Revision: 20590
http://sourceforge.net/p/jmol/code/20590
Author: hansonr
Date: 2015-06-19 08:29:26 +0000 (Fri, 19 Jun 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.3.15_2015.06.18"
new feature: cleaning empty array values using .find()
- arrays of hash info:
array = array.find()
bug fix: msCIF reader can hang if occupancy is not fractional
bug fix: JSmol applet not returning full set of parameters in animFrameCallback
bug fix: load FILL command can fail if base unit cell is not part of the needed
set for the specified volume
Modified Paths:
--------------
trunk/Jmol/src/javajs/util/Measure.java
trunk/Jmol/src/org/jmol/appletjs/Jmol.java
trunk/Jmol/src/org/jmol/script/SV.java
trunk/Jmol/src/org/jmol/script/ScriptCompiler.java
trunk/Jmol/src/org/jmol/script/ScriptExpr.java
trunk/Jmol/src/org/jmol/scriptext/MathExt.java
trunk/Jmol/src/org/jmol/viewer/JC.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/ShapeManager.java
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/javajs/util/Measure.java
===================================================================
--- trunk/Jmol/src/javajs/util/Measure.java 2015-06-18 19:51:21 UTC (rev
20589)
+++ trunk/Jmol/src/javajs/util/Measure.java 2015-06-19 08:29:26 UTC (rev
20590)
@@ -179,21 +179,22 @@
public static float distanceToPlane(P4 plane, T3 pt) {
return (plane == null ? Float.NaN
- : (plane.x * pt.x + plane.y * pt.y + plane.z * pt.z + plane.w)
- / (float) Math.sqrt(plane.x * plane.x + plane.y * plane.y + plane.z
- * plane.z));
+ : (plane.dot(pt) + plane.w) / (float) Math.sqrt(plane.dot(plane)));
}
+ public static float directedDistanceToPlane(P3 pt, P4 plane, P3 ptref) {
+ float f = plane.dot(pt) + plane.w;
+ float f1 = plane.dot(ptref) + plane.w;
+ return Math.signum(f1) * f / (float) Math.sqrt(plane.dot(plane));
+ }
+
public static float distanceToPlaneD(P4 plane, float d, P3 pt) {
- return (plane == null ? Float.NaN : (plane.x * pt.x + plane.y
- * pt.y + plane.z * pt.z + plane.w) / d);
+ return (plane == null ? Float.NaN : (plane.dot(pt) + plane.w) / d);
}
public static float distanceToPlaneV(V3 norm, float w, P3 pt) {
return (norm == null ? Float.NaN
- : (norm.x * pt.x + norm.y * pt.y + norm.z * pt.z + w)
- / (float) Math.sqrt(norm.x * norm.x + norm.y * norm.y + norm.z
- * norm.z));
+ : (norm.dot(pt) + w) / (float) Math.sqrt(norm.dot(norm)));
}
/**
Modified: trunk/Jmol/src/org/jmol/appletjs/Jmol.java
===================================================================
--- trunk/Jmol/src/org/jmol/appletjs/Jmol.java 2015-06-18 19:51:21 UTC (rev
20589)
+++ trunk/Jmol/src/org/jmol/appletjs/Jmol.java 2015-06-19 08:29:26 UTC (rev
20590)
@@ -230,7 +230,7 @@
* o = o[tokens[i]];
* for (var i = 0; i < data.length; i++)
* data[i] && data[i].booleanValue && (data[i] =
data[i].booleanValue());
- * return
o(data[0],data[1],data[2],data[3],data[4],data[5],data[6],data[7]);
+ * return o.apply(null,data)
* } catch (e) { System.out.println(callback + " failed " +
e); }
*/
{
Modified: trunk/Jmol/src/org/jmol/script/SV.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/SV.java 2015-06-18 19:51:21 UTC (rev
20589)
+++ trunk/Jmol/src/org/jmol/script/SV.java 2015-06-19 08:29:26 UTC (rev
20590)
@@ -849,8 +849,9 @@
case string:
break;
default:
- return ((tokenIn instanceof SV) && ((SV) tokenIn).myName != null ?
newI(0)
- .setv((SV) tokenIn) : tokenIn);
+ return ((tokenIn instanceof SV) && ((SV) tokenIn).myName != null
+ ? newI(0).setv((SV) tokenIn)
+ : tokenIn);
}
// negative number is a count from the end
Modified: trunk/Jmol/src/org/jmol/script/ScriptCompiler.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptCompiler.java 2015-06-18 19:51:21 UTC
(rev 20589)
+++ trunk/Jmol/src/org/jmol/script/ScriptCompiler.java 2015-06-19 08:29:26 UTC
(rev 20590)
@@ -65,7 +65,7 @@
*/
/**
- * @param vwr
+ * @param vwr
* @j2sIgnoreSuperConstructor
*
*/
@@ -906,20 +906,19 @@
private void getPrefixToken() {
ident = script.substring(ichToken, ichToken + cchToken);
identLC = ident.toLowerCase();
- boolean isUserVar = (lastToken.tok != T.per && !isDotDot &&
isContextVariable(identLC));
- String myName = (isUserVar ? ident : null);
+ boolean isUserVar = isContextVariable(identLC);
+ String myName = ident;//(isUserVar ? ident : null);
String preserveCase = null;
if (nTokens == 0)
isUserToken = isUserVar;
if (nTokens == 1
- && (tokCommand == T.function || tokCommand == T.parallel
- || tokCommand == T.var)
-
- || nTokens != 0 && isUserVar
-
- || !isDotDot && isUserFunction(identLC) && ((preserveCase = ident) !=
null)
-
-
+ && (tokCommand == T.function || tokCommand == T.parallel || tokCommand
== T.var)
+
+ || nTokens != 0 && isUserVar
+
+ || !isDotDot && isUserFunction(identLC)
+ && ((preserveCase = ident) != null)
+
&& (thisFunction == null || !thisFunction.name.equals(identLC))) {
// we need to allow:
@@ -954,8 +953,8 @@
if (identLC.indexOf("property_") == 0) {
theToken = T.o(T.property, identLC);
} else if (myName != null) {
- theToken = SV.newSV(T.identifier, 0, ident);
- ((SV)theToken).myName = myName;
+ theToken = SV.newSV(T.identifier, Integer.MAX_VALUE, ident);
+ ((SV) theToken).myName = myName;
} else {
theToken = T.o(T.identifier, ident);
}
@@ -986,8 +985,9 @@
&& lastToken.tok == T.defaultdirectory || tokCommand == T.load
|| tokCommand == T.background || tokCommand == T.script));
iHaveQuotedString = true;
- if ((tokCommand == T.load || tokCommand == T.cgo) && lastToken.tok ==
T.data
- || tokCommand == T.data && str.indexOf("@") < 0) {
+ if ((tokCommand == T.load || tokCommand == T.cgo)
+ && lastToken.tok == T.data || tokCommand == T.data
+ && str.indexOf("@") < 0) {
if (!getData(str)) {
return ERROR(ERROR_missingEnd, "data");
}
@@ -1034,6 +1034,7 @@
cchToken = 1;
switch (ch) {
case '[':
+ tokLastMath = 1;
addTokenToPrefix(T.tokenArrayOpen);
bracketCount++;
return CONTINUE;
@@ -1071,9 +1072,9 @@
if (nTokens == 2) {
if (lastToken.tok == T.image)
iHaveQuotedString = true;
- } else
- if (!iHaveQuotedString && lastToken.tok != T.domains && lastToken.tok
!= T.validation) {
- return OK;
+ } else if (!iHaveQuotedString && lastToken.tok != T.domains
+ && lastToken.tok != T.validation) {
+ return OK;
}
//$FALL-THROUGH$
case T.load:
@@ -1130,8 +1131,8 @@
}
}
if (!iHaveQuotedString
- && lookingAtImpliedString(tokCommand == T.show, tokCommand ==
T.load, nTokens > 1
- || tokCommand != T.script)) {
+ && lookingAtImpliedString(tokCommand == T.show, tokCommand == T.load,
+ nTokens > 1 || tokCommand != T.script)) {
String str = script.substring(ichToken, ichToken + cchToken);
if (tokCommand == T.script) {
if (str.startsWith("javascript:")) {
@@ -1268,7 +1269,8 @@
boolean isBondOrMatrix = (script.charAt(ichToken) == '[');
BS bs = lookingAtBitset();
if (bs != null) {
- addTokenToPrefix(T.o(T.bitset, isBondOrMatrix ? BondSet.newBS(bs,
null) : bs));
+ addTokenToPrefix(T.o(T.bitset, isBondOrMatrix ? BondSet.newBS(bs, null)
+ : bs));
return CONTINUE;
}
if (isBondOrMatrix) {
@@ -1905,8 +1907,8 @@
}
private static ScriptFunction newScriptParallelProcessor(String name, int
tok) {
- ScriptFunction jpp = (ScriptFunction) Interface
- .getInterface("org.jmol.script.ScriptParallelProcessor", null, null);
+ ScriptFunction jpp = (ScriptFunction) Interface.getInterface(
+ "org.jmol.script.ScriptParallelProcessor", null, null);
jpp.set(name, tok);
return jpp;
}
@@ -1920,18 +1922,16 @@
ptNewSetModifier = (isNewSet ? (ident.equals("(") ? 2 : 1)
: Integer.MAX_VALUE);
// unfortunately we have to look here for defaultLattice, because it must
not turn into a string.
- return ((isSetBrace || theToken.tok == T.leftparen
- || theToken.tok == T.defaultlattice
- || theToken.tok == T.plusPlus || theToken.tok == T.minusMinus) ?
theToken
+ return ((isSetBrace || theToken.tok == T.leftparen
+ || theToken.tok == T.defaultlattice || theToken.tok == T.plusPlus ||
theToken.tok == T.minusMinus) ? theToken
: T.o(T.identifier, ident));
}
private void checkUnquotedFileName() {
int ichT = ichToken;
char ch;
- while (++ichT < cchScript
- && !PT.isWhitespace(ch = script.charAt(ichT)) && ch != '#'
- && ch != ';' && ch != '}') {
+ while (++ichT < cchScript && !PT.isWhitespace(ch = script.charAt(ichT))
+ && ch != '#' && ch != ';' && ch != '}') {
}
String name = script.substring(ichToken, ichT).replace('\\', '/');
cchToken = ichT - ichToken;
@@ -2774,10 +2774,10 @@
tokLastMath = 1;
// last is hack for insertion codes embedded in an atom expression :-(
// select c3^a
- while (PT.isLetterOrDigit(ch = charAt(ichT)) || ch == '_'
- || ch == '*' && charAt(ichT - 1) == '?' || ch == '?' || ch == '~'
- || ch == '\'' || ch == '\\' && charAt(ichT + 1) == '?' || ch == '^'
- && ichT > ichT0 && PT.isDigit(charAt(ichT - 1)))
+ while (PT.isLetterOrDigit(ch = charAt(ichT)) || ch == '_' || ch == '*'
+ && charAt(ichT - 1) == '?' || ch == '?' || ch == '~' || ch == '\''
+ || ch == '\\' && charAt(ichT + 1) == '?' || ch == '^' && ichT > ichT0
+ && PT.isDigit(charAt(ichT - 1)))
++ichT;
break;
}
Modified: trunk/Jmol/src/org/jmol/script/ScriptExpr.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptExpr.java 2015-06-18 19:51:21 UTC
(rev 20589)
+++ trunk/Jmol/src/org/jmol/script/ScriptExpr.java 2015-06-19 08:29:26 UTC
(rev 20590)
@@ -522,7 +522,7 @@
if (!isWhere) {
rpn.addX(SV.newT(theToken));
break;
- }
+ }//$FALL-THROUGH$
default:
if (theTok == T.leftsquare && tokAt(i + 2) == T.colon) {
v = getAssocArray(i);
Modified: trunk/Jmol/src/org/jmol/scriptext/MathExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2015-06-18 19:51:21 UTC
(rev 20589)
+++ trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2015-06-19 08:29:26 UTC
(rev 20590)
@@ -839,13 +839,15 @@
* 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
+ * x = {atomset1}.distance.all({atomset2}) returns an array or array of
arrays
+ * of values
*
- * @param mp
- * @param args
- * @param intValue optional .min .max
+ * @param mp
+ * @param args
+ * @param intValue
+ * optional .min .max
* @return true if successful
- * @throws ScriptException
+ * @throws ScriptException
*/
private boolean evaluateDotDist(ScriptMathProcessor mp, SV[] args,
@@ -933,7 +935,10 @@
float f = Float.NaN;
try {
if (isDist) {
- f = (plane1 == null ? (plane2 == null ? pt2.distance(pt1) : Measure
+ if (plane2 != null && args.length == 2)
+ f = Measure.directedDistanceToPlane(pt1, plane2,
SV.ptValue(args[1]));
+ else
+ f = (plane1 == null ? (plane2 == null ? pt2.distance(pt1) : Measure
.distanceToPlane(plane2, pt1)) : Measure.distanceToPlane(plane1,
pt2));
} else {
@@ -1013,8 +1018,6 @@
private boolean evaluateFind(ScriptMathProcessor mp, SV[] args)
throws ScriptException {
- if (args.length == 0)
- return false;
// {*}.find("CF",true|false)
// {*}.find("MF")
@@ -1031,7 +1034,8 @@
SV x1 = mp.getX();
boolean isList = (x1.tok == T.varray);
- String sFind = SV.sValue(args[0]);
+ boolean isEmpty = (args.length == 0);
+ String sFind = (isEmpty ? "" : SV.sValue(args[0]));
String flags = (args.length > 1 && args[1].tok != T.on
&& args[1].tok != T.off ? SV.sValue(args[1]) : "");
boolean isSequence = !isList && sFind.equalsIgnoreCase("SEQUENCE");
@@ -1082,17 +1086,22 @@
(BS) x1.value, false,
(isMF ? null : vwr.ms.getCellWeights((BS) x1.value)), isON));
if (isSequence)
- return mp.addXStr(vwr.getSmilesOpt((BS) x1.value, -1, -1,
- JC.SMILES_BIO
- | (isAll ? JC.SMILES_BIO_ALLOW_UNMACHED_RINGS |
JC.SMILES_BIO_CROSSLINK : 0)));
+ return mp.addXStr(vwr.getSmilesOpt((BS) x1.value, -1, -1,
+ JC.SMILES_BIO
+ | (isAll ? JC.SMILES_BIO_ALLOW_UNMACHED_RINGS
+ | JC.SMILES_BIO_CROSSLINK : 0)));
if (isSmiles || isSearch)
sFind = flags;
BS bsMatch3D = bs2;
if (asBonds) {
// this will return a single match
- int[][] map = vwr.getSmilesMatcher().getCorrelationMaps(sFind,
- vwr.ms.at, vwr.ms.ac, (BS) x1.value,
- (isSmiles ? JC.SMILES_TYPE_SMILES : JC.SMILES_TYPE_SMARTS) |
JC.SMILES_RETURN_FIRST);
+ int[][] map = vwr.getSmilesMatcher().getCorrelationMaps(
+ sFind,
+ vwr.ms.at,
+ vwr.ms.ac,
+ (BS) x1.value,
+ (isSmiles ? JC.SMILES_TYPE_SMILES : JC.SMILES_TYPE_SMARTS)
+ | JC.SMILES_RETURN_FIRST);
ret = (map.length > 0 ? vwr.ms.getDihedralMap(map[0]) : new
int[0]);
} else {
ret = e.getSmilesExt().getSmilesMatches(sFind, null, (BS) x1.value,
@@ -1114,27 +1123,46 @@
if (isList || isPattern) {
JmolPatternMatcher pm = getPatternMatcher();
Pattern pattern = null;
- try {
- pattern = (sFind.length() == 0 ? null : pm.compile(sFind,
isCaseInsensitive));
- } catch (Exception ex) {
- e.evalError(ex.toString(), null);
+ String[] list = null;
+ Lst<SV> svlist = (isList ? x1.getList() : null);
+ if (sFind.length() > 0) {
+ try {
+ pattern = (sFind.length() == 0 ? null : pm.compile(sFind,
+ isCaseInsensitive));
+ list = SV.strListValue(x1);
+ } catch (Exception ex) {
+ e.evalError(ex.toString(), null);
+ }
}
- String[] list = SV.strListValue(x1);
- Lst<SV> svlist = (isList ? x1.getList() : null);
+ int nlist = (list == null ? svlist.size() : list.length);
if (Logger.debugging)
Logger.debug("finding " + sFind);
BS bs = new BS();
int n = 0;
Matcher matcher = null;
Lst<String> v = (asMatch ? new Lst<String>() : null);
- for (int i = 0; i < list.length; i++) {
- String what = list[i];
+ String what = "";
+ for (int i = 0; i < nlist; i++) {
boolean isMatch;
if (pattern == null) {
- isMatch = (what.length() != 0);
+ SV o = svlist.get(i);
+ switch (o.tok) {
+ case T.hash:
+ isMatch = (o.getMap().isEmpty() != isEmpty);
+ break;
+ case T.varray:
+ isMatch = ((o.getList().size() == 0) != isEmpty);
+ break;
+ case T.string:
+ isMatch = ((o.asString().length() == 0) != isEmpty);
+ break;
+ default:
+ isMatch = true;
+ }
} else {
- matcher = pattern.matcher(what);
- isMatch = matcher.find();
+ what = list[i];
+ matcher = pattern.matcher(what);
+ isMatch = matcher.find();
}
if (asMatch && isMatch || !asMatch && isMatch == !isReverse) {
n++;
@@ -1150,9 +1178,9 @@
.addXStr(n == 0 ? "" : matcher.group()) : mp.addXInt(n == 0 ? 0
: matcher.start() + 1));
}
- // removed in 14.2/3.14 -- not documented and not expected if (n == 1)
-// return mp.addXStr(asMatch ? (String) v.get(0) : list[ipt]);
-
+ // removed in 14.2/3.14 -- not documented and not expected if (n ==
1)
+ // return mp.addXStr(asMatch ? (String) v.get(0) : list[ipt]);
+
if (asMatch) {
String[] listNew = new String[n];
if (n > 0)
@@ -1165,8 +1193,8 @@
}
Lst<SV> l = new Lst<SV>();
for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1))
- l.addLast(svlist.get(i));
- return mp.addXList(l);
+ l.addLast(svlist.get(i));
+ return mp.addXList(l);
}
if (isSequence) {
return mp.addXStr(vwr.getJBR().toStdAmino3(SV.sValue(x1)));
Modified: trunk/Jmol/src/org/jmol/viewer/JC.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/JC.java 2015-06-18 19:51:21 UTC (rev
20589)
+++ trunk/Jmol/src/org/jmol/viewer/JC.java 2015-06-19 08:29:26 UTC (rev
20590)
@@ -66,7 +66,7 @@
};
- public final static String copyright = "(C) 2012 Jmol Development";
+ public final static String copyright = "(C) 2015 Jmol Development";
public final static String version;
public final static String date;
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-06-18 19:51:21 UTC
(rev 20589)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-06-19 08:29:26 UTC
(rev 20590)
@@ -16,6 +16,13 @@
Jmol.___JmolVersion="14.3.15_2015.06.18"
+new feature: cleaning empty array values using .find()
+ - arrays of hash info:
+
+ array = array.find()
+
+bug fix: msCIF reader can hang if occupancy is not fractional
+bug fix: JSmol applet not returning full set of parameters in animFrameCallback
bug fix: load FILL command can fail if base unit cell is not part of the
needed set for the specified volume
JmolVersion="14.3.15_2015.06.18"
@@ -56,15 +63,6 @@
print b.format(["energy", "pointGroup"]).sort(1).reverse.format("%5.3f
%5s")
-new feature: cleaning empty array values using .find()
- - arrays of hash info:
-
- array = array.find(":")
-
- - arrays of numbers:
-
- array = array.find("")
-
new feature: polyhedra highlight with select ON or set selectionHalos ON
Modified: trunk/Jmol/src/org/jmol/viewer/ShapeManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/ShapeManager.java 2015-06-18 19:51:21 UTC
(rev 20589)
+++ trunk/Jmol/src/org/jmol/viewer/ShapeManager.java 2015-06-19 08:29:26 UTC
(rev 20590)
@@ -439,7 +439,7 @@
ms.getAtomsInFrame(bs);
Vibration[] vibrationVectors = ms.vibrations;
boolean vibs = (vibrationVectors != null && tm.vibrationOn);
- boolean checkOccupancy = (ms.bsModulated != null);
+ boolean checkOccupancy = (ms.bsModulated != null && ms.occupancies !=
null);
Atom[] atoms = ms.at;
int occ;
boolean haveMods = false;
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-06-18 19:51:21 UTC (rev
20589)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-06-19 08:29:26 UTC (rev
20590)
@@ -488,10 +488,14 @@
display = info.get("display");
isSingleThreaded = apiPlatform.isSingleThreaded();
noGraphicsAllowed = checkOption2("noGraphics", "-n");
+ System.out.println("nographics " + noGraphicsAllowed);
+ headless = apiPlatform.isHeadless();
haveDisplay = (isWebGL || display != null && !noGraphicsAllowed
&& !headless && !dataOnly);
noGraphicsAllowed &= (display == null);
- headless = (noGraphicsAllowed || apiPlatform.isHeadless());
+ System.out.println("nographics " + noGraphicsAllowed);
+ headless |= noGraphicsAllowed;
+ System.out.println("headless " + headless + commandOptions);
if (haveDisplay) {
mustRender = true;
multiTouch = checkOption2("multiTouch", "-multitouch");
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