Revision: 21480
http://sourceforge.net/p/jmol/code/21480
Author: hansonr
Date: 2017-04-04 15:44:44 +0000 (Tue, 04 Apr 2017)
Log Message:
-----------
Jmol.___JmolVersion="14.11.2" // 2017-04-04
bug fix: NBO fixes
bug fix: backboneSteps moved to cartoonSteps
// order of checking for TRUE is:
// cartoonBlocks, cartoonBaseEdges, cartoonSteps, cartoonLadders,
cartoonRibose
Modified Paths:
--------------
trunk/Jmol/src/org/gennbo/NBOConfig.java
trunk/Jmol/src/org/gennbo/NBODialog.java
trunk/Jmol/src/org/gennbo/NBOModel.java
trunk/Jmol/src/org/gennbo/NBOSearch.java
trunk/Jmol/src/org/gennbo/NBOService.java
trunk/Jmol/src/org/gennbo/NBOView.java
Modified: trunk/Jmol/src/org/gennbo/NBOConfig.java
===================================================================
--- trunk/Jmol/src/org/gennbo/NBOConfig.java 2017-04-04 13:48:07 UTC (rev
21479)
+++ trunk/Jmol/src/org/gennbo/NBOConfig.java 2017-04-04 15:44:44 UTC (rev
21480)
@@ -343,7 +343,7 @@
}
protected void doSettingShowHalos() {
- dialog.runScriptNow("select " + jCheckSelHalo.isSelected());
+ dialog.runScriptQueued("select " + jCheckSelHalo.isSelected());
}
protected void doSettingWireMesh() {
@@ -376,7 +376,7 @@
if (isJmol) {
if (!dialog.jmolOptionNONBO)
- dialog.runScriptNow("background gray;set defaultcolors Jmol;refresh;");
+ dialog.runScriptQueued("background gray;set defaultcolors
Jmol;refresh;");
} else {
if (jCheckWireMesh.isSelected())
jCheckWireMesh.doClick();
@@ -387,7 +387,7 @@
String atomColors = "";
atomColors = GuiMap.getResourceString(this,
"org/gennbo/assets/atomColors.txt");
- dialog.runScriptNow(atomColors + ";refresh");
+ dialog.runScriptQueued(atomColors + ";refresh");
} catch (IOException e) {
dialog.logError("atomColors.txt not found");
}
Modified: trunk/Jmol/src/org/gennbo/NBODialog.java
===================================================================
--- trunk/Jmol/src/org/gennbo/NBODialog.java 2017-04-04 13:48:07 UTC (rev
21479)
+++ trunk/Jmol/src/org/gennbo/NBODialog.java 2017-04-04 15:44:44 UTC (rev
21480)
@@ -777,7 +777,7 @@
public void close() {
if (modulePanel != null)
inputFileHandler.clearInputFile(false);
- runScriptNow("select off");
+ runScriptQueued("select off");
dispose();
}
@@ -861,7 +861,7 @@
iAmLoading = false;
if (NBOConfig.nboView)
- runScriptNow("select 1.1;color bonds lightgrey;"
+ runScriptQueued("select 1.1;color bonds lightgrey;"
+ "wireframe 0.1;select none");
isOpenShell = vwr.ms.getModelAuxiliaryInfo(0).containsKey("isOpenShell");
switch (dialogMode) {
@@ -1141,8 +1141,15 @@
}
protected String loadModelFileNow(String s) {
- return runScriptNow("load " + s.replace('\\', '/'));
+ String script = "load " + s.replace('\\', '/');
+ logInfo("!$ " + script, Logger.LEVEL_DEBUG);
+ script = script.replace('"', '\'');
+ return PT.trim(vwr.runScript(script), "\n");
}
+
+ public String getCFIData() {
+ return evaluateJmolString("data({*},'cfi')");
+ }
protected boolean checkEnabled() {
return (jmolOptionNONBO || nboService.isEnabled()
@@ -1212,11 +1219,6 @@
return isOpenShell;
}
- synchronized protected String runScriptNow(String script) {
- logInfo("!$ " + script, Logger.LEVEL_DEBUG);
- return PT.trim(vwr.runScript(script.replace('"', '\'')), "\n");
- }
-
class HelpBtn extends JButton {
String page;
Modified: trunk/Jmol/src/org/gennbo/NBOModel.java
===================================================================
--- trunk/Jmol/src/org/gennbo/NBOModel.java 2017-04-04 13:48:07 UTC (rev
21479)
+++ trunk/Jmol/src/org/gennbo/NBOModel.java 2017-04-04 15:44:44 UTC (rev
21480)
@@ -1016,7 +1016,7 @@
protected void loadModelToNBO(String s, boolean undoRedo) {
boolean alsoLoadJmol = true;
if (s == null) {
- s = dialog.runScriptNow(";print data({*},'cfi');");
+ s = dialog.getCFIData();
alsoLoadJmol = false;
}
// if (undoRedo)
@@ -1041,8 +1041,9 @@
protected void loadModelFromNBO(String path, String fname, String ext) {
if (PT.isOneOf(ext, NBOConfig.JMOL_EXTENSIONS)) {
notFromNBO = true;
- dialog.runScriptNow("set refreshing false"); // a bit risky
+ dialog.runScriptQueued("set refreshing false");
dialog.loadModelFileQueued(new File(path + "\\" + fname + "." + ext),
false);
+ dialog.runScriptQueued("set refreshing true");
return;
}
String ess = getEss(ext, true);
@@ -1127,7 +1128,7 @@
*
*/
protected void notifyPick(int[] picked) {
- dialog.runScriptNow("measure delete;"
+ dialog.runScriptQueued("measure delete;"
+ (resetOnAtomClick ? "select none" : ""));
if (resetOnAtomClick) {
clearSelected(false);
@@ -1184,13 +1185,13 @@
*/
protected void notifyFileLoaded() {
- String fileContents = dialog.runScriptNow("print data({*},'cfi')");
+ String fileContents = dialog.getCFIData();
if (notFromNBO) {
notFromNBO = false;
loadModelToNBO(fileContents, false);
return;
}
- dialog.runScriptNow(NBOConfig.JMOL_FONT_SCRIPT);
+ dialog.runScriptQueued(NBOConfig.JMOL_FONT_SCRIPT);
// + ";select 1.1;"); // NOT rotate best, because these may be symmetry
designed
dialog.doSetStructure(null);
showComponents(true);
@@ -1214,7 +1215,7 @@
updateSelected(false);
showSelectedOnFileLoad = false;
} else {
- dialog.runScriptNow("select none; select on;refresh");
+ dialog.runScriptQueued("select none; select on;refresh");
}
}
Modified: trunk/Jmol/src/org/gennbo/NBOSearch.java
===================================================================
--- trunk/Jmol/src/org/gennbo/NBOSearch.java 2017-04-04 13:48:07 UTC (rev
21479)
+++ trunk/Jmol/src/org/gennbo/NBOSearch.java 2017-04-04 15:44:44 UTC (rev
21480)
@@ -525,7 +525,7 @@
.append("measurements off;select add {*}.bonds; color bonds
lightgrey; select none;");
}
script.append("isosurface delete; select off;refresh");
- dialog.runScriptNow(script.toString());
+ dialog.runScriptQueued(script.toString());
buildHome();
}
@@ -537,7 +537,7 @@
keyWdBtn.setText("<html><font color=black>" + getKeyword()
+ "</font></html>");
keyWdBtn.setVisible(true);
- dialog.runScriptNow("isosurface delete;refresh");
+ dialog.runScriptQueued("isosurface delete;refresh");
opList.removeAll();
ButtonGroup btnGroup = new ButtonGroup();
@@ -618,7 +618,7 @@
changeKey(bend);
break;
case KEYWD_NRT:
- dialog.runScriptNow("set bondpicking true");
+ dialog.runScriptQueued("set bondpicking true");
if (dialog.isOpenShell())
setKeyword("s a a' rs".split(" "), new String[] { "Spin: ", "Atom A: ",
"Atom A': ", "Res Struct: " });
@@ -672,7 +672,7 @@
changeKey(new String[] {});
break;
case KEYWD_BAS1BAS2:
- dialog.runScriptNow("set bondpicking true");
+ dialog.runScriptQueued("set bondpicking true");
setKeyword("b1 b2 r c".split(" "), new String[] { "Basis 1:", "Basis 2:",
"Row:", "Column:" });
getBasisOperationsB1B2();
@@ -687,8 +687,8 @@
private void load(int nn, boolean withBondPicking) {
dialog.iAmLoading = true;
- if (dialog.loadModelFileNow(dialog.inputFileHandler.newNBOFileForExt(""
- + nn)
+ if (dialog.loadModelFileNow(
+ PT.esc(dialog.inputFileHandler.newNBOFileForExt("" +
nn).toString().replace('\\', '/'))
+ (withBondPicking ? ";set bondpicking true" : "")) == null)
dialog.iAmLoading = false;
}
@@ -1279,7 +1279,7 @@
*
*/
protected void notifyPick_s(int[] picked) {
- dialog.runScriptNow("isosurface delete");
+ dialog.runScriptQueued("isosurface delete");
int at1 = picked[0];
int at2 = picked[1];
if (at2 == Integer.MIN_VALUE) {
@@ -1467,7 +1467,7 @@
protected void notifyFileLoaded_s() {
if (vwr.ms.ac == 0)
return;
- dialog.runScriptNow("isosurface delete");
+ dialog.runScriptQueued("isosurface delete");
optionSelected = -1;
if (dialog.isOpenShell()) {
Modified: trunk/Jmol/src/org/gennbo/NBOService.java
===================================================================
--- trunk/Jmol/src/org/gennbo/NBOService.java 2017-04-04 13:48:07 UTC (rev
21479)
+++ trunk/Jmol/src/org/gennbo/NBOService.java 2017-04-04 15:44:44 UTC (rev
21480)
@@ -483,7 +483,7 @@
}
// standard expectation
- System.out.println("*start*\n" + s);
+ //System.out.println("*start*\n" + s);
if (currentRequest == null) {
if (haveLicense) {
System.out.println("TRANSMISSION ERROR: UNSOLICITED!");
Modified: trunk/Jmol/src/org/gennbo/NBOView.java
===================================================================
--- trunk/Jmol/src/org/gennbo/NBOView.java 2017-04-04 13:48:07 UTC (rev
21479)
+++ trunk/Jmol/src/org/gennbo/NBOView.java 2017-04-04 15:44:44 UTC (rev
21480)
@@ -211,7 +211,7 @@
JPanel panel = new JPanel(new BorderLayout());
viewState = VIEW_STATE_MAIN;
///panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS));
- dialog.runScriptNow("set bondpicking true");
+ dialog.runScriptQueued("set bondpicking true");
Box b = createViewSearchJobBox(NBOFileHandler.MODE_VIEW);
if (!dialog.jmolOptionNONBO)
@@ -437,7 +437,7 @@
*/
protected void doViewPlane() {
viewPlanePt = 0;
- dialog.runScriptNow("set bondpicking false");
+ dialog.runScriptQueued("set bondpicking false");
viewState = VIEW_STATE_PLANE;
Box box = NBOUtil.createTitleBox(" Definiton of Plane ", null);
final JPanel plane = new JPanel(new BorderLayout());
@@ -483,8 +483,7 @@
d.addWindowListener(new WindowAdapter() {
@Override
public void windowClosing(WindowEvent e) {
- dialog.runScriptQueued("select off");
- dialog.runScriptNow("set bondpicking true");
+ dialog.runScriptQueued("select off;set bondpicking true");
viewState = VIEW_STATE_MAIN;
}
});
@@ -492,8 +491,7 @@
@Override
public void actionPerformed(ActionEvent e) {
d.dispose();
- dialog.runScriptQueued("select off");
- dialog.runScriptNow("set bondpicking true");
+ dialog.runScriptQueued("select off;set bondpicking true");
viewState = VIEW_STATE_MAIN;
}
});
@@ -512,7 +510,7 @@
* Vector dialog
*/
protected void doViewAxis() {
- dialog.runScriptNow("set bondpicking false");
+ dialog.runScriptQueued("set bondpicking false");
viewState = VIEW_STATE_VECTOR;
viewVectorPt = 0;
Box box = NBOUtil.createTitleBox(" Vector Definition ", null);
@@ -561,8 +559,7 @@
d.addWindowListener(new WindowAdapter() {
@Override
public void windowClosing(WindowEvent e) {
- dialog.runScriptQueued("select off");
- dialog.runScriptNow("set bondpicking true");
+ dialog.runScriptQueued("select off;set bondpicking true");
viewState = VIEW_STATE_MAIN;
}
});
@@ -570,8 +567,7 @@
@Override
public void actionPerformed(ActionEvent e) {
d.dispose();
- dialog.runScriptQueued("select off");
- dialog.runScriptNow("set bondpicking true");
+ dialog.runScriptQueued("select off;set bondpicking true");
viewState = VIEW_STATE_MAIN;
}
});
@@ -1209,7 +1205,7 @@
private void initializeImage() {
//testingView = NBOConfig.debugVerbose;
- dialog.runScriptNow("image close");
+ dialog.runScriptQueued("image close");
dialog.nboService.restart();
setDefaultParameterArrays();
if (jmolView)
@@ -1227,7 +1223,7 @@
*
*/
protected void notifyPick_v(int[] picked) {
- dialog.runScriptNow("isosurface delete");
+ dialog.runScriptQueued("isosurface delete");
int at1 = picked[0];
int at2 = picked[1];
switch (viewState) {
@@ -1333,7 +1329,7 @@
return;
orbitals.bsOn.clearAll();
orbitals.bsNeg.clearAll();
- dialog.runScriptNow("isosurface * off");
+ dialog.runScriptQueued("isosurface * off");
orbitals.updateIsosurfacesInJmol(i);
}
@@ -1826,7 +1822,7 @@
String id = "id " + PT.esc(title.toString().trim());
String script = "image " + id + " close;image id \"\" "
+ PT.esc(f.toString().replace('\\', '/'));
- dialog.runScriptNow(script);
+ dialog.runScriptQueued(script);
break;
case NBOService.MODE_RAW:
break;
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