Revision: 20396
http://sourceforge.net/p/jmol/code/20396
Author: hansonr
Date: 2015-03-21 02:12:09 +0000 (Sat, 21 Mar 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.2.13_2015.03.20b"
bug fix: popup menu Symmetry broken
bug fix: PDB reader does not save unit cell on simple load
Modified Paths:
--------------
branches/v14_2/Jmol/src/org/jmol/adapter/readers/pdb/PdbReader.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/popup/JmolGenericPopup.java
branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: branches/v14_2/Jmol/src/org/jmol/adapter/readers/pdb/PdbReader.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/adapter/readers/pdb/PdbReader.java
2015-03-21 02:11:19 UTC (rev 20395)
+++ branches/v14_2/Jmol/src/org/jmol/adapter/readers/pdb/PdbReader.java
2015-03-21 02:12:09 UTC (rev 20396)
@@ -422,6 +422,7 @@
protected void finalizeReaderPDB() throws Exception {
checkNotPDB();
+ checkUnitCellParams();
if (!isCourseGrained)
connectAll(maxSerial, isConnectStateBug);
SymmetryInterface symmetry;
@@ -474,6 +475,14 @@
}
}
+ private void checkUnitCellParams() {
+ if (iHaveUnitCell) {
+ asc.setCurrentModelInfo("unitCellParams", unitCellParams);
+ if (sgName != null)
+ asc.setCurrentModelInfo("spaceGroup", sgName);
+ }
+ }
+
private void checkForResidualBFactors(SymmetryInterface symmetry) {
Atom[] atoms = asc.atoms;
boolean isResidual = false;
@@ -649,8 +658,7 @@
*/
- @SuppressWarnings("unchecked")
- private void remark350() throws Exception {
+ private void remark350() throws Exception {
Lst<M4> biomts = null;
Lst<String> biomtchains = null;
vBiomolecules = new Lst<Map<String, Object>>();
@@ -1318,6 +1326,7 @@
haveMappedSerials = false;
sbConect = null;
asc.newAtomSet();
+ checkUnitCellParams();
if (!isCourseGrained)
setModelPDB(true);
asc.setCurrentAtomSetNumber(modelNumber);
@@ -1344,7 +1353,7 @@
a = Float.NaN; // 1 for a means no unit cell
setUnitCell(a, getFloat(15, 9), getFloat(24, 9), getFloat(33,
7), getFloat(40, 7), getFloat(47, 7));
- if (sgName == null)
+ if (sgName == null || sgName.equals("unspecified!"))
setSpaceGroupName(PT.parseTrimmedRange(line, 55, 66));
}
Modified: branches/v14_2/Jmol/src/org/jmol/modelset/ModelLoader.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/modelset/ModelLoader.java 2015-03-21
02:11:19 UTC (rev 20395)
+++ branches/v14_2/Jmol/src/org/jmol/modelset/ModelLoader.java 2015-03-21
02:12:09 UTC (rev 20396)
@@ -1097,15 +1097,15 @@
// 1. apply CONECT records and set bsExclude to omit them
// 2. apply stereochemistry from JME
- BS bsExclude = (ms
- .getInfoM("someModelsHaveCONECT") == null ? null
+ BS bsExclude = (ms.getInfoM("someModelsHaveCONECT") == null ? null
: new BS());
if (bsExclude != null)
ms.setPdbConectBonding(baseAtomIndex, baseModelIndex, bsExclude);
// 2. for each model in the collection,
int modelAtomCount = 0;
- boolean symmetryAlreadyAppliedToBonds =
vwr.getBoolean(T.applysymmetrytobonds);
+ boolean symmetryAlreadyAppliedToBonds = vwr
+ .getBoolean(T.applysymmetrytobonds);
boolean doAutoBond = vwr.getBoolean(T.autobond);
boolean forceAutoBond = vwr.getBoolean(T.forceautobond);
BS bs = null;
@@ -1115,15 +1115,12 @@
if (!noAutoBond)
for (int i = baseModelIndex; i < modelCount; i++) {
modelAtomCount = models[i].bsAtoms.cardinality();
- int modelBondCount = ms.getInfoI(i,
- "initialBondCount");
+ int modelBondCount = ms.getInfoI(i, "initialBondCount");
boolean modelIsPDB = models[i].isBioModel;
if (modelBondCount < 0) {
modelBondCount = ms.bondCount;
}
- boolean modelHasSymmetry = ms.getInfoB(i,
- "hasSymmetry");
// check for PDB file with fewer than one bond per every two atoms
// this is in case the PDB format is being usurped for non-RCSB uses
// In other words, say someone uses the PDB format to indicate atoms
and
@@ -1135,12 +1132,8 @@
// automatic bonding, and additional bonds might be made.
boolean doBond = (forceAutoBond || doAutoBond
&& (modelBondCount == 0
- || modelIsPDB
- && jmolData == null
- && (ms
- .getMSInfoB("havePDBHeaderName") || modelBondCount <
modelAtomCount / 2) || modelHasSymmetry
- && !symmetryAlreadyAppliedToBonds
- && !ms.getInfoB(i, "hasBonds")));
+ || modelIsPDB && jmolData == null &&
(ms.getMSInfoB("havePDBHeaderName") || modelBondCount < modelAtomCount / 2)
+ || ms.getInfoB(i, "hasSymmetry") &&
!symmetryAlreadyAppliedToBonds && !ms.getInfoB(i, "hasBonds")));
if (!doBond)
continue;
autoBonding = true;
@@ -1154,8 +1147,8 @@
if (modulationOn)
ms.setModulation(null, true, modulationTUV, false);
if (autoBonding) {
- ms.autoBondBs4(bs, bs, bsExclude, null,
- ms.defaultCovalentMad, vwr.getBoolean(T.legacyautobonding));
+ ms.autoBondBs4(bs, bs, bsExclude, null, ms.defaultCovalentMad,
+ vwr.getBoolean(T.legacyautobonding));
Logger
.info("ModelSet: autobonding; use autobond=false to not generate
bonds automatically");
} else {
Modified: branches/v14_2/Jmol/src/org/jmol/modelset/ModelSet.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/modelset/ModelSet.java 2015-03-21
02:11:19 UTC (rev 20395)
+++ branches/v14_2/Jmol/src/org/jmol/modelset/ModelSet.java 2015-03-21
02:12:09 UTC (rev 20396)
@@ -904,11 +904,23 @@
}
public SymmetryInterface getUnitCell(int modelIndex) {
- return (!haveUnitCells || modelIndex < 0 || modelIndex >= mc ? null
- : am[modelIndex].simpleCage != null ? am[modelIndex].simpleCage
- : unitCells == null || modelIndex >= unitCells.length
- || !unitCells[modelIndex].haveUnitCell() ? null
- : unitCells[modelIndex]);
+ if (modelIndex < 0 || modelIndex >= mc)
+ return null;
+ if (am[modelIndex].simpleCage != null)
+ return am[modelIndex].simpleCage;
+ if (unitCells != null && modelIndex < unitCells.length
+ && unitCells[modelIndex].haveUnitCell())
+ return unitCells[modelIndex];
+ if (getInfo(modelIndex, "unitCellParams") != null) {
+ if (unitCells == null)
+ unitCells = new SymmetryInterface[mc];
+ getSymTemp(true).setSymmetryInfo(modelIndex,
am[modelIndex].auxiliaryInfo, null);
+ SymmetryInterface unitCell = symTemp;
+ symTemp = null;
+ haveUnitCells = true;
+ return unitCells[modelIndex] = unitCell;
+ }
+ return null;
}
public void setModelCage(int modelIndex, SymmetryInterface simpleCage) {
Modified: branches/v14_2/Jmol/src/org/jmol/popup/JmolGenericPopup.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/popup/JmolGenericPopup.java
2015-03-21 02:11:19 UTC (rev 20395)
+++ branches/v14_2/Jmol/src/org/jmol/popup/JmolGenericPopup.java
2015-03-21 02:12:09 UTC (rev 20396)
@@ -105,7 +105,7 @@
private boolean isMultiConfiguration;
private boolean isMultiFrame;
private boolean isPDB;
- private boolean isSymmetry;
+ private boolean hasSymmetry;
private boolean isUnitCell;
private boolean isVibration;
private boolean isZapped;
@@ -377,7 +377,7 @@
modelInfo = new Hashtable<String, Object>();
isPDB = checkBoolean("isPDB");
isMultiFrame = (modelCount > 1);
- isSymmetry = checkBoolean("hasSymmetry");
+ hasSymmetry = modelInfo.containsKey("hasSymmetry");
isUnitCell = modelInfo.containsKey("unitCellParams");
fileHasUnitCell = (isPDB && isUnitCell || checkBoolean("fileHasUnitCell"));
isLastFrame = (modelIndex == modelCount - 1);
@@ -604,7 +604,7 @@
for (int i = VibrationOnly.size(); --i >= 0;)
menuEnable(VibrationOnly.get(i), isVibration);
for (int i = SymmetryOnly.size(); --i >= 0;)
- menuEnable(SymmetryOnly.get(i), isSymmetry && isUnitCell);
+ menuEnable(SymmetryOnly.get(i), hasSymmetry && isUnitCell);
for (int i = ChargesOnly.size(); --i >= 0;)
menuEnable(ChargesOnly.get(i), haveCharges);
for (int i = TemperatureOnly.size(); --i >= 0;)
@@ -722,7 +722,7 @@
return;
menuRemoveAll(menu, 0);
menuEnable(menu, false);
- if (!isSymmetry || modelIndex < 0)
+ if (!hasSymmetry || modelIndex < 0)
return;
Map<String, Object> info = (Map<String, Object>) vwr.getProperty(
"DATA_API", "spaceGroupInfo", null);
@@ -763,7 +763,7 @@
return;
menuRemoveAll(menu, 0);
menuEnable(menu, false);
- if (!isSymmetry || modelIndex < 0)
+ if (!hasSymmetry || modelIndex < 0)
return;
String[] list = (String[]) modelInfo.get("symmetryOperations");
if (list == null)
Modified: branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties 2015-03-21
02:11:19 UTC (rev 20395)
+++ branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties 2015-03-21
02:12:09 UTC (rev 20396)
@@ -4,8 +4,13 @@
# THIS IS THE RELEASE BRANCH
# BUG FIXES ONLY, PLEASE
-Jmol.___JmolVersion="14.2.13_2015.03.20"
+Jmol.___JmolVersion="14.2.13_2015.03.20b"
+bug fix: popup menu Symmetry broken
+bug fix: PDB reader does not save unit cell on simple load
+
+JmolVersion="14.2.13_2015.03.20"
+
bug fix: use of {*}.xxxx = for(i;{*};....) fails
JmolVersion="14.2.13_2015.03.19"
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