Revision: 21346
http://sourceforge.net/p/jmol/code/21346
Author: hansonr
Date: 2017-01-25 20:52:14 +0000 (Wed, 25 Jan 2017)
Log Message:
-----------
adding NBOPlugin and JmolPlugin
Modified Paths:
--------------
trunk/Jmol/src/org/gennbo/NBODialog.java
trunk/Jmol/src/org/gennbo/NBODialogConfig.java
trunk/Jmol/src/org/gennbo/NBODialogRun.java
trunk/Jmol/src/org/gennbo/NBODialogSearch.java
trunk/Jmol/src/org/gennbo/NBODialogView.java
trunk/Jmol/src/org/gennbo/NBOFileHandler.java
trunk/Jmol/src/org/gennbo/NBOService.java
trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/JmolPanel.java
trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/StatusListener.java
Added Paths:
-----------
trunk/Jmol/src/org/gennbo/NBOPlugin.java
trunk/Jmol/src/org/openscience/jmol/app/JmolPlugin.java
Modified: trunk/Jmol/src/org/gennbo/NBODialog.java
===================================================================
--- trunk/Jmol/src/org/gennbo/NBODialog.java 2017-01-25 18:12:49 UTC (rev
21345)
+++ trunk/Jmol/src/org/gennbo/NBODialog.java 2017-01-25 20:52:14 UTC (rev
21346)
@@ -45,7 +45,6 @@
import java.io.IOException;
import java.net.URI;
import java.net.URISyntaxException;
-import java.net.URL;
import javajs.swing.SwingConstants;
import javajs.util.PT;
@@ -109,8 +108,6 @@
private JPanel topPanel;
protected JButton modelButton, runButton, viewButton, searchButton;
- protected JPanel settingsPanel;
-
private JPanel homePanel;
boolean isJmolNBO;
@@ -119,6 +116,8 @@
protected JLabel statusLab;
protected JPanel nboOutput;
+
+ private NBOPlugin nboPlugin;
static final char DIALOG_CONFIG = 'c';
static final char DIALOG_MODEL = 'm';
@@ -137,19 +136,20 @@
* @param vwr
* The interacting display we are reproducing (source of view angle
* info etc)
+ * @param plugin
*/
- public NBODialog(JFrame jmolFrame, Viewer vwr) {
+ public NBODialog(NBOPlugin plugin, JFrame jmolFrame, Viewer vwr) {
super(jmolFrame);
- setTitle("NBOPro6@Jmol");
+ setTitle("NBOPro6@Jmol " + plugin.getVersion());
+ nboPlugin = plugin;
this.vwr = vwr;
- this.nboService = new NBOService(vwr);
+ this.nboService = new NBOService(this, vwr);
this.setIconImage(getIcon("nbo6logo20x20").getImage());
this.setLayout(new BorderLayout());
sendDefaultScript();
+
//get saved properties
- nboService.nboDialog = this;
-
createDialog(jmolFrame.getBounds());
}
@@ -171,14 +171,10 @@
addWindowListener(new WindowAdapter() {
@Override
public void windowClosing(WindowEvent e) {
- //TODO
-// nboService.manager.clearQueue();
-// //nboService.manager.
-// nboService.closeProcess();
+ nboService.closeProcess();
close();
}
});
- //final NBODialog dialog = this;
placeNBODialog(this);
helpBtn = new HelpBtn(""){
@@ -225,11 +221,12 @@
//centerPanel.setLeftComponent(mainPage());
this.dialogMode = DIALOG_HOME;
this.getContentPane().add(topPanel,BorderLayout.NORTH);
- settingsPanel = buildSettingsPanel();
settingsDialog = new JDialog(this,"Settings");
- settingsDialog.add(settingsPanel);
settingsDialog.setSize(new Dimension(350,400));
settingsDialog.setLocation(this.getX() + 100,this.getY()+100);
+ settingsPanel = new JPanel();
+ buildSettingsPanel(settingsPanel);
+ settingsDialog.add(settingsPanel);
this.setVisible(true);
if (nboService.isOffLine())
settingsDialog.setVisible(true);
@@ -643,7 +640,7 @@
runScriptNow("mo delete; nbo delete; select off");
break;
}
- nboService.jobQueue.clear();
+ nboService.clearQueue();
nboService.isWorking = false;
this.settingsBox.setVisible(false);
if (!checkEnabled())
@@ -840,5 +837,4 @@
else
loadModelFileQueued(file, false, false);
}
-
}
Modified: trunk/Jmol/src/org/gennbo/NBODialogConfig.java
===================================================================
--- trunk/Jmol/src/org/gennbo/NBODialogConfig.java 2017-01-25 18:12:49 UTC
(rev 21345)
+++ trunk/Jmol/src/org/gennbo/NBODialogConfig.java 2017-01-25 20:52:14 UTC
(rev 21346)
@@ -33,10 +33,7 @@
import java.awt.Rectangle;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
-import java.io.BufferedReader;
import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
import java.io.IOException;
import java.net.URI;
import java.net.URISyntaxException;
@@ -64,7 +61,6 @@
import javax.swing.ListCellRenderer;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
-import javax.swing.filechooser.FileNameExtensionFilter;
import javax.swing.plaf.basic.BasicComboPopup;
import javax.swing.plaf.basic.ComboPopup;
import javax.swing.plaf.metal.MetalComboBoxUI;
@@ -111,7 +107,11 @@
protected JTextPane jpNBOLog;
protected JSlider opacity = new JSlider();
+ protected JPanel settingsPanel;
+ protected JComboBox<Color> colorBox1, colorBox2;
+ protected JCheckBox jCheckAtomNum, jCheckSelHalo, jCheckDebugVerbose,
jCheckNboView, jCheckWireMesh;
+
protected String bodyText = "";
protected boolean showAtNum, nboView, useWireMesh;
@@ -149,22 +149,33 @@
/**
* Creates a dialog for getting info related to output frames in nbo format.
+ * @param settingsPanel
*
* @return settings panel
*/
@SuppressWarnings("unchecked")
- protected JPanel buildSettingsPanel() {
+ protected JPanel buildSettingsPanel(JPanel settingsPanel) {
+ settingsPanel.removeAll();
checkNBOStatus();
String viewOpts = getOrbitalDisplayOptions();
- JPanel filePanel = new JPanel();
- filePanel.setLayout(new BoxLayout(filePanel, BoxLayout.Y_AXIS));
- addPathSetting(filePanel, MODE_PATH_SERVICE);
- addPathSetting(filePanel, MODE_PATH_WORKING);
+ settingsPanel.setLayout(new BoxLayout(settingsPanel, BoxLayout.Y_AXIS));
+ addPathSetting(settingsPanel, MODE_PATH_SERVICE);
+ addPathSetting(settingsPanel, MODE_PATH_WORKING);
//Settings
- filePanel.add(createTitleBox(" Settings ", null));
- JCheckBox jCheckAtomNum = new JCheckBox("Show Atom
Numbers");//.setAlignmentX(0.5f);
+
+ JButton jbDefaults = new JButton("Set Defaults");
+ jbDefaults.addActionListener(new ActionListener() {
+
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ setDefaults();
+ }
+
+ });
+ settingsPanel.add(createTitleBox(" Settings ", jbDefaults));
+ jCheckAtomNum = new JCheckBox("Show Atom Numbers");//.setAlignmentX(0.5f);
jCheckAtomNum.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
@@ -176,22 +187,18 @@
jCheckAtomNum.setSelected(true);
Box settingsBox = createBorderBox(true);
settingsBox.add(jCheckAtomNum);
-
- JCheckBox jCheckSelHalo = new JCheckBox("Show selection halos on atoms");
+
+ jCheckSelHalo = new JCheckBox("Show selection halos on atoms");
jCheckSelHalo.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
- runScriptNow("select " + ((JCheckBox) e.getSource()).isSelected());
+ runScriptNow("select " + jCheckSelHalo.isSelected());
}
});
jCheckSelHalo.doClick();
settingsBox.add(jCheckSelHalo);
- color1 = "[" + orbColor1.getRed() + " " + orbColor1.getGreen() + " "
- + orbColor1.getBlue() + "]";
- color2 = "[" + orbColor2.getRed() + " " + orbColor2.getGreen() + " "
- + orbColor2.getBlue() + "]";
- final JCheckBox jCheckWireMesh = new JCheckBox(
+ jCheckWireMesh = new JCheckBox(
"Use wire mesh for orbital display");
settingsBox.add(jCheckWireMesh);
@@ -199,8 +206,9 @@
Color.cyan, Color.blue, Color.magenta, };
JPanel displayOps = new JPanel(new GridLayout(1, 4));
- displayOps.add(new JLabel("(+) color: "));
- final JComboBox<Color> colorBox1 = new JComboBox<Color>(colors);
+ JLabel label = new JLabel(" (+) color: ");
+ displayOps.add(label);
+ colorBox1 = new JComboBox<Color>(colors);
colorBox1.setRenderer(new ColorRenderer());
colorBox1.setSelectedItem(orbColor1);
displayOps.add(colorBox1);
@@ -208,20 +216,16 @@
@Override
public void actionPerformed(ActionEvent e) {
orbColor1 = ((Color) colorBox1.getSelectedItem());
- color1 = "[" + orbColor1.getRed() + " " + orbColor1.getGreen() + " "
- + orbColor1.getBlue() + "]";
setOrbitalDisplayOptions();
}
});
- displayOps.add(new JLabel(" (-) color: "));
- final JComboBox<Color> colorBox2 = new JComboBox<Color>(colors);
+ displayOps.add(new JLabel(" (-) color: "));
+ colorBox2 = new JComboBox<Color>(colors);
colorBox2.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
orbColor2 = ((Color) colorBox2.getSelectedItem());
- color2 = "[" + orbColor2.getRed() + " " + orbColor2.getGreen() + " "
- + orbColor2.getBlue() + "]";
setOrbitalDisplayOptions();
}
});
@@ -266,7 +270,8 @@
});
if (useWireMesh)
jCheckWireMesh.setSelected(true);
- JCheckBox jCheckNboView = new JCheckBox("Emulate NBO View");
+
+ jCheckNboView = new JCheckBox("Emulate NBO View");
settingsBox.add(jCheckNboView);
jCheckNboView.addActionListener(new ActionListener() {
@Override
@@ -278,14 +283,15 @@
if (jCheckWireMesh.isSelected())
jCheckWireMesh.doClick();
opacity.setValue(3);
- } else
- resetColorScheme();
-
+ } else {
+ setDefaults();
+ runScriptNow("background black;set defaultcolors Jmol;refresh;");
+ }
}
});
- JCheckBox jb = new JCheckBox("Verbose Debugging");
- settingsBox.add(jb);
- jb.addActionListener(new ActionListener() {
+ jCheckDebugVerbose = new JCheckBox("Verbose Debugging");
+ settingsBox.add(jCheckDebugVerbose);
+ jCheckDebugVerbose.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
debugVerbose = ((JCheckBox) e.getSource()).isSelected();
@@ -297,11 +303,35 @@
opacity.setValue((int) (opacityOp * 10));
}
settingsBox.setBorder(BorderFactory.createLineBorder(Color.black));
- filePanel.add(settingsBox);
- return filePanel;
+ settingsPanel.add(settingsBox);
+ return settingsPanel;
}
+ protected void setDefaults() {
+
+ nboService.setNBOProperty("orbitalDisplayOptions", "default");
+ getOrbitalDisplayOptions();
+ opacity.setValue((int) (opacityOp * 10));
+ colorBox1.setSelectedItem(orbColor1);
+ colorBox2.setSelectedItem(orbColor2);
+
+ jCheckWireMesh.setSelected(useWireMesh);
+ //jCheckWireMesh.doClick();
+ jCheckAtomNum.setSelected(true);
+ //jCheckAtomNum.doClick();
+ jCheckSelHalo.setSelected(true);
+ //jCheckSelHalo.doClick();
+ jCheckDebugVerbose.setSelected(false);
+ //jCheckDebugVerbose.doClick();
+ jCheckNboView.setSelected(false);
+ //jCheckNboView.doClick();
+ }
+
protected void setOrbitalDisplayOptions() {
+ color1 = "[" + orbColor1.getRed() + " " + orbColor1.getGreen() + " "
+ + orbColor1.getBlue() + "]";
+ color2 = "[" + orbColor2.getRed() + " " + orbColor2.getGreen() + " "
+ + orbColor2.getBlue() + "]";
String script = "nbo color " + color2 + " " + color1 + ";mo color "
+ color2 + " " + color1 + ";";
script += (useWireMesh ? "nbo nofill mesh;mo nofill mesh"
@@ -314,8 +344,8 @@
}
private String getOrbitalDisplayOptions() {
- String options = nboService.getNBOProperty("orbitalDisplayOptions", null);
- if (options == null) {
+ String options = nboService.getNBOProperty("orbitalDisplayOptions",
"default");
+ if (options.equals("default")) {
orbColor1 = Color.blue;
orbColor2 = Color.red;
opacityOp = 0;
@@ -336,7 +366,7 @@
return options;
}
- private void addPathSetting(JPanel filePanel, final int mode) {
+ private void addPathSetting(JPanel panel, final int mode) {
//GUI for NBO path selection
String title = "";
String path = "";
@@ -359,11 +389,11 @@
}
});
- filePanel.add(createTitleBox(title, null));
+ panel.add(createTitleBox(title, null));
Box serverBox = createBorderBox(true);
serverBox.add(createPathBox(tfPath, mode));
serverBox.setMaximumSize(new Dimension(350, 50));
- filePanel.add(serverBox);
+ panel.add(serverBox);
//Job files
//
@@ -499,25 +529,16 @@
* Sets color scheme to emulate look of NBO view
*/
protected void setNBOColorScheme() {
- nboView = true;
- String atomColors = "";
- String fname = "org/openscience/jmol/app/nbo/help/atomColors.txt";
try {
- atomColors = GuiMap.getResourceString(this, fname);
+ String atomColors = "";
+ atomColors = GuiMap.getResourceString(this,
"org/gennbo/help/atomColors.txt");
+ runScriptNow(atomColors + ";refresh");
+ nboView = true;
} catch (IOException e) {
alertError("Atom colors not found");
}
- runScriptNow(atomColors + ";refresh");
}
- /**
- * Resets Jmol look and feel
- */
- protected void resetColorScheme() {
- nboView = false;
- runScriptNow("background black;set defaultcolors Jmol;refresh;");
- }
-
// /**
// * sets components visible recursively
// * @param c
@@ -539,7 +560,7 @@
*/
protected void showAtomNums(boolean alpha) {
if (!showAtNum) {
- runScriptNow("select {*};label off; select remove {*}");
+ runScriptNow("select {*};label off; select none");
return;
}
SB sb = new SB();
@@ -550,7 +571,7 @@
sb.append("select {*};color labels white;");
sb.append("select {H*};color labels " + color + ";"
- + "set labeloffset 0 0 {*}; select remove {*};");
+ + "set labeloffset 0 0 {*}; select none;");
runScriptNow(sb.toString());
}
@@ -617,8 +638,7 @@
* p, b, r ("red"), i, etc.
*/
protected synchronized void log(String line, char chFormat) {
- if (line.trim().equals("") || jpNBOLog == null || !debugVerbose
- && "b|r".indexOf("" + chFormat) < 0)
+ if (dontLog(line, chFormat))
return;
if (line.trim().length() >= 1) {
line = PT.rep(line.trim(), "<", "<");
@@ -640,6 +660,13 @@
jpNBOLog.setCaretPosition(jpNBOLog.getDocument().getLength());
}
+ private boolean dontLog(String line, char chFormat) {
+ return (jpNBOLog == null
+ || line.trim().equals("")
+ || line.indexOf("read/unit=5/attempt to read past end") >= 0
+ || !debugVerbose && "b|r".indexOf("" + chFormat) < 0);
+ }
+
protected void alertError(String line) {
log(line, 'r');
vwr.alert(line);
Modified: trunk/Jmol/src/org/gennbo/NBODialogRun.java
===================================================================
--- trunk/Jmol/src/org/gennbo/NBODialogRun.java 2017-01-25 18:12:49 UTC (rev
21345)
+++ trunk/Jmol/src/org/gennbo/NBODialogRun.java 2017-01-25 20:52:14 UTC (rev
21346)
@@ -331,6 +331,44 @@
// return true;
// }
+
+ /**
+ * gets a valid $CHOOSE list from nbo file if it exists and corrects the
bonds
+ * in the Jmol model
+ *
+ *
+ * @return false if output contains error
+ */
+ protected boolean getChooseList() {
+ File f = NBOFileHandler.newNBOFile(inputFileHandler.inputFile, "nbo");
+ if (!f.exists() || f.length() == 0)
+ return false;
+ String fdata = inputFileHandler.getFileData(f.toString());
+ String[] tokens = PT.split(fdata, "\n $CHOOSE");
+ int i = 1;
+ if (tokens.length < 2) {
+ logInfo("$CHOOSE record was not found in " + f,
+ Logger.LEVEL_INFO);
+ return false;
+ }
+ if (tokens[1].trim().startsWith("keylist")) {
+ if (!tokens[1].contains("Structure accepted:")) {
+ if (tokens[1].contains("missing END?")) {
+ logInfo("Plot files not found. Have you used RUN yet?",
+ Logger.LEVEL_ERROR);
+ return false;
+ } else if (tokens[2].contains("ignoring")) {
+ System.out.println("Ignoring $CHOOSE list");
+ } else {
+ return false;
+ }
+ }
+ i = 3;
+ }
+ setChooseList(tokens[i].substring(0, tokens[i].indexOf("$END")));
+ return true;
+ }
+
protected void setChooseList(String data) {
chooseList = new ChooseList();
String[] tokens = PT.split(data, "END");
@@ -652,15 +690,10 @@
fileData = inputFileHandler.read47File();
nboKeywords = cleanNBOKeylist(fileData[1]);
- if (inputFileHandler.useExt.equals("47")) {
- if (!inputFileHandler.getChooseList()) {
- File f = NBOFileHandler.newNBOFile(inputFileHandler.inputFile, "nbo");
- if (f.exists())
- logInfo("Error reading $CHOOSE list", Logger.LEVEL_ERROR);
- } else
- setBonds(true);
- }
+ if (inputFileHandler.useExt.equals("47"))
+ getChooseList();
showAtomNums(true);
+ setBonds(true);
addNBOKeylist();
for (Component c : panel.getComponents())
c.setVisible(true);
Modified: trunk/Jmol/src/org/gennbo/NBODialogSearch.java
===================================================================
--- trunk/Jmol/src/org/gennbo/NBODialogSearch.java 2017-01-25 18:12:49 UTC
(rev 21345)
+++ trunk/Jmol/src/org/gennbo/NBODialogSearch.java 2017-01-25 20:52:14 UTC
(rev 21346)
@@ -1000,7 +1000,7 @@
if (list.equals(list3)) {
changeKey(nrt);
//Parsing RS list here ensures RS list will be in .nbo file
- parseRsList(inputFileHandler.getRSList());
+ parseRsList(getRSList());
unit.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
@@ -1046,6 +1046,29 @@
}
}
+ protected String[] getRSList() {
+ String data = inputFileHandler.getInputFile("nbo");
+ String[] toks = PT.split(data,
+ "TOPO matrix for the leading resonance structure:\n");
+ if (toks.length < 2) {
+ if (toks[0].contains("0 candidate reference structure(s)"))
+ alertError("0 candidate reference structure(s) calculated by SR LEWIS"
+ + "Candidate reference structure taken from NBO search");
+ return null;
+ }
+ String[] toks2 = PT
+ .split(toks[1],
+
"---------------------------------------------------------------------------");
+ String[] rsList = new String[2];
+ rsList[0] = toks2[0].substring(toks2[0].lastIndexOf('-'),
+ toks2[0].indexOf("Res")).trim();
+ rsList[0] = rsList[0].replace("-\n", "");
+ rsList[1] = toks2[1];
+ return rsList;
+ }
+
+
+
/**
* Takes two strings from .nbo file and parses RS list information toks[0] =
* primary rs matrix toks[1] = change list using accountants notation
@@ -1361,8 +1384,8 @@
alphaSpin.setVisible(false);
betaSpin.setVisible(false);
}
- if (!inputFileHandler.getChooseList())
- alertError("Error reading $CHOOSE list");
+
+ getChooseList();
showAtomNums(true);
setBonds(true);
Modified: trunk/Jmol/src/org/gennbo/NBODialogView.java
===================================================================
--- trunk/Jmol/src/org/gennbo/NBODialogView.java 2017-01-25 18:12:49 UTC
(rev 21345)
+++ trunk/Jmol/src/org/gennbo/NBODialogView.java 2017-01-25 20:52:14 UTC
(rev 21346)
@@ -481,6 +481,7 @@
protected void setOrbitalColors(char plusMinus) {
currSign = plusMinus;
+ // just for one orbital?
runScriptNow("nbo color "
+ (plusMinus == '+' ? color2 + " " + color1 : color1 + " " + color2));
}
@@ -1427,10 +1428,7 @@
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);
+ getChooseList();
showAtomNums(true);
colorMeshes();
alphaSpin.setVisible(isOpenShell);
Modified: trunk/Jmol/src/org/gennbo/NBOFileHandler.java
===================================================================
--- trunk/Jmol/src/org/gennbo/NBOFileHandler.java 2017-01-25 18:12:49 UTC
(rev 21345)
+++ trunk/Jmol/src/org/gennbo/NBOFileHandler.java 2017-01-25 20:52:14 UTC
(rev 21346)
@@ -153,6 +153,8 @@
//return false;
if (dialog.dialogMode == NBODialog.DIALOG_MODEL)
return true;
+ // DP? if(!inputFile.getAbsolutePath().endsWith(".47"))
+ // DP? inputFile = newNBOFile(inputFile, "47");
if (!useExt.equals("47")) {
jobStem = NBOFileHandler.getJobStem(inputFile);
dialog.loadModelFromNBO(fileDir, jobStem, useExt);
@@ -287,67 +289,6 @@
return false;
}
- /**
- * gets a valid $CHOOSE list from nbo file if it exists and corrects the
bonds
- * in the jmol model
- *
- * @return false if output contains error
- */
- protected boolean getChooseList() {
- File f = newNBOFile(inputFile, "nbo");
- if (!f.exists() || f.length() == 0)
- return false;
- String fdata = getFileData(f.toString());
- String[] tokens = PT.split(fdata, "\n $CHOOSE");
- int i = 1;
- if (tokens.length < 2) {
- dialog.logInfo("$CHOOSE record was not found in " + f,
- Logger.LEVEL_INFO);
- return false;
- }
- if (tokens[1].trim().startsWith("keylist")) {
- if (!tokens[1].contains("Structure accepted:")) {
- if (tokens[1].contains("missing END?")) {
- dialog.logInfo("Plot files not found. Have you used RUN yet?",
- Logger.LEVEL_ERROR);
- return false;
- } else if (tokens[2].contains("ignoring")) {
- dialog.alert("Ignoring $CHOOSE list");
- } else {
- return false;
- }
- }
- i = 3;
- }
- String data = tokens[i].substring(0, tokens[i].indexOf("$END"));
-
- dialog.setChooseList(data);
-
- return true;
- }
-
- protected String[] getRSList() {
- String data = getFileData(newNBOFile(inputFile, "nbo").toString());
- String[] toks = PT.split(data,
- "TOPO matrix for the leading resonance structure:\n");
- if (toks.length < 2) {
- if (toks[0].contains("0 candidate reference structure(s)"))
- dialog
- .alertError("0 candidate reference structure(s) calculated by SR
LEWIS"
- + "Candidate reference structure taken from NBO search");
- return null;
- }
- String[] toks2 = PT
- .split(toks[1],
-
"---------------------------------------------------------------------------");
- String[] rsList = new String[2];
- rsList[0] = toks2[0].substring(toks2[0].lastIndexOf('-'),
- toks2[0].indexOf("Res")).trim();
- rsList[0] = rsList[0].replace("-\n", "");
- rsList[1] = toks2[1];
- return rsList;
- }
-
public void clear() {
tfName.setText("");
tfExt.setText("");
@@ -412,4 +353,8 @@
btnBrowse.setEnabled(b);
}
+ public String getInputFile(String name) {
+ return getFileData(newNBOFile(inputFile, name).toString());
+ }
+
}
Added: trunk/Jmol/src/org/gennbo/NBOPlugin.java
===================================================================
--- trunk/Jmol/src/org/gennbo/NBOPlugin.java (rev 0)
+++ trunk/Jmol/src/org/gennbo/NBOPlugin.java 2017-01-25 20:52:14 UTC (rev
21346)
@@ -0,0 +1,78 @@
+/* $RCSfile$
+ * $Author: hansonr $
+ * $Date: 2014-12-13 22:43:17 -0600 (Sat, 13 Dec 2014) $
+ * $Revision: 20162 $
+ *
+ * Copyright (C) 2002-2005 The Jmol Development Team
+ *
+ * Contact: jmol-develop...@lists.sf.net
+ *
+ * This library is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation; either
+ * version 2.1 of the License, or (at your option) any later version.
+ *
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this library; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+ */
+package org.gennbo;
+
+import javax.swing.JFrame;
+
+import org.jmol.c.CBK;
+import org.jmol.viewer.Viewer;
+import org.openscience.jmol.app.JmolPlugin;
+
+public class NBOPlugin implements JmolPlugin {
+
+ protected NBODialog nboDialog;
+ protected Viewer vwr;
+
+ public final static String version = "0.1.1";
+
+ @Override
+ public void start(JFrame frame, Viewer vwr) {
+ this.vwr = vwr;
+ nboDialog = new NBODialog(this, frame, vwr);
+ System.out.println("NBO Plugin started.");
+ }
+
+ @Override
+ public String getName() {
+ return "NBO";
+ }
+
+ @Override
+ public String getVersion() {
+ return version;
+ }
+
+ @Override
+ public void setVisible(boolean b) {
+ if (nboDialog == null)
+ return;
+ nboDialog.setVisible(b);
+ }
+
+ @Override
+ public void destroy() {
+ if (nboDialog == null)
+ return;
+ nboDialog.close();
+ nboDialog = null;
+ }
+
+ @Override
+ public void notifyCallback(CBK type, Object[] data) {
+ if (nboDialog == null)
+ return;
+ nboDialog.notifyCallback(type, data);
+ }
+
+}
Property changes on: trunk/Jmol/src/org/gennbo/NBOPlugin.java
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property
Modified: trunk/Jmol/src/org/gennbo/NBOService.java
===================================================================
--- trunk/Jmol/src/org/gennbo/NBOService.java 2017-01-25 18:12:49 UTC (rev
21345)
+++ trunk/Jmol/src/org/gennbo/NBOService.java 2017-01-25 20:52:14 UTC (rev
21346)
@@ -82,7 +82,7 @@
// 1 1 2
//
// jmol_outfile.txt is:
-
+
// DATA " "
// 1 1 2
// NBOServe: NATURAL BOND ORBITAL PROGRAM SUITE
@@ -128,21 +128,18 @@
// GLOBAL C_PATH C:\temp
// GLOBAL C_JOBSTEM ch3nh2
// CMD VIEW 1
-
-
-
+
// modes of operation
-
+
// NOTE: There was a problem in that View and Raw were both 4 here
-
+
static final int MODE_ERROR = -1;
static final int MODE_RAW = 0;// leave this 0; it is referred to that in
StatusListener
-
// these are for panel state
static final int MODE_MODEL = 1; // don't change this number -- it is used
for LOAD NBO
static final int MODE_RUN = 20;
-
+
// these are for rawCmdNew only
static final int MODE_VALUE = 45;
static final int MODE_LIST = 46;
@@ -153,44 +150,44 @@
//static final int MODE_VALUE_M = 60;
static final int MODE_GETRS = 61;
static final int MODE_LABEL_BONDS = 62;
+
protected int count;
+ protected boolean isWorking;
protected Viewer vwr;
-
- NBODialog nboDialog;
-
protected Process nboServer;
protected Thread nboListener;
- private InputStream stdout;
protected BufferedReader nboReader;
+ protected NBODialog nboDialog;
+ protected NBOJob currJob;
+ protected Object lock;
+ protected Queue<NBOJob> jobQueue;
+
private PrintWriter stdinWriter;
+ private InputStream stdout;
private SB sbRet;
-
private boolean inData;
- protected boolean isWorking;
+ private boolean cantStartServer;
private String serverPath;
- private String serverDir;
private String nboModel;
-
- NBOJob currJob;
- Queue<NBOJob> jobQueue;
- protected Object lock;
- private boolean cantStartServer;
+
private String exeName = "NBOServe.exe";
-
+
/**
* Manage communication between Jmol and NBOServer
+ * @param nboDialog
*
* @param vwr
* The interacting display we are reproducing (source of view angle
* info etc)
*/
- public NBOService(Viewer vwr) {
+ public NBOService(NBODialog nboDialog, Viewer vwr) {
+ this.nboDialog = nboDialog;
this.vwr = vwr;
sbRet = new SB();
- setServerPath(getNBOProperty("serverPath",
- System.getProperty("user.home") + "/NBOServe"));
+ setServerPath(getNBOProperty("serverPath", System.getProperty("user.home")
+ + "/NBOServe"));
jobQueue = new ArrayDeque<NBOJob>();
lock = new Object();
}
@@ -198,11 +195,12 @@
boolean isOffLine() {
return cantStartServer;
}
-
+
/**
* Return path to NBOServe directory.
*
- * @param fileName or null for path itself, without slash
+ * @param fileName
+ * or null for path itself, without slash
*
* @return path
*/
@@ -224,7 +222,6 @@
return serverPath != null;
}
-
protected String getNBOProperty(String name, String defaultValue) {
return JmolPanel.getPluginOption("NBO", name, defaultValue);
}
@@ -234,14 +231,14 @@
JmolPanel.setPluginOption("NBO", name, option);
}
-
/**
* @param job
*/
protected void sendToNBO(NBOJob job) {
String s = "<" + job.cmd + ">";
currJob = job;
- nboDialog.inputFileHandler.writeToFile(serverDir + "/" + job.cmd,
job.sb.toString());
+ nboDialog.inputFileHandler.writeToFile(getServerPath(job.cmd),
+ job.sb.toString());
nboDialog.setStatus(job.statusInfo + " (sending job.cmd)");
sendCmd(s);
}
@@ -249,7 +246,7 @@
private void sendCmd(String s) {
count = 1;
System.out.println("sending " + s);
- if(stdinWriter == null)
+ if (stdinWriter == null)
restart();
stdinWriter.println(s);
stdinWriter.flush();
@@ -294,13 +291,13 @@
int pt = line.indexOf("\n");
return (pt < 0 ? line + s : line.substring(0, pt) + s +
line.substring(pt));
}
-
+
String startProcess(boolean sync, @SuppressWarnings("unused") final int
mode) {
try {
System.out.println("starting NBO process sync=" + sync);
- File pathToExecutable = new File(serverPath + "/" + exeName );
- ProcessBuilder builder = new ProcessBuilder(serverPath + "/" + exeName);
- builder.directory(new File(pathToExecutable.getParent())); // this is
where you set the root folder for the executable to run with
+ String path = getServerPath(exeName);
+ ProcessBuilder builder = new ProcessBuilder(path);
+ builder.directory(new File(new File(path).getParent())); // root folder
for executable
builder.redirectErrorStream(true);
nboServer = builder.start();
stdout = nboServer.getInputStream();
@@ -427,13 +424,13 @@
nboAddModelLine(line);
}
break;
-// case MODE_VALUE_M:
-// if (line.indexOf("DATA") >= 0)
-// isWorking = inRequest = false;
-// if (inRequest && isWorking)
-// nboDialog.processModelLine(line);
-// break;
-//
+ // case MODE_VALUE_M:
+ // if (line.indexOf("DATA") >= 0)
+ // isWorking = inRequest = false;
+ // if (inRequest && isWorking)
+ // nboDialog.processModelLine(line);
+ // break;
+ //
case MODE_GETRS:
if (inRequest && isWorking) {
int cnt = Integer.parseInt(line.trim());
@@ -469,14 +466,15 @@
}
private int lineNo = 0;
+
protected void logServerLine(String line) {
- nboDialog.logInfo((++lineNo) + "< " + line, isFortranError(line) ?
Logger.LEVEL_ERROR : Logger.LEVEL_DEBUG);
- }
-
+ nboDialog.logInfo((++lineNo) + "< " + line,
+ isFortranError(line) ? Logger.LEVEL_ERROR : Logger.LEVEL_DEBUG);
+ }
+
protected boolean isFortranError(String line) {
return line.indexOf("Permission denied") >= 0
- || line.indexOf("PGFIO-F") >= 0
- || line.indexOf("Invalid command") >= 0;
+ || line.indexOf("PGFIO-F") >= 0 || line.indexOf("Invalid command") >=
0;
}
public void closeProcess() {
@@ -493,7 +491,7 @@
}
nboReader = null;
try {
- nboListener.interrupt();
+ nboListener.interrupt();
} catch (Exception e) {
System.out.println("can't interrupt");
}
@@ -515,46 +513,44 @@
startProcess(false, MODE_RAW);
return (nboServer != null);
}
-
/**
* The interface for ALL communication with NBOServe from NBODialog.
+ *
* @param cmd
* @param data
- * @param dialogMode
- * @param list
- * @param status
+ * @param dialogMode
+ * @param list
+ * @param status
*/
protected void rawCmdNew(String cmd, SB data, int dialogMode,
DefaultComboBoxModel<String> list, String status) {
- if(dialogMode == MODE_LABEL){
- nboDialog.runScriptNow("mo delete; nbo delete");
+ if (dialogMode == MODE_LABEL) {
+ nboDialog.runScriptNow("mo delete; nbo delete");
+ }
+ String fname = null;
+ synchronized (lock) {
+ if (data == null) {
+ nboDialog.logInfo("> " + cmd, Logger.LEVEL_DEBUG);
+ } else {
+ fname = cmd + "_cmd.txt";
+ nboDialog.logInfo("> " + fname + "\n" + data, Logger.LEVEL_DEBUG);
+ cmd = "<" + fname + ">";
+ isWorking = true;
}
- String fname = null;
- synchronized(lock){
- if (data == null) {
- nboDialog.logInfo("> " + cmd, Logger.LEVEL_DEBUG);
- } else {
- fname = cmd + "_cmd.txt";
- nboDialog.logInfo("> " + fname + "\n" + data, Logger.LEVEL_DEBUG);
- cmd = "<" + fname + ">";
- isWorking = true;
- }
- if(jobQueue.isEmpty()){
- currJob = new NBOJob(fname,data, status, list);
- jobQueue.add(currJob);
- currJob.dialogMode = dialogMode;
- sendToNBO(currJob);
- }
- else{
- NBOJob j = new NBOJob(fname,data, status, list);
- j.dialogMode = dialogMode;
- jobQueue.add(j);
- }
- }
+ if (jobQueue.isEmpty()) {
+ currJob = new NBOJob(fname, data, status, list);
+ jobQueue.add(currJob);
+ currJob.dialogMode = dialogMode;
+ sendToNBO(currJob);
+ } else {
+ NBOJob j = new NBOJob(fname, data, status, list);
+ j.dialogMode = dialogMode;
+ jobQueue.add(j);
+ }
+ }
}
-
class NBOJob {
String cmd;
String statusInfo;
@@ -577,7 +573,8 @@
String arch = System.getenv("PROCESSOR_ARCHITECTURE");
File f = new File(getServerPath("gennbo.bat"));
if (!f.exists()) {
- vwr.alert(f + " not found, make sure gennbo.bat is in same directory as
" + exeName);
+ vwr.alert(f + " not found, make sure gennbo.bat is in same directory as "
+ + exeName);
return false;
}
String wow64Arch = System.getenv("PROCESSOR_ARCHITEW6432");
@@ -603,6 +600,8 @@
return true;
}
+ public void clearQueue() {
+ jobQueue.clear();
+ }
-
-}
\ No newline at end of file
+}
Added: trunk/Jmol/src/org/openscience/jmol/app/JmolPlugin.java
===================================================================
--- trunk/Jmol/src/org/openscience/jmol/app/JmolPlugin.java
(rev 0)
+++ trunk/Jmol/src/org/openscience/jmol/app/JmolPlugin.java 2017-01-25
20:52:14 UTC (rev 21346)
@@ -0,0 +1,15 @@
+package org.openscience.jmol.app;
+
+import javax.swing.JFrame;
+
+import org.jmol.c.CBK;
+import org.jmol.viewer.Viewer;
+
+public interface JmolPlugin {
+ void start(JFrame frame, Viewer viewer);
+ void destroy();
+ String getVersion();
+ String getName();
+ void setVisible(boolean b);
+ void notifyCallback(CBK type, Object[] data);
+}
Property changes on: trunk/Jmol/src/org/openscience/jmol/app/JmolPlugin.java
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property
Modified: trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/JmolPanel.java
===================================================================
--- trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/JmolPanel.java
2017-01-25 18:12:49 UTC (rev 21345)
+++ trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/JmolPanel.java
2017-01-25 20:52:14 UTC (rev 21346)
@@ -52,8 +52,10 @@
import java.util.Hashtable;
import java.util.List;
import java.util.Map;
+import java.util.Map.Entry;
import java.util.Properties;
+import javajs.util.Lst;
import javajs.util.PT;
import javax.swing.AbstractAction;
@@ -94,6 +96,7 @@
import org.openscience.jmol.app.HistoryFile;
import org.openscience.jmol.app.Jmol;
import org.openscience.jmol.app.JmolApp;
+import org.openscience.jmol.app.JmolPlugin;
import org.openscience.jmol.app.SplashInterface;
import org.openscience.jmol.app.jmolpanel.console.AppConsole;
import org.openscience.jmol.app.jmolpanel.console.ConsoleTextArea;
@@ -118,19 +121,13 @@
StatusBar status;
int startupWidth, startupHeight;
JsonNioServer serverService;
- public NBOService nboService;
// Called by NBODialog
- public void setNBOService(NBOService service) {
- this.nboService = service;
- }
-
protected String appletContext;
protected PropertyChangeSupport pcs = new PropertyChangeSupport(this);
protected DisplayPanel display;
protected GaussianDialog gaussianDialog;
- protected NBODialog nboDialog;
protected RecentFilesDialog recentFiles;
protected AtomSetChooser atomSetChooser;
public JFrame frame;
@@ -285,23 +282,6 @@
say(GT._("Initializing Script Window..."));
vwr.getProperty("DATA_API", "getAppConsole", Boolean.TRUE);
- // Setup Plugin system
- // say(GT._("Loading plugins..."));
- // pluginManager = new CDKPluginManager(
- // System.getProperty("user.home") + System.getProperty("file.separator")
- // + ".jmol", new JmolEditBus(vwr)
- // );
- //
pluginManager.loadPlugin("org.openscience.cdkplugin.dirbrowser.DirBrowserPlugin");
- //
pluginManager.loadPlugin("org.openscience.cdkplugin.dirbrowser.DadmlBrowserPlugin");
- // pluginManager.loadPlugins(
- // System.getProperty("user.home") + System.getProperty("file.separator")
- // + ".jmol/plugins"
- // );
- // feature to allow for globally installed plugins
- // if (System.getProperty("plugin.dir") != null) {
- // pluginManager.loadPlugins(System.getProperty("plugin.dir"));
- // }
-
// install the command table
say(GT._("Building Command Hooks..."));
commands = new Hashtable<String, Action>();
@@ -608,6 +588,8 @@
dispose(frame, saveSize);
return true;
}
+
+ Map<String, JmolPlugin> plugins = new Hashtable<String, JmolPlugin>();
void dispose(JFrame f, boolean saveSize) {
// Save window positions and status in the history
@@ -623,14 +605,16 @@
serverService.close();
serverService = null;
}
- if(nboDialog != null){
- nboDialog.close();
- nboDialog = null;
+
+ for (Entry<String, JmolPlugin> e : plugins.entrySet()) {
+ try {
+ e.getValue().destroy();
+ } catch (Throwable err) {
+ // ignore
+ }
}
- if(nboService != null){
- nboService.closeProcess();
- nboService = null;
- }
+ plugins.clear();
+
if (numWindows <= 1) {
// Close Jmol
report(GT._("Closing Jmol..."));
@@ -1173,19 +1157,24 @@
*/
void startNBO(String type) {
- String nboServerPath = historyFile.getProperty("nboServerPath", null);
+ String nboServerPath = getPluginOption("NBO", "serverPath", null);
if (nboServerPath == null) {
vwr.alert("NBOServe.exe has not been installed. See
http://nbo6.chem.wisc.edu/new6_css.htm for additional information");
- return;
}
+ showPlugin("NBO", "org.gennbo.NBOPlugin");
+ }
- if (nboDialog == null)
- nboDialog = (NBODialog) getInstanceWithParams("org.gennbo.NBODialog",
- new Class[] { JFrame.class, Viewer.class }, frame, vwr );
- if (nboDialog == null) {
- vwr.alert("The NBODialog class could not be found.");
- } else {
- nboDialog.setVisible(true);
+ private void showPlugin(String name, String path) {
+ try {
+ JmolPlugin p = plugins.get(name);
+ if (p == null) {
+ plugins.put(name, p = (JmolPlugin) Interface.getInterface(path, vwr,
+ "plugin"));
+ p.start(frame, vwr);
+ }
+ p.setVisible(true);
+ } catch (Throwable e) {
+ System.out.println("Error creating plugin " + name);
}
}
@@ -1708,10 +1697,8 @@
gaussianDialog.dispose();
gaussianDialog = null;
}
- if (nboDialog != null) {
- nboDialog.dispose();
- nboDialog = null;
- }
+
+
boolean doTranslate = GT.setDoTranslate(true);
getDialogs();
GT.setDoTranslate(doTranslate);
Modified: trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/StatusListener.java
===================================================================
--- trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/StatusListener.java
2017-01-25 18:12:49 UTC (rev 21345)
+++ trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/StatusListener.java
2017-01-25 20:52:14 UTC (rev 21346)
@@ -43,6 +43,7 @@
import org.jmol.dialog.Dialog;
import org.jmol.util.Logger;
import org.jmol.viewer.Viewer;
+import org.openscience.jmol.app.JmolPlugin;
import org.openscience.jmol.app.jmolpanel.console.AppConsole;
import org.openscience.jmol.app.webexport.WebExport;
@@ -122,8 +123,9 @@
@SuppressWarnings("unchecked")
@Override
public void notifyCallback(CBK type, Object[] data) {
- if (jmol.nboDialog != null)
- jmol.nboDialog.notifyCallback(type, data);
+ if (!jmol.plugins.isEmpty())
+ for (JmolPlugin p : jmol.plugins.values())
+ p.notifyCallback(type, data);
String strInfo = (data == null || data[1] == null ? null : data[1]
.toString());
Map<String, Object> info;
@@ -149,10 +151,10 @@
if (jmol.frame != null) {
//Font f = jmol.frame.getFont();
//if (f != null) {
- //int m = jmol.frame.getFontMetrics(f).stringWidth("M");
- //int n = jmol.frame.getWidth() / m;
- //if (n < menuName.length())
- //menuName = menuName.substring(0, n) + "...";
+ //int m = jmol.frame.getFontMetrics(f).stringWidth("M");
+ //int n = jmol.frame.getWidth() / m;
+ //if (n < menuName.length())
+ //menuName = menuName.substring(0, n) + "...";
//}
jmol.frame.setTitle(menuName);
}
@@ -190,7 +192,7 @@
String service = (String) info.get("service");
if ("nbo".equals(service)) {
if ("showPanel".equals(info.get("action")))
- jmol.startNBO(null);
+ jmol.startNBO(null);
//else
//jmol.getNBOService().processRequest(info, 0);
}
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