Revision: 20672
http://sourceforge.net/p/jmol/code/20672
Author: hansonr
Date: 2015-08-02 03:03:52 +0000 (Sun, 02 Aug 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.2.15_2015.08.01"
bug fix: SMARTS matching broken for [r5] ring designation
bug fix: reference to functions as commands requires lower case:
-- for example:
function F(a){ print a }
F("test") // OK
f("test") // OK
f "test" // OK
F "test" // fails
Revision Links:
--------------
http://sourceforge.net/p/jmol/code/5
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/modelset/BondCollection.java
trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java
trunk/Jmol/src/org/jmol/script/ScriptTokenParser.java
trunk/Jmol/src/org/jmol/script/T.java
trunk/Jmol/src/org/jmol/smiles/SmilesAtom.java
trunk/Jmol/src/org/jmol/smiles/SmilesParser.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/modelset/BondCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/BondCollection.java 2015-07-31
13:04:18 UTC (rev 20671)
+++ trunk/Jmol/src/org/jmol/modelset/BondCollection.java 2015-08-02
03:03:52 UTC (rev 20672)
@@ -128,8 +128,7 @@
Bond bond = bo[iBond];
boolean isSelected1 = bsAtoms.get(bond.atom1.i);
boolean isSelected2 = bsAtoms.get(bond.atom2.i);
- if ((!bondSelectionModeOr & isSelected1 & isSelected2)
- || (bondSelectionModeOr & (isSelected1 | isSelected2)))
+ if (bondSelectionModeOr ? isSelected1 || isSelected2 : isSelected1 &&
isSelected2)
bs.set(iBond);
}
return bs;
Modified: trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java 2015-07-31
13:04:18 UTC (rev 20671)
+++ trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java 2015-08-02
03:03:52 UTC (rev 20672)
@@ -1775,17 +1775,16 @@
}
break;
case T.bitset:
- if (op.intValue == T.bonds && x2.value instanceof BondSet)
+ boolean isAtoms = (op.intValue != T.bonds);
+ if (!isAtoms && x2.value instanceof BondSet)
return addX(x2);
BS bs = SV.bsSelectVar(x2);
- if (bs.cardinality() == 1 && (op.intValue & T.minmaxmask) == 0)
+ if (isAtoms && bs.cardinality() == 1 && (op.intValue & T.minmaxmask) ==
0)
op.intValue |= T.min;
Object val = eval.getBitsetProperty(bs, op.intValue, null, null,
x2.value, op.value, false, x2.index, true);
- if (op.intValue != T.bonds)
- return addXObj(val);
- return addX(SV.newV(T.bitset, BondSet.newBS(
- (BS) val, vwr.ms.getAtomIndices(bs))));
+ return (isAtoms ? addXObj(val) : addX(SV.newV(T.bitset, BondSet.newBS(
+ (BS) val, vwr.ms.getAtomIndices(bs)))));
}
return false;
}
Modified: trunk/Jmol/src/org/jmol/script/ScriptTokenParser.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptTokenParser.java 2015-07-31
13:04:18 UTC (rev 20671)
+++ trunk/Jmol/src/org/jmol/script/ScriptTokenParser.java 2015-08-02
03:03:52 UTC (rev 20672)
@@ -264,6 +264,7 @@
protected Map<String, Boolean> htUserFunctions;
protected boolean isUserFunction(String name) {
+ name = name.toLowerCase();
return (!isStateScript && (vwr.isFunction(name) ||
htUserFunctions.containsKey(name)));
}
Modified: trunk/Jmol/src/org/jmol/script/T.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/T.java 2015-07-31 13:04:18 UTC (rev
20671)
+++ trunk/Jmol/src/org/jmol/script/T.java 2015-08-02 03:03:52 UTC (rev
20672)
@@ -1149,7 +1149,7 @@
public final static int basepair = misc | 40;
public final static int binary = misc | 42;
public final static int blockdata = misc | 44;
- public final static int bondset = misc | 46;
+ public final static int bondset = misc | 46; // never used
public final static int bottom = misc | 47;
public final static int brillouin = misc | 48;
public final static int cancel = misc | 50;
Modified: trunk/Jmol/src/org/jmol/smiles/SmilesAtom.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmilesAtom.java 2015-07-31 13:04:18 UTC
(rev 20671)
+++ trunk/Jmol/src/org/jmol/smiles/SmilesAtom.java 2015-08-02 03:03:52 UTC
(rev 20672)
@@ -202,6 +202,7 @@
int ringSize = Integer.MIN_VALUE;
int ringConnectivity = -1;
private Node matchingNode;
+ public boolean hasSubpattern;
public SmilesAtom setAll(int iComponent, int ptAtom, int flags, int
atomicNumber,
int charge) {
Modified: trunk/Jmol/src/org/jmol/smiles/SmilesParser.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmilesParser.java 2015-07-31 13:04:18 UTC
(rev 20671)
+++ trunk/Jmol/src/org/jmol/smiles/SmilesParser.java 2015-08-02 03:03:52 UTC
(rev 20672)
@@ -339,7 +339,7 @@
for (int i = molecule.ac; --i >= 0;) {
SmilesAtom atom = molecule.patternAtoms[i];
if (molecule.isTopology &&
- (atom.elementNumber != -2 || atom.nAtomsOr > 0 || atom.nPrimitives >
0))
+ (atom.hasSubpattern || atom.elementNumber != -2 || atom.nAtomsOr > 0
|| atom.nPrimitives > 0))
molecule.isTopology = false;
atom.setBondArray();
if (!isSmarts && atom.bioType == '\0' &&
!atom.setHydrogenCount(molecule))
@@ -550,6 +550,7 @@
subPattern += ".0";
currentAtom = parseAtom(molecule, null, subPattern, currentAtom,
bond, ch == '[', false, isBranchAtom);
+ currentAtom.hasSubpattern = true;
if (bond.order != SmilesBond.TYPE_UNKNOWN
&& bond.order != SmilesBond.TYPE_NONE)
bond.set2a(null, currentAtom);
@@ -766,7 +767,6 @@
SmilesAtom newAtom = (atomSet == null ? molecule.addAtom()
: isPrimitive ? atomSet.addPrimitive() : atomSet.addAtomOr());
-
if (braceCount > 0)
newAtom.selected = true;
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-07-31 13:04:18 UTC
(rev 20671)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-08-02 03:03:52 UTC
(rev 20672)
@@ -51,8 +51,21 @@
TODO: curved arrows overextend and with width settings do not truncate shaft
properly
-Jmol.___JmolVersion="14.2.15_2015.07.30b"
+Jmol.___JmolVersion="14.3.15_2015.08.01"
+bug fix: SMARTS matching broken for [r5] ring designation
+
+bug fix: reference to functions as commands requires lower case:
+ -- for example:
+ function F(a){ print a }
+ F("test") // OK
+ f("test") // OK
+ f "test" // OK
+ F "test" // fails
+
+
+JmolVersion="14.3.15_2015.07.30b"
+
bug fix: JavaScript deletion of array elements fails for int[] arrays.
JmolVersion="14.3.15_2015.07.30"
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