Revision: 20250
http://sourceforge.net/p/jmol/code/20250
Author: hansonr
Date: 2015-01-28 00:19:08 +0000 (Wed, 28 Jan 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.2.12_2015.01.27"
bug fix: CGO LINE_LOOP not closing
bug fix: configuration 1 broken
bug fix: display configuration=1 broken (in Jmol 12.0, 2011)
JmolVersion="14.2.12_2015.01.25"
bug fix: image echos broken
bug fix: MOPAC reader loses two atoms in IRC calculation for MOPAC 2012
bug fix: _slabPlane and _depthPlane not set immediately when slab and depth are
set
Modified Paths:
--------------
branches/v14_2/Jmol/src/org/jmol/modelset/AtomCollection.java
branches/v14_2/Jmol/src/org/jmol/modelset/ModelLoader.java
branches/v14_2/Jmol/src/org/jmol/modelset/ModelSet.java
branches/v14_2/Jmol/src/org/jmol/script/ScriptEval.java
branches/v14_2/Jmol/src/org/jmol/script/ScriptExpr.java
branches/v14_2/Jmol/src/org/jmol/script/T.java
branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties
branches/v14_2/Jmol/src/org/jmol/viewer/TransformManager.java
branches/v14_2/Jmol/src/org/jmol/viewer/Viewer.java
Modified: branches/v14_2/Jmol/src/org/jmol/modelset/AtomCollection.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/modelset/AtomCollection.java
2015-01-27 23:56:55 UTC (rev 20249)
+++ branches/v14_2/Jmol/src/org/jmol/modelset/AtomCollection.java
2015-01-28 00:19:08 UTC (rev 20250)
@@ -572,6 +572,11 @@
taintAtom(i, TAINT_ATOMNO);
setAtomNumber(i, iValue);
break;
+ case T.bonded:
+ for (i = ac; --i >= 0;)
+ if (at[i].getCovalentBondCount() > 0)
+ bs.set(i);
+ break;
case T.seqid:
taintAtom(i, TAINT_SEQID);
setAtomSeqID(i, iValue);
Modified: branches/v14_2/Jmol/src/org/jmol/modelset/ModelLoader.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/modelset/ModelLoader.java 2015-01-27
23:56:55 UTC (rev 20249)
+++ branches/v14_2/Jmol/src/org/jmol/modelset/ModelLoader.java 2015-01-28
00:19:08 UTC (rev 20250)
@@ -1228,7 +1228,7 @@
groups[groupIndex] = group;
group.groupIndex = groupIndex;
- for (int i = lastAtomIndex; --i >= firstAtomIndex;)
+ for (int i = lastAtomIndex + 1; --i >= firstAtomIndex;)
ms.at[i].setGroup(group);
}
Modified: branches/v14_2/Jmol/src/org/jmol/modelset/ModelSet.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/modelset/ModelSet.java 2015-01-27
23:56:55 UTC (rev 20249)
+++ branches/v14_2/Jmol/src/org/jmol/modelset/ModelSet.java 2015-01-28
00:19:08 UTC (rev 20250)
@@ -4078,20 +4078,5 @@
return ret;
}
- public BS getAtomsFromAtomNumberInFrame(int atomNumber) {
- BS bs = new BS();
- BS bsModels = vwr.getVisibleFramesBitSet();
- for (int i = ac; --i >= 0;) {
- Atom atom = at[i];
- if (!bsModels.get(atom.mi)) {
- i = am[atom.mi].firstAtomIndex;
- continue;
- }
- if (atom.getAtomNumber() == atomNumber)
- bs.set(i);
- }
- return bs;
- }
-
}
Modified: branches/v14_2/Jmol/src/org/jmol/script/ScriptEval.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/script/ScriptEval.java 2015-01-27
23:56:55 UTC (rev 20249)
+++ branches/v14_2/Jmol/src/org/jmol/script/ScriptEval.java 2015-01-28
00:19:08 UTC (rev 20250)
@@ -2229,7 +2229,6 @@
}
if (theToken == null)
continue;
- //System.out.println(pc + " thetoken = " + theToken);
int tok = theToken.tok;
if (T.tokAttr(tok, T.flowCommand)) {
isForCheck = cmdFlow(tok, isForCheck, vProcess);
Modified: branches/v14_2/Jmol/src/org/jmol/script/ScriptExpr.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/script/ScriptExpr.java 2015-01-27
23:56:55 UTC (rev 20249)
+++ branches/v14_2/Jmol/src/org/jmol/script/ScriptExpr.java 2015-01-28
00:19:08 UTC (rev 20250)
@@ -200,7 +200,7 @@
v = parameterExpressionToken(++i);
i = iToken;
} else if (tokAt(i) == T.integer) {
- v = vwr.ms.getAtomsFromAtomNumberInFrame(st[i].intValue);
+ v = vwr.ms.getAtoms(T.atomno, Integer.valueOf(st[i].intValue));
break;
} else {
v = getParameter(SV.sValue(st[i]), T.variable, true);
@@ -805,6 +805,7 @@
rpn.addXBs(lookupIdentifierValue("_" + value));
}
break;
+ case T.bonded:
case T.carbohydrate:
case T.dna:
case T.hetero:
@@ -876,7 +877,7 @@
(int) Math.floor(pt.y * 1000), (int) Math.floor(pt.z * 1000)
}));
break;
case T.thismodel:
- rpn.addXBs(vwr.getModelUndeletedAtomsBitSet(vwr.am.cmi));
+ rpn.addXBs(vwr.am.cmi < 0 ? vwr.getFrameAtoms() :
vwr.getModelUndeletedAtomsBitSet(vwr.am.cmi));
break;
case T.hydrogen:
case T.amino:
Modified: branches/v14_2/Jmol/src/org/jmol/script/T.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/script/T.java 2015-01-27 23:56:55 UTC
(rev 20249)
+++ branches/v14_2/Jmol/src/org/jmol/script/T.java 2015-01-28 00:19:08 UTC
(rev 20250)
@@ -431,6 +431,7 @@
public final static int spec_seqcode_range = expression | 39;
public final static int amino = predefinedset | 2;
+ public final static int bonded = predefinedset | 3;
public final static int dna = predefinedset | 4;
public final static int hetero = predefinedset | 6 | deprecatedparam;
public final static int helixalpha = predefinedset | 7; // Jmol
12.1.14
@@ -1898,6 +1899,7 @@
"best",
"bin",
"bondCount",
+ "bonded",
"bottom",
"branch",
"brillouin",
@@ -2921,6 +2923,7 @@
best, // "best"
bin, // "bin"
bondcount, // "bondCount"
+ bonded, // "bonded"
bottom, // "bottom"
branch, // "branch"
brillouin, // "brillouin"
Modified: branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties 2015-01-27
23:56:55 UTC (rev 20249)
+++ branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties 2015-01-28
00:19:08 UTC (rev 20250)
@@ -5,12 +5,8 @@
# THIS IS THE RELEASE BRANCH
# BUG FIXES ONLY, PLEASE
-Jmol.___JmolVersion="14.2.12_2015.01.26"
+Jmol.___JmolVersion="14.2.12_2015.01.27"
-bug fix: @3 for "atomno=3" should not extend to models that are not part of
the current model set
- -- commonly used for shortcut at the console
- -- provides a function distinct from "atomno=3" when there are multiple models
-
bug fix: CGO LINE_LOOP not closing
bug fix: configuration 1 broken
bug fix: display configuration=1 broken (in Jmol 12.0, 2011)
Modified: branches/v14_2/Jmol/src/org/jmol/viewer/TransformManager.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/viewer/TransformManager.java
2015-01-27 23:56:55 UTC (rev 20249)
+++ branches/v14_2/Jmol/src/org/jmol/viewer/TransformManager.java
2015-01-28 00:19:08 UTC (rev 20250)
@@ -1426,6 +1426,7 @@
zSlabValue = zValueFromPercent(zSlabPercentSetting);
zDepthValue = zValueFromPercent(zDepthPercentSetting);
}
+
if (zSlabPoint != null) {
try {
transformPt3f(zSlabPoint, pointT2);
@@ -2461,6 +2462,7 @@
// so that's sppa = (spc / vR) * rPO * (vR / 2) / mR * rPO = spc/2/mR
modelRadiusPixels = modelRadius * scalePixelsPerAngstrom; // (s)
+
// System.out.println("transformman zoom scalppa modelrad " +
zoomPercent + " " +
// scalePixelsPerAngstrom + " " + modelRadiusPixels + " " +
visualRange
// + " -- "+ vwr.dimScreen.width+ " "+ vwr.dimScreen.height);
Modified: branches/v14_2/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/viewer/Viewer.java 2015-01-27 23:56:55 UTC
(rev 20249)
+++ branches/v14_2/Jmol/src/org/jmol/viewer/Viewer.java 2015-01-28 00:19:08 UTC
(rev 20250)
@@ -9167,4 +9167,9 @@
if (jmolpopup != null)
jmolpopup.jpiUpdateComputedMenus();
}
+
+ public BS getFrameAtoms() {
+ return getModelUndeletedAtomsBitSetBs(getVisibleFramesBitSet());
+ }
+
}
This was sent by the SourceForge.net collaborative development platform, the
world's largest Open Source development site.
------------------------------------------------------------------------------
Dive into the World of Parallel Programming. The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/
_______________________________________________
Jmol-commits mailing list
Jmol-commits@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-commits
