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Jmol: an open-source Java viewer for chemical structures in 3D
/* $RCSfile$
* $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: [email protected]
*
* 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 java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Component;
import java.awt.Container;
import java.awt.Cursor;
import java.awt.Dimension;
import java.awt.Font;
import java.awt.GridBagConstraints;
import java.awt.GridBagLayout;
import java.awt.GridLayout;
import java.awt.Image;
import java.awt.Insets;
import java.awt.Rectangle;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
import java.io.File;
import java.util.Map;
import javajs.swing.SwingConstants;
import javajs.util.PT;
import javax.swing.BorderFactory;
import javax.swing.Box;
import javax.swing.BoxLayout;
import javax.swing.ImageIcon;
import javax.swing.JButton;
import javax.swing.JComboBox;
import javax.swing.JDialog;
import javax.swing.JFileChooser;
import javax.swing.JFrame;
import javax.swing.JLabel;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.JSplitPane;
import javax.swing.JTextField;
import javax.swing.JTextPane;
import javax.swing.Timer;
import javax.swing.border.LineBorder;
import javax.swing.filechooser.FileNameExtensionFilter;
import org.jmol.c.CBK;
import org.jmol.java.BS;
import org.jmol.util.Logger;
import org.jmol.viewer.Viewer;
import org.openscience.jmol.app.jmolpanel.JmolPanel;
/**
* A dialog for interacting with NBOServer
*
* MEMO: all save/restore orientation is turned off.
*
*/
public class NBODialog extends JDialog {
protected JLabel licenseInfo;
private JButton helpBtn;
private JDialog settingsDialog;
private JPanel topPanel;
protected JButton modelButton, runButton, viewButton, searchButton;
protected JPanel settingsPanel;
private JPanel homePanel;
protected JPanel nboOutput;
protected String lastOutputSaveName;
protected NBOModel modelPanel;
protected NBORun runPanel;
private NBOSearch searchPanel;
protected NBOView viewPanel;
protected JPanel viewSettingsBox;
protected static final int DIALOG_HOME = 0;
protected static final int DIALOG_MODEL = 1;
protected static final int DIALOG_RUN = 2;
protected static final int DIALOG_VIEW = 3;
protected static final int DIALOG_SEARCH = 4;
protected static final int DIALOG_CONFIG = 5;
protected static final int DIALOG_HELP = 6;
final private static String[] dialogNames = new String[] { "Home", "Model",
"Run", "View", "Search", "Settings", "Help" };
protected static String getDialogName(int type) {
return dialogNames[type];
}
protected static final int ORIGIN_UNKNOWN = 0;
protected static final int ORIGIN_NIH = 1;
protected static final int ORIGIN_LINE_FORMULA = 2;
protected static final int ORIGIN_FILE_INPUT = 3;
protected static final int ORIGIN_NBO_ARCHIVE = 4;
protected int modelOrigin = ORIGIN_UNKNOWN;
protected boolean jmolOptionNOZAP = false; // do no zap between modules
protected boolean jmolOptionNOSET = false; // do not use NBO settings by default
protected boolean jmolOptionVIEW = false; // present only the VIEW option
protected boolean jmolOptionNONBO = false; // do not try to contact NBOServe
/**
* Allowing passage of Jmol options. Currently: NOZAP;NOSET;JMOL;VIEW
*
* @param jmolOptions
*/
protected void setJmolOptions(Map jmolOptions) {
String options = ("" + (jmolOptions == null ? "" : jmolOptions
.get("options"))).toUpperCase();
if (options.equals("VIEW"))
options = "VIEW;NOZAP;NOSET;NONBO";
jmolOptionVIEW = (options.indexOf("VIEW") >= 0);
jmolOptionNOZAP = (options.indexOf("NOZAP") >= 0);
jmolOptionNOSET = (options.indexOf("NOSET") >= 0);
jmolOptionNONBO = (options.indexOf("NONBO") >= 0);
}
protected Viewer vwr;
protected NBOService nboService;
/**
* Jmol plugin object for NBO
*
*/
protected NBOPlugin nboPlugin;
// private/protected variables
// /**
// * Tracks the last resonance structure type (nrtstra, nrtstrb, alpha, beta);
// * reset to “alpha” by openPanel()
// */
// private String rsTypeLast = "alpha";
/**
* String value of what is showing in the session dialog -- persistent
*/
protected String nboOutputBodyText = "";
/**
* The input file handler; recreated via openPanel()
*/
protected NBOFileHandler inputFileHandler;
protected JLabel icon;
protected JSplitPane centerPanel;
protected JPanel modulePanel;
protected JLabel statusLab;
protected JTextPane jpNBODialog;
/**
* true if NBOServe has successfully restarted-- persistent
*/
protected boolean haveService;
/**
* the dialog that is currently open, for example DIALOG_MODEL-- persistent
*/
protected int dialogMode;
/**
* configuration information source
*/
protected NBOConfig config;
private boolean isOpenShell;
private boolean isCaretEnabled = true;
protected void setCaretEnabled(boolean tf) {
isCaretEnabled = tf;
if (tf)
log("\n", 'b');
}
/**
* Creates a dialog for getting info related to output frames in nbo format.
*
* @param jmolFrame
* The Jmol frame associated with the dialog
* @param vwr
* The interacting display we are reproducing (source of view angle
* info etc)
* @param plugin
* @param jmolOptions
*/
public NBODialog(NBOPlugin plugin, JFrame jmolFrame, Viewer vwr,
Map jmolOptions) {
super(jmolFrame);
setName(plugin.getName());
setTitle(getName() + " " + plugin.getVersion());
setJmolOptions(jmolOptions);
this.vwr = vwr;
nboPlugin = plugin;
nboService = new NBOService(this, vwr, !jmolOptionNONBO);
config = new NBOConfig(this);
setIconImage(nboPlugin.getIcon("nbo6logo20x20").getImage());
setLayout(new BorderLayout());
if (!jmolOptionNOSET)
runScriptQueued(NBOConfig.DEFAULT_SCRIPT);
modelPanel = new NBOModel(this);
runPanel = new NBORun(this);
viewPanel = searchPanel = new NBOSearch(this);
createDialog(jmolFrame);
if (!jmolOptionNOSET)
config.doSetDefaults(false);
if (jmolOptionVIEW || jmolOptionNONBO)
doOpenPanel(DIALOG_VIEW);
}
protected void doOpenPanel(int type) {
if (jmolOptionNONBO && "rsm".indexOf("" + type) >= 0) {
vwr.alert("This option requires NBOServe");
return;
}
if (type == DIALOG_CONFIG) {
settingsDialog.setVisible(true);
return;
}
if (nboService.isWorking()) {
int i = JOptionPane.showConfirmDialog(this,
"NBOServe is working. Cancel current job?\n"
+ "This could affect input/output files\n"
+ "if GenNBO is running.", "Message", JOptionPane.YES_NO_OPTION);
if (i == JOptionPane.NO_OPTION) {
return;
}
}
logCmd("Entering " + getDialogName(type));
nboService.restart();
// nboService.restartIfNecessary();
nboService.clearQueue();
if (!checkEnabled()) {
doOpenPanel(DIALOG_CONFIG);
return;
}
if (type != DIALOG_CONFIG) {
if (dialogMode == DIALOG_HOME) {
remove(homePanel);
add(centerPanel, BorderLayout.CENTER);
}
resetModuleVariables();
}
viewSettingsBox.setVisible(false);
if (topPanel != null)
topPanel.remove(icon);
switch (dialogMode = type) {
case DIALOG_CONFIG:
break;
case DIALOG_MODEL:
centerPanel.setLeftComponent(modulePanel = modelPanel.buildModelPanel());
icon = new JLabel(nboPlugin.getIcon("nbomodel_logo"));
setThis(modelButton);
break;
case DIALOG_RUN:
centerPanel.setLeftComponent(modulePanel = runPanel.buildRunPanel());
icon = new JLabel(nboPlugin.getIcon("nborun_logo"));
setThis(runButton);
break;
case DIALOG_VIEW:
centerPanel.setLeftComponent(modulePanel = viewPanel.buildViewPanel());
icon = new JLabel(nboPlugin.getIcon("nboview_logo"));
if (NBOConfig.nboView)
setThis(viewButton);
break;
case DIALOG_SEARCH:
centerPanel.setLeftComponent(modulePanel = searchPanel.buildSearchPanel());
//settingsBox.setVisible(true);
icon = new JLabel(nboPlugin.getIcon("nbosearch_logo"));
setThis(searchButton);
break;
}
resetDivider();
if (topPanel != null)
topPanel.add(icon, BorderLayout.EAST);
setStatus("");
invalidate();
setVisible(true);
runScriptQueued(jmolOptionNOZAP ? "select none" : "zap");
}
/**
* Rest all variables that might be an issue
*
*/
private void resetModuleVariables() {
// Anything here that looks like it needs resetting prior to changing panels.
viewPanel.resetCurrentOrbitalClicked();
resetVariables_c();
}
private void createDialog(JFrame jmolFrame) {
dialogMode = DIALOG_HOME;
Rectangle bounds = jmolFrame.getBounds();
if (bounds.height < 630)
jmolFrame.setSize(bounds.width, 630);
// createDialog(Math.max(570, 615);
setBounds(bounds.x + bounds.width, bounds.y, 650,
Math.max(bounds.height, 630));
addWindowListener(new WindowAdapter() {
@Override
public void windowClosing(WindowEvent e) {
nboService.closeProcess(false);
close();
}
});
placeNBODialog(this);
licenseInfo = new JLabel("License not found", SwingConstants.CENTER);
//licenseInfo.setBackground(null);
licenseInfo.setOpaque(true);
licenseInfo.setForeground(Color.white);
licenseInfo.setBackground(Color.black);
createOutputDialog();
centerPanel = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT, new JPanel(),
nboOutput);
topPanel = buildTopPanel();
getContentPane().add((homePanel = mainPage()), BorderLayout.CENTER);
getContentPane().add(licenseInfo, BorderLayout.SOUTH);
resetDivider();
//centerPanel.setLeftComponent(mainPage());
this.dialogMode = DIALOG_HOME;
this.getContentPane().add(topPanel, BorderLayout.NORTH);
settingsDialog = new JDialog(this, "Settings");
settingsDialog.setSize(new Dimension(350, 400));
settingsDialog.setLocation(this.getX() + 100, this.getY() + 100);
settingsPanel = new JPanel();
config.buildSettingsPanel(settingsPanel);
settingsDialog.add(settingsPanel);
this.setVisible(true);
if (!jmolOptionNONBO && nboService.isOffLine())
settingsDialog.setVisible(true);
}
/**
* Places main dialog adjacent to main jmol window
*
* @param d
*/
private void placeNBODialog(JDialog d) {
Dimension screenSize = d.getToolkit().getScreenSize();
Dimension size = d.getSize();
int x = Math.min(screenSize.width - size.width, d.getParent().getX()
+ d.getParent().getWidth()) - 10;
int y = d.getParent().getY();
//System.out.println("------" + x + " " + y);
d.setLocation(x, y);
}
private JButton getMainButton(final JButton b, final int mode, Font font) {
b.setBorder(null);
b.setMargin(new Insets(5, 5, 5, 5));
b.setContentAreaFilled(false);
b.setForeground(Color.white);
b.setFont(font);
switch (mode) {
case DIALOG_HELP:
case DIALOG_HOME:
break;
default:
b.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
doOpenPanel(mode);
}
});
}
return b;
}
/**
* Top panel with logo/modules/file choosing options
*
* @return top panel
*/
private JPanel buildTopPanel() {
modelButton = new JButton("Model");
runButton = new JButton("Run");
viewButton = new JButton("View");
searchButton = new JButton("Search");
helpBtn = new HelpBtn(null);
JPanel p = new JPanel(new BorderLayout());
if (!jmolOptionNONBO) {
Box b = Box.createHorizontalBox();
b.add(Box.createRigidArea(new Dimension(20, 0)));
b.add(getMainButton(modelButton, DIALOG_MODEL, NBOConfig.topFont));
b.add(Box.createRigidArea(new Dimension(20, 0)));
b.add(getMainButton(runButton, DIALOG_RUN, NBOConfig.topFont));
b.add(Box.createRigidArea(new Dimension(20, 0)));
b.add(getMainButton(viewButton, DIALOG_VIEW, NBOConfig.topFont));
b.add(Box.createRigidArea(new Dimension(20, 0)));
b.add(getMainButton(searchButton, DIALOG_SEARCH, NBOConfig.topFont));
b.add(Box.createRigidArea(new Dimension(30, 50)));
b.add(getMainButton(new JButton("Settings"), DIALOG_CONFIG,
NBOConfig.settingHelpFont));
b.add(Box.createRigidArea(new Dimension(20, 0)));
b.add(getMainButton(helpBtn, DIALOG_HELP, NBOConfig.settingHelpFont));
b.add(Box.createRigidArea(new Dimension(20, 0)));
b.add(getMainButton(new HelpBtn("Manual", "NBOPro6_man.pdf", "NBOPro6"), DIALOG_HOME, NBOConfig.settingHelpFont));
p.add(b, BorderLayout.CENTER);
}
icon = new JLabel();
icon.setFont(NBOConfig.nboFont);
icon.setForeground(Color.white);
p.add(icon, BorderLayout.EAST);
p.setBackground(Color.BLACK);
p.setPreferredSize(new Dimension(500, 60));
return p;
}
/**
* sets components colors in container recursively
*
* @param comp
* @param foregroundColor
* @param backgroundColor
*/
private void setComponents(Component comp, Color foregroundColor,
Color backgroundColor) {
if (comp instanceof JTextField || comp instanceof JTextPane
|| comp instanceof JButton)
return;
if (comp instanceof JComboBox)
comp.setBackground(new Color(248, 248, 248));
if (foregroundColor != null)
comp.setForeground(foregroundColor);
if (backgroundColor != null)
comp.setBackground(backgroundColor);
if (comp instanceof Container) {
for (Component c : ((Container) comp).getComponents()) {
setComponents(c, foregroundColor, backgroundColor);
}
}
}
private JPanel mainPage() {
JPanel p = new JPanel();
p.setBackground(Color.white);
haveService = nboService.restartIfNecessary(); // BH temporarily
p.setLayout(new BoxLayout(p, BoxLayout.Y_AXIS));
//Header stuff////////////
ImageIcon imageIcon = nboPlugin.getIcon("nbo6logo");
Image image = imageIcon.getImage();
Image newimg = image.getScaledInstance(20, 20, java.awt.Image.SCALE_SMOOTH);
imageIcon = new ImageIcon(newimg);
JLabel lab = new JLabel(imageIcon);
Box b = Box.createHorizontalBox();
b.add(lab);
lab = new JLabel("NBOServe (v6) toolbox");
b.add(lab);
b.add(Box.createRigidArea(new Dimension(370, 0)));
icon.setOpaque(true);
icon.setBackground(Color.LIGHT_GRAY);
icon.setText(haveService ? " Connected "
: "Not
Connected ");
icon.setForeground(haveService ? Color.black : Color.red);
icon.setBorder(BorderFactory.createLineBorder(Color.black));
p.add(b);
lab = new JLabel(getName());
lab.setFont(NBOConfig.nboProTitleFont);
lab.setForeground(Color.red);
p.add(lab);
lab.setAlignmentX(0.5f);
lab = new JLabel("Frank Weinhold, Dylan Phillips, and Bob Hanson");
lab.setAlignmentX(0.5f);
p.add(lab);
//Body/////////////
JPanel p2 = new JPanel(new GridBagLayout());
GridBagConstraints c = new GridBagConstraints();
p2.setBorder(BorderFactory.createLineBorder(Color.black));
JButton btn = new JButton("Model");
btn.setForeground(Color.WHITE);
btn.setBackground(Color.BLUE);
btn.setMinimumSize(new Dimension(150, 30));
btn.setFont(NBOConfig.homeButtonFont);
btn.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
doOpenPanel(DIALOG_MODEL);
}
});
c.gridx = 0;
c.gridy = 0;
c.gridwidth = 1;
c.gridheight = 1;
p2.add(btn, c);
c.gridx = 1;
c.gridy = 0;
c.gridwidth = 3;
p2.add(lab = new JLabel(" Create & edit molecular model and input files"),
c);
c.gridx = 5;
c.gridwidth = 1;
p2.add(Box.createRigidArea(new Dimension(60, 10)), c);
lab.setFont(NBOConfig.homeTextFont);
JTextPane tp = new JTextPane();
tp.setContentType("text/html");
tp.setText("Frank Weinhold
(Acknowledgments: Eric Glendening, John Carpenter, "
+ "Mark Muyskens, Isaac Mades, Scott Ostrander, John Blair, Craig Weinhold) ");
tp.setEditable(false);
tp.setBackground(null);
tp.setPreferredSize(new Dimension(430, 60));
c.gridx = 1;
c.gridy = 1;
c.gridwidth = 3;
c.fill = GridBagConstraints.HORIZONTAL;
p2.add(tp, c);
c.weightx = 0;
//RUN/////////////
btn = new JButton("Run");
btn.setForeground(Color.WHITE);
btn.setBackground(Color.BLUE);
btn.setMinimumSize(new Dimension(150, 30));
btn.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
doOpenPanel(DIALOG_RUN);
}
});
c.gridx = 0;
c.gridy = 2;
c.gridwidth = 1;
btn.setFont(NBOConfig.homeButtonFont);
p2.add(btn, c);
c.gridx = 1;
c.gridy = 2;
c.gridwidth = 3;
p2.add(lab = new JLabel(" Launch NBO analysis for chosen archive file"), c);
lab.setFont(NBOConfig.homeTextFont);
tp = new JTextPane();
tp.setContentType("text/html");
tp.setBackground(null);
tp.setText("Eric Glendening, Jay Badenhoop, Alan Reed, John Carpenter, Jon Bohmann, "
+ "Christine Morales, and Frank Weinhold ");
c.gridx = 1;
c.gridy = 3;
c.gridwidth = 3;
p2.add(tp, c);
//VIEW//////////////
btn = new JButton("View");
btn.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
doOpenPanel(DIALOG_VIEW);
}
});
btn.setFont(NBOConfig.homeButtonFont);
btn.setForeground(Color.WHITE);
btn.setBackground(Color.BLUE);
btn.setMinimumSize(new Dimension(150, 30));
c.gridx = 0;
c.gridy = 4;
c.gridwidth = 1;
p2.add(btn, c);
c.gridx = 1;
c.gridy = 4;
c.gridwidth = 3;
p2.add(lab = new JLabel(" Display NBO orbitals in 1D/2D/3D imagery"), c);
lab.setFont(NBOConfig.homeTextFont);
tp = new JTextPane();
tp.setMaximumSize(new Dimension(430, 60));
tp.setContentType("text/html");
tp.setBackground(null);
tp.setText("Mark Wendt and Frank Weinhold
(Acknowledgments: Eric Glendening, John Carpenter, "
+ "Mark Muyskens, Scott Ostrander, Zdenek Havlas, Dave Anderson) ");
c.gridx = 1;
c.gridy = 5;
c.gridwidth = 3;
p2.add(tp, c);
//SEARCH/////////////
btn = new JButton("Search");
btn.setForeground(Color.WHITE);
btn.setBackground(Color.BLUE);
btn.setMinimumSize(new Dimension(150, 30));
btn.setFont(NBOConfig.homeButtonFont);
btn.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
doOpenPanel(DIALOG_SEARCH);
}
});
c.gridx = 0;
c.gridy = 6;
c.gridwidth = 1;
p2.add(btn, c);
c.gridx = 1;
c.gridy = 6;
c.gridwidth = 3;
p2.add(lab = new JLabel(" Search NBO output interactively"), c);
lab.setFont(NBOConfig.homeTextFont);
tp = new JTextPane();
tp.setMaximumSize(new Dimension(430, 60));
tp.setContentType("text/html");
tp.setBackground(null);
tp.setText("Frank Weinhold ");
c.gridx = 1;
c.gridy = 7;
c.gridwidth = 3;
p2.add(tp, c);
p.add(p2);
JTextPane t = new JTextPane();
t.setContentType("text/html");
t.setText("\u00a9Copyright 2017 Board of Regents of the University of Wisconsin System "
+ "on behalf of \nthe Theoretical Chemistry Institute. All Rights Reserved ");
t.setForeground(Color.RED);
t.setBackground(null);
t.setAlignmentX(0.5f);
t.setMaximumSize(new Dimension(10000, 80));
p.add(t);
return p;
}
private void resetDivider() {
centerPanel.setDividerLocation(365);
}
private void createOutputDialog() {
nboOutput = new JPanel(new BorderLayout());
viewSettingsBox = new JPanel(new BorderLayout());
viewSettingsBox.add(new JLabel("Settings"), BorderLayout.NORTH);
JPanel s = new JPanel(new BorderLayout());
s.add(viewSettingsBox, BorderLayout.NORTH);
viewSettingsBox.setVisible(!jmolOptionNONBO);
nboOutput.add(viewSettingsBox, BorderLayout.NORTH);
nboOutput.add(s, BorderLayout.CENTER);
JLabel lab = new JLabel("Session Dialog");
lab.setFont(NBOConfig.monoFont);
s.add(lab, BorderLayout.PAGE_START);
JScrollPane p1 = new JScrollPane();
if (jpNBODialog == null) {
jpNBODialog = new JTextPane();
jpNBODialog.setEditable(false);
jpNBODialog.setBorder(null);
//jpNBODialog.setFont(new Font("Arial", Font.PLAIN, 16));
nboOutputBodyText = "";
}
jpNBODialog.setContentType("text/html");
//jpNBODialog.setFont(new Font("Arial",Font.PLAIN,10));
setComponents(s, Color.WHITE, Color.BLACK);
p1.getViewport().add(jpNBODialog);
p1.setBorder(null);
s.add(p1, BorderLayout.CENTER);
JPanel box = new JPanel(new GridLayout(2, 1));
statusLab = new JLabel();
statusLab.setForeground(Color.red);
statusLab.setBackground(Color.white);
statusLab.setFont(NBOConfig.statusFont);
statusLab.setOpaque(true);
box.add(statusLab);
Box box2 = Box.createHorizontalBox();
JButton clear = new JButton("Clear");
clear.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
doClearOutput();
}
});
box2.add(clear);
JButton btn = new JButton("Save Output");
btn.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
doSaveOutput();
}
});
box2.add(btn);
box.add(box2);
s.add(box, BorderLayout.SOUTH);
}
protected void doSaveOutput() {
if (jpNBODialog == null)
return;
JFileChooser myChooser = new JFileChooser();
if (lastOutputSaveName == null)
lastOutputSaveName = inputFileHandler.tfDir.getText()
+ "/nboDialog.txt";
String savePath = lastOutputSaveName;
myChooser.setSelectedFile(new File(savePath));
myChooser.setFileFilter(new FileNameExtensionFilter(".txt", ".txt"));
myChooser.setFileHidingEnabled(true);
int button = myChooser.showSaveDialog(jpNBODialog);
if (button == JFileChooser.APPROVE_OPTION) {
saveDialogOutput(myChooser.getSelectedFile().toString());
}
}
protected void saveDialogOutput(String saveFileName) {
String output = nboOutputBodyText.replaceAll("
", NBOUtil.sep);
output = output.replaceAll("", "");
output = output.replaceAll("", "");
output = output.replaceAll("", "");
output = output.replaceAll("", "");
inputFileHandler.writeToFile(saveFileName, output);
}
public void close() {
if (modulePanel != null)
inputFileHandler.clearInputFile(false);
runScriptQueued("select off");
dispose();
}
private void setThis(JButton btn) {
for (Component c : ((Container) topPanel.getComponent(0)).getComponents()) {
if (c instanceof JButton) {
if (((JButton) c).equals(btn)) {
btn.setEnabled(false);
btn.setBorder(new LineBorder(Color.WHITE, 2));
} else {
((JButton) c).setBorder(null);
((JButton) c).setEnabled(true);
}
}
}
invalidate();
}
/**
* Callback from Jmol Viewer indicating user actions
*
* @param type
* @param data
*/
@SuppressWarnings("incomplete-switch")
public void notifyCallback(CBK type, Object[] data) {
//System.out.println(type + "" + data[1]);
if (!isVisible())
return;
switch (type) {
case STRUCTUREMODIFIED:
if (dialogMode == DIALOG_MODEL) {
}
break;
case PICK:
int[] picked = NBOUtil.getAtomsPicked(data);
if (picked[0] < 0)
return; // not an atom or a bond -- maybe draw picking is on
switch (dialogMode) {
case DIALOG_MODEL:
modelPanel.notifyPick(picked);
return;
case DIALOG_VIEW:
viewPanel.notifyPick_v(picked);
return;
case DIALOG_SEARCH:
searchPanel.notifyPick_s(picked);
return;
}
break;
case LOADSTRUCT:
if (vwr.ms.ac == 0)
return;
String f = "" + vwr.getParameter("_modelFile");
if (!iAmLoading) {
if (!f.endsWith(".47")) {
if (dialogMode != DIALOG_MODEL) {
doOpenPanel(DIALOG_MODEL);
return;
}
}
if (dialogMode == DIALOG_MODEL) {
modelPanel.setModelNotFromNBO();
} else {
if (dialogMode != DIALOG_RUN) {
doOpenPanel(DIALOG_RUN);
return;
}
if (f.startsWith("http")) {
runPanel.retrieveFile(f, null);
return;
}
if (f.startsWith("file:"))
f = PT.trim(f.substring(5), "/");
if (!f.contains(":"))
f = "/" + f;
inputFileHandler.loadSelectedFile(new File(f));
return;
}
}
iAmLoading = false;
if (NBOConfig.nboView)
runScriptQueued("select 1.1;color bonds lightgrey;"
+ "wireframe 0.1;select none");
isOpenShell = vwr.ms.getModelAuxiliaryInfo(0).containsKey("isOpenShell");
switch (dialogMode) {
case DIALOG_MODEL:
modelPanel.notifyFileLoaded();
return;
case DIALOG_RUN:
runPanel.notifyFileLoaded();
return;
case DIALOG_VIEW:
viewPanel.notifyFileLoaded_v();
return;
case DIALOG_SEARCH:
searchPanel.notifyFileLoaded_s();
return;
}
break;
}
}
/**
* clear output panel
*/
protected void doClearOutput() {
nboOutputBodyText = "";
// String fontFamily = jpNBOLog.getFont().getFamily();
if (jpNBODialog != null)
jpNBODialog.setText("");
}
// protected boolean checkJmolNBO(){
// return(vwr.ms.getInfo(vwr.am.cmi, "nboType") != null ||
// NBOFileHandler.getExt(inputFileHandler.inputFile).equals("47"));
// }
/**
* user has made changes to the settings, so we need to update panels
*/
protected void updatePanelSettings() {
switch (dialogMode) {
case DIALOG_VIEW:
viewPanel.doSetNewBasis(false, false);
break;
}
}
/**
* Carry out all functions to load a new file or basis
*
* @param file
*/
void loadNewFile(File file) {
viewPanel.isNewModel = true;
switch (dialogMode) {
case DIALOG_VIEW:
// switch to desired file.
viewPanel.loadNewFileIfAble();
break;
default:
loadModelFileQueued(file, false);
}
}
void setLicense(String data) {
String[] lines = PT.split(data, "\n");
licenseInfo.setText("" + lines[1]
+ "");
}
// protected Component getComponentatPoint(Point p, Component top){
// Component c = null;
// if(top.isShowing()) {
// do{
// c = ((Container) top).findComponentAt(p);
// }while(!(c instanceof Container));
// }
// return c;
// }
protected void setStatus(String statusInfo) {
boolean isBusy = (statusInfo != null && statusInfo.length() > 0);
statusLab.setText(statusInfo);
centerPanel.setCursor(Cursor
.getPredefinedCursor(isBusy ? Cursor.WAIT_CURSOR
: Cursor.DEFAULT_CURSOR));
if (isBusy) {
logStatus(statusInfo);
if (statusInfo.indexOf("...") >= 0) {
if (runTimer != null) {
runTimer.stop();
}
runTimer = new Timer(1000, new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
doShowRunTime();
}
});
runStartTime = System.currentTimeMillis();
runTimer.setRepeats(true);
runTimer.start();
}
} else if (runTimer != null) {
runTimer.stop();
runTimer = null;
}
}
Timer runTimer;
private long runStartTime;
protected synchronized void doShowRunTime() {
String t = statusLab.getText();
int pt = t.indexOf("...");
if (pt < 0)
return;
try {
int time = (int) (System.currentTimeMillis() - runStartTime);
int minutes = time / 60000;
int seconds = (time % 60000) / 1000;
String s = "00" + seconds;
s = minutes + ":" + s.substring(s.length() - 2);
statusLab.setText(t.substring(0, pt + 3) + " " + s);
} catch (Exception e) {
if (runTimer != null) {
runTimer.stop();
runTimer = null;
}
}
}
/**
* add selection halos to atoms in s
*
* @param s
* - array containing atomnums
*/
protected void showSelected(String s) {
BS bs = new BS();
for (String x : PT.getTokens(s))
bs.set((Integer.parseInt(x) - 1));
String script = "select on " + bs + ";";
runScriptQueued(script);
}
protected String getJmolWorkingPath() {
String path = JmolPanel.getJmolProperty("workingPath",
System.getProperty("user.home"));
saveWorkingPath(path);
return path;
}
protected String getWorkingPath() {
String path = nboPlugin.getNBOProperty("workingPath", null);
return (path == null ? getJmolWorkingPath() : path);
}
protected void saveWorkingPath(String path) {
nboPlugin.setNBOProperty("workingPath", path);
}
protected static void colorMeshes() {
// yeiks! causes file load again! updatePanelSettings();
}
protected void resetVariables_c() {
// rsTypeLast = "alpha";
}
protected void alertRequiresNBOServe() {
vwr.alert("This functionality requires NBOServe.");
}
protected void logCmd(String msg) {
log(msg, 'I');
}
protected void logValue(String msg) {
log(msg, 'b');
}
protected void logStatus(String msg) {
log(msg, 'p');
}
protected void logError(String msg) {
log(msg, 'r');
}
/**
* appends output to session dialog panel
*
* @param line
* output message to append
* @param chFormat
* p, b, r ("red"), i, etc.
*/
protected synchronized void log(String line, char chFormat) {
if (dontLog(line, chFormat))
return;
if (line.equals("\n") || line.trim().length() >= 1) {
line = PT.rep(line.trim(), "<", "<");
line = PT.rep(line, ">", ">");
line = PT.rep(line, "<br>", "
");
String format0 = "" + chFormat;
String format1 = format0;
// String fontFamily = jpNBOLog.getFont().getFamily();
if (chFormat == 'r') {
format0 = "b style=color:red";
format1 = "b";
setStatus("");
}
if (!format0.equals("p"))
line = "<" + format0 + ">" + line + "";
jpNBODialog.setText(""
+ (nboOutputBodyText = nboOutputBodyText + line + "\n
")
+ "");
}
if (isCaretEnabled )
jpNBODialog.setCaretPosition(jpNBODialog.getDocument().getLength());
}
private boolean dontLog(String line, char chFormat) {
return (jpNBODialog == null
|| line.indexOf("read/unit=5/attempt to read past end") >= 0
|| line.indexOf("*end*") >= 0 || !NBOConfig.debugVerbose
&& "b|r|I".indexOf("" + chFormat) < 0);
}
protected void alertError(String line) {
line = PT.rep(line.replace('\r', ' '), "\n\n", "\n");
logError(line);
vwr.alert(line);
}
protected void logInfo(String msg, int mode) {
Logger.info(msg);
log(msg, mode == Logger.LEVEL_INFO ? 'p' : mode == Logger.LEVEL_ERROR ? 'r'
: mode == Logger.LEVEL_WARN ? 'b' : 'i');
}
protected void runScriptQueued(String script) {
if (script.indexOf("easure") >= 0)
System.out.println("TESTING NBOD");
logInfo("_$ " + PT.rep(script, "\n", "
"), Logger.LEVEL_DEBUG);
vwr.script(script);
}
protected boolean iAmLoading;
protected void loadModelFileQueued(File f, boolean saveOrientation) {
// BH removing re-orientation for now
saveOrientation = false;
iAmLoading = true;
String s = "load \"" + f.getAbsolutePath().replace('\\', '/') + "\""
+ NBOConfig.JMOL_FONT_SCRIPT;
if (saveOrientation)
s = "save orientation o1;" + s + ";restore orientation o1";
runScriptQueued(s);
}
/**
* Uses the LOAD DATA option to load data from NBO; just getting all the
* "load xxx" methods in the same place.
*
*
* @param s
*/
protected void loadModelDataQueued(String s) {
iAmLoading = true;
runScriptQueued(s);
}
protected String loadModelFileNow(String s) {
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()
&& nboService.restartIfNecessary());
}
String evaluateJmolString(String expr) {
return vwr.evaluateExpressionAsVariable(expr).asString();
}
protected String getJmolFilename() {
return evaluateJmolString("getProperty('filename')");
}
/**
* not used for MODEL
*
* @param mode
*/
protected void getNewInputFileHandler(int mode) {
inputFileHandler = new NBOFileHandler(inputFileHandler == null ? ""
: inputFileHandler.jobStem, "47", mode, "47", this);
}
/**
* label atoms: (number lone pairs)+atomnum
*
* @param type
* alpha or beta or null
*/
protected void doSetStructure(String type) {
doSearchSetResStruct(type, -1);
}
/**
* Changes bonds and labels on the Jmol model when new resonance structure is
* selected
*
* @param type
* one of rsa, rsb, alpha, beta, or null
* @param rsNum
* - index of RS in Combo Box
*/
protected void doSearchSetResStruct(String type, int rsNum) {
if (type == null || !isOpenShell() && type.equals("beta")) {
type = "alpha";
}
String script = "measurements off;isosurface off;select 1.1;"
+ "select 1.1;color labels white;"
+ "select 1.1 & _H;color labels "
+ ((NBOConfig.nboView) ? "black" : "gray") + ";"
+ "set labeloffset 0 0 {1.1}; select none;"
+ ";select 1.1;connect nbo " + type + (rsNum >= 0 ? "_" + (rsNum + 1) : "")
+ (NBOConfig.showAtNum ? "; label %[nbo];" : "off");
if (NBOConfig.nboView)
script += "select 1.1;color bonds lightgrey;" + "wireframe 0.1;";
script += NBOConfig.JMOL_FONT_SCRIPT;
runScriptQueued(script);
}
protected boolean isOpenShell() {
return isOpenShell;
}
class HelpBtn extends JButton {
String page;
protected HelpBtn(String page) {
this("Help", page, null);
}
protected HelpBtn(String label, String page, String tooltip) {
super(label);
setBackground(Color.black);
setForeground(Color.white);
this.page = page;
tooltip = "Help for "
+ (tooltip != null ? tooltip
: page == null || page.length() == 1 ? "this module" : page);
setToolTipText(tooltip);
addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent arg0) {
doHelp();
}
});
}
protected void doHelp() {
vwr.showUrl(NBOConfig.NBO_WEB_SITE + "/jmol_help/" + getHelpPage());
}
/**
* Get the proper help page for this context
*
* @return a web page URI
*/
protected String getHelpPage() {
if (page != null)
return page;
switch (dialogMode) {
case DIALOG_MODEL:
return "model_help.htm";
case DIALOG_RUN:
return "run_help.htm";
case DIALOG_VIEW:
return "view_help.htm";
case DIALOG_SEARCH:
return "search_help.htm";
case DIALOG_CONFIG:
case DIALOG_HOME:
default:
return "Jmol_NBOPro6_help.htm";
}
}
}
}
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