Revision: 20830
http://sourceforge.net/p/jmol/code/20830
Author: hansonr
Date: 2015-10-17 23:11:03 +0000 (Sat, 17 Oct 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.5.0_2015.10.17"
bug fix: if (...) \n { .... not working
bug fix: CIF reader will read empty second model for IUCr files with terminal
data_global block
bug fix: polyhedra bonds unitcell can cause error in HTML5
bug fix: nucleic backbone should include O atoms on P and C
bug fix: nucleic spine should not include C2'
bug fix: pmesh/isosurface RESOLUTION 0.0001 with plane can cause loss of some
or all of the plane
-- resolution 0.0001 creates just a minimum of triangles to construct
the plane.
bug fix: set testflag4;isosurface ... ; does not generate normals
bug fix: (Application) set refreshing false shows Jmol console in model frame
(Java bug??)
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java
trunk/Jmol/src/org/jmol/jvxl/readers/VolumeDataReader.java
trunk/Jmol/src/org/jmol/modelsetbio/Resolver.java
trunk/Jmol/src/org/jmol/rendersurface/IsosurfaceRenderer.java
trunk/Jmol/src/org/jmol/script/ScriptCompiler.java
trunk/Jmol/src/org/jmol/shapespecial/Polyhedra.java
trunk/Jmol/src/org/jmol/viewer/JC.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java 2015-10-15
00:01:37 UTC (rev 20829)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java 2015-10-17
23:11:03 UTC (rev 20830)
@@ -356,7 +356,10 @@
@Override
protected void finalizeSubclassReader() throws Exception {
- if (!isMMCIF || !finalizeSubclass())
+ // added check for final data_global
+ if (asc.iSet > 0 && asc.getAtomSetAtomCount(asc.iSet) == 0)
+ asc.atomSetCount--;
+ else if (!isMMCIF || !finalizeSubclass())
applySymmetryAndSetTrajectory();
int n = asc.atomSetCount;
if (n > 1)
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/VolumeDataReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/VolumeDataReader.java 2015-10-15
00:01:37 UTC (rev 20829)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/VolumeDataReader.java 2015-10-17
23:11:03 UTC (rev 20830)
@@ -203,6 +203,8 @@
nGrid = gridMax;
}
}
+ if (nGrid == 1)
+ nGrid = 2;
ptsPerAngstrom = (nGrid - 1) / range;
if (ptsPerAngstrom < minPointsPerAngstrom) {
ptsPerAngstrom = minPointsPerAngstrom;
Modified: trunk/Jmol/src/org/jmol/modelsetbio/Resolver.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/Resolver.java 2015-10-15 00:01:37 UTC
(rev 20829)
+++ trunk/Jmol/src/org/jmol/modelsetbio/Resolver.java 2015-10-17 23:11:03 UTC
(rev 20830)
@@ -1419,7 +1419,7 @@
"C5'", // 7 - sugar 5' carbon SPINE
"C4'", // 8 - sugar ring 4' carbon SPINE
"C3'", // 9 - sugar ring 3' carbon SPINE
- "O3'", // 10 - sugar 3' oxygen
+ "O3'", // 10 - sugar 3' oxygen SPINE
"C2'", // 11 - sugar ring 2' carbon
"C1'", // 12 - sugar ring 1' carbon
// Phosphorus is not required for a nucleic group because
@@ -1541,8 +1541,8 @@
"H2''",
"HO2'",
- "O3P", // - third equivalent oxygen on phosphorus of phosphate
- "OP3", // - third equivalent oxygen on phosphorus of phosphate -- new
designation
+ "O3P", // 99 - third equivalent oxygen on phosphorus of phosphate
+ "OP3", //100 - third equivalent oxygen on phosphorus of phosphate --
new designation
};
Modified: trunk/Jmol/src/org/jmol/rendersurface/IsosurfaceRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/rendersurface/IsosurfaceRenderer.java
2015-10-15 00:01:37 UTC (rev 20829)
+++ trunk/Jmol/src/org/jmol/rendersurface/IsosurfaceRenderer.java
2015-10-17 23:11:03 UTC (rev 20830)
@@ -529,17 +529,15 @@
for (int i = vertexCount; --i >= 0;) {
if (vertexValues != null && Float.isNaN(vertexValues[i]))
continue;
- if (i > 100)
- continue;
pt1f.setT(vertices[i]);
short n = mesh.normixes[i];
// -n is an intensity2sided and does not correspond to a true normal
// index
if (n >= 0) {
- pt1f.scaleAdd2(3, vertexVectors[n], pt1f);
- tm.transformPtScrT3(pt1f, pt1f);
+ pt2f.scaleAdd2(0.3f, vertexVectors[n], pt1f);
+ tm.transformPtScrT3(pt2f, pt2f);
pt1f.set(screens[i].x, screens[i].y, screens[i].z);
- g3d.drawLineAB(pt1f, pt1f);
+ g3d.drawLineAB(pt1f, pt2f);
}
}
}
Modified: trunk/Jmol/src/org/jmol/script/ScriptCompiler.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptCompiler.java 2015-10-15 00:01:37 UTC
(rev 20829)
+++ trunk/Jmol/src/org/jmol/script/ScriptCompiler.java 2015-10-17 23:11:03 UTC
(rev 20830)
@@ -721,11 +721,10 @@
if (lastFlowCommand == null) {
parenCount = setBraceCount = braceCount = 0;
ltoken.remove(0);
- iBrace++;
T t = ContextToken.newContext(true);
addTokenToPrefix(setCommand(t));
pushContext(t);
- vBraces.addLast(tokenCommand);
+ addBrace(tokenCommand);
} else {
parenCount = setBraceCount = 0;
setCommand(lastFlowCommand);
@@ -813,7 +812,8 @@
}
if (endOfLine) {
- if (!haveENDIF && flowContext != null &&
flowContext.checkForceEndIf(-1)) {
+ if (!haveENDIF && flowContext != null
+ && flowContext.checkForceEndIf(-1)) {
boolean isOneLine = (flowContext.addLine == 0); // if (....) xxxxx;
if (isComment) {
if (!isOneLine) {
@@ -855,6 +855,14 @@
return OK;
}
+ /**
+ * @param t could be { or } or a command such as FOR or WHILE
+ */
+ private void addBrace(T t) {
+ vBraces.addLast(t);
+ iBrace++;
+ }
+
private void pushContext(T t) {
pushCount++;
vPush.addLast(t);
@@ -869,16 +877,16 @@
*
* more than two tokens:
*
- * not a script function xxxx.spt(3,4,5)
+ * xxxx.spt(3,4,5)
*
* @return true if found
*/
private boolean wasImpliedScript() {
- if (nTokens >= 2 && (tokCommand == T.script || tokCommand == T.macro) &&
checkImpliedScriptCmd) {
+ if (checkImpliedScriptCmd && nTokens >= 2 && (tokCommand == T.script ||
tokCommand == T.macro)) {
String s = (nTokens == 2 ? lastToken.value.toString().toUpperCase()
: null);
- if (nTokens > 2 ? !(tokAt(2) == T.leftparen && ltoken.get(1).value
- .toString().endsWith(".spt")) : s.endsWith(".SORT")
+ if (nTokens > 2 ? !(tokAt(2) == T.leftparen &&
ltoken.get(1).value.toString().endsWith(".spt"))
+ : s.endsWith(".SORT")
|| s.endsWith(".REVERSE") || s.endsWith(".POP")
|| s.indexOf(".SORT(") >= 0 || s.indexOf(".REVERSE(") >= 0
|| s.indexOf(".POP(") >= 0 || s.indexOf(".PUSH(") >= 0
@@ -983,7 +991,7 @@
ltoken.add(0, setCommand(token));
}
- private void getPrefixToken() {
+ private int getPrefixToken() {
ident = script.substring(ichToken, ichToken + cchToken);
identLC = ident.toLowerCase();
boolean isUserVar = lastToken.tok != T.per && !isDotDot &&
isContextVariable(identLC);
@@ -1033,7 +1041,7 @@
// myName is just in case this is being used as a key to a hash
theToken = SV.newSV((identLC.indexOf("property_") == 0 ? T.property :
T.identifier), Integer.MAX_VALUE, ident).setName(myName);
}
- theTok = theToken.tok;
+ return theTok = theToken.tok;
}
/**
@@ -1381,14 +1389,14 @@
private int parseKnownToken() {
- getPrefixToken();
+ int tok = getPrefixToken();
// specific token-based issues depend upon where we are in the command
T token;
if (isDotDot) {
- if (theTok == T.leftsquare) {
+ if (tok == T.leftsquare) {
bracketCount++;
} else {
addTokenToPrefix(T.o(T.string, ident));
@@ -1398,16 +1406,16 @@
return CONTINUE;
}
if (tokLastMath != 0)
- tokLastMath = theTok;
+ tokLastMath = tok;
if (flowContext != null && flowContext.token.tok == T.switchcmd
- && flowContext.var != null && theTok != T.casecmd
- && theTok != T.defaultcmd && lastToken.tok != T.switchcmd)
+ && flowContext.var != null && tok != T.casecmd
+ && tok != T.defaultcmd && lastToken.tok != T.switchcmd)
return ERROR(ERROR_badContext, ident);
- if (lastToken.tok == T.define && theTok != T.leftbrace && nTokens != 1) {
- addTokenToPrefix(theTok == T.define ? lastToken : T.o(T.string, ident));
+ if (lastToken.tok == T.define && tok != T.leftbrace && nTokens != 1) {
+ addTokenToPrefix(tok == T.define ? lastToken : T.o(T.string, ident));
return CONTINUE;
}
- switch (theTok) {
+ switch (tok) {
case T.identifier:
if (nTokens == 0 && !checkImpliedScriptCmd) {
if (ident.charAt(0) == '\'') {
@@ -1500,13 +1508,13 @@
checkNewSetCommand();
if (isNewSet && parenCount == 0 && bracketCount == 0
&& ichToken <= setEqualPt) {
- tokenizePlusPlus(theTok, false);
+ tokenizePlusPlus(tok, false);
return CONTINUE;
} else if (nSemiSkip == forPoint3 && nTokens == ptSemi + 2) {
token = lastToken;
addTokenToPrefix(T.tokenEquals);
addTokenToPrefix(token);
- addTokenToPrefix(theTok == T.minusMinus ? T.tokenMinus : T.tokenPlus);
+ addTokenToPrefix(tok == T.minusMinus ? T.tokenMinus : T.tokenPlus);
addTokenToPrefix(T.i(1));
return CONTINUE;
}
@@ -1562,10 +1570,10 @@
if (!wasImpliedScript()) {
// because if we need to repeat due to a.xxx = ....
// then we don't want to force the end yet
+ // for (a in {selected}) { wrap(a, vnm, f) }
+
braceCount = parenCount = nSemiSkip = 0;
- if (theToken.tok != T.casecmd && theToken.tok != T.defaultcmd)
- vBraces.addLast(theToken);
- iBrace++;
+ addBrace(theToken);
isEndOfCommand = true;
ichEnd = ichToken;
}
@@ -1677,13 +1685,13 @@
if (lltoken.get(iCommand - 1)[0].tok == T.end
&& lastFlowContext != null && lastFlowContext.forceEndIf
&& lastFlowContext.addLine > 0
- && isFlowIfContextOK(lastFlowContext, tokCommand)) {
+ && isFlowIfContextOK(lastFlowContext)) {
flowContext = lastFlowContext;
flowContext.forceEndIf = true;
lltoken.remove(--iCommand);
} else if (flowContext != null && flowContext.addLine > 0) {
while (flowContext != null
- && !isFlowIfContextOK(flowContext, tokCommand)) {
+ && !isFlowIfContextOK(flowContext)) {
if (flowContext.checkForceEndIf(0)) {
forceFlowEnd(flowContext.token);
processTokenList(iLine, isFull);
@@ -1736,8 +1744,7 @@
}
if (theTok == T.rightbrace) {
// if }, just push onto vBrace, but NOT onto ltoken
- vBraces.addLast(tokenCommand);
- iBrace++;
+ addBrace(tokenCommand);
tokCommand = T.nada;
return CONTINUE;
}
@@ -2075,19 +2082,36 @@
private boolean checkFlowStartBrace(boolean atEnd) {
int tok = tokCommand;
- if ((!T.tokAttr(tok, T.flowCommand) || tok == T.breakcmd || tok ==
T.continuecmd))
+ switch (tok) {
+ default:
+ if (T.tokAttr(tok, T.flowCommand)) {
+ if (atEnd) {
+ switch (tok) {
+ case T.casecmd:
+ case T.defaultcmd:
+ break;
+ default:
+ flowContext.addLine = 0;
+ addBrace(tokenCommand);
+ lastFlowCommand = null;
+ break;
+ }
+ parenCount = braceCount = 0;
+ }
+ return true;
+ }
+ //$FALL-THROUGH$
+ case T.breakcmd:
+ case T.continuecmd:
return false;
- if (atEnd) {
- if (tokenCommand.tok != T.casecmd && tokenCommand.tok != T.defaultcmd) {
- iBrace++;
- vBraces.addLast(tokenCommand);
- lastFlowCommand = null;
- }
- parenCount = braceCount = 0;
}
- return true;
}
+ /**
+ * process a pending explicit right brace }
+ *
+ * @return continuation status
+ */
private int checkFlowEndBrace() {
if (iBrace <= 0 || vBraces.get(iBrace - 1).tok != T.rightbrace)
@@ -2096,6 +2120,10 @@
vBraces.remove(--iBrace);
T token = vBraces.remove(--iBrace);
if (theTok == T.leftbrace) {
+ //
+ // }
+ // {
+ //
braceCount--;
parenCount--;
}
@@ -2163,7 +2191,7 @@
int pt = lltoken.size();
switch (tokCommand) {
case T.endifcmd:
- if (!isFlowIfContextOK(flowContext, tokCommand)){
+ if (!isFlowIfContextOK(flowContext)){
if (!haveENDIF)
return RESTART;
errorStr(ERROR_badContext, ident);
@@ -2206,10 +2234,10 @@
break;
case T.elseif:
case T.elsecmd:
- if (flowContext != null && !isFlowIfContextOK(flowContext, tokCommand)) {
+ if (flowContext != null && !isFlowIfContextOK(flowContext)) {
flowContext = flowContext.parent;
}
- if (!isFlowIfContextOK(flowContext, tokCommand)) {
+ if (!isFlowIfContextOK(flowContext)) {
if (!haveENDIF)
return RESTART;
errorStr(ERROR_badContext, ident);
@@ -2269,23 +2297,42 @@
return OK;
}
+ /**
+ * generate a new end token with pointer to the start or to default as the
intValue
+ * and set it as the command token
+ *
+ * @param tokCommand end or endif
+ * @param ident "end" or "endif"
+ */
private void setFlowEnd(int tokCommand, String ident) {
setCommand(T.tv(tokCommand,
(flowContext.ptDefault > 0 ? flowContext.ptDefault
: -flowContext.pt0), ident)); //copy
}
-
- private boolean isFlowIfContextOK(ScriptFlowContext f, int tokCommand) {
+ /**
+ * check for proper sequence: if...[any number of elseif]...[zero or one
else]...[endif]
+ * @param f
+ * @return true if OK
+ */
+ private boolean isFlowIfContextOK(ScriptFlowContext f) {
switch (f == null ? T.nada : f.token.tok) {
- case T.elsecmd:
- return tokCommand != T.elsecmd;
case T.ifcmd:
case T.elseif:
return true;
+ case T.elsecmd:
+ return tokCommand != T.elsecmd;
}
return false;
}
+ /**
+ *
+ * @param tok the XXX in END XXX
+ * @param ident
+ * @param pt1
+ * @param isExplicitEnd actual END IF or END FOR, etc.
+ * @return true if no error
+ */
private boolean checkFlowEnd(int tok, String ident, int pt1,
boolean isExplicitEnd) {
if (isExplicitEnd) {
@@ -2296,8 +2343,7 @@
switch (flowContext.token.tok) {
case T.function:
case T.parallel:
- case T.trycmd:
-
+ case T.trycmd:
break;
default:
setFlowEnd(T.end, "end");
Modified: trunk/Jmol/src/org/jmol/shapespecial/Polyhedra.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapespecial/Polyhedra.java 2015-10-15 00:01:37 UTC
(rev 20829)
+++ trunk/Jmol/src/org/jmol/shapespecial/Polyhedra.java 2015-10-17 23:11:03 UTC
(rev 20830)
@@ -871,7 +871,14 @@
p10[3] = -((-p10[3]) ^ (1 << i0));
p1[3] = -((-p1[3]) ^ (1 << i));
b = (int[])((Object[]) o)[2];
- faceList.removeObj(b);
+ for (int j = faceList.size(); --j >= 0;) {
+ int[] f = faceList.get(j);
+ if (f[0] == b[0] && f[1] == b[1]) {
+ faceList.remove(j);
+ break;
+ }
+ }
+ // not supported for JavaScript faceList.removeObj(b);
}
return true;
}
Modified: trunk/Jmol/src/org/jmol/viewer/JC.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/JC.java 2015-10-15 00:01:37 UTC (rev
20829)
+++ trunk/Jmol/src/org/jmol/viewer/JC.java 2015-10-17 23:11:03 UTC (rev
20830)
@@ -621,9 +621,9 @@
// structure related
//
"@alpha _a=2", // rasmol doc says "approximately *.CA" - whatever?
- "@_bb protein&_a>=1&_a<6 | nucleic& _a>=6&_a<14", // no H atoms
+ "@_bb protein&_a>=1&_a<6 |
nucleic&(_a>=6&_a<14|_a>=73&&_a<=79||_a==99||_a=100)", // no H atoms
"@backbone _bb | _H && connected(single, _bb)",
- "@spine protein&_a>=1&_a<4|nucleic&_a>=6&_a<14&_a!=12",
+ "@spine protein&_a>=1&_a<4|nucleic&(_a>=6&_a<11|_a=13)",
"@sidechain (protein,nucleic) & !backbone",
"@base nucleic & !backbone",
"@dynamic_flatring search('[a]')"
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-10-15 00:01:37 UTC
(rev 20829)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-10-17 23:11:03 UTC
(rev 20830)
@@ -62,8 +62,24 @@
TODO: consider if models with no atoms will cause issues in relation to
model.firstAtomIndex
-Jmol.___JmolVersion="14.5.0_2015.10.14"
+Jmol.___JmolVersion="14.5.0_2015.10.17"
+bug fix: if (...) \n { .... not working
+bug fix: CIF reader will read empty second model for IUCr files with terminal
data_global block
+bug fix: polyhedra bonds unitcell can cause error in HTML5
+bug fix: nucleic backbone should include O atoms on P and C
+bug fix: nucleic spine should not include C2'
+bug fix: pmesh/isosurface RESOLUTION 0.0001 with plane can cause loss of some
or all of the plane
+ -- resolution 0.0001 creates just a minimum of triangles to construct
the plane.
+bug fix: set testflag4;isosurface ... ; does not generate normals
+bug fix: (Application) set refreshing false shows Jmol console in model frame
(Java bug??)
+
+JmolVersion="14.5.0_2015.10.14"
+
+NOTE: GoDaddy's inadvertent forcing of revocation of the secure certificate
for Jmol
+ has disabled ALL applets created since Oct 15, 2014. This is a mandatory
upgrade.
+
+
bug fix: SHOW PROPERTY IDENTIFY crashes Jmol.
JmolVersion="14.5.0_2015.10.13"
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-10-15 00:01:37 UTC (rev
20829)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-10-17 23:11:03 UTC (rev
20830)
@@ -3558,7 +3558,7 @@
private boolean updateWindow(int width, int height) {
//System.out.println("Viewer updateWindow " + width + " " + height);
if (!refreshing || creatingImage)
- return false;
+ return (refreshing ? false : !isJS);
if (isTainted || tm.slabEnabled)
setModelVisibility();
isTainted = false;
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