Revision: 21331
http://sourceforge.net/p/jmol/code/21331
Author: hansonr
Date: 2017-01-23 23:31:55 +0000 (Mon, 23 Jan 2017)
Log Message:
-----------
GenNBO tool - avoid reset of orientation when different bases are loaded.
Modified Paths:
--------------
trunk/Jmol/src/org/openscience/jmol/app/nbo/NBODialogView.java
trunk/Jmol/src/org/openscience/jmol/app/nbo/NBOFileHandler.java
Modified: trunk/Jmol/src/org/openscience/jmol/app/nbo/NBODialogView.java
===================================================================
--- trunk/Jmol/src/org/openscience/jmol/app/nbo/NBODialogView.java
2017-01-23 19:08:22 UTC (rev 21330)
+++ trunk/Jmol/src/org/openscience/jmol/app/nbo/NBODialogView.java
2017-01-23 23:31:55 UTC (rev 21331)
@@ -1002,8 +1002,7 @@
betaList = list;
else
alphaList = list;
- String s = getJmolFilename();
- loadModelFileQueued(f, f.getAbsolutePath().equals(s), false);
+ loadModelFileQueued(f,
NBOFileHandler.pathWithoutExtension(f.getAbsolutePath()).equals(NBOFileHandler.pathWithoutExtension(getJmolFilename())),
false);
}
protected void setLastOrbitalSelection() {
@@ -1390,47 +1389,51 @@
runScriptQueued("select bonds " + bonds + ";wireframe 0");
return;
}
-
+
Map<String, Object> moData = (Map<String, Object>) vwr
.getCurrentModelAuxInfo().get("moData");
String type = basis.getSelectedItem().toString();
if (type.charAt(0) == 'P')
type = type.substring(1);
boolean isBeta = isOpenShell && !alphaSpin.isSelected();
- String[] a = ((Map<String, String[]>) moData.get("nboLabelMap"))
- .get((isBeta ? "beta_" : "") + type);
- DefaultComboBoxModel<String> list = (isBeta ? betaList : alphaList);
- for (int i = 0; i < a.length; i++)
- list.addElement((i + 1) + ". " + a[i]);
- orbitals.setModel(list);
- setLastOrbitalSelection();
+ try {
+ String[] a = ((Map<String, String[]>) moData.get("nboLabelMap"))
+ .get((isBeta ? "beta_" : "") + type);
+ DefaultComboBoxModel<String> list = (isBeta ? betaList : alphaList);
+ for (int i = 0; i < a.length; i++)
+ list.addElement((i + 1) + ". " + a[i]);
+ orbitals.setModel(list);
+ setLastOrbitalSelection();
- resetValues();
- settingsBox.setVisible(true);
- // for(int i = 0; i < 5; i++)
- // panel.getComponents()[i].setVisible(true);
- if (!inputFileHandler.getChooseList())
- logInfo("Error reading $CHOOSE list", Logger.LEVEL_ERROR);
- showAtomNums(true);
+ resetValues();
+ settingsBox.setVisible(true);
+ // for(int i = 0; i < 5; i++)
+ // panel.getComponents()[i].setVisible(true);
+ if (!inputFileHandler.getChooseList())
+ logInfo("Error reading $CHOOSE list", Logger.LEVEL_ERROR);
+ showAtomNums(true);
- if (!useWireMesh) {
- runScriptQueued("nbo nomesh fill translucent " + opacityOp);
- runScriptQueued("mo nomesh fill translucent " + opacityOp);
- }
+ if (!useWireMesh) {
+ runScriptQueued("nbo nomesh fill translucent " + opacityOp);
+ runScriptQueued("mo nomesh fill translucent " + opacityOp);
+ }
- runScriptQueued("nbo color " + color2 + " " + color1);
- runScriptQueued("mo color " + color2 + " " + color1);
- if (isOpenShell) {
- alphaSpin.setVisible(true);
- betaSpin.setVisible(true);
- } else {
- alphaSpin.setVisible(false);
- betaSpin.setVisible(false);
+ runScriptQueued("nbo color " + color2 + " " + color1);
+ runScriptQueued("mo color " + color2 + " " + color1);
+ if (isOpenShell) {
+ alphaSpin.setVisible(true);
+ betaSpin.setVisible(true);
+ } else {
+ alphaSpin.setVisible(false);
+ betaSpin.setVisible(false);
+ }
+ setBonds(true);
+ for (int i = 0; i < panel.getComponentCount(); i++) {
+ panel.getComponent(i).setVisible(true);
+ }
+ } catch (NullPointerException e) {
+ log(e.getMessage() + " reading file", 'r');
}
- setBonds(true);
- for (int i = 0; i < panel.getComponentCount(); i++) {
- panel.getComponent(i).setVisible(true);
- }
}
protected void setViewerBasis() {
Modified: trunk/Jmol/src/org/openscience/jmol/app/nbo/NBOFileHandler.java
===================================================================
--- trunk/Jmol/src/org/openscience/jmol/app/nbo/NBOFileHandler.java
2017-01-23 19:08:22 UTC (rev 21330)
+++ trunk/Jmol/src/org/openscience/jmol/app/nbo/NBOFileHandler.java
2017-01-23 23:31:55 UTC (rev 21331)
@@ -345,11 +345,15 @@
//useful file manipulation methods /////////////////////////////
protected static File newNBOFile(File f, String ext) {
- String fname = f.toString().replace('\\', '/');
+ return new File(pathWithoutExtension(f.toString().replace('\\', '/')) +
"." + ext);
+ }
+
+ protected static String pathWithoutExtension(String fname) {
int pt = fname.lastIndexOf(".");
- return new File((pt < 0 ? fname : fname.substring(0, pt)) + "." + ext);
+ return (pt < 0 ? fname : fname.substring(0, pt));
}
+
protected void clearInputFile() {
// if (jobStem.length() == 0)
// return;
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