Revision: 20296
http://sourceforge.net/p/jmol/code/20296
Author: hansonr
Date: 2015-02-15 18:32:52 +0000 (Sun, 15 Feb 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.3.12_2015.02.14"
new feature: x.dot(y) for planes and points -- was present but undocumented
and not working correctly
new feature: (undocumented) x.distance.all(y)
new feature: load MUTATE "==LYS"
-- loads using set appendNew false
-- bypasses regeneration of secondary structure
-- not to be documented
-- issued by MUTATE command only
bug fix: MUTATE command adjustments for saving state
bug fix: MUTATE command should not force recreation of shapes
bug fix: MUTATE command should not change backbone atoms
bug fix: x = measure(a,b) where b is {none} crashes Jmol
bug fix: compare({atomA},{atomsB}) should return standard 4x4 matrix, not one
involving a rotation
about an atom center
-- (not adjusted when ROTATESELECTED was fixed in 14.3.11_2014.12.17; Angel
Herraez)
code: org.jmol.modelsetbio.BioExt
-- extracts struts, quaternion plots, polymerInfo, mutate into optional module
-- saves 15K in corebio.js
Modified Paths:
--------------
trunk/Jmol/src/javajs/util/A4.java
trunk/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
trunk/Jmol/src/org/jmol/jvxl/calc/MarchingCubes.java
trunk/Jmol/src/org/jmol/jvxl/data/MeshData.java
trunk/Jmol/src/org/jmol/minimize/Minimizer.java
trunk/Jmol/src/org/jmol/minimize/forcefield/ForceFieldUFF.java
trunk/Jmol/src/org/jmol/modelset/ModelLoader.java
trunk/Jmol/src/org/jmol/modelsetbio/BioExt.java
trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java
trunk/Jmol/src/org/jmol/script/ScriptCompiler.java
trunk/Jmol/src/org/jmol/script/ScriptEval.java
trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java
trunk/Jmol/src/org/jmol/scriptext/MathExt.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/console/AppConsole.java
Modified: trunk/Jmol/src/javajs/util/A4.java
===================================================================
--- trunk/Jmol/src/javajs/util/A4.java 2015-02-15 00:51:11 UTC (rev 20295)
+++ trunk/Jmol/src/javajs/util/A4.java 2015-02-15 18:32:52 UTC (rev 20296)
@@ -190,7 +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);
+ if (sin == 0 && cos == 1) {
+ x = y = 0;
+ z = 1;
+ } else {
+ angle = (float) Math.atan2(sin, cos);
+ }
// no need to normalize
// x /= n;
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
2015-02-15 00:51:11 UTC (rev 20295)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
2015-02-15 18:32:52 UTC (rev 20296)
@@ -71,6 +71,8 @@
protected void initSubclass() {
setIsPDB();
isMMCIF = true;
+ if (htParams.containsKey("isMutate"))
+ asc.setInfo("isMutate",Boolean.TRUE);
byChain = checkFilterKey("BYCHAIN");
bySymop = checkFilterKey("BYSYMOP");
isCourseGrained = byChain || bySymop;
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
2015-02-15 00:51:11 UTC (rev 20295)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
2015-02-15 18:32:52 UTC (rev 20296)
@@ -467,7 +467,7 @@
return asc.errorMessage + "\nfor file " + filePath
+ "\ntype " + name;
if ((asc.bsAtoms == null ? asc.ac
- : asc.bsAtoms.cardinality()) == 0
+ : asc.bsAtoms.nextSetBit(0)) <= 0
&& fileType.indexOf("DataOnly") < 0 && asc.atomSetInfo.get("dataOnly")
== null)
return "No atoms found\nfor file " + filePath + "\ntype " + name;
fixBaseIndices();
Modified: trunk/Jmol/src/org/jmol/jvxl/calc/MarchingCubes.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/calc/MarchingCubes.java 2015-02-15
00:51:11 UTC (rev 20295)
+++ trunk/Jmol/src/org/jmol/jvxl/calc/MarchingCubes.java 2015-02-15
18:32:52 UTC (rev 20296)
@@ -277,7 +277,7 @@
break;
}
allInside = (colorDensity && (cutoff == 0
- || mode == MODE_JVXL && bsVoxels.cardinality() == 0));
+ || mode == MODE_JVXL && bsVoxels.nextSetBit(0) < 0));
boolean colorDensityAll = (colorDensity && cutoff == 0);
float v = 0;
for (int x = x0; x != x1; x += xStep, ptX += ptStep, pt = ptX) {
Modified: trunk/Jmol/src/org/jmol/jvxl/data/MeshData.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/data/MeshData.java 2015-02-15 00:51:11 UTC
(rev 20295)
+++ trunk/Jmol/src/org/jmol/jvxl/data/MeshData.java 2015-02-15 18:32:52 UTC
(rev 20296)
@@ -236,7 +236,7 @@
return;
int nNull = 0;
for (int i = 0; i < nSets; i++) {
- if (surfaceSet[i] != null && surfaceSet[i].cardinality() == 0)
+ if (surfaceSet[i] != null && surfaceSet[i].nextSetBit(0) < 0)
surfaceSet[i] = null;
if (surfaceSet[i] == null)
nNull++;
Modified: trunk/Jmol/src/org/jmol/minimize/Minimizer.java
===================================================================
--- trunk/Jmol/src/org/jmol/minimize/Minimizer.java 2015-02-15 00:51:11 UTC
(rev 20295)
+++ trunk/Jmol/src/org/jmol/minimize/Minimizer.java 2015-02-15 18:32:52 UTC
(rev 20296)
@@ -223,7 +223,7 @@
}
Logger.info("minimize: initializing " + pFF.name + " (steps = " + steps +
" criterion = "
+ crit + ") ...");
- if (bsSelected.cardinality() == 0) {
+ if (bsSelected.nextSetBit(0) < 0) {
Logger.error(GT._("No atoms selected -- nothing to do!"));
return false;
}
Modified: trunk/Jmol/src/org/jmol/minimize/forcefield/ForceFieldUFF.java
===================================================================
--- trunk/Jmol/src/org/jmol/minimize/forcefield/ForceFieldUFF.java
2015-02-15 00:51:11 UTC (rev 20295)
+++ trunk/Jmol/src/org/jmol/minimize/forcefield/ForceFieldUFF.java
2015-02-15 18:32:52 UTC (rev 20296)
@@ -171,12 +171,12 @@
if (!(v instanceof BS))
return null;
BS bs = (BS) v;
- if (isAromatic && bs.cardinality() > 0) {
+ if (isAromatic && bs.nextSetBit(0) >= 0) {
if (bsAromatic == null)
bsAromatic = (BS)
minimizer.vwr.evaluateExpression(tokenTypes[TOKEN_AROMATIC]);
bs.and(bsAromatic);
}
- if (Logger.debugging && bs.cardinality() > 0)
+ if (Logger.debugging && bs.nextSetBit(0) >= 0)
Logger.debug(smarts + " minimize atoms=" + bs);
return bs;
}
Modified: trunk/Jmol/src/org/jmol/modelset/ModelLoader.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelLoader.java 2015-02-15 00:51:11 UTC
(rev 20295)
+++ trunk/Jmol/src/org/jmol/modelset/ModelLoader.java 2015-02-15 18:32:52 UTC
(rev 20296)
@@ -144,7 +144,7 @@
private boolean someModelsHaveUnitcells;
private boolean someModelsAreModulated;
- private boolean is2D;
+ private boolean is2D, isMutate;
public boolean isTrajectory;
private boolean isPyMOLsession;
private boolean doMinimize;
@@ -167,6 +167,7 @@
ms.modelSetProperties = (Properties) ms.getInfoM("properties");
//isMultiFile = getModelSetAuxiliaryInfoBoolean("isMultiFile"); -- no
longer necessary
ms.haveBioModels = ms.getMSInfoB("isPDB");
+ isMutate = ms.getMSInfoB("isMutate");
if (ms.haveBioModels)
jbr = vwr.getJBR().setLoader(this);
jmolData = (String) ms.getInfoM("jmolData");
@@ -285,7 +286,7 @@
adapterModelCount = (adapter == null ? 1 : adapter
.getAtomSetCount(asc));
// cannot append a trajectory into a previous model
- appendNew = (!merging || adapter == null || adapterModelCount > 1
+ appendNew = !isMutate && (!merging || adapter == null || adapterModelCount
> 1
|| isTrajectory || vwr.getBoolean(T.appendnew));
htAtomMap.clear();
chainOf = new Chain[defaultGroupCount];
@@ -574,7 +575,6 @@
if (loadScript.indexOf("load append ") >= 0)
loadScript.append("; set appendNew true");
m.loadScript.append(" ").appendSB(loadScript).append(";\n");
-
}
if (isTrajectory) {
// fill in the rest of the data
@@ -1299,7 +1299,7 @@
// finalize all structures
- if (!ms.haveBioModels || isPyMOLsession) {
+ if (!ms.haveBioModels || isPyMOLsession || isMutate) {
ms.freezeModels();
return;
}
Modified: trunk/Jmol/src/org/jmol/modelsetbio/BioExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/BioExt.java 2015-02-15 00:51:11 UTC
(rev 20295)
+++ trunk/Jmol/src/org/jmol/modelsetbio/BioExt.java 2015-02-15 18:32:52 UTC
(rev 20296)
@@ -955,7 +955,6 @@
return false;
String[] info = vwr.fm.getFileInfo();
- boolean b = vwr.getBoolean(T.appendnew);
Group g = ms.at[iatom].group;
//try {
// get the initial group -- protein for now
@@ -975,9 +974,7 @@
"try{\n"
+ " var atoms0 = {*}\n"
+ " var res0 = " + BS.escape(bsRes0,'(',')') + "\n"
- + " set appendNew false\n"
- + " load append "+fileName+"\n"
- + " set appendNew " + b + "\n"
+ + " load mutate "+fileName+"\n"
+ " var res1 = {!atoms0};var r1 = res1[1];var r0 = res1[0]\n"
+ " if ({r1 & within(group, r0)}){\n"
+ " var haveHs = ({_H & connected(res0)} != 0)\n"
@@ -999,13 +996,20 @@
+ " connect {N2} {keyatoms & *.C}\n"
+ " }\n"
+ " if (C0) {\n" // not terminal
- + " if ({res1 and _H & connected(*.N)} == 1) {\n" // proline
or proline-like
- + " delete *.H and res1\n"
- + " } else {\n"
- + " var x = angle({*.C and res1},{*.CA and res1},{*.N and
res1},{*.H and res1})\n"
+ + " var h1 = {*.H and res1}\n"
+ + " var n = (h1 ? 0 + {res1 and _H & connected(*.N)} : 0)\n"
+ + " switch (n) {\n"
+ + " case 0:\n" // no hydrogens
+ + " break\n"
+ + " case 1:\n" // proline or proline-like
+ + " delete h1\n"
+ + " break\n"
+ + " default:\n"
+ + " var x = angle({*.C and res1},{*.CA and res1},{*.N and
res1},h1)\n"
+ " rotate branch {*.CA and res1} {*.N and res1}
@{angleH-x}\n"
+ " delete *.H2 and res1\n"
+ " delete *.H3 and res1\n"
+ + " break\n"
+ " }\n"
+ " connect {C0} {keyatoms & *.N}\n"
+ " }\n"
@@ -1017,13 +1021,16 @@
Logger.debug(script);
vwr.eval.runScript(script);
} catch (Exception e) {
- // TODO
+ // serious Jmol bug here!
+ if (!vwr.isJS)
+ e.printStackTrace();
+ System.out.println(e);
}
ms = vwr.ms;
if (ms.ac == ac)
return false;
SB sb = ms.am[iModel].loadScript;
- String s = PT.rep(sb.toString(), "load append", "mutate ({" + iatom +
"})");
+ String s = PT.rep(sb.toString(), "load mutate ", "mutate ({" + iatom +
"})");
sb.setLength(0);
sb.append(s);
// check for protein monomer
@@ -1048,7 +1055,6 @@
//} catch (Exception e) {
// System.out.println("" + e);
// }
- vwr.setBooleanProperty("appendNew", b);
vwr.fm.setFileInfo(info);
return true;
Modified: trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java 2015-02-15 00:51:11 UTC
(rev 20295)
+++ trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java 2015-02-15 18:32:52 UTC
(rev 20296)
@@ -589,10 +589,10 @@
} else {
for (int i = 0; i < specInfo.length();) {
bsA = ms.getSequenceBits(specInfo.substring(i, ++i), null);
- if (bsA.cardinality() == 0)
+ if (bsA.nextSetBit(0) < 0)
continue;
bsB = ms.getSequenceBits(specInfo.substring(i, ++i), null);
- if (bsB.cardinality() == 0)
+ if (bsB.nextSetBit(0) < 0)
continue;
calcAllRasmolHydrogenBonds(bsA, bsB, vHBonds, true, 1, false, null);
}
Modified: trunk/Jmol/src/org/jmol/script/ScriptCompiler.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptCompiler.java 2015-02-15 00:51:11 UTC
(rev 20295)
+++ trunk/Jmol/src/org/jmol/script/ScriptCompiler.java 2015-02-15 18:32:52 UTC
(rev 20296)
@@ -1069,7 +1069,7 @@
return OK;
}
if (tokCommand == T.load) {
- if (nTokens == 1 || nTokens == 2 && tokAt(1) == T.append) {
+ if (nTokens == 1 || nTokens == 2 && (tokAt(1) == T.append)) {
boolean isDataBase = Viewer.isDatabaseCode(charAt(ichToken));
if (lookingAtLoadFormat(isDataBase)) {
String strFormat = script.substring(ichToken, ichToken + cchToken);
@@ -1079,6 +1079,7 @@
case T.orientation:
case T.append:
case T.history:
+ case T.mutate:
case T.nbo:
if (nTokens != 1)
return ERROR;
Modified: trunk/Jmol/src/org/jmol/script/ScriptEval.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEval.java 2015-02-15 00:51:11 UTC
(rev 20295)
+++ trunk/Jmol/src/org/jmol/script/ScriptEval.java 2015-02-15 18:32:52 UTC
(rev 20296)
@@ -2184,7 +2184,7 @@
continue;
}
thisCommand = getCommand(pc, false, true);
- if (debugScript)
+ if (debugHigh || debugScript)
Logger.info(thisCommand);
String nextCommand = getCommand(pc + 1, false, true);
fullCommand = thisCommand
@@ -4037,6 +4037,7 @@
boolean isAppend = false;
boolean isInline = false;
boolean isSmiles = false;
+ boolean isMutate = false;
boolean isData = false;
boolean isAsync = vwr.async;
boolean isConcat = false;
@@ -4145,6 +4146,13 @@
i += 2; // skip END "key"
}
break;
+ case T.mutate:
+ isMutate = isAppend = true;
+ appendNew = false;
+ loadScript.append(" mutate");
+ modelName = optParameterAsString(++i);
+ tok = T.getTokFromName(modelName);
+ break;
case T.append:
isAppend = true;
loadScript.append(" append");
@@ -4503,6 +4511,8 @@
Logger.startTimer("load");
if (!isStateScript && !isAppend)
vwr.setBooleanProperty("legacyJavaFloat", false);
+ if (isMutate)
+ htParams.put("isMutate", Boolean.TRUE);
errMsg = vwr.loadModelFromFile(null, filename, filenames, null, isAppend,
htParams, loadScript, sOptions, tokType, isConcat);
if (timeMsg)
Modified: trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java 2015-02-15
00:51:11 UTC (rev 20295)
+++ trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java 2015-02-15
18:32:52 UTC (rev 20296)
@@ -900,10 +900,8 @@
m4.transpose();
return addXM4(m4);
case T.bitset:
- return addXBs(BSUtil.copyInvert(
- SV.bsSelectVar(x2),
- (x2.value instanceof BondSet ? vwr.ms.bondCount : vwr
- .ms.ac)));
+ return addXBs(BSUtil.copyInvert(SV.bsSelectVar(x2),
+ (x2.value instanceof BondSet ? vwr.ms.bondCount : vwr.ms.ac)));
}
return addXFloat(-x2.asFloat());
case T.opNot:
@@ -919,10 +917,8 @@
case T.matrix4f:
return addXM4(M4.newM4((M4) x2.value).invert());
case T.bitset:
- return addXBs(BSUtil.copyInvert(
- SV.bsSelectVar(x2),
- (x2.value instanceof BondSet ? vwr.ms.bondCount : vwr
- .ms.ac)));
+ return addXBs(BSUtil.copyInvert(SV.bsSelectVar(x2),
+ (x2.value instanceof BondSet ? vwr.ms.bondCount : vwr.ms.ac)));
default:
return addXBool(!x2.asBoolean());
}
@@ -949,12 +945,8 @@
switch (iv) {
case T.identifier:
// special flag to get all properties.
- return (x2.tok == T.bitset && getAllProperties(x2, (String) op.value));
- case T.type:
- return addXStr(typeOf(x2));
- case T.keys:
- return getKeys(x2, (op.intValue & T.minmaxmask) == T.minmaxmask);
- case T.length:
+ return (x2.tok == T.bitset && (chk ? addXStr("") : getAllProperties(x2,
+ (String) op.value)));
case T.count:
case T.size:
if (iv == T.length && x2.value instanceof BondSet)
@@ -1246,16 +1238,14 @@
case T.times:
switch (x1.tok) {
case T.integer:
- return (isDecimal(x2) ?
- addXFloat(x1.intValue * x2.asFloat())
- : addXInt(x1.intValue * x2.asInt()));
+ return (isDecimal(x2) ? addXFloat(x1.intValue * x2.asFloat())
+ : addXInt(x1.intValue * x2.asInt()));
case T.string:
- return (isDecimal(x2) || isDecimal(x1) ?
- 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);
+ return (isDecimal(x2) || isDecimal(x1) ? addXFloat(x1.asFloat()
+ * x2.asFloat()) : addXInt(x1.asInt() * x2.asInt()));
+ }
+ 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
@@ -1268,15 +1258,14 @@
M3 m3b = M3.newM3((M3) x2.value);
m3b.transpose();
m3b.rotate(pt);
- if (x1.tok == T.varray)
- return addX(SV.getVariableAF(new float[] { pt.x, pt.y, pt.z }));
- return addXPt(pt);
+ return (x1.tok == T.varray ? addX(SV.getVariableAF(new float[] {
+ pt.x, pt.y, pt.z })) : addXPt(pt));
}
if (pt4 != null)
// q * m --> q
- return addXPt4((Quat.newP4(pt4).mulQ(Quat
- .newM((M3) x2.value))).toPoint4f());
- break;
+ return addXPt4((Quat.newP4(pt4).mulQ(Quat.newM((M3) x2.value)))
+ .toPoint4f());
+ break;
case T.matrix4f:
// pt4 * m4
// [a b c d] * m4
@@ -1284,10 +1273,8 @@
M4 m4b = M4.newM4((M4) x2.value);
m4b.transpose();
m4b.transform(pt4);
- if (x1.tok == T.varray)
- return addX(SV.getVariableAF(new float[] { pt4.x, pt4.y, pt4.z,
- pt4.w }));
- return addXPt4(pt4);
+ return (x1.tok == T.varray ? addX(SV.getVariableAF(new float[] {
+ pt4.x, pt4.y, pt4.z, pt4.w })) : addXPt4(pt4));
}
break;
}
@@ -1296,9 +1283,8 @@
M3 m3 = (M3) x1.value;
if (pt != null) {
m3.rotate(pt);
- if (x2.tok == T.varray)
- return addX(SV.getVariableAF(new float[] { pt.x, pt.y, pt.z }));
- return addXPt(pt);
+ return (x2.tok == T.varray ? addX(SV.getVariableAF(new float[] {
+ pt.x, pt.y, pt.z })) : addXPt(pt));
}
switch (x2.tok) {
case T.matrix3f:
@@ -1307,8 +1293,8 @@
return addXM3(m);
case T.point4f:
// m * q
- return addXM3(Quat.newM(m3)
- .mulQ(Quat.newP4((P4) x2.value)).getMatrix());
+ return addXM3(Quat.newM(m3).mulQ(Quat.newP4((P4) x2.value))
+ .getMatrix());
}
f = x2.asFloat();
A4 aa = new A4();
@@ -1319,16 +1305,13 @@
M4 m4 = (M4) x1.value;
if (pt != null) {
m4.rotTrans(pt);
- if (x2.tok == T.varray)
- return addX(SV.getVariableAF(new float[] { pt.x, pt.y, pt.z }));
- return addXPt(pt);
+ return (x2.tok == T.varray ? addX(SV.getVariableAF(new float[] {
+ pt.x, pt.y, pt.z })) : addXPt(pt));
}
if (pt4 != null) {
m4.transform(pt4);
- if (x2.tok == T.varray)
- return addX(SV.getVariableAF(new float[] { pt4.x, pt4.y, pt4.z,
- pt4.w }));
- return addXPt4(pt4);
+ return (x2.tok == T.varray ? addX(SV.getVariableAF(new float[] {
+ pt4.x, pt4.y, pt4.z, pt4.w })) : addXPt4(pt4));
}
if (x2.tok == T.matrix4f) {
M4 m4b = M4.newM4((M4) x2.value);
@@ -1352,8 +1335,7 @@
// quaternion notation as well here.
return addXPt4(Quat.newP4((P4) x1.value)
.mulQ(Quat.newP4((P4) x2.value)).toPoint4f());
- return addXPt4(Quat.newP4((P4) x1.value).mul(x2.asFloat())
- .toPoint4f());
+ return addXPt4(Quat.newP4((P4)
x1.value).mul(x2.asFloat()).toPoint4f());
}
return addXFloat(x1.asFloat() * x2.asFloat());
case T.divide:
@@ -1377,21 +1359,20 @@
Float.NaN) : P3.new3(pt.x / f2, pt.y / f2, pt.z / f2));
case T.point4f:
return addXPt4(x2.tok == T.point4f ? Quat.newP4((P4) x1.value)
- .div(Quat.newP4((P4) x2.value)).toPoint4f() : (f2 = x2
- .asFloat()) == 0 ? P4.new4(Float.NaN, Float.NaN, Float.NaN,
- Float.NaN) : Quat.newP4((P4) x1.value).mul(1 / f2)
- .toPoint4f());
+ .div(Quat.newP4((P4) x2.value)).toPoint4f()
+ : (f2 = x2.asFloat()) == 0 ? P4.new4(Float.NaN, Float.NaN,
+ Float.NaN, Float.NaN) : Quat.newP4((P4) x1.value).mul(1 / f2)
+ .toPoint4f());
}
return addXFloat(x1.asFloat() / x2.asFloat());
case T.leftdivide:
f = x2.asFloat();
if (x1.tok == T.point4f) {
- if (f == 0)
- return addXPt4(P4.new4(Float.NaN, Float.NaN, Float.NaN, Float.NaN));
- if (x2.tok == T.point4f)
- return addXPt4(Quat.newP4((P4) x1.value)
- .divLeft(Quat.newP4((P4) x2.value)).toPoint4f());
- return addXPt4(Quat.newP4((P4) x1.value).mul(1 / f).toPoint4f());
+ return (f == 0 ? addXPt4(P4.new4(Float.NaN, Float.NaN, Float.NaN,
+ Float.NaN)) : x2.tok == T.point4f ? addXPt4(Quat
+ .newP4((P4) x1.value).divLeft(Quat.newP4((P4) x2.value))
+ .toPoint4f()) : addXPt4(Quat.newP4((P4) x1.value).mul(1 / f)
+ .toPoint4f()));
}
return addXInt(f == 0 ? 0 : (int) Math.floor(x1.asFloat() /
x2.asFloat()));
case T.timestimes:
@@ -1428,15 +1409,9 @@
return addXStr(s);
case T.string:
s = (String) x1.value;
- if (n == 0)
- return addXStr(PT.trim(s, "\n\t "));
- if (n == 9999)
- return addXStr(s.toUpperCase());
- if (n == -9999)
- return addXStr(s.toLowerCase());
- if (n > 0)
- return addXStr(PT.formatS(s, n, n, false, false));
- return addXStr(PT.formatS(s, n, n - 1, true, false));
+ return addXStr(n == 0 ? PT.trim(s, "\n\t ") : n == 9999 ? s
+ .toUpperCase() : n == -9999 ? s.toLowerCase() : n > 0 ? PT.formatS(
+ s, n, n, false, false) : PT.formatS(s, n, n - 1, true, false));
case T.varray:
String[] list = SV.strListValue(x1);
for (int i = 0; i < list.length; i++) {
@@ -1455,7 +1430,8 @@
case T.point4f:
pt4 = (P4) x1.value;
if (x2.tok == T.point3f)
- return addXPt((P3) (Quat.newP4(pt4)).transform2((P3) x2.value, new
P3()));
+ return addXPt((P3) (Quat.newP4(pt4)).transform2((P3) x2.value,
+ new P3()));
if (x2.tok == T.point4f) {
P4 v4 = P4.newPt((P4) x2.value);
(Quat.newP4(pt4)).getThetaDirected(v4);
@@ -1546,15 +1522,16 @@
.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();
switch (x.tok) {
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));
@@ -1562,21 +1539,15 @@
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) {
- if (chk)
- return new P4();
switch (x.tok) {
case T.point4f:
return (P4) x.value;
@@ -1617,8 +1588,6 @@
private boolean getAllProperties(SV x2, String abbr)
throws ScriptException {
- if (chk)
- return addXStr("");
BS bs = SV.bsSelectVar(x2);
Lst<T> tokens;
int n = bs.cardinality();
@@ -1652,8 +1621,6 @@
private boolean getBoundBox(SV x2) {
if (x2.tok != T.bitset)
return false;
- if (chk)
- return addXStr("");
BoxInfo b = vwr.ms.getBoxInfo(SV.bsSelectVar(x2), 1);
P3[] pts = b.getBoundBoxPoints(true);
Lst<P3> list = new Lst<P3>();
Modified: trunk/Jmol/src/org/jmol/scriptext/MathExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2015-02-15 00:51:11 UTC
(rev 20295)
+++ trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2015-02-15 18:32:52 UTC
(rev 20296)
@@ -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:
@@ -744,24 +745,67 @@
// }
}
- private boolean evaluateDot(ScriptMathProcessor mp, SV[] args, int tok,
- int intValue) throws ScriptException {
+ /**
+ * 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 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;
@@ -813,9 +857,8 @@
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,
@@ -823,7 +866,32 @@
}
}
}
- 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)
@@ -841,9 +909,9 @@
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);
@@ -1556,8 +1624,10 @@
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]));
@@ -1647,7 +1717,7 @@
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,
@@ -1662,8 +1732,8 @@
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);
@@ -1679,7 +1749,7 @@
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);
@@ -1714,13 +1784,13 @@
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();
@@ -1747,8 +1817,11 @@
// 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));
}
}
@@ -1868,7 +1941,7 @@
&& (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;
@@ -1940,7 +2013,7 @@
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);
@@ -2280,8 +2353,26 @@
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);
@@ -2301,14 +2392,14 @@
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;
@@ -2596,32 +2687,6 @@
}
- 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;
- }
-
- if (plane1 == null)
- return (plane2 == null ? pt2.distance(pt1) : Measure.distanceToPlane(
- plane2, pt1));
- return Measure.distanceToPlane(plane1, pt2);
- }
-
@Override
@SuppressWarnings("unchecked")
public Object getMinMax(Object floatOrSVArray, int tok) {
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-02-15 00:51:11 UTC
(rev 20295)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-02-15 18:32:52 UTC
(rev 20296)
@@ -17,12 +17,26 @@
Jmol.___JmolVersion="14.3.12_2015.02.14"
+new feature: x.dot(y) for planes and points -- was present but undocumented
and not working correctly
+new feature: (undocumented) x.distance.all(y)
+
+new feature: load MUTATE "==LYS"
+ -- loads using set appendNew false
+ -- bypasses regeneration of secondary structure
+ -- not to be documented
+ -- issued by MUTATE command only
+
+bug fix: MUTATE command adjustments for saving state
+bug fix: MUTATE command should not force recreation of shapes
+bug fix: MUTATE command should not change backbone atoms
+bug fix: x = measure(a,b) where b is {none} crashes Jmol
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)
-bug fix: mutation should not force recreation of shapes
+ about an atom center
+ -- (not adjusted when ROTATESELECTED was fixed in 14.3.11_2014.12.17; Angel
Herraez)
code: org.jmol.modelsetbio.BioExt
-- extracts struts, quaternion plots, polymerInfo, mutate into optional module
+ -- saves 15K in corebio.js
JmolVersion="14.3.12_2015.02.11"
Modified:
trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/console/AppConsole.java
===================================================================
--- trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/console/AppConsole.java
2015-02-15 00:51:11 UTC (rev 20295)
+++ trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/console/AppConsole.java
2015-02-15 18:32:52 UTC (rev 20296)
@@ -878,8 +878,8 @@
pt = caretPosition.getOffset();
consoleTextPane.setCaretPosition(pt);
try {
- vBar.setValue(Integer.MAX_VALUE);
- } catch (Exception e) {
+ vBar.setValue(vBar.getMaximum());
+ } catch (Throwable e) {
//
}
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