Revision: 20304
http://sourceforge.net/p/jmol/code/20304
Author: hansonr
Date: 2015-02-18 22:39:06 +0000 (Wed, 18 Feb 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.2.12_2015.02.18b"
bug fix: POV-Ray renderer does not show proper backbone
bug fix: POV-Ray renderer with a translucent surface shows bonds that should be
hidden
JmolVersion="14.2.12_2015.02.16"
bug fix: write isosurface "./xxx.jvxl" broken -- concatenates "isosurface"
with filename
bug fix: write ISOSURFACE by itself broken (similarly for write POINTGROUP and
others)
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
14.2.11_2014.12.17)
Modified Paths:
--------------
branches/v14_2/Jmol/src/javajs/util/A4.java
branches/v14_2/Jmol/src/org/jmol/g3d/Graphics3D.java
branches/v14_2/Jmol/src/org/jmol/renderbio/BackboneRenderer.java
branches/v14_2/Jmol/src/org/jmol/script/ScriptCompiler.java
branches/v14_2/Jmol/src/org/jmol/script/ScriptMathProcessor.java
branches/v14_2/Jmol/src/org/jmol/scriptext/CmdExt.java
branches/v14_2/Jmol/src/org/jmol/scriptext/MathExt.java
branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties
branches/v14_2/Jmol/src/org/openscience/jmol/app/jmolpanel/console/AppConsole.java
Modified: branches/v14_2/Jmol/src/javajs/util/A4.java
===================================================================
--- branches/v14_2/Jmol/src/javajs/util/A4.java 2015-02-18 05:14:51 UTC (rev
20303)
+++ branches/v14_2/Jmol/src/javajs/util/A4.java 2015-02-18 22:39:06 UTC (rev
20304)
@@ -190,12 +190,12 @@
y = (float) (m02 - m20);
z = (float) (m10 - m01);
double sin = 0.5 * Math.sqrt(x * x + y * y + z * z);
- angle = (float) Math.atan2(sin, cos);
-
- // no need to normalize
- // x /= n;
- // y /= n;
- // z /= n;
+ if (sin == 0 && cos == 1) {
+ x = y = 0;
+ z = 1;
+ } else {
+ angle = (float) Math.atan2(sin, cos);
+ }
}
/**
Modified: branches/v14_2/Jmol/src/org/jmol/g3d/Graphics3D.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/g3d/Graphics3D.java 2015-02-18
05:14:51 UTC (rev 20303)
+++ branches/v14_2/Jmol/src/org/jmol/g3d/Graphics3D.java 2015-02-18
22:39:06 UTC (rev 20304)
@@ -392,8 +392,7 @@
}
platform.setBackgroundColor(bgcolor);
platform.notifyEndOfRendering();
- //setWidthHeight(antialiasEnabled);
- currentlyRendering = false;
+ currentlyRendering = isPass2 = false;
}
public static void mergeBufferPixel(int[] pbuf, int offset, int argbB,
Modified: branches/v14_2/Jmol/src/org/jmol/renderbio/BackboneRenderer.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/renderbio/BackboneRenderer.java
2015-02-18 05:14:51 UTC (rev 20303)
+++ branches/v14_2/Jmol/src/org/jmol/renderbio/BackboneRenderer.java
2015-02-18 22:39:06 UTC (rev 20304)
@@ -64,11 +64,11 @@
}
}
- private void drawSegment(Atom atomA, Atom atomB, short colixA, short colixB,
float max) {
- if (atomA.nBackbonesDisplayed == 0
- || atomB.nBackbonesDisplayed == 0
- || ms.isAtomHidden(atomB.i)
- || !isDataFrame && atomA.distanceSquared(atomB) > max)
+ private void drawSegment(Atom atomA, Atom atomB, short colixA, short colixB,
+ float max) {
+ if (atomA.nBackbonesDisplayed == 0 || atomB.nBackbonesDisplayed == 0
+ || ms.isAtomHidden(atomB.i) || !isDataFrame
+ && atomA.distanceSquared(atomB) > max)
return;
colixA = C.getColixInherited(colixA, atomA.colixAtom);
colixB = C.getColixInherited(colixB, atomB.colixAtom);
@@ -82,8 +82,8 @@
if (mad < 0) {
g3d.drawLine(colixA, colixB, xA, yA, zA, xB, yB, zB);
} else {
- int width = (int) (exportType == GData.EXPORT_CARTESIAN ? mad : vwr
- .tm.scaleToScreen((zA + zB) / 2, mad));
+ int width = (int) (isExport ? mad : vwr.tm.scaleToScreen((zA + zB) / 2,
+ mad));
g3d.fillCylinderXYZ(colixA, colixB, GData.ENDCAPS_SPHERICAL, width, xA,
yA, zA, xB, yB, zB);
}
Modified: branches/v14_2/Jmol/src/org/jmol/script/ScriptCompiler.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/script/ScriptCompiler.java 2015-02-18
05:14:51 UTC (rev 20303)
+++ branches/v14_2/Jmol/src/org/jmol/script/ScriptCompiler.java 2015-02-18
22:39:06 UTC (rev 20304)
@@ -1158,7 +1158,7 @@
if (lookingAtImpliedString(true, true, true)) {
int pt = cchToken;
String str = script.substring(ichToken, ichToken + cchToken);
- if (str.indexOf(" ") < 0) {
+ if (str.indexOf(" ") < 0 && str.indexOf(".") >= 0) {
addTokenToPrefix(T.o(T.string, str));
iHaveQuotedString = true;
return CONTINUE;
Modified: branches/v14_2/Jmol/src/org/jmol/script/ScriptMathProcessor.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/script/ScriptMathProcessor.java
2015-02-18 05:14:51 UTC (rev 20303)
+++ branches/v14_2/Jmol/src/org/jmol/script/ScriptMathProcessor.java
2015-02-18 22:39:06 UTC (rev 20304)
@@ -1060,6 +1060,7 @@
@SuppressWarnings("unchecked")
public boolean binaryOp(T op, SV x1, SV x2) throws ScriptException {
+ // chk only does not get here
P3 pt;
P4 pt4;
M3 m;
@@ -1254,8 +1255,8 @@
addXFloat(x1.asFloat() * x2.asFloat()) :
addXInt(x1.asInt() * x2.asInt()));
}
- pt = (x1.tok == T.matrix3f ? ptValue(x2, false)
- : x2.tok == T.matrix3f ? ptValue(x1, false) : null);
+ pt = (x1.tok == T.matrix3f ? ptValue(x2)
+ : x2.tok == T.matrix3f ? ptValue(x1) : null);
pt4 = (x1.tok == T.matrix4f ? planeValue(x2)
: x2.tok == T.matrix4f ? planeValue(x1) : null);
// checking here to make sure arrays remain arrays and
@@ -1546,7 +1547,7 @@
.lastIndexOf("-") > 0));
}
- public P3 ptValue(SV x, boolean allowFloat) throws ScriptException {
+ public P3 ptValue(SV x) throws ScriptException {
Object pt;
if (chk)
return new P3();
@@ -1554,7 +1555,10 @@
case T.point3f:
return (P3) x.value;
case T.bitset:
- return (P3) eval.getBitsetProperty(SV.bsSelectVar(x), T.xyz, null, null,
+ BS bs = SV.bsSelectVar(x);
+ if (bs.nextSetBit(0) < 0)
+ break;
+ return (P3) eval.getBitsetProperty(bs, T.xyz, null, null,
x.value, null, false, Integer.MAX_VALUE, false);
case T.string:
pt = Escape.uP(SV.sValue(x));
@@ -1562,19 +1566,15 @@
return (P3) pt;
break;
case T.varray:
-
pt = Escape.uP("{" + SV.sValue(x).replace(']',' ').replace('[',' ') +
"}");
if (pt instanceof P3)
return (P3) pt;
break;
}
- if (!allowFloat)
- return null;
- float f = SV.fValue(x);
- return P3.new3(f, f, f);
+ return null;
}
- public P4 planeValue(T x) {
+ public P4 planeValue(SV x) {
if (chk)
return new P4();
switch (x.tok) {
Modified: branches/v14_2/Jmol/src/org/jmol/scriptext/CmdExt.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-02-18
05:14:51 UTC (rev 20303)
+++ branches/v14_2/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-02-18
22:39:06 UTC (rev 20304)
@@ -3168,19 +3168,6 @@
case T.identifier:
case T.string:
fileName = SV.sValue(tokenAt(pt, args));
- if (pt == argCount - 3 && tokAtArray(pt + 1, args) == T.per) {
- // write filename.xxx gets separated as filename .spt
- // write isosurface filename.xxx also
- fileName += "." + SV.sValue(tokenAt(pt + 2, args));
- }
- if (type != "VAR" && pt == pt0 && !isCoord)
- type = "IMAGE";
- else if (fileName.length() > 0 && fileName.charAt(0) == '.'
- && (pt == pt0 + 1 || pt == pt0 + 2)) {
- fileName = SV.sValue(tokenAt(pt - 1, args)) + fileName;
- if (type != "VAR" && pt == pt0 + 1)
- type = "IMAGE";
- }
if (fileName.equalsIgnoreCase("clipboard")
|| !vwr.haveAccess(ACCESS.ALL))
fileName = null;
Modified: branches/v14_2/Jmol/src/org/jmol/scriptext/MathExt.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/scriptext/MathExt.java 2015-02-18
05:14:51 UTC (rev 20303)
+++ branches/v14_2/Jmol/src/org/jmol/scriptext/MathExt.java 2015-02-18
22:39:06 UTC (rev 20304)
@@ -138,10 +138,11 @@
return evaluateCross(mp, args);
case T.data:
return evaluateData(mp, args);
+ case T.dot:
+ return evaluateDotDist(mp, args, 0);
case T.distance:
- case T.dot:
if (op.tok == T.propselector)
- return evaluateDot(mp, args, tok, op.intValue);
+ return evaluateDotDist(mp, args, op.intValue);
//$FALL-THROUGH$
case T.angle:
case T.measure:
@@ -401,7 +402,8 @@
} 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 +413,24 @@
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 +444,19 @@
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 +468,8 @@
//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 +487,18 @@
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 +512,8 @@
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);
@@ -738,25 +739,69 @@
// {selected atoms} XYZ, MOL, PDB file format
return mp.addXStr(vwr.getData(selected, type));
}
+
+
+ /**
+ * x = y.distance({atoms}) the average distance from elements of y to the
+ * CENTER of {atoms}
+ *
+ * x = {atomset1}.distance.min({atomset2}, asAtomSet) If asAtomSet is true,
+ * returns the closest atom in atomset1 to any atom of atomset2; if false or
+ * omitted, returns an array listing the distance of each atom in atomset1 to
+ * the closest atom in atomset2. This array can be used to assign properties
+ * to atomset1: {1.1}.property_d = {1.1}.distance.min({2.1}); color {1.1}
+ * property_d.
+ *
+ * x = {atomset1}.distance.min({point}, asAtomSet) If asAtomSet is true,
+ * returns the atom in atomset1 closest to the specified point;if false or
+ * omitted, returns the closest distance to the specified point from any atom
+ * in atomset1.
+ *
+ * x = {atomset1}.distance.min({atomset2}).min returns the shortest distance
+ * from any atom in atomset1 to any atom in atomset2.
+ *
+ * x = {atomset1}.distance.max({atomset2}, asAtomSet) If asAtomSet is true,
+ * returns the furthest atom in atomset1 to any atom of atomset2; if false or
+ * omitted, returns an array listing the distance of each atom in atomset1 to
+ * the furthest atom in atomset2.
+ *
+ * x = {atomset1}.distance.max({point}, asAtomSet) If asAtomSet is true,
+ * returns the atom in atomset1 furthest from the specified point;if false or
+ * omitted, returns the furthest distance to the specified point from any
atom
+ * in atomset1.
+ *
+ * x = {atomset1}.distance.max({atomset2}).max returns the furthest distance
+ * from any atom in atomset1 to any atom in atomset2.
+ *
+ * x = {atomset1}.distance.all({atomset2}) returns an array or array of
arrays of values
+ *
+ * @param mp
+ * @param args
+ * @param intValue optional .min .max
+ * @return true if successful
+ * @throws ScriptException
+ */
- private boolean evaluateDot(ScriptMathProcessor mp, SV[] args, int tok,
- int intValue) throws ScriptException {
+ private boolean evaluateDotDist(ScriptMathProcessor mp, SV[] args,
+ int intValue) throws ScriptException {
// distance and dot
+
+ boolean isDist = (intValue != 0);
switch (args.length) {
case 1:
- if (tok == T.dot)
- return false;
+ break;
+ case 2:
+ if (isDist)
+ break;
//$FALL-THROUGH$
- case 2:
- break;
default:
return false;
}
SV x1 = mp.getX();
SV x2 = args[0];
- P3 pt2 = (x2.tok == T.varray ? null : mp.ptValue(x2, false));
+ P3 pt2 = (x2.tok == T.varray ? null : mp.ptValue(x2));
P4 plane2 = mp.planeValue(x2);
- if (tok == T.distance) {
+ if (isDist) {
int minMax = intValue & T.minmaxmask;
boolean isMinMax = (minMax == T.min || minMax == T.max);
boolean isAll = minMax == T.minmaxmask;
@@ -808,9 +853,8 @@
float[] data = new float[bs.cardinality()];
for (int i = bs.nextSetBit(0), p = 0; i >= 0; i = bs
.nextSetBit(i + 1))
- data[p++] = ((Float) e.getBitsetProperty(bs2, intValue,
- atoms[i], plane2, x1.value, null, false, x1.index, false))
- .floatValue();
+ data[p++] = ((Float) e.getBitsetProperty(bs2, intValue, atoms[i],
+ plane2, x1.value, null, false, x1.index,
false)).floatValue();
return mp.addXAF(data);
}
return mp.addXObj(e.getBitsetProperty(bs, intValue, pt2, plane2,
@@ -818,7 +862,32 @@
}
}
}
- return mp.addXFloat(getDistance(mp, x1, x2, tok));
+ P3 pt1 = mp.ptValue(x1);
+ P4 plane1 = mp.planeValue(x1);
+ float f = Float.NaN;
+ try {
+ if (isDist) {
+ f = (plane1 == null ? (plane2 == null ? pt2.distance(pt1) : Measure
+ .distanceToPlane(plane2, pt1)) : Measure.distanceToPlane(plane1,
+ pt2));
+ } else {
+ if (plane1 != null && plane2 != null) {
+ // q1.dot(q2) assume quaternions
+ f = plane1.x * plane2.x + plane1.y * plane2.y + plane1.z * plane2.z
+ + plane1.w * plane2.w;
+ // plane.dot(point) =
+ } else {
+ if (plane1 != null)
+ pt1 = P3.new3(plane1.x, plane1.y, plane1.z);
+ // point.dot(plane)
+ else if (plane2 != null)
+ pt2 = P3.new3(plane2.x, plane2.y, plane2.z);
+ f = pt1.dot(pt2);
+ }
+ }
+ } catch (Exception e) {
+ }
+ return mp.addXFloat(f);
}
private boolean evaluateHelix(ScriptMathProcessor mp, SV[] args)
@@ -836,9 +905,9 @@
int tok = T.getTokFromName(type);
if (args.length > 2) {
// helix(pt1, pt2, dq ...)
- P3 pta = mp.ptValue(args[0], true);
- P3 ptb = mp.ptValue(args[1], true);
- if (tok == T.nada || args[2].tok != T.point4f)
+ P3 pta = mp.ptValue(args[0]);
+ P3 ptb = mp.ptValue(args[1]);
+ if (tok == T.nada || args[2].tok != T.point4f || pta == null || ptb ==
null)
return false;
Quat dq = Quat.newP4((P4) args[2].value);
T3[] data = Measure.computeHelicalAxis(pta, ptb, dq);
@@ -884,7 +953,8 @@
// {*}.find("CF",true|false)
// {*}.find("MF")
// {*}.find("MF", "C2H4")
- // {*}.find("SEQENCE")
+ // {*}.find("SEQUENCE")
+ // "AVA".find("SEQUENCE")
// {*}.find("SMARTS", "CCCC")
// "CCCC".find("SMARTS", "CC")
// "CCCC".find("SMILES", "MF")
@@ -1058,6 +1128,7 @@
propertyValue = new BS[] { (BS) propertyValue,
SV.bsSelectVar(args[pt]) };
break;
+ case T.hash:
case T.string:
if (vwr.checkPropertyParameter(propertyName))
propertyValue = args[pt++].value;
@@ -1546,8 +1617,10 @@
return false;
}
P3[] pts = new P3[nPoints];
- for (int i = 0; i < nPoints; i++)
- pts[i] = mp.ptValue(args[i], true);
+ for (int i = 0; i < nPoints; i++) {
+ if ((pts[i] = mp.ptValue(args[i])) == null)
+ return false;
+ }
switch (nPoints) {
case 2:
return mp.addXFloat(pts[0].distance(pts[1]));
@@ -1637,7 +1710,7 @@
return mp.addXStr("");
return mp.addXList(list);
}
- pt2 = mp.ptValue(args[0], false);
+ pt2 = mp.ptValue(args[0]);
if (pt2 == null)
return mp.addXStr("");
return mp.addXPt(Measure.getIntersection(pt2, null, plane, pt3, norm,
@@ -1652,8 +1725,8 @@
return mp.addXPt4(e.getHklPlane(P3.new3(SV.fValue(args[0]),
SV.fValue(args[1]), SV.fValue(args[2]))));
case T.intersection:
- pt1 = mp.ptValue(args[0], false);
- pt2 = mp.ptValue(args[1], false);
+ pt1 = mp.ptValue(args[0]);
+ pt2 = mp.ptValue(args[1]);
if (pt1 == null || pt2 == null)
return mp.addXStr("");
V3 vLine = V3.newV(pt2);
@@ -1669,7 +1742,7 @@
return mp.addXStr("");
return mp.addXPt(pt1);
}
- pt3 = mp.ptValue(args[2], false);
+ pt3 = mp.ptValue(args[2]);
if (pt3 == null)
return mp.addXStr("");
// intersection(ptLine, vLine, pt2);
@@ -1704,13 +1777,13 @@
break;
case T.bitset:
case T.point3f:
- pt1 = mp.ptValue(args[0], false);
- pt2 = mp.ptValue(args[1], false);
+ pt1 = mp.ptValue(args[0]);
+ pt2 = mp.ptValue(args[1]);
if (pt2 == null)
return false;
pt3 = (args.length > 2
&& (args[2].tok == T.bitset || args[2].tok == T.point3f) ? mp
- .ptValue(args[2], false) : null);
+ .ptValue(args[2]) : null);
norm = V3.newV(pt2);
if (pt3 == null) {
plane = new P4();
@@ -1737,8 +1810,11 @@
// plane(<point1>,<point2>,<point3>)
// plane(<point1>,<point2>,<point3>,<pointref>)
V3 vAB = new V3();
+ P3 ptref = (args.length == 4 ? mp.ptValue(args[3]) : null);
+ if (ptref == null)
+ return false;
float nd = Measure.getDirectedNormalThroughPoints(pt1, pt2, pt3,
- (args.length == 4 ? mp.ptValue(args[3], true) : null), norm, vAB);
+ ptref, norm, vAB);
return mp.addXPt4(P4.new4(norm.x, norm.y, norm.z, nd));
}
}
@@ -1858,7 +1934,7 @@
&& (args[1].tok == T.integer || args[1].tok == T.bitset))
break;
}
- if ((pt0 = mp.ptValue(args[0], false)) == null || tok != T.quaternion
+ if ((pt0 = mp.ptValue(args[0])) == null || tok != T.quaternion
&& args[1].tok == T.point3f)
return false;
break;
@@ -1930,7 +2006,7 @@
break;
}
}
- P3 pt1 = mp.ptValue(args[1], false);
+ P3 pt1 = mp.ptValue(args[1]);
p4 = mp.planeValue(args[0]);
if (pt1 != null)
q = Quat.getQuaternionFrame(P3.new3(0, 0, 0), pt0, pt1);
@@ -2270,8 +2346,26 @@
private boolean evaluateSymop(ScriptMathProcessor mp, SV[] args,
boolean haveBitSet) throws ScriptException {
- // {xxx}.symop()
- // symop({xxx}
+
+ // x = y.symop(op,atomOrPoint)
+ // Returns the point that is the result of the transformation of
atomOrPoint
+ // via a crystallographic symmetry operation. The atom set y selects the
unit
+ // cell and spacegroup to be used. If only one model is present, this can
simply be all.
+ // Otherwise, it could be any atom or group of atoms from any model, for
example
+ // {*/1.2} or {atomno=1}. The first parameter, op, is a symmetry
operation.
+ // This can be the 1-based index of a symmetry operation in a file (use
show spacegroup to get this listing)
+ // or a specific Jones-Faithful expression in quotes such as "x,1/2-y,z".
+ //
+ // x = y.symop(op,"label")
+ // This form of the .symop() function returns a set of draw commands that
describe
+ // the symmetry operation in terms of rotation axes, inversion centers,
planes, and
+ // translational vectors. The draw objects will all have IDs starting with
whatever
+ // is given for the label.
+ //
+ // x = symop("x,y,-z")
+ // x = symop(3)
+
+
if (args.length == 0)
return false;
SV x1 = (haveBitSet ? mp.getX() : null);
@@ -2291,14 +2385,14 @@
xyz = null;
}
int iOp = (xyz == null ? args[0].asInt() : 0);
- P3 pt = (args.length > 1 ? mp.ptValue(args[1], true) : null);
- if (args.length == 2 && !Float.isNaN(pt.x))
+ P3 pt = (args.length > 1 ? mp.ptValue(args[1]) : null);
+ if (args.length == 2 && pt != null)
return mp.addXObj(vwr.ms.getSymTemp(false).getSymmetryInfoAtom(vwr.ms,
bs, xyz, iOp, pt, null, null,
T.point));
- String desc = (args.length == 1 ? "" : SV.sValue(args[args.length - 1]))
+ String desc = (args.length == 1 ? "matrix" : SV.sValue(args[args.length -
1]))
.toLowerCase();
int tok = T.draw;
- if (args.length == 1 || desc.equalsIgnoreCase("matrix")) {
+ if (desc.equalsIgnoreCase("matrix")) {
tok = T.matrix4f;
} else if (desc.equalsIgnoreCase("array") ||
desc.equalsIgnoreCase("list")) {
tok = T.list;
@@ -2558,7 +2652,7 @@
private BS getAtomsNearSurface(float distance, String surfaceId) {
Object[] data = new Object[] { surfaceId, null, null };
if (e.getShapePropertyData(JC.SHAPE_ISOSURFACE, "getVertices", data))
- return vwr.ms.getAtomsNearPts(distance, (T3[]) data[1], (BS) data[2]);
+ return getAtomsNearPts(distance, (T3[]) data[1], (BS) data[2]);
data[1] = Integer.valueOf(0);
data[2] = Integer.valueOf(-1);
if (e.getShapePropertyData(JC.SHAPE_DRAW, "getCenter", data))
@@ -2566,32 +2660,26 @@
return new BS();
}
- private float getDistance(ScriptMathProcessor mp, SV x1, SV x2, int tok)
- throws ScriptException {
- P3 pt1 = mp.ptValue(x1, true);
- P4 plane1 = mp.planeValue(x1);
- P3 pt2 = mp.ptValue(x2, true);
- P4 plane2 = mp.planeValue(x2);
- if (tok == T.dot) {
- if (plane1 != null && plane2 != null)
- // q1.dot(q2) assume quaternions
- return plane1.x * plane2.x + plane1.y * plane2.y + plane1.z * plane2.z
- + plane1.w * plane2.w;
- // plane.dot(point) =
- if (plane1 != null)
- pt1 = P3.new3(plane1.x, plane1.y, plane1.z);
- // point.dot(plane)
- if (plane2 != null)
- pt2 = P3.new3(plane2.x, plane2.y, plane2.z);
- return pt1.x * pt2.x + pt1.y * pt2.y + pt1.z * pt2.z;
+ private BS getAtomsNearPts(float distance, T3[] points, BS bsInclude) {
+ BS bsResult = new BS();
+ if (points.length == 0 || bsInclude != null && bsInclude.cardinality() ==
0)
+ return bsResult;
+ if (bsInclude == null)
+ bsInclude = BSUtil.setAll(points.length);
+ Atom[] at = vwr.ms.at;
+ for (int i = vwr.ms.ac; --i >= 0;) {
+ Atom atom = at[i];
+ for (int j = bsInclude.nextSetBit(0); j >= 0; j = bsInclude
+ .nextSetBit(j + 1))
+ if (atom.distance(points[j]) < distance) {
+ bsResult.set(i);
+ break;
+ }
}
-
- if (plane1 == null)
- return (plane2 == null ? pt2.distance(pt1) : Measure.distanceToPlane(
- plane2, pt1));
- return Measure.distanceToPlane(plane1, pt2);
+ return bsResult;
}
+
@Override
@SuppressWarnings("unchecked")
public Object getMinMax(Object floatOrSVArray, int tok) {
Modified: branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties 2015-02-18
05:14:51 UTC (rev 20303)
+++ branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties 2015-02-18
22:39:06 UTC (rev 20304)
@@ -5,8 +5,16 @@
# THIS IS THE RELEASE BRANCH
# BUG FIXES ONLY, PLEASE
-Jmol.___JmolVersion="14.2.12_2015.02.14"
+Jmol.___JmolVersion="14.2.12_2015.02.18b"
+bug fix: POV-Ray renderer does not show proper backbone
+bug fix: POV-Ray renderer with a translucent surface shows bonds that should
be hidden
+
+JmolVersion="14.2.12_2015.02.16"
+
+bug fix: write isosurface "./xxx.jvxl" broken -- concatenates "isosurface"
with filename
+bug fix: write ISOSURFACE by itself broken (similarly for write POINTGROUP
and others)
+
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
14.2.11_2014.12.17)
Modified:
branches/v14_2/Jmol/src/org/openscience/jmol/app/jmolpanel/console/AppConsole.java
===================================================================
---
branches/v14_2/Jmol/src/org/openscience/jmol/app/jmolpanel/console/AppConsole.java
2015-02-18 05:14:51 UTC (rev 20303)
+++
branches/v14_2/Jmol/src/org/openscience/jmol/app/jmolpanel/console/AppConsole.java
2015-02-18 22:39:06 UTC (rev 20304)
@@ -877,7 +877,7 @@
pt = caretPosition.getOffset();
consoleTextPane.setCaretPosition(pt);
- vBar.setValue(Integer.MAX_VALUE);
+ vBar.setValue(vBar.getMaximum());
} catch (Exception e) {
e.printStackTrace();
consoleTextPane.setCaretPosition(getLength());
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