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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.Dimension;
import java.awt.EventQueue;
import java.awt.GridLayout;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.KeyEvent;
import java.awt.event.KeyListener;
import java.awt.event.MouseEvent;
import java.awt.event.MouseListener;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
import java.io.File;
import java.util.Map;
import javajs.util.PT;
import javajs.util.SB;
import javax.swing.AbstractListModel;
import javax.swing.BorderFactory;
import javax.swing.Box;
import javax.swing.BoxLayout;
import javax.swing.ButtonGroup;
import javax.swing.DefaultListModel;
import javax.swing.JButton;
import javax.swing.JComboBox;
import javax.swing.JDialog;
import javax.swing.JLabel;
import javax.swing.JList;
import javax.swing.JPanel;
import javax.swing.JRadioButton;
import javax.swing.JScrollPane;
import javax.swing.JTextField;
import javax.swing.ListCellRenderer;
import javax.swing.ScrollPaneConstants;
import javax.swing.Timer;
import javax.swing.event.ListSelectionEvent;
import javax.swing.event.ListSelectionListener;
import org.jmol.awt.AwtColor;
import org.jmol.java.BS;
import org.jmol.util.C;
import org.jmol.viewer.Viewer;
class NBOView {
protected NBODialog dialog;
protected Viewer vwr;
private static final int MODE_VIEW_IMAGE = 13;
private static final int MODE_VIEW_LIST = 23;
protected NBOView(NBODialog dialog) {
this.dialog = dialog;
this.vwr = dialog.vwr;
}
protected final int BASIS_AO = 0;
protected final int BASIS_PNAO = 1;
protected final int BASIS_NAO = 2;
protected final int BASIS_PNHO = 3;
protected final int BASIS_NHO = 4;
protected final int BASIS_PNBO = 5;
protected final int BASIS_NBO = 6;
protected final int BASIS_PNLMO = 7;
protected final int BASIS_NLMO = 8;
protected final int BASIS_MO = 9;
protected final static String[] basSet =
{ "AO", // 0
"PNAO", "NAO", // 1,2
"PNHO", "NHO", // 3,4
"PNBO", "NBO", "PNLMO", "NLMO", // 5-8
"MO" }; // 9
protected final static int[] basisLabelKey =
{//AO NAO NHOab NBOab MO
0, 1, 1, 2, 2, 3, 3, 3, 3, 4, // alpha
0, 1, 1, 5, 5, 6, 6, 6, 6, 4 // beta
};
private String[][] orbitalLabels;
private void clearLabelSet() {
orbitalLabels = new String[7][];
}
private String[] getLabelSet(int ibas, boolean isAlpha) {
return orbitalLabels[getIbasKey(ibas, isAlpha)];
}
private int getIbasKey(int ibas, boolean isBeta) {
return basisLabelKey[ibas + (isBeta ? 10 : 0)];
}
private void addBasisLabel(int ikey, String[] tokens) {
orbitalLabels[ikey] = tokens;
}
private JScrollPane orbScroll;
private Box centerBox, bottomBox;
private Box vecBox;
private Box planeBox;
private JRadioButton profileBtn, contourBtn, viewBtn;
private JRadioButton atomOrient;
private DefaultListModel alphaList, betaList; // useful for no-NBOServe use?
/**
* "Jmol" vs. "Atom" perspective chosen
*/
private boolean jmolView;
// effectively private, but need to be protected
// because they are used by private inner classes
protected OrbitalList orbitals;
/**
* The state of the VIEW panel, in terms of what modal dialogs are open; reset
* to VIEW_STATE_MAIN each time openPanel() is run.
*/
protected int viewState;
protected final static int VIEW_STATE_MAIN = 0;
protected final static int VIEW_STATE_PLANE = 1;
protected final static int VIEW_STATE_VECTOR = 2;
protected final static int VIEW_STATE_CAMERA = 3;
// used in SEARCH and in some cases NBODialg itself:
protected JComboBox comboBasis1;
protected JRadioButton alphaSpin, betaSpin;
protected boolean isNewModel = true;
// used by SEARCH; cleared by openPanel() using
protected String currOrb = "";
protected int currOrbIndex;
//NBOServe view settings
private String[] plVal, vecVal, lineVal;
/**
* reset the arrays of values that will be sent to NBOServe to their default
* values.
*
*/
protected void setDefaultParameterArrays() {
plVal = new String[] { "1", "2", "3", "0.5", "0.0", "0.0", "0.0", "-3.0",
"3.0", "-3.0", "3.0", "25" };
vecVal = new String[] { "1", "2", "0.5", "-2.0", "2.0", "-1.0", "1.0",
"100" };
lineVal = new String[] { "0.03", "0.05", "4", "0.05", "0.05", "0.1", "0.1" };
}
private final JTextField[] vectorFields = new JTextField[8];
private final JTextField[] planeFields = new JTextField[12];
private final JTextField[] camFields = new JTextField[53];
private final JTextField[] lineFields = new JTextField[7];
private String[] camVal = { "6.43", "0.0", "0.0", "50.0", "2.0", "2.0",
"0.0", "0.60", "1.0", "1.0", "40.0", "0.0", "0.60", "1.0", "1.0", "40.0",
"0.0", "0.60", "1.0", "1.0", "40.0", "0.0", "0.60", "1.0", "1.0", "40.0",
"0.5", "1.0", "1.0", "1.0", "0.8", "0.0", "0.0", "1.0", "0.8", "0.4",
"0.0", "1.0", "1.0", "0.5", "0.5", "0.5", "0.0", "0.7", "1.0", "0.22",
"0.40", "0.10", "0.05", "0.0316", "0.0001", "0.4000", "1" };
private String[] camFieldIDs = {
// 0 - 6
"1a", "1b", "1c", "1d", "1e", "1f",
"1g",
// 7 - 26
"2a", "2b", "2c", "2d", "2e", "2f", "2g", "2h", "2i", "2j", "2k", "2l",
"2m", "2n", "2o", "2p", "2q", "2r", "2s", "2t",
// 27 - 44
"3a", "3b", "3c", "3d", "3e", "3f", "3g", "3h", "3i", "3j", "3k", "3l",
"3m", "3n", "3o", "3p", "3q", "3r",
// 45 - 48
"4a", "4b", "4c", "4d",
// 49 - 51
"5a", "5b", "5c", "6" };
protected JPanel buildViewPanel() {
JPanel panel = new JPanel(new BorderLayout());
viewState = VIEW_STATE_MAIN;
///panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS));
dialog.runScriptQueued("set bondpicking true");
Box b = createViewSearchJobBox(NBOFileHandler.MODE_VIEW);
if (!dialog.jmolOptionNONBO)
panel.add(b, BorderLayout.NORTH);
centerBox = NBOUtil.createTitleBox(" Select Orbital(s) ",
createSelectOrbitalBox());
centerBox.setVisible(false);
centerBox.add(createOrbitalPanel());
panel.add(centerBox, BorderLayout.CENTER);
panel.add(createBottomBox(), BorderLayout.SOUTH);
updateViewSettings();
dialog.inputFileHandler.setBrowseEnabled(true);
// String fileType = dialog.runScriptNow("print _fileType");
// if (fileType.equals("GenNBO")) {
// File f = new File(
// dialog.runScriptNow("select within(model, visible); print _modelFile"));
// dialog.inputFileHandler.setInputFile(NBOFileHandler.newNBOFile(f, "47"));
// }
return panel;
}
protected Box createViewSearchJobBox(int mode) {
Box topBox = NBOUtil.createTitleBox(" Select Job ", dialog.new HelpBtn(
(mode == NBOFileHandler.MODE_SEARCH ? "search" : "view")
+ "_job_help.htm"));
Box inputBox = NBOUtil.createBorderBox(true);
inputBox.setPreferredSize(new Dimension(360, 50));
inputBox.setMaximumSize(new Dimension(360, 50));
topBox.add(inputBox);
dialog.getNewInputFileHandler(mode);
inputBox.add(Box.createVerticalStrut(5));
inputBox.add(dialog.inputFileHandler);
return topBox;
}
private Component createBottomBox() {
bottomBox = NBOUtil.createTitleBox(" Display Type ", dialog.new HelpBtn(
"view_display_help.htm"));
JPanel profBox = new JPanel(new GridLayout(2, 3, 0, 0));
profBox.setBorder(BorderFactory.createLineBorder(Color.BLACK));
profBox.setAlignmentX(0.0f);
ButtonGroup bg = new ButtonGroup();
profileBtn = new JRadioButton("1D Profile");
profileBtn.setToolTipText("Produce profile plot from axis parameters");
bg.add(profileBtn);
final JButton goBtn = new JButton("GO");
goBtn.setEnabled(false);
ActionListener goEnableAction = new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
goBtn.setEnabled(true);
}
};
profileBtn.addActionListener(goEnableAction);
profBox.add(profileBtn);//.setFont(nboFont);
contourBtn = new JRadioButton("2D Contour");
contourBtn.setToolTipText("Produce contour plot from plane parameters");
profBox.add(contourBtn);//.setFont(nboFont);
contourBtn.addActionListener(goEnableAction);
bg.add(contourBtn);
viewBtn = new JRadioButton("3D view");
viewBtn.addActionListener(goEnableAction);
bg.add(viewBtn);
profBox.add(viewBtn);//.setFont(nboFont);
vecBox = Box.createHorizontalBox();
vecBox.setAlignmentX(0.0f);
vecBox.setMaximumSize(new Dimension(120, 25));
profBox.add(vecBox);
planeBox = Box.createHorizontalBox();
planeBox.setAlignmentX(0.0f);
planeBox.setMaximumSize(new Dimension(120, 25));
profBox.add(planeBox);
goBtn.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
doGoPressed();
}
});
profBox.add(goBtn);
bottomBox.add(profBox);
bottomBox.setVisible(false);
return bottomBox;
}
private Component createSelectOrbitalBox() {
Box horizBox = Box.createHorizontalBox();
alphaList = betaList = null;
comboBasis1 = new JComboBox(basSet);
comboBasis1.setMaximumSize(new Dimension(70, 25));
//comboBasis1.setUI(new StyledComboBoxUI(180, -1));
horizBox.add(comboBasis1);
comboBasis1.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
if (comboBasis1.isEnabled())
doSetNewBasis(false, true);
}
});
betaSpin = new JRadioButton("β");
alphaSpin = new JRadioButton("α");
alphaSpin.setSelected(true);
ButtonGroup spinSelection = new ButtonGroup();
spinSelection.add(alphaSpin);
spinSelection.add(betaSpin);
betaSpin.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
EventQueue.invokeLater(new Runnable() {
@Override
public void run() {
doSetSpin(isAlphaSpin() ? null : "beta");
}
});
}
});
alphaSpin.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
EventQueue.invokeLater(new Runnable() {
@Override
public void run() {
doSetSpin(isAlphaSpin() ? "alpha" : null);
}
});
}
});
horizBox.add(alphaSpin);
horizBox.add(betaSpin);
alphaSpin.setVisible(dialog.isOpenShell());
betaSpin.setVisible(dialog.isOpenShell());
horizBox.add(dialog.new HelpBtn("view_orbital_help.htm"));
return horizBox;
}
private Component createOrbitalPanel() {
JPanel orbPanel = new JPanel(new BorderLayout());
orbPanel.setBorder(BorderFactory.createLineBorder(Color.black));
orbScroll = new JScrollPane();
orbScroll.setMaximumSize(new Dimension(355, 400));
orbScroll.getViewport().setMinimumSize(new Dimension(250, 400));
orbScroll
.setVerticalScrollBarPolicy(ScrollPaneConstants.VERTICAL_SCROLLBAR_NEVER);
orbPanel.add(orbScroll, BorderLayout.CENTER);
orbPanel.setAlignmentX(0.0f);
orbPanel.add(new JLabel(
"click to turn up to 9 orbitals on/off; hold to reverse phase"),
BorderLayout.SOUTH);
newOrbitals();
return orbPanel;
}
protected void doGoPressed() {
int n = orbitals.bsOn.cardinality();
if (n > 9) {
vwr.alert("More than 9 orbitals are selected!");
return;
}
if (orbitals.bsOn.isEmpty()) {
vwr.alert("Pick an orbital to plot.");
return;
}
initializeImage();
if (profileBtn.isSelected()) {
createImage1or2D(true);
} else if (contourBtn.isSelected()) {
createImage1or2D(false);
} else if (viewBtn.isSelected())
createImage3D();
}
protected void doSetSpin(String type) {
if (type != null) {
dialog.doSetStructure(type);
}
if (NBOConfig.nboView) {
dialog.runScriptQueued("select *;color bonds lightgrey");
}
doSetNewBasis(false, false);
}
/**
* Check to see if we have a given plot file and that it is not zero length.
* If we don't, run gennbo (if available) using the PLOT keyword and return
* null.
*
* @param fileNum
* 31-39 or 0 to set to the current value of comboBasis
* @return a new File object or null
*/
private File ensurePlotFile(int fileNum) {
if (fileNum == 0)
fileNum = 31 + comboBasis1.getSelectedIndex();
File f = dialog.inputFileHandler.newNBOFileForExt("" + fileNum);
if (!f.exists() || f.length() == 0) {
dialog.runPanel.doRunGenNBOJob("PLOT");
return null;
}
return f;
}
/**
* Plane dialog
*/
protected void doViewPlane() {
viewPlanePt = 0;
dialog.runScriptQueued("set bondpicking false");
viewState = VIEW_STATE_PLANE;
Box box = NBOUtil.createTitleBox(" Definiton of Plane ", null);
final JPanel plane = new JPanel(new BorderLayout());
JPanel labs = new JPanel(new GridLayout(6, 1, 5, 0));
labs.add(new JLabel("Enter fraction to locate origin:"));
labs.add(new JLabel("Enter two rotation angles:"));
labs.add(new JLabel("Enter shift of plane along normal:"));
labs.add(new JLabel("Enter min and max X values:"));
labs.add(new JLabel("Enter min and max Y values:"));
labs.add(new JLabel("Enter number of steps NX:"));
plane.add(labs, BorderLayout.WEST);
JPanel in = new JPanel(new GridLayout(6, 1, 5, 0));
in.add(planeFields[3]);
Box bo = Box.createHorizontalBox();
bo.add(planeFields[4]);
bo.add(planeFields[5]);
in.add(bo);
in.add(planeFields[6]);
bo = Box.createHorizontalBox();
bo.add(planeFields[7]);
bo.add(planeFields[8]);
in.add(bo);
bo = Box.createHorizontalBox();
bo.add(planeFields[9]);
bo.add(planeFields[10]);
in.add(bo);
in.add(planeFields[11]);
plane.add(in, BorderLayout.CENTER);
JButton b = new JButton("OK");
plane.add(b, BorderLayout.SOUTH);
Box box2 = Box.createVerticalBox();
box2.setBorder(BorderFactory.createLineBorder(Color.black));
box2.add(plane);
box2.setAlignmentX(0.0f);
box2.setMaximumSize(new Dimension(355, 250));
box.add(box2);
final JDialog d = new JDialog(dialog, "Vector definition");
d.setSize(new Dimension(300, 300));
d.setVisible(true);
d.add(box);
centerDialog(d, 175);
showSelected(planeFields);
d.addWindowListener(new WindowAdapter() {
@Override
public void windowClosing(WindowEvent e) {
dialog.runScriptQueued("select off;set bondpicking true");
viewState = VIEW_STATE_MAIN;
}
});
b.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
d.dispose();
dialog.runScriptQueued("select off;set bondpicking true");
viewState = VIEW_STATE_MAIN;
}
});
plane.setVisible(true);
}
private void showSelected(JTextField[] t) {
String s = "";
for (int i = t.length; --i >= 0;)
s += " " + t[i].getText();
dialog.showSelected(s);
}
/**
* Vector dialog
*/
protected void doViewAxis() {
dialog.runScriptQueued("set bondpicking false");
viewState = VIEW_STATE_VECTOR;
viewVectorPt = 0;
Box box = NBOUtil.createTitleBox(" Vector Definition ", null);
JPanel vect = new JPanel(new BorderLayout());
JPanel labs = new JPanel(new GridLayout(4, 1, 4, 0));
// labs.add(new JLabel("Enter or select two atom numbers:"));
labs.add(new JLabel("Enter fraction to locate origin:"));
labs.add(new JLabel("Enter min and max X values:"));
labs.add(new JLabel("Enter min and max function values:"));
labs.add(new JLabel("Enter number of steps NX:"));
vect.add(labs, BorderLayout.WEST);
JPanel in = new JPanel(new GridLayout(4, 1, 4, 0));
// Box bo = Box.createHorizontalBox();
// bo.add(vectorFields[0]);
// bo.add(vectorFields[1]);
// in.add(bo);
in.add(vectorFields[2]);
Box bo = Box.createHorizontalBox();
bo.add(vectorFields[3]);
bo.add(vectorFields[4]);
in.add(bo);
bo = Box.createHorizontalBox();
bo.add(vectorFields[5]);
bo.add(vectorFields[6]);
in.add(bo);
in.add(vectorFields[7]);
vect.add(in, BorderLayout.CENTER);
JButton b = new JButton("OK");
Box box2 = Box.createVerticalBox();
vect.add(b, BorderLayout.SOUTH);
vect.setAlignmentX(0.0f);
box2.setAlignmentX(0.0f);
box.setAlignmentX(0.0f);
box2.setBorder(BorderFactory.createLineBorder(Color.black));
box2.add(vect);
box2.setMaximumSize(new Dimension(355, 250));
box.add(box2);
final JDialog d = new JDialog(dialog, "Vector definition");
d.setSize(new Dimension(300, 300));
d.setVisible(true);
d.add(box);
centerDialog(d, 150);
showSelected(vectorFields);
d.addWindowListener(new WindowAdapter() {
@Override
public void windowClosing(WindowEvent e) {
dialog.runScriptQueued("select off;set bondpicking true");
viewState = VIEW_STATE_MAIN;
}
});
b.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
d.dispose();
dialog.runScriptQueued("select off;set bondpicking true");
viewState = VIEW_STATE_MAIN;
}
});
}
/**
* Vector dialog
*/
protected void doViewLines() {
Box box = NBOUtil.createTitleBox(" Contour lines ", null);
JPanel lines = new JPanel(new BorderLayout());
JPanel labs = new JPanel(new GridLayout(5, 1, 5, 0));
labs.add(new JLabel("Enter first contour line:"));
labs.add(new JLabel("Enter contour step size:"));
labs.add(new JLabel("Enter number of contours:"));
labs.add(new JLabel("Enter length of dash (cm):"));
labs.add(new JLabel("Enter length of space (cm):"));
lines.add(labs, BorderLayout.WEST);
JPanel in = new JPanel(new GridLayout(5, 1, 5, 0));
in.add(lineFields[0]);
in.add(lineFields[1]);
in.add(lineFields[2]);
in.add(lineFields[3]);
in.add(lineFields[4]);
lines.add(in, BorderLayout.CENTER);
Box box2 = Box.createVerticalBox();
box2.setBorder(BorderFactory.createLineBorder(Color.black));
box2.add(lines);
box.add(box2);
box2.setAlignmentX(0.0f);
final JDialog d = new JDialog(dialog, "Line settings");
d.setSize(new Dimension(300, 300));
d.setVisible(true);
d.add(box);
box = NBOUtil.createTitleBox(" Orbital diagram lines ", null);
lines = new JPanel(new BorderLayout());
labs = new JPanel(new GridLayout(2, 1, 5, 0));
labs.add(new JLabel("Enter length of dash (cm):"));
labs.add(new JLabel("Enter length of space (cm):"));
lines.add(labs, BorderLayout.WEST);
in = new JPanel(new GridLayout(2, 1, 5, 0));
in.add(lineFields[5]);
in.add(lineFields[6]);
lines.add(in, BorderLayout.CENTER);
box2 = Box.createVerticalBox();
box2.setAlignmentX(0.0f);
box2.setBorder(BorderFactory.createLineBorder(Color.black));
box2.add(lines);
box.add(box2);
JButton b = new JButton("OK");
lines.add(b, BorderLayout.SOUTH);
d.add(box, BorderLayout.SOUTH);
centerDialog(d, 150);
b.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
d.dispose();
viewState = VIEW_STATE_MAIN;
}
});
lines.setVisible(true);
}
private void centerDialog(JDialog d, int h) {
int x = (dialog.getX() + dialog.getWidth()) / 2 + 150;
int y = (dialog.getY() + dialog.getHeight()) / 2 - h;
d.setLocation(x, y);
}
/**
* Camera settings panel
*/
protected void doCam1() {
viewState = VIEW_STATE_CAMERA;
JPanel panel = new JPanel();
JPanel cam1 = new JPanel();//(dialog, "Camera and Light-Source:", false);
cam1.setLayout(new BorderLayout());
cam1.setMinimumSize(new Dimension(350, 200));
cam1.setVisible(true);
//centerDialog(cam1);
cam1.setBorder(BorderFactory.createLineBorder(Color.black));
Box box = NBOUtil.createTitleBox(" Camera and Light-Source ", null);
JPanel labs = new JPanel(new GridLayout(5, 1, 5, 0));
labs.add(new JLabel("Bounding sphere radius"));
labs.add(new JLabel("Camera distance from screen center:"));
labs.add(new JLabel("Two rotation angles (about X, Y):"));
labs.add(new JLabel("Camera view angle:"));
labs.add(new JLabel("Lighting (RL, UD, BF w.r.t. camera):"));
cam1.add(labs, BorderLayout.WEST);
JPanel in = new JPanel(new GridLayout(5, 1, 5, 0));
Box bo = Box.createHorizontalBox();
in.add(camFields[52]);
in.add(camFields[0]);
bo.add(camFields[1]);
bo.add(camFields[2]);
in.add(bo);
in.add(camFields[3]);
bo = Box.createHorizontalBox();
bo.add(camFields[4]);
bo.add(camFields[5]);
bo.add(camFields[6]);
in.add(bo);
cam1.add(in, BorderLayout.CENTER);
cam1.setAlignmentX(0.0f);
box.add(cam1);
panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS));
panel.add(box);
cam2(panel);
cam3(panel);
cam4(panel);
cam5(panel);
JScrollPane sp = new JScrollPane();
sp.setMaximumSize(new Dimension(350, 500));
sp.getViewport().add(panel);
final JDialog d = new JDialog(dialog, "Camera parameters");
d.setSize(new Dimension(360, 500));
d.setVisible(true);
d.add(sp, BorderLayout.CENTER);
centerDialog(d, 250);
JButton b = new JButton("OK");
d.add(b, BorderLayout.SOUTH);
b.setAlignmentX(0.0f);
b.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
d.dispose();
}
});
}
private void cam2(JPanel panel) {
Box box = NBOUtil.createTitleBox(" Surface Optical Parameters: ", null);
JPanel cam2 = new JPanel(new BorderLayout());
cam2.setBorder(BorderFactory.createLineBorder(Color.black));
JPanel labs = new JPanel(new GridLayout(4, 1, 5, 0));
labs.add(new JLabel("atoms:"));
labs.add(new JLabel("bonds:"));
labs.add(new JLabel("H-bonds:"));
labs.add(new JLabel("orbitals:"));
cam2.add(labs, BorderLayout.WEST);
JPanel in = new JPanel(new GridLayout(4, 1, 5, 0));
Box bo = Box.createHorizontalBox();
bo.add(camFields[7]);
bo.add(camFields[8]);
bo.add(camFields[9]);
bo.add(camFields[10]);
bo.add(camFields[11]);
in.add(bo);
bo = Box.createHorizontalBox();
bo.add(camFields[12]);
bo.add(camFields[13]);
bo.add(camFields[14]);
bo.add(camFields[15]);
bo.add(camFields[16]);
in.add(bo);
bo = Box.createHorizontalBox();
bo.add(camFields[17]);
bo.add(camFields[18]);
bo.add(camFields[19]);
bo.add(camFields[20]);
bo.add(camFields[21]);
in.add(bo);
bo = Box.createHorizontalBox();
bo.add(camFields[22]);
bo.add(camFields[23]);
bo.add(camFields[24]);
bo.add(camFields[25]);
bo.add(camFields[26]);
in.add(bo);
cam2.add(in, BorderLayout.CENTER);
cam2.add(
new JLabel(
" amb diff spec pow transp"),
BorderLayout.NORTH);
//JButton b = new JButton("OK");
//cam2.add(b, BorderLayout.SOUTH);
cam2.setAlignmentX(0.0f);
box.add(cam2);
panel.add(box);
// b.addActionListener(new ActionListener() {
// @Override
// public void actionPerformed(ActionEvent e) {
// cam2.dispose();
// cam3();
// }
// });
}
private void cam3(JPanel panel) {
JPanel cam3 = new JPanel(new BorderLayout());
Box box = NBOUtil.createTitleBox(" Color (Blue/Green/Red) Parameters: ",
null);
cam3.setBorder(BorderFactory.createLineBorder(Color.black));
JPanel labs = new JPanel(new GridLayout(6, 1, 5, 0));
labs.add(new JLabel("light source color:"));
labs.add(new JLabel("background color:"));
labs.add(new JLabel("orbital (+ phase) color:"));
labs.add(new JLabel("orbital (- phase) color:"));
labs.add(new JLabel("bond color"));
labs.add(new JLabel("H-Bond color"));
cam3.add(labs, BorderLayout.WEST);
JPanel in = new JPanel(new GridLayout(6, 1, 5, 0));
Box bo = Box.createHorizontalBox();
bo.add(camFields[27]);
bo.add(camFields[28]);
bo.add(camFields[29]);
in.add(bo);
bo = Box.createHorizontalBox();
bo.add(camFields[30]);
bo.add(camFields[31]);
bo.add(camFields[32]);
in.add(bo);
bo = Box.createHorizontalBox();
bo.add(camFields[33]);
bo.add(camFields[34]);
bo.add(camFields[35]);
in.add(bo);
bo = Box.createHorizontalBox();
bo.add(camFields[36]);
bo.add(camFields[37]);
bo.add(camFields[38]);
in.add(bo);
bo = Box.createHorizontalBox();
bo.add(camFields[39]);
bo.add(camFields[40]);
bo.add(camFields[41]);
in.add(bo);
bo = Box.createHorizontalBox();
bo.add(camFields[42]);
bo.add(camFields[43]);
bo.add(camFields[44]);
in.add(bo);
cam3.add(in, BorderLayout.CENTER);
cam3.add(
new JLabel(
" Blue Green Red"),
BorderLayout.NORTH);
cam3.setAlignmentX(0.0f);
box.add(cam3);
panel.add(box);
}
private void cam4(JPanel panel) {
JPanel cam4 = new JPanel(new BorderLayout());
Box box = NBOUtil.createTitleBox(" Atomic and Bond Radii: ", null);
cam4.setBorder(BorderFactory.createLineBorder(Color.black));
JPanel labs = new JPanel(new GridLayout(4, 1, 5, 0));
labs.add(new JLabel("Atomic radius for H:"));
labs.add(new JLabel("Atomic radius for C:"));
labs.add(new JLabel("Bond radius:"));
labs.add(new JLabel("H-bond radius:"));
cam4.add(labs, BorderLayout.WEST);
JPanel in = new JPanel(new GridLayout(4, 1, 5, 0));
in.add(camFields[45]);
in.add(camFields[46]);
in.add(camFields[47]);
in.add(camFields[48]);
cam4.add(in, BorderLayout.CENTER);
cam4.setAlignmentX(0.0f);
box.add(cam4);
panel.add(box);
}
private void cam5(JPanel panel) {
JPanel cam5 = new JPanel(new BorderLayout());
Box box = NBOUtil.createTitleBox(" Contour Parameters: ", null);
cam5.setBorder(BorderFactory.createLineBorder(Color.black));
JPanel labs = new JPanel(new GridLayout(3, 1, 5, 0));
labs.add(new JLabel("Contour value:"));
labs.add(new JLabel("Contour tolerance:"));
labs.add(new JLabel("Stepsize:"));
cam5.add(labs, BorderLayout.WEST);
JPanel in = new JPanel(new GridLayout(3, 1, 5, 0));
in.add(camFields[49]);
in.add(camFields[50]);
in.add(camFields[51]);
cam5.add(in, BorderLayout.CENTER);
cam5.setAlignmentX(0.0f);
box.add(cam5);
panel.add(box);
}
//////////////////////// general methods ////////////////////
private void newOrbitals() {
if (orbitals != null) {
orbitals.removeListSelectionListener(orbitals);
orbitals.removeMouseListener(orbitals);
orbScroll.getViewport().remove(orbitals);
}
orbScroll.getViewport().add(orbitals = new OrbitalList());
}
private void updateViewSettings() {
dialog.viewSettingsBox.removeAll();
dialog.viewSettingsBox.setLayout(new BorderLayout());
//Box top = Box.createVerticalBox();
JLabel lab = new JLabel("Settings:");
lab.setBackground(Color.black);
lab.setForeground(Color.white);
lab.setOpaque(true);
lab.setFont(NBOConfig.nboFont);
//top.add(lab);
Box middle = Box.createVerticalBox();
Box tmp = Box.createHorizontalBox();
tmp.add(new JLabel("Orientation: "));
atomOrient = new JRadioButton("Atoms");
atomOrient.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent arg0) {
doViewByAtoms();
}
});
tmp.add(atomOrient);
final JRadioButton jmolOrient = new JRadioButton("Jmol");
jmolOrient.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent arg0) {
doViewByJmol();
}
});
tmp.add(jmolOrient);
ButtonGroup bg = new ButtonGroup();
bg.add(jmolOrient);
bg.add(atomOrient);
dialog.viewSettingsBox.add(lab, BorderLayout.NORTH);
middle.add(tmp);
tmp = Box.createHorizontalBox();
final JButton btnVec = new JButton("Axis");
final JButton btnPla = new JButton("Plane");
final JButton btnLines = new JButton("Lines");
btnVec.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
doViewAxis();
}
});
btnPla.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
doViewPlane();
}
});
btnLines.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
doViewLines();
}
});
btnPla.setMargin(null);
tmp.add(btnVec);
tmp.add(btnPla);
tmp.add(btnLines);
middle.add(tmp);
dialog.viewSettingsBox.add(middle, BorderLayout.CENTER);
final JButton btnCam = new JButton("Camera");
btnCam.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
doCam1();
}
});
atomOrient.setSelected(true);
dialog.viewSettingsBox.add(btnCam, BorderLayout.SOUTH);
dialog.repaint();
dialog.revalidate();
}
protected void doViewByJmol() {
planeBox.setVisible(false);
jmolView = true;
}
protected void doViewByAtoms() {
planeBox.setVisible(true);
dialog.nboService.restartIfNecessary();
setDefaultParameterArrays();
jmolView = false;
}
protected File doSetNewBasis(boolean isFileLoading, boolean clearAlphaBeta) {
if (clearAlphaBeta) {
alphaList = betaList = null;
}
dialog.runScriptQueued("isosurface delete");
resetCurrentOrbitalClicked();
if (comboBasis1.getSelectedIndex() == BASIS_MO) {
if (!dialog.runPanel.cleanNBOKeylist(
dialog.inputFileHandler.read47File(false)[1], true).contains("CMO")) {
dialog.runPanel.doRunGenNBOJob("CMO");
return null;
}
}
if (orbitals == null)
return null;
isNewModel = true;
orbitals.removeAll();
File f = ensurePlotFile(0);
if (f == null) {
// NBOServe is probably sending a job.
return null;
}
boolean isBeta = dialog.isOpenShell() && !isAlphaSpin();
DefaultListModel list = (isBeta ? betaList : alphaList);
if (list != null && list.size() > 0) {
orbitals.setModelList(list, false);
return null;
}
list = new DefaultListModel();
if (isBeta)
betaList = list;
else
alphaList = list;
if (isFileLoading) {
return f;
}
dialog.logCmd("select " + comboBasis1.getSelectedItem() + " "
+ (isBeta ? "beta" : dialog.isOpenShell() ? "alpha" : ""));
int ibasis = comboBasis1.getSelectedIndex();
String[] tokens = this.getLabelSet(ibasis, isBeta);
if (tokens != null) {
orbitals.loadList(tokens, list);
return f;
}
if (dialog.jmolOptionNONBO)
return f;
postNBO_v(NBOUtil.postAddCmd(getMetaHeader(true), "LABEL"),
MODE_VIEW_LIST, getIbasKey(ibasis, isBeta), list, "Getting list", null, null);
return null;
}
/////////////////////// RAW NBOSERVE API ////////////////////
/**
* get the standard header for a set of META commands, specifically C_PATH and
* C_JOBSTEM and I_SPIN; possibly I_BAS_1
*
* @param addBasis
* if desired, from comboBasis
*
* @return a new string buffer using javajs.util.SB
*
*/
protected SB getMetaHeader(boolean addBasis) {
SB sb = new SB();
NBOUtil.postAddGlobalC(sb, "PATH",
dialog.inputFileHandler.inputFile.getParent());
NBOUtil.postAddGlobalC(sb, "JOBSTEM", dialog.inputFileHandler.jobStem);
if (addBasis)
NBOUtil.postAddGlobalI(sb, "BAS_1", 1, comboBasis1);
NBOUtil.postAddGlobalI(sb, "SPIN",
(!dialog.isOpenShell() ? 0 : isAlphaSpin() ? 1 : -1), null);
return sb;
}
/**
* add in camera parameters
*
* @param sb
*/
private void appendCameraParams(SB sb) {
int n = camFields.length;
for (int i = 0; i < n; i++) {
// //if (!camFields[i].getText().equals(camVal[i])) {
// camVal[i] = camFields[i].getText();
NBOUtil.postAddGlobalT(sb, "CAMERA_" + camFieldIDs[i], camFields[i]);
}
}
/**
* add in the SIGN parameter
*
* @param sb
* @param i
*/
private void appendOrbitalPhaseSign(SB sb, int i) {
NBOUtil.postAddGlobal(sb, "SIGN", (orbitals.bsNeg.get(i) ? "-1" : "+1"));
}
//contour/profile selected orbital in orbital list
protected void createImage1or2D(boolean oneD) {
if (jmolView)
setJmolView(true);
if (orbitals.bsOn.cardinality() > 1) {
createImage1or2DMultiple(oneD);
return;
}
// ? needed ? sendJmolOrientation();
SB sb = getMetaHeader(true);
int ind = orbitals.bsOn.nextSetBit(0);
appendOrbitalPhaseSign(sb, ind);
appendLineParams(sb);
if (oneD) {
appendVectorParams(sb);
} else {
appendPlaneParams(sb);
}
String cmd = (oneD ? "Profile " : "Contour ") + (ind + 1);
dialog.logCmd(cmd);
NBOUtil.postAddCmd(sb, cmd);
postNBO_v(sb, MODE_VIEW_IMAGE, -1, null,
(oneD ? "Profiling.." : "Contouring.."), null, null);
}
private void appendLineParams(SB sb) {
for (int i = 0; i < lineFields.length; i++)
NBOUtil.postAddGlobal(sb, "LINES_" + (char) ('a' + i), lineVal[i] = lineFields[i].getText());
}
private void appendVectorParams(SB sb) {
for (int i = 0; i < vectorFields.length; i++)
NBOUtil.postAddGlobal(sb, "VECTOR_" + (char) ('a' + i), vecVal[i] = vectorFields[i].getText());
}
private void appendPlaneParams(SB sb) {
for (int i = 0; i < planeFields.length; i++)
NBOUtil.postAddGlobal(sb, "PLANE_" + (char) ('a' + i), plVal[i] = planeFields[i].getText());
}
private void setJmolView(boolean is2D) {
String key = (is2D ? "a U" : "a V_U");
SB sb = new SB();
for (int i = 1; i <= 3; i++) {
String tmp2 = "";
for (int j = 1; j <= 3; j++) {
Object oi = vwr.getProperty("string", "orientationInfo.rotationMatrix["
+ j + "][" + i + "]", null);
tmp2 += oi.toString() + " ";
}
sb.append(key + i + " " + tmp2 + NBOUtil.sep);
}
// I do not understand why a LABEL command has to be given here. A bug?
postNBO_v(NBOUtil.postAddCmd(getMetaHeader(true), "LABEL"),
NBOService.MODE_RAW, -1, null, "", "jview.txt", sb.toString());
postNBO_v(NBOUtil.postAddCmd(new SB(), "JVIEW"), NBOService.MODE_RAW, -1, null,
"Sending Jmol orientation", null, null);
// sb = getMetaHeader(true);
// sb.append("CMD LABEL");
// nboService.rawCmdNew("v", sb, MODE_RAW, null, "");
}
protected void createImage1or2DMultiple(boolean oneD) {
// sb = getMetaHeader(true);
// sb.append("CMD LABEL");
// nboService.rawCmdNew("v", sb, MODE_RAW, null, "");
//
SB sb = new SB();
String msg = (oneD) ? "Profile" : "Contour";
String profileList = "";
for (int pt = 0, i = orbitals.bsOn.nextSetBit(0); i >= 0; i = orbitals.bsOn
.nextSetBit(i + 1)) {
sb = getMetaHeader(true);
appendOrbitalPhaseSign(sb, i);
NBOUtil.postAddCmd(sb, (oneD ? "PROFILE " : "CONTOUR ") + (i + 1));
msg += " " + (i + 1);
profileList += " " + (++pt);
postNBO_v(sb, NBOService.MODE_RAW, -1, null, "Sending " + msg, null, null);
}
dialog.logCmd(msg);
sb = getMetaHeader(false);
appendLineParams(sb);
NBOUtil.postAddCmd(sb, "DRAW" + profileList);
postNBO_v(sb, MODE_VIEW_IMAGE, -1, null, "Drawing...", null, null);
}
protected void createImage3D() {
SB sb = new SB();
String tmp = "View";
String list = "";
BS bs = orbitals.bsOn;
for (int pt = 0, i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
sb = getMetaHeader(true);
appendOrbitalPhaseSign(sb, i);
NBOUtil.postAddCmd(sb, "PROFILE " + (i + 1));
postNBO_v(sb, NBOService.MODE_RAW, -1, null, "Sending profile " + (i + 1),
null, null);
tmp += " " + (i + 1);
list += " " + (++pt);
}
dialog.logCmd(tmp);
String jviewData = sb.toString();
// BH: It turns out it is CRITICAL that if you send camera parameters, you MUST NOT SEND basis information.
// (no idea why!)
sb = getMetaHeader(false);
appendCameraParams(sb);
NBOUtil.postAddCmd(sb, "VIEW" + list);
postNBO_v(sb, MODE_VIEW_IMAGE, -1, null, "Raytracing...", null, jviewData);
}
private void initializeImage() {
//testingView = NBOConfig.debugVerbose;
dialog.runScriptQueued("image close");
dialog.nboService.restart();
setDefaultParameterArrays();
if (jmolView)
setJmolView(false);
}
private int viewVectorPt = 0;
private int viewPlanePt = 0;
/**
* callback notification from Jmol
*
* @param picked
* [atomno1, atomno2] or [atomno1, Integer.MIN_VALUE]
*
*/
protected void notifyPick_v(int[] picked) {
dialog.runScriptQueued("isosurface delete");
int at1 = picked[0];
int at2 = picked[1];
switch (viewState) {
case VIEW_STATE_VECTOR:
if (at2 != Integer.MIN_VALUE)
return;
vectorFields[viewVectorPt++].setText("" + at1);
showSelected(vectorFields);
viewVectorPt = viewVectorPt % 2;
break;
case VIEW_STATE_PLANE:
if (at2 != Integer.MIN_VALUE)
return;
planeFields[viewPlanePt++].setText("" + at1);
showSelected(planeFields);
viewPlanePt = viewPlanePt % 3;
break;
case VIEW_STATE_MAIN:
if (at2 == Integer.MIN_VALUE) {
showOrbital(nextOrbitalForAtomPick(at1,
(DefaultListModel) orbitals.getModel()));
return;
}
switch (comboBasis1.getSelectedIndex()) {
case BASIS_AO:
case BASIS_PNAO:
case BASIS_NAO:
case BASIS_MO:
break;
case BASIS_PNHO:
case BASIS_NHO: {
String sat1 = vwr.ms.at[at1 - 1].getElementSymbol() + at1;
String sat2 = vwr.ms.at[at2 - 1].getElementSymbol() + at2;
showOrbital(nextOrbitalForBondPick(sat1 + "(" + sat2 + ")", sat2 + "("
+ at1 + ")"));
}
break;
case BASIS_PNBO:
case BASIS_NBO:
case BASIS_PNLMO:
case BASIS_NLMO: {
String sat1 = vwr.ms.at[at1 - 1].getElementSymbol() + at1;
String sat2 = vwr.ms.at[at2 - 1].getElementSymbol() + at2;
showOrbital(nextOrbitalForBondPick(sat1 + "-" + sat2, sat2 + "-" + sat1));
}
break;
}
}
}
private boolean includeRydberg = false; // BH thinking this is not necessary
/**
* Determine the next orbital in the cycle for bond picking
*
* @param atomno
* @param list
* @return the new index
*/
protected int nextOrbitalForAtomPick(int atomno,
AbstractListModel list) {
String at = vwr.ms.at[atomno - 1].getElementSymbol() + atomno + "(";
int curr = (currOrb.contains(at) ? currOrbIndex : -1);
for (int i = curr + 1, size = list.getSize(); i < size + curr; i++) {
int ipt = i % size;
String str = list.getElementAt(ipt).replaceAll(" ", "");
if (str.contains(at + "lp)") || str.contains(at + "lv)")
|| includeRydberg && str.contains(at + "ry)")) {
orbitals.setSelectedIndex(ipt);
currOrb = str;
currOrbIndex = ipt;
return ipt;
}
}
return curr;
}
/**
* check for the next orbital upon bond clicking
*
* @param b1
* @param b2
* @return the next orbital index, or -1
*/
private int nextOrbitalForBondPick(String b1, String b2) {
int size = orbitals.getModel().getSize();
int curr = (currOrb.contains(b1) ? currOrbIndex : -1);
for (int i = curr + 1; i < size + curr; i++) {
int ipt = i % size;
String listOrb = orbitals.getModel().getElementAt(ipt);
String str = listOrb.replace(" ", "");
if (str.contains(b1) || b2 != null && str.contains(b2)) {
orbitals.setSelectedIndex(ipt);
currOrb = str;
currOrbIndex = ipt;
return ipt;
}
}
return curr;
}
protected void resetCurrentOrbitalClicked() {
currOrb = "";
currOrbIndex = -1;
}
protected void showOrbital(int i) {
if (i < 0)
return;
orbitals.bsOn.clearAll();
orbitals.bsNeg.clearAll();
dialog.runScriptQueued("isosurface * off");
orbitals.updateIsosurfacesInJmol(i);
}
protected void notifyList(AbstractListModel list) {
if (list != null) {
orbitals.setLayoutOrientation(JList.VERTICAL_WRAP);
orbitals.requestFocus();
}
}
@SuppressWarnings("unchecked")
protected void notifyFileLoaded_v() {
if (vwr.ms.ac == 0)
return;
clearLabelSet();
centerBox.setVisible(true);
bottomBox.setVisible(!dialog.jmolOptionNONBO);
//OLD
// if (!newModel) {
// String frame = (startingModelCount + modelCount - 1) + ".1";
// dialog.runScriptQueued("frame " + frame + ";refesh");
// colorMeshes();
// dialog.runScriptQueued("var b = {visible}.bonds;select bonds @b;wireframe 0;refresh");
// return;
// }
//<--
// retrieve model from currently loaded model
Map moData = (Map) vwr
.getCurrentModelAuxInfo().get("moData");
String type = comboBasis1.getSelectedItem().toString();
int ibas = comboBasis1.getSelectedIndex();
if (type.charAt(0) == 'P')
type = type.substring(1);
boolean isBeta = dialog.isOpenShell() && !isAlphaSpin()
&& betaList != null;
try {
boolean needab = (getIbasKey(ibas, true) != getIbasKey(ibas, false));
alphaSpin.setVisible(needab && dialog.isOpenShell()); // old
betaSpin.setVisible(needab && dialog.isOpenShell()); // old
setDefaultParameterArrays();
for (int i = 0; i < planeFields.length; i++)
planeFields[i] = new JTextField(plVal[i]);
for (int i = 0; i < vectorFields.length; i++)
vectorFields[i] = new JTextField(vecVal[i]);
for (int i = 0; i < lineFields.length; i++)
lineFields[i] = new JTextField(lineVal[i]);
for (int i = 0; i < camFields.length; i++)
camFields[i] = new JTextField(camVal[i]);
vecBox.removeAll();
vecBox.add(new JLabel("Axis: "));
vecBox.add(vectorFields[0]);
vecBox.add(vectorFields[1]);
planeBox.removeAll();
planeBox.add(new JLabel("Plane: "));
planeBox.add(planeFields[0]);
planeBox.add(planeFields[1]);
planeBox.add(planeFields[2]);
dialog.viewSettingsBox.setVisible(!dialog.jmolOptionNONBO);
// set list
DefaultListModel list = (isBeta ? betaList : alphaList);
if (dialog.jmolOptionNONBO) {
if (type.startsWith("P"))
type = type.substring(1);
if (type.equalsIgnoreCase("NLMO"))
type = "NBO";
String[] a = ((Map) moData.get("nboLabelMap"))
.get((isBeta ? "beta_" : "") + type);
list.clear();
for (int i = 0; i < a.length; i++)
list.addElement((i + 1) + ". " + a[i] + " ");
} else {
doSetNewBasis(false, true);
}
// orbitals.setModelList(list, true);
} catch (NullPointerException e) {
//not a problem? dialog.log(e.getMessage() + " reading file", 'r');
e.printStackTrace();
}
NBODialog.colorMeshes();
// showAtomNums(true);
// setBonds(true);
}
protected void loadNewFileIfAble() {
dialog.nboService.restart();
comboBasis1.setEnabled(false);
if (comboBasis1.getSelectedIndex() != BASIS_MO)
comboBasis1.setSelectedIndex(BASIS_PNBO);
else
comboBasis1.setSelectedIndex(BASIS_MO);
comboBasis1.setEnabled(true);
File f = doSetNewBasis(true, true);
if (f == null)
return;
dialog.loadModelFileQueued(
f,
NBOUtil.pathWithoutExtension(f.getAbsolutePath()).equals(
NBOUtil.pathWithoutExtension(dialog.getJmolFilename())));
}
protected void showLewisStructure() {
dialog.doSetStructure(isAlphaSpin() ? "alpha" : "beta");
}
protected boolean isAlphaSpin() {
return alphaSpin.isSelected() || !alphaSpin.isVisible();
}
/**
* Indicate that we have a new model and clear all bit sets.
*
* Called by NBOFileHandler.clearInputFile
*
*/
protected void resetView() {
isNewModel = true;
orbitals.clearOrbitals(true);
clearLabelSet();
}
class OrbitalList extends JList implements ListSelectionListener,
MouseListener, KeyListener {
protected BS bsOn = new BS();
protected BS bsNeg = new BS();
protected BS bsKnown = new BS();
public OrbitalList() {
super();
setLayoutOrientation(JList.VERTICAL_WRAP);
setVisibleRowCount(-1); // indicates to automatically calculate max number of rows
setFont(NBOConfig.nboFontLarge);
//setColorScheme();
setFont(NBOConfig.listFont);
setModel(new DefaultListModel() {
@Override
public void addElement(String s) {
s += " ";
super.addElement(s);
}
});
setCellRenderer(new ListCellRenderer() {
@Override
public Component getListCellRendererComponent(JList list,
String value, int index,
boolean isSelected,
boolean cellHasFocus) {
return renderCell(index);
}
});
addListSelectionListener(this);
addMouseListener(this);
}
public void loadList(String[] lines, DefaultListModel list) {
list.clear();
for (int i = 0; i < lines.length; i++)
list.addElement(lines[i]);
setModelList(list, true);
}
/**
* @param list
* @param isNew
* unused
*/
void setModelList(DefaultListModel list, boolean isNew) {
setSelectedIndices(new int[0]);
setModel(list);
clearOrbitals(true);
showLewisStructure();
updateIsosurfacesInJmol(Integer.MIN_VALUE);
}
private JLabel cellLabel;
protected boolean myTurn;
protected boolean toggled;
protected Component renderCell(int index) {
if (cellLabel == null) {
cellLabel = new JLabel() {
@Override
public void setBackground(Color bg) {
if (myTurn)
super.setBackground(bg);
}
};
cellLabel.setFont(NBOConfig.listFont);
cellLabel.setMinimumSize(new Dimension(180, 20));
cellLabel.setPreferredSize(new Dimension(180, 20));
cellLabel.setMaximumSize(new Dimension(180, 20));
cellLabel.setOpaque(true);
}
cellLabel.setText(getModel().getElementAt(index));
myTurn = true;
Color bgcolor = (!bsOn.get(index) ? Color.WHITE
: bsNeg.get(index) ? NBOConfig.orbColor2 : NBOConfig.orbColor1);
cellLabel.setBackground(bgcolor);
cellLabel.setForeground(getContrastColor(bgcolor));
myTurn = false;
return cellLabel;
}
private Color getContrastColor(Color bgcolor) {
return new AwtColor(C.getArgb(C.getBgContrast(bgcolor.getRGB())));
}
/**
* Clear the orbital display bitsets.
*
* @param clearAll
*/
void clearOrbitals(boolean clearAll) {
bsKnown.clearAll();
if (clearAll) {
bsOn.clearAll();
bsNeg.clearAll();
}
}
// /**
// *
// */
// protected void setLastOrbitalSelection() {
// updateIsosurfacesInJmol(-1);
// }
//
/**
* Create, display, or hide a given orbital zero-based index. Optionally (in
* the case of a key release) use the current selection set from Java but
* otherwise use the bsON bit set.
*
*
* @param iClicked
* negative: set the current list selection using BsON
* Integer.MAX_VALUE: set the current BsON from the list selection
* (keyboard drag, for example) otherwise: toggle the specified
* orbital index on or off
*
*/
protected void updateIsosurfacesInJmol(int iClicked) {
DefaultListModel model = (DefaultListModel) getModel();
boolean isBeta = betaSpin.isSelected();
String type = comboBasis1.getSelectedItem().toString();
String script = "select 1.1;";
if (iClicked == Integer.MAX_VALUE)
script += updateBitSetFromModel();
else
updateModelFromBitSet();
//System.out.println("update " + bsOn + " " + bsKnown + " " + iClicked);
for (int i = 0, n = model.getSize(); i < n; i++) {
boolean isOn = bsOn.get(i);
if (i == iClicked || isOn && !bsKnown.get(i)
|| isSelectedIndex(i) != isOn) {
String id = "mo" + i;
if (!isOn || bsKnown.get(i)) {
if (isOn && bsNeg.get(i)) {
bsKnown.clear(i);
bsNeg.clear(i);
}
bsOn.setBitTo(i, isOn = !isOn);
}
boolean isKnown = bsKnown.get(i);
if (!bsOn.get(i)) {
// just turn it off
script += "isosurface mo" + i + " off;";
} else if (isKnown) {
// just turn it on
script += "isosurface mo" + i + " on;";
} else {
bsKnown.set(i);
// create the isosurface
script += NBOConfig.getJmolIsosurfaceScript(id, type, i + 1,
isBeta, bsNeg.get(i));
}
}
// if (bsOn.get(i)) {
// dialog.logCmd("...orbital " + orbitals.getModel().getElementAt(i)
// + (bsNeg.get(i) ? " [-]" : ""));
// }
}
updateModelFromBitSet();
dialog.runScriptQueued(script);
//System.out.println("known" + bsKnown + " on" + bsOn + " neg" + bsNeg + " " + script);
}
private String updateBitSetFromModel() {
int[] a = getSelectedIndices();
BS bsModel = new BS();
for (int i = a.length; --i >= 0;)
bsModel.set(i);
String script = "";
for (int i = getModel().getSize(); --i >= 0;) {
if (bsModel.get(i) != bsOn.get(i)) {
if (bsOn.get(i)) {
script += "isosurface mo" + i + " off;";
bsOn.clear(i);
} else {
bsOn.set(i);
}
}
}
return script;
}
private void updateModelFromBitSet() {
int[] a = new int[bsOn.cardinality()];
for (int i = bsOn.nextSetBit(0), pt = 0; i >= 0; i = bsOn
.nextSetBit(i + 1))
a[pt++] = i;
try {
setSelectedIndices(a);
//System.out.println("on neg " + bsOn + " " + bsNeg + " " + PT.toJSON(null, a));
} catch (Exception e) {
System.out.println("render error " + e);
// this is due to underlying list changing. Ignore
}
}
@Override
public void valueChanged(ListSelectionEvent e) {
}
// protected void setLabel(int i) {
// String label0 = getModel().getElementAt(i);
// int pt = label0.indexOf('[');
// if (pt > 0)
// label0 = label0.substring(0, pt);
// ((DefaultListModel) getModel()).set(i, label0.trim() + " ");
// }
@Override
public void mousePressed(MouseEvent e) {
killMouseTimer();
mouseTimer = getMouseTimer();
// System.out.println("PRESS" + e);
// System.out.println("press " + PT.toJSON(null, getSelectedIndices()) + e.getClickCount());
}
@Override
public void mouseReleased(MouseEvent e) {
// System.out.println("RELEASE" + e);
// System.out.println("release " + PT.toJSON(null, getSelectedIndices()));
//boolean toggled = this.toggled;
killMouseTimer();
int i = getSelectedIndex();
// if (toggled)
// this.toggleOrbitalNegation(i);
toggled = false;
updateIsosurfacesInJmol(i);
}
private void killMouseTimer() {
if (mouseTimer != null)
mouseTimer.stop();
mouseTimer = null;
toggled = false;
}
private final static int DBLCLICK_THRESHOLD_MS = 300;
private Timer mouseTimer;
private Timer getMouseTimer() {
Timer t = new Timer(DBLCLICK_THRESHOLD_MS, new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
doHoldTimerEvent();
}
});
t.setRepeats(false);
t.start();
System.out.println("timer started");
return t;
}
protected void doHoldTimerEvent() {
int i = getSelectedIndex();
if (bsOn.get(i)) {
toggled = true;
// toggle:
bsNeg.setBitTo(i, !bsNeg.get(i));
bsKnown.clear(i); // to - just switch colors?
// toggleOrbitalNegation(i);
repaint();
}
}
@Override
public void mouseClicked(MouseEvent e) {
}
@Override
public void mouseEntered(MouseEvent e) {
}
@Override
public void mouseExited(MouseEvent e) {
}
@Override
public void keyPressed(KeyEvent e) {
// System.out.println("KEYDN" + orbitals.getSelectedIndex() + " " + e);
}
@Override
public void keyReleased(KeyEvent e) {
// System.out.println("KEYUP" + orbitals.getSelectedIndex() + " " + e);
updateIsosurfacesInJmol(Integer.MAX_VALUE);
}
@Override
public void keyTyped(KeyEvent e) {
}
}
/**
* Post a request to NBOServe with a callback to processNBO_s.
*
* @param sb
* command data
* @param mode
* type of request
* @param ikey
* @param list
* optional list to fill
* @param statusMessage
* @param dataFileName
* optional
* @param fileData
* optional
*/
private void postNBO_v(SB sb, final int mode, final int ikey,
final DefaultListModel list,
String statusMessage, String dataFileName,
String fileData) {
final NBORequest req = new NBORequest();
req.set(new Runnable() {
@Override
public void run() {
processNBO_v(req, mode, ikey, list);
}
}, false, statusMessage, "v_cmd.txt", sb.toString(), dataFileName, fileData);
dialog.nboService.postToNBO(req);
}
/**
* Process the reply from NBOServe.
*
*
* @param req
* @param mode
* @param ikey
* @param list
*/
protected void processNBO_v(NBORequest req, int mode, int ikey,
DefaultListModel list) {
String[] lines = req.getReplyLines();
switch (mode) {
case MODE_VIEW_LIST:
addBasisLabel(ikey, lines);
orbitals.loadList(lines, list);
break;
case MODE_VIEW_IMAGE:
String fname = dialog.inputFileHandler.inputFile.getParent() + "\\"
+ dialog.inputFileHandler.jobStem + ".bmp";
File f = new File(fname);
final SB title = new SB();
String id = "id " + PT.esc(title.toString().trim());
String script = "image " + id + " close;image id \"\" "
+ PT.esc(f.toString().replace('\\', '/'));
dialog.runScriptQueued(script);
break;
case NBOService.MODE_RAW:
break;
}
}
}