms != null && endPositions != null) {
+ if (dihedralList != null) {
+ viewer.setDihedrals(dihedralList, bsBranches, 0F);
+ } else if (bsAtoms != null && endPositions != null) {
// when the standard deviations of the end points was
// exact, we know that we want EXACTLY those final positions
viewer.setAtomCoords(bsAtoms, T.xyz, endPositions);
@@ -180,7 +191,11 @@
}
private void doTransform() {
- if (isNav) {
+ if (dihedralList != null) {
+ float f = 1f / myFps / endDegrees;
+ viewer.setDihedrals(dihedralList, bsBranches, f);
+ nDegrees += 1f / myFps;
+ } else if (isNav) {
transformManager.setNavigationOffsetRelative();//navigatingSurface);
} else if (transformManager.isSpinInternal
|| transformManager.isSpinFixed) {
Modified: trunk/Jmol/src/org/jmol/util/Measure.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Measure.java 2013-06-14 12:43:25 UTC (rev
18329)
+++ trunk/Jmol/src/org/jmol/util/Measure.java 2013-06-14 12:44:40 UTC (rev
18330)
@@ -458,7 +458,7 @@
P3[] cptsB = getCenterAndPoints(ptsB);
float[] retStddev = new float[2];
Quaternion q = calculateQuaternionRotation(new P3[][] { cptsA,
- cptsB }, retStddev, false);
+ cptsB }, retStddev, true); // was false
V3 v = V3.newV(cptsB[0]);
v.sub(cptsA[0]);
m.setMV(q.getMatrix(), v);
Modified: trunk/Jmol/src/org/jmol/viewer/ActionManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/ActionManager.java 2013-06-14 12:43:25 UTC
(rev 18329)
+++ trunk/Jmol/src/org/jmol/viewer/ActionManager.java 2013-06-14 12:44:40 UTC
(rev 18330)
@@ -1870,7 +1870,7 @@
int[] points = new int[nb];
int ni = 0;
for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1),
ni++) {
- lengths[ni] = viewer.getBranchBitSet(i, atomIndex).cardinality();
+ lengths[ni] = viewer.getBranchBitSet(i, atomIndex,
true).cardinality();
points[ni] = i;
}
for (int j = 0; j < nb - 2; j++) {
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-06-14 12:43:25 UTC
(rev 18329)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-06-14 12:44:40 UTC
(rev 18330)
@@ -9,8 +9,14 @@
# The quotes above look odd for a parameter file, but they are
# important for the JavaScript version of Jmol.
-___JmolVersion="13.1.17_dev_2013.06.13"
+___JmolVersion="13.1.17_dev_2013.06.14"
+bug fix: COMPARE could rotate to less-good fit with SMARTS search
+bug fix: draw ARROW ATOM/BOND broken
+
+new feature: compare({atomset1} {atomset2} "ccCCN" "bonds")
+new feature: {1.1}.find("ccCCN", "BONDS")
+
bug fix: animation MORPH broken for non-PyMOL files
-- load trajectory ({0 6}) 1cdr.pdb
-- animation MORPH 10
Modified: trunk/Jmol/src/org/jmol/viewer/TransformManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/TransformManager.java 2013-06-14
12:43:25 UTC (rev 18329)
+++ trunk/Jmol/src/org/jmol/viewer/TransformManager.java 2013-06-14
12:44:40 UTC (rev 18330)
@@ -223,7 +223,7 @@
unTransformPoint(pt2, pt2);
viewer.setInMotion(false);
rotateAboutPointsInternal(null, pt2, pt1, 10 * speed, Float.NaN, false,
- true, null, true, null, null);
+ true, null, true, null, null, null);
}
final V3 arcBall0 = new V3();
@@ -361,7 +361,7 @@
isSpinInternal = false;
isSpinFixed = true;
isSpinSelected = (bsAtoms != null);
- setSpin(eval, true, endDegrees, null, bsAtoms, false);
+ setSpin(eval, true, endDegrees, null, null, bsAtoms, false);
return false;
}
float radians = endDegrees * JC.radiansPerDegree;
@@ -388,7 +388,7 @@
float endDegrees, boolean isClockwise,
boolean isSpin, BS bsAtoms,
boolean isGesture, V3 translation,
- JmolList<P3> finalPoints) {
+ JmolList<P3> finalPoints, float[]
dihedralList) {
// *THE* Viewer INTERNAL frame rotation entry point
@@ -401,7 +401,7 @@
isSpin = false;
}
- if ((translation == null || translation.length() < 0.001)
+ if (dihedralList == null && (translation == null || translation.length() <
0.001)
&& (!isSpin || endDegrees == 0 || Float.isNaN(degreesPerSecond) ||
degreesPerSecond == 0)
&& (isSpin || endDegrees == 0))
return false;
@@ -420,6 +420,7 @@
boolean isSelected = (bsAtoms != null);
if (isSpin) {
// we need to adjust the degreesPerSecond to match a multiple of the
frame rate
+ if (dihedralList == null) {
int nFrames = (int) (Math.abs(endDegrees) / Math.abs(degreesPerSecond)
* spinFps + 0.5);
if (Float.isNaN(endDegrees)) {
@@ -433,7 +434,10 @@
isSpinInternal = true;
isSpinFixed = false;
isSpinSelected = isSelected;
- setSpin(eval, true, endDegrees, finalPoints, bsAtoms, isGesture);
+ } else {
+ endDegrees = degreesPerSecond;
+ }
+ setSpin(eval, true, endDegrees, finalPoints, dihedralList, bsAtoms,
isGesture);
return false;
}
float radians = endDegrees * JC.radiansPerDegree;
@@ -1964,15 +1968,16 @@
private SpinThread spinThread;
public void setSpinOn() {
- setSpin(null, true, Float.MAX_VALUE, null, null, false);
+ setSpin(null, true, Float.MAX_VALUE, null, null, null, false);
}
public void setSpinOff() {
- setSpin(null, false, Float.MAX_VALUE, null, null, false);
+ setSpin(null, false, Float.MAX_VALUE, null, null, null, false);
}
private void setSpin(JmolScriptEvaluator eval, boolean spinOn,
- float endDegrees, JmolList<P3> endPositions, BS bsAtoms,
+ float endDegrees, JmolList<P3> endPositions, float[]
dihedralList,
+ BS bsAtoms,
boolean isGesture) {
if (navOn && spinOn)
setNavOn(false);
@@ -1980,7 +1985,7 @@
viewer.getGlobalSettings().setB("_spinning", spinOn);
if (spinOn) {
if (spinThread == null) {
- spinThread = new SpinThread(this, viewer, endDegrees, endPositions,
+ spinThread = new SpinThread(this, viewer, endDegrees, endPositions,
dihedralList,
bsAtoms, false, isGesture);
spinThread.setEval(eval);
if (bsAtoms == null) {
@@ -2000,7 +2005,7 @@
return;
boolean wasOn = this.navOn;
if (navOn && spinOn)
- setSpin(null, false, 0, null, null, false);
+ setSpin(null, false, 0, null, null, null, false);
this.navOn = navOn;
viewer.getGlobalSettings().setB("_navigating", navOn);
if (!navOn)
@@ -2011,7 +2016,7 @@
if (navFps == 0)
navFps = 10;
if (spinThread == null) {
- spinThread = new SpinThread(this, viewer, 0, null, null, true, false);
+ spinThread = new SpinThread(this, viewer, 0, null, null, null, true,
false);
spinThread.start();
}
} else if (wasOn) {
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2013-06-14 12:43:25 UTC (rev
18329)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2013-06-14 12:44:40 UTC (rev
18330)
@@ -3343,12 +3343,12 @@
return modelSet.getAtomsConnected(min, max, intType, bs);
}
- public BS getBranchBitSet(int atomIndex, int atomIndexNot) {
+ public BS getBranchBitSet(int atomIndex, int atomIndexNot, boolean
allowCyclic) {
if (atomIndex < 0 || atomIndex >= getAtomCount())
return new BS();
return JmolMolecule.getBranchBitSet(modelSet.atoms, atomIndex,
getModelUndeletedAtomsBitSet(modelSet.atoms[atomIndex].modelIndex),
- null, atomIndexNot, true, true);
+ null, atomIndexNot, allowCyclic, true);
}
public int getAtomIndexFromAtomNumber(int atomNumber) {
@@ -7938,11 +7938,11 @@
P3 point2, float degreesPerSecond,
float endDegrees, boolean isSpin,
BS bsSelected, V3 translation,
- JmolList<P3> finalPoints) {
+ JmolList<P3> finalPoints, float[]
dihedralList) {
// Eval: rotate INTERNAL
boolean isOK = transformManager.rotateAboutPointsInternal(eval, point1,
point2, degreesPerSecond, endDegrees, false, isSpin, bsSelected, false,
- translation, finalPoints);
+ translation, finalPoints, dihedralList);
if (isOK)
refresh(-1, "rotateAxisAboutPointsInternal");
return isOK;
@@ -7958,7 +7958,7 @@
}
transformManager.rotateAboutPointsInternal(null, pt1, pt2,
global.pickingSpinRate, Float.MAX_VALUE, isClockwise, true, null,
- false, null, null);
+ false, null, null, null);
}
public V3 getModelDipole() {
@@ -8154,7 +8154,7 @@
statusManager.setStatusAtomMoved(bs);
}
- void moveAtoms(Matrix3f mNew, Matrix3f matrixRotate, V3 translation,
+ public void moveAtoms(Matrix3f mNew, Matrix3f matrixRotate, V3 translation,
P3 center, boolean isInternal, BS bsAtoms) {
// from TransformManager exclusively
if (bsAtoms.cardinality() == 0)
@@ -8294,7 +8294,7 @@
}
if (Measure.computeAngleABC(pt, atom1, atom2, true) > 90
|| Measure.computeAngleABC(pt, atom2, atom1, true) > 90) {
- bsBranch = getBranchBitSet(atom2.index, atom1.index);
+ bsBranch = getBranchBitSet(atom2.index, atom1.index, true);
}
if (bsBranch != null)
for (int n = 0, i = atom1.getBonds().length; --i >= 0;) {
@@ -8323,7 +8323,7 @@
bs.andNot(selectionManager.getMotionFixedAtoms());
rotateAboutPointsInternal(eval, atom1, atom2, 0, degrees, false, bs, null,
- null);
+ null, null);
}
public void refreshMeasures(boolean andStopMinimization) {
@@ -10036,4 +10036,16 @@
modelSet.setBondParametersBS(modelIndex, i, bsBonds, rad, pymolValence,
argb, trans);
}
+ public int[][] getDihedralMap(int[] atoms) {
+ return modelSet.getDihedralMap(atoms);
+ }
+
+ public void setDihedrals(float[] dihedralList, BS[] bsBranches, float rate) {
+ modelSet.setDihedrals(dihedralList, bsBranches, rate);
+ }
+
+ public BS[] getBsBranches(float[] dihedralList) {
+ return modelSet.getBsBranches(dihedralList);
+ }
+
}
This was sent by the SourceForge.net collaborative development platform, the
world's largest Open Source development site.
------------------------------------------------------------------------------
This SF.net email is sponsored by Windows:
Build for Windows Store.
http://p.sf.net/sfu/windows-dev2dev
_______________________________________________
Jmol-commits mailing list
Jmol-commits@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-commits
