Revision: 20854
http://sourceforge.net/p/jmol/code/20854
Author: hansonr
Date: 2015-11-03 12:17:44 +0000 (Tue, 03 Nov 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.4.0_2015.11.03"
bug fix: FOR without {} but with ";" after sole statement
followed immediately by second FOR improperly loops
for (var i from [1,5])
print i;
for (var i from [1,5])
print i
bug fix: OXT missing from BACKBONE selection
bug fix: (JSmol) CIF parser fails to read CIF files containing only a single
(non-loop) _struct_ref_seq_dif.align_id
bug fix: slabbing should reset area and volume of isosurface
bug fix: meshSlicer may fail to add edge to sliced pmesh
bug fix: polyhedron volume will be incorrect if there is a
face triangle that has no edges visible (requires a six or more sided
face)
bug fix: nested if...{...if... } else {...} gives compiler syntax error:
if (i=1) {
print "i=1"
if (j=1)
print "j != 1"
} else { // } closes if (j=1) instead of if (i=1) {
print "i != 1"
}
bug fix: empty format crashes Jmol -- print "testing".format("")
bug fix: after CALCULATE HYDROGENS TRUE and then deleting hydrogens, hydrogens
are not added to aromatic rings in PDB models
bug fix: reading saved state after adding hydrogen atoms results in infinite
loop
Modified Paths:
--------------
branches/v14_4/Jmol/src/org/jmol/jvxl/readers/SurfaceGenerator.java
branches/v14_4/Jmol/src/org/jmol/script/ScriptCompiler.java
branches/v14_4/Jmol/src/org/jmol/script/ScriptEval.java
branches/v14_4/Jmol/src/org/jmol/shapesurface/Isosurface.java
branches/v14_4/Jmol/src/org/jmol/util/MeshSlicer.java
branches/v14_4/Jmol/src/org/jmol/viewer/JC.java
branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: branches/v14_4/Jmol/src/org/jmol/jvxl/readers/SurfaceGenerator.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/jvxl/readers/SurfaceGenerator.java
2015-11-01 18:15:50 UTC (rev 20853)
+++ branches/v14_4/Jmol/src/org/jmol/jvxl/readers/SurfaceGenerator.java
2015-11-03 12:17:44 UTC (rev 20854)
@@ -314,9 +314,10 @@
return true;
} else if (AU.isAS(value)) {
params.title = (String[]) value;
- for (int i = 0; i < params.title.length; i++)
- if (params.title[i].length() > 0)
- Logger.info(params.title[i]);
+ if (Logger.debugging)
+ for (int i = 0; i < params.title.length; i++)
+ if (params.title[i].length() > 0)
+ Logger.info(params.title[i]);
}
return true;
}
Modified: branches/v14_4/Jmol/src/org/jmol/script/ScriptCompiler.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/script/ScriptCompiler.java 2015-11-01
18:15:50 UTC (rev 20853)
+++ branches/v14_4/Jmol/src/org/jmol/script/ScriptCompiler.java 2015-11-03
12:17:44 UTC (rev 20854)
@@ -732,13 +732,12 @@
ltoken.remove(0);
lastFlowCommand = null;
forceFlowContext = flowContext;
-// lastFlowImplicitEnd = flowContext.nextFlowImplicitEnd;
+ // lastFlowImplicitEnd = flowContext.nextFlowImplicitEnd;
}
}
if (bracketCount > 0 || setBraceCount > 0 || parenCount > 0
|| braceCount == 1 && !checkFlowStartBrace(true)) {
- error(n == 1 ? ERROR_commandExpected
- : ERROR_endOfCommandUnexpected);
+ error(n == 1 ? ERROR_commandExpected : ERROR_endOfCommandUnexpected);
return ERROR;
}
if (needRightParen) {
@@ -811,16 +810,27 @@
setEqualPt = Integer.MAX_VALUE;
}
+ boolean isOneLine = (flowContext != null && flowContext.addLine == 0); //
if (....) xxxxx;
+ boolean isEndFlow = ((endOfLine || !isOneLine) && !haveENDIF &&
flowContext != null && flowContext.checkForceEndIf(-1));
if (endOfLine) {
- if (!haveENDIF && flowContext != null
- && flowContext.checkForceEndIf(-1)) {
- boolean isOneLine = (flowContext.addLine == 0); // if (....) xxxxx;
+ if (isEndFlow) {
if (isComment) {
if (!isOneLine) {
flowContext.addLine++;
flowContext.forceEndIf = true;
}
} else if (n > 0 && !haveENDIF || isOneLine) {
+ // looking for
+ // for (...)
+ // print ...
+ //
+ // but not
+ //
+ // for (...)
+ //
+ // print ...
+ //
+
forceFlowEnd(flowContext.token);
if (!isOneLine) {
forceFlowContext.forceEndIf = true;
@@ -829,13 +839,19 @@
isEndOfCommand = true;
cchToken = 0;
ichCurrentCommand = ichToken;
-// if (n > 0 || isOneLine)
- // lineCurrent--;
return CONTINUE;
}
isComment = false;
isShowCommand = false;
++lineCurrent;
+ } else if (isEndFlow) {
+ // looking at something like
+ //
+ // for (...)
+ // print ... ;
+ //
+ forceFlowEnd(flowContext.token);
+ forceFlowContext.forceEndIf = true;
}
if (ichToken >= cchScript) {
// check for end of all brace work
Modified: branches/v14_4/Jmol/src/org/jmol/script/ScriptEval.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/script/ScriptEval.java 2015-11-01
18:15:50 UTC (rev 20853)
+++ branches/v14_4/Jmol/src/org/jmol/script/ScriptEval.java 2015-11-03
12:17:44 UTC (rev 20854)
@@ -97,6 +97,7 @@
* extends ScriptError -- error handling
*
* scriptext.CmdExt -- optionally loaded, less-used commands
+ * scriptext.IsoExt -- optionally loaded, less-used commands
* scriptext.MathExt -- optionally loaded, less-used functions
* scriptext.SmilesExt -- optionally loaded methods for cmds and math
*
Modified: branches/v14_4/Jmol/src/org/jmol/shapesurface/Isosurface.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/shapesurface/Isosurface.java
2015-11-01 18:15:50 UTC (rev 20853)
+++ branches/v14_4/Jmol/src/org/jmol/shapesurface/Isosurface.java
2015-11-03 12:17:44 UTC (rev 20854)
@@ -764,6 +764,8 @@
}
protected void slabPolygons(Object[] slabInfo) {
+ thisMesh.calculatedVolume = null;
+ thisMesh.calculatedArea = null;
thisMesh.getMeshSlicer().slabPolygons(slabInfo, false);
thisMesh.reinitializeLightingAndColor(vwr);
}
Modified: branches/v14_4/Jmol/src/org/jmol/util/MeshSlicer.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/util/MeshSlicer.java 2015-11-01
18:15:50 UTC (rev 20853)
+++ branches/v14_4/Jmol/src/org/jmol/util/MeshSlicer.java 2015-11-03
12:17:44 UTC (rev 20854)
@@ -583,7 +583,7 @@
if (iD == i2 && iE == i3) {
// cap but don't toss if tossing 23
doClear = !toss23;
- return false;
+ return !doClear; // was FALSE, but we need to recreate the edge
}
if (iD == i1 || iE == i1) {
// other is i2 or i3 -- along an edge
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/JC.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/JC.java 2015-11-01 18:15:50 UTC
(rev 20853)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/JC.java 2015-11-03 12:17:44 UTC
(rev 20854)
@@ -621,7 +621,7 @@
// structure related
//
"@alpha _a=2", // rasmol doc says "approximately *.CA" - whatever?
- "@_bb protein&_a>=1&_a<6 |
nucleic&(_a>=6&_a<14|_a>=73&&_a<=79||_a==99||_a=100)", // no H atoms
+ "@_bb protein&(_a>=1&_a<6|_a=64) |
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<11|_a=13)",
"@sidechain (protein,nucleic) & !backbone",
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2015-11-01
18:15:50 UTC (rev 20853)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2015-11-03
12:17:44 UTC (rev 20854)
@@ -7,8 +7,19 @@
# see also http://chemapps.stolaf.edu/jmol/zip for daily updates
-Jmol.___JmolVersion="14.4.0_2015.10.30"
+Jmol.___JmolVersion="14.4.0_2015.11.03"
+bug fix: FOR without {} but with ";" after sole statement
+ followed immediately by second FOR improperly loops
+ for (var i from [1,5])
+ print i;
+ for (var i from [1,5])
+ print i
+bug fix: OXT missing from BACKBONE selection
+bug fix: (JSmol) CIF parser fails to read CIF files containing only a single
(non-loop) _struct_ref_seq_dif.align_id
+bug fix: slabbing should reset area and volume of isosurface
+bug fix: meshSlicer may fail to add edge to sliced pmesh
+
bug fix: polyhedron volume will be incorrect if there is a
face triangle that has no edges visible (requires a six or more sided
face)
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