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Jmol: an open-source Java viewer for chemical structures in 3D
/* $RCSfile$
* $Author: turnera $
* $Date: 2007-05-08 22:52:24 +0100 (Tue, 08 May 2007) $
* $Revision: 7642 $
*
* 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.openscience.jmol.app.jmolpanel;
import org.jmol.i18n.GT;
import org.jmol.viewer.Viewer;
import java.io.File;
import java.io.Writer;
import java.io.FileWriter;
import java.io.BufferedWriter;
import java.awt.Font;
import java.awt.GridLayout;
import java.awt.Dimension;
import java.awt.FlowLayout;
import java.awt.BorderLayout;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.MouseEvent;
import java.awt.event.MouseListener;
import javajs.util.PT;
import javax.swing.JDialog;
import javax.swing.JButton;
import javax.swing.JLabel;
import javax.swing.JPanel;
import javax.swing.JFrame;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
import javax.swing.border.TitledBorder;
import javax.swing.BorderFactory;
import javax.swing.JSplitPane;
import javax.swing.JTextField;
import javax.swing.JSpinner;
import javax.swing.JTextPane;
import javax.swing.SpinnerModel;
import javax.swing.SpinnerNumberModel;
import javax.swing.JComboBox;
import javax.swing.JFileChooser;
import javax.swing.JScrollPane;
import javax.swing.SwingUtilities;
public class GaussianDialog extends JDialog implements ActionListener,
ChangeListener,
MouseListener {
/*
* By Andy Turner, [email protected]
* modified and integrated into Jmol by Bob Hanson, [email protected], 10/12/2008
*/
Viewer vwr;
private JPanel container;
private JTextField checkField, optsField, fileField, selectField;
private JComboBox memBox, methBox, basisBox, dfBox;
private JSpinner procSpinner, chargeSpinner, multSpinner;
private JButton fileButton, saveButton, closeButton, refreshButton;
private JFileChooser fileChooser;
protected JTextPane editArea;
//private JTabbedPane inputTabs;
private String check, mem, proc, file, meth, route, charge, mult, select;
protected JScrollPane editPane;
protected int iscroll;
private static final String DEFAULT_METHOD = "HF";
private static final String DEFAULT_BASIS = "3-21G**";
private static final String DEFAULT_CHARGE = "0";
private static final String DEFAULT_MULT = "1";
private static final String[] BASIS_LIST = {"Gen",
"3-21G",
"3-21G*",
"3-21G**",
"6-21G",
"4-31G",
"6-31G",
"6-311G",
"D95V",
"D95",
"SHC",
"CEP-4G",
"CEP-31G",
"CEP-121G",
"LanL2MB",
"LanL2DZ",
"SDD",
"SDDAll",
"cc-pVDZ",
"cc-pVTZ",
"cc-pVQZ",
"cc-pV5Z",
"cc-pV6Z",
"aug-cc-pVDZ",
"aug-cc-pVTZ",
"aug-cc-pVQZ",
"aug-cc-pV5Z",
"aug-cc-pV6Z",
"SV",
"SVP",
"TZV",
"TZVP",
"MidiX",
"EPR-II",
"EPR-III",
"UGBS",
"UGBS1P",
"UGBS2P",
"UGBS3P",
"MTSmall",
"DGDZVP",
"DGDZVP2",
"DGTZVP"};
private static final String[] METHOD_LIST = {"HF",
"MP2",
"MP3",
"MP4",
"CCSD(T)",
"CIS",
"CISD",
"LSDA",
"BLYP",
"BP86",
"BPW91",
"OLYP",
"OP86",
"OPW91",
"PBEPBE",
"VSXC",
"HCTH93",
"HCTH147",
"HCTH407",
"TPSSTPSS",
"B3LYP",
"B3PW91",
"AM1",
"PM3",
"CNDO",
"INDO",
"MNDO",
"MINDO3",
"ZINDO",
"UFF",
"AMBER",
"DREIDING",
"Huckel"};
private static final String[] DF_LIST = {"None",
"Auto",
"DGA1",
"DGA2"};
private static final String[] MEMORY_LIST = {"Default",
"100MB",
"500MB",
"1GB",
"2GB",
"4GB",
"7GB",
"15GB"};
private static final String NOBASIS_LIST =
"AM1 PM3 CNDO INDO MNDO MINDO3 ZINDO UFF AMBER DREIDING Huckel";
private static final String DFT_LIST =
"LSDA BLYP BP86 BPW91 OLYP OP86 OPW91 PBEPBE VSXC HCTH93 NCTH147 HCTH407 TPSSTPSS B3LYP B3PW91";
public GaussianDialog(JFrame f, Viewer vwr) {
super(f, false);
this.vwr = vwr;
setTitle(GT._("Create Gaussian Input File"));
container = new JPanel();
container.setLayout(new BorderLayout());
//inputTabs = new JTabbedPane();
JPanel basicPanel = buildBasicPanel();
//inputTabs.addTab(GT._("Basic"), null, basicPanel);
JPanel advancedPanel = buildAdvancedPanel();
//inputTabs.addTab(GT._("Advanced"), null, advancedPanel);
JPanel filePanel = buildFilePanel();
JPanel buttonPanel = buildButtonPanel();
JSplitPane splitPane = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT,
basicPanel, advancedPanel);
container.add(splitPane, BorderLayout.NORTH);
container.add(filePanel, BorderLayout.CENTER);
container.add(buttonPanel, BorderLayout.SOUTH);
getContentPane().add(container);
pack();
centerDialog();
updateUI();
}
private JPanel buildBasicPanel() {
JPanel showPanel = new JPanel(new BorderLayout());
JPanel linkPanel = new JPanel(new BorderLayout());
TitledBorder linkTitle = BorderFactory.createTitledBorder("link0 Section");
linkPanel.setBorder(linkTitle);
JPanel linkLabels = new JPanel(new GridLayout(3,1));
JPanel linkControls = new JPanel(new GridLayout(3,1));
JLabel checkLabel = new JLabel(GT._("Checkpoint File: "));
linkLabels.add(checkLabel);
checkField = new JTextField(20);
linkControls.add(checkField);
checkField.addActionListener(this);
JLabel memLabel = new JLabel(GT._("Memory:"));
linkLabels.add(memLabel);
memBox = new JComboBox(MEMORY_LIST);
linkControls.add(memBox);
memBox.setSelectedIndex(0);
memBox.addActionListener(this);
JLabel procLabel = new JLabel(GT._("Processors:"));
linkLabels.add(procLabel);
SpinnerModel procModel = new SpinnerNumberModel(1, 1, 16, 1);
procSpinner = new JSpinner(procModel);
procSpinner.setEditor(new JSpinner.NumberEditor(procSpinner, "#"));
linkControls.add(procSpinner);
procSpinner.addChangeListener(this);
linkPanel.add(linkLabels, BorderLayout.LINE_START);
linkPanel.add(linkControls, BorderLayout.CENTER);
showPanel.add(linkPanel, BorderLayout.NORTH);
JPanel routePanel = new JPanel(new BorderLayout());
TitledBorder routeTitle = BorderFactory.createTitledBorder(GT._("Route"));
routePanel.setBorder(routeTitle);
JPanel routeLabels = new JPanel(new GridLayout(4,1));
JPanel routeControls = new JPanel(new GridLayout(4,1));
JLabel methLabel = new JLabel(GT._("Method: "));
routeLabels.add(methLabel);
methBox = new JComboBox(METHOD_LIST);
routeControls.add(methBox);
methBox.setSelectedIndex(0);
methBox.addActionListener(this);
JLabel basisLabel = new JLabel(GT._("Basis Set: "));
routeLabels.add(basisLabel);
basisBox = new JComboBox(BASIS_LIST);
routeControls.add(basisBox);
basisBox.setSelectedIndex(3);
basisBox.addActionListener(this);
JLabel dfLabel =
new JLabel(GT._("DFT Density Fit: "));
routeLabels.add(dfLabel);
dfBox = new JComboBox(DF_LIST);
routeControls.add(dfBox);
dfBox.setSelectedIndex(0);
dfBox.addActionListener(this);
JLabel optsLabel = new JLabel(GT._("Job Options: "));
routeLabels.add(optsLabel);
optsField = new JTextField(20);
routeControls.add(optsField);
optsField.setText("opt pop=full gfprint");
optsField.addActionListener(this);
routePanel.add(routeLabels, BorderLayout.LINE_START);
routePanel.add(routeControls, BorderLayout.CENTER);
showPanel.add(routePanel, BorderLayout.CENTER);
JPanel molPanel = new JPanel(new BorderLayout());
TitledBorder molTitle =
BorderFactory.createTitledBorder(GT._("Molecular Properties"));
molPanel.setBorder(molTitle);
JPanel molLabels = new JPanel(new GridLayout(3,1));
JPanel molControls = new JPanel(new GridLayout(3,1));
JLabel chargeLabel = new JLabel(GT._("Total Charge: "));
molLabels.add(chargeLabel);
SpinnerModel chargeModel = new SpinnerNumberModel(0, -10, 10, 1);
chargeSpinner = new JSpinner(chargeModel);
chargeSpinner.setEditor(new JSpinner.NumberEditor(chargeSpinner, "#"));
molControls.add(chargeSpinner);
chargeSpinner.addChangeListener(this);
JLabel multLabel = new JLabel(GT._("Multiplicity: "));
molLabels.add(multLabel);
SpinnerModel multModel = new SpinnerNumberModel(1, 0, 10, 1);
multSpinner = new JSpinner(multModel);
multSpinner.setEditor(new JSpinner.NumberEditor(multSpinner, "#"));
molControls.add(multSpinner);
multSpinner.addChangeListener(this);
molPanel.add(molLabels, BorderLayout.LINE_START);
molPanel.add(molControls, BorderLayout.CENTER);
showPanel.add(molPanel, BorderLayout.SOUTH);
return showPanel;
}
private JPanel buildAdvancedPanel() {
JPanel editPanel = new JPanel(new BorderLayout());
TitledBorder editTitle =
BorderFactory.createTitledBorder("Edit Gaussian Input File");
editPanel.setBorder(editTitle);
editArea = new JTextPane();
editArea.setContentType("text/html");
editArea.setFont(new Font("Monospaced", Font.PLAIN, 8));
editArea.addMouseListener(this);
editPane = new JScrollPane(editArea);
editPane.setPreferredSize(new Dimension(150,100));
editPanel.add(editPane, BorderLayout.CENTER);
return editPanel;
}
private JPanel buildFilePanel() {
JPanel showPanel = new JPanel(new FlowLayout(FlowLayout.RIGHT));
TitledBorder fileTitle =
BorderFactory.createTitledBorder(GT._("Gaussian Input File Name"));
showPanel.setBorder(fileTitle);
fileField = new JTextField(30);
showPanel.add(fileField);
fileField.setText(new File("my_input.com").getAbsolutePath());
fileButton = new JButton(GT._("File..."));
fileButton.addActionListener(this);
showPanel.add(fileButton);
return showPanel;
}
private JPanel buildButtonPanel() {
JPanel buttonPanel = new JPanel();
buttonPanel.setLayout(new FlowLayout(FlowLayout.RIGHT));
JLabel selectLabel = new JLabel(GT._("Selection: "));
buttonPanel.add(selectLabel);
selectField = new JTextField(20);
selectField.setText("visible");
buttonPanel.add(selectField);
selectField.addActionListener(this);
refreshButton = new JButton(GT._("Refresh"));
refreshButton.addActionListener(this);
buttonPanel.add(refreshButton);
saveButton = new JButton(GT._("Save"));
saveButton.addActionListener(this);
buttonPanel.add(saveButton);
closeButton = new JButton(GT._("Close"));
closeButton.addActionListener(this);
buttonPanel.add(closeButton);
getRootPane().setDefaultButton(saveButton);
return buttonPanel;
}
protected void centerDialog() {
Dimension screenSize = this.getToolkit().getScreenSize();
Dimension size = this.getSize();
screenSize.height = screenSize.height / 2;
screenSize.width = screenSize.width / 2;
size.height = size.height / 2;
size.width = size.width / 2;
int y = screenSize.height - size.height;
int x = screenSize.width - size.width;
this.setLocation(x, y);
}
private void updateVars() {
check = checkField.getText();
mem = memBox.getSelectedItem().toString();
proc = procSpinner.getValue().toString();
select = selectField.getText();
if (select.length() == 0) {
select = "visible";
selectField.setText(select);
}
charge = chargeSpinner.getValue().toString();
if (charge.equals("")) charge = DEFAULT_CHARGE;
mult = multSpinner.getValue().toString();
if (mult.equals("")) mult = DEFAULT_MULT;
String basis = (String) basisBox.getSelectedItem();
if (basis.equals("")) basis = DEFAULT_BASIS;
meth = methBox.getSelectedItem().toString();
if (meth.equals("")) meth = DEFAULT_METHOD;
if (NOBASIS_LIST.lastIndexOf(meth, NOBASIS_LIST.length()) >= 0) basis = "";
if (!basis.equals("")) basis = "/" + basis;
String df = dfBox.getSelectedItem().toString();
if (DFT_LIST.lastIndexOf(meth, DFT_LIST.length()) < 0) df = "None";
if (df.equals("None")) {
df = "";
} else {
df = "/" + df;
}
file = fileField.getText();
if (file.equals("")) file = "my_input.com";
String opts = optsField.getText();
route = "# " + meth + basis + df + " " + opts;
}
private void updateUI() {
updateVars();
if (NOBASIS_LIST.lastIndexOf(meth, NOBASIS_LIST.length()) >= 0) {
basisBox.setEnabled(false);
} else {
basisBox.setEnabled(true);
}
if (DFT_LIST.lastIndexOf(meth, DFT_LIST.length()) >= 0) {
dfBox.setEnabled(true);
} else {
dfBox.setEnabled(false);
}
getCommand(-2, true);
return;
}
private void save() {
// if (inputTabs.getSelectedIndex() == 0)
// getCommand(-1);
Writer output = null;
try {
String s = editArea.getText();
if (s.indexOf("") < 0) {
getCommand(-1, true);
s = editArea.getText();
}
File outputFile = new File(fileField.getText());
fileField.setText(outputFile.getAbsolutePath());
output = new BufferedWriter(new FileWriter(outputFile));
output.write(asHTML(s, false));
output.close();
} catch (Exception err) {
return;
}
//dispose();
}
private void cancel() {
dispose();
}
@Override
public void dispose() {
vwr.script("select off");
super.dispose();
}
private void setFile() {
fileChooser = new JFileChooser();
String fname = fileField.getText();
fileChooser.setSelectedFile(new File(fname));
int ierr = fileChooser.showDialog(this, "Set");
if (ierr == JFileChooser.APPROVE_OPTION) {
File file = fileChooser.getSelectedFile();
fileField.setText(file.getAbsolutePath());
}
}
// private void tabSwitched() {
// if (inputTabs.getSelectedIndex() == 1) {
// getCommand(-1);
// }
// }
protected void getCommand(int iAtom, boolean doScroll) {
updateVars();
String c = check;
if (!c.equals(""))
c = "%chk=" + c + "\n";
String m = mem;
if (!m.equals("Default")) {
m = "%mem=" + m + "\n";
} else {
m = "";
}
String p = proc;
if (!p.equals("1")) {
p = "%nproc=" + p + "\n";
} else {
p = "";
}
String format = "USER:%-2e %10.5x %10.5y %10.5z";
String data = vwr.getData(select, format);
iscroll = 0;
if (iAtom >= 0) {
String a = vwr.getData("atomIndex=" + iAtom, format);
iscroll = data.indexOf(a);
if (iscroll >= 0) {
data = PT.rep(data, a, "" + PT.rep(a, "\n", "")
+ " <<<\n");
}
int mm = editPane.getVerticalScrollBar().getMaximum();
iscroll = (int) (iscroll * 1.0 / data.length() * mm);
} else if (iAtom == -1) {
iscroll = -1;
}
if (!doScroll)
iscroll = editPane.getVerticalScrollBar().getValue();
editArea.setText(asHTML(c + m + p + route + "\n\n"
+ "Title: Created by Jmol version " + Viewer.getJmolVersion()
+ "\n\n" + charge + " " + mult + "\n" + data + "\n", true));
if (iscroll >= 0)
SwingUtilities.invokeLater(new Runnable() {
@Override
public void run() {
try {
editPane.getVerticalScrollBar().setValue(iscroll);
} catch (Exception e) {
editPane.getVerticalScrollBar().setValue(0);
}
}
});
}
protected String asHTML(String s, boolean toHTML) {
if (toHTML)
return "" + s + "
";
if (s.indexOf("") >= 0) {
s = PT.rep(s, "", "");
s = PT.rep(s, "", "");
s = PT.rep(s, "", "");
s = PT.rep(s, "", "");
s = PT.rep(s, "<", "");
s = PT.rep(s, " ", "");
s = PT.split(s, "")[1];
s = PT.split(s, "")[0];
}
return s.trim() + "\n";
}
@Override
public void actionPerformed(ActionEvent event) {
Object c = event.getSource();
if (c == saveButton) {
save();
} else if (c == closeButton) {
cancel();
} else if (c == fileButton) {
setFile();
} else if (c == refreshButton) {
getCommand(-2, true);
} else {
updateUI();
}
}
// @Override
// public void stateChanged(ChangeEvent event) {
// if (event.getSource() == inputTabs) {
// tabSwitched();
// }
// }
public void updateModel(int iAtom) {
getCommand(iAtom, true);
if (iAtom >= 0)
vwr.script("select on atomindex=" + iAtom);
}
@Override
public void stateChanged(ChangeEvent e) {
getCommand(-2, true);
}
@Override
public void mouseClicked(MouseEvent e) {
if (e.getSource() == editArea) {
SwingUtilities.invokeLater(new Runnable() {
@Override
public void run() {
try {
String s = asHTML(editArea.getText(), false);
int pt = editArea.getCaretPosition();
int i0 = s.lastIndexOf("\n", pt) + 5;
int i1 = s.indexOf("\n", pt);
String coord = s.substring(i0, i1);
if (Float.isNaN(PT.parseFloat(coord)))
return;
vwr.scriptWait("select on within(0.1,{" + coord + "})");
getCommand(vwr.bsA().nextSetBit(0), false);
} catch (Exception e) {
//
}
}
});
}
}
@Override
public void mouseEntered(MouseEvent arg0) {
}
@Override
public void mouseExited(MouseEvent arg0) {
}
@Override
public void mousePressed(MouseEvent arg0) {
}
@Override
public void mouseReleased(MouseEvent arg0) {
}
}