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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.Rectangle;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import javajs.util.PT;
import javajs.util.SB;
import javax.swing.BorderFactory;
import javax.swing.Box;
import javax.swing.JComboBox;
import javax.swing.JLabel;
import javax.swing.JPanel;
import javax.swing.JTextField;
import javax.swing.plaf.basic.BasicComboPopup;
import javax.swing.plaf.basic.ComboPopup;
import javax.swing.plaf.metal.MetalComboBoxUI;
public class NBOUtil {
public static void postAddGlobalC(SB sb, String label, String val) {
sb.append("GLOBAL C_").append(label).append(" ").append(val).append(sep);
}
public static void postAddGlobalI(SB sb, String label, int offset, JComboBox cb) {
sb.append("GLOBAL I_").append(label).append(" ").appendI(cb == null ? offset : cb.getSelectedIndex() + offset).append(sep);
}
public static void postAddGlobalT(SB sb, String key, JTextField t) {
sb.append("GLOBAL ").append(key).append(" ").append(t.getText()).append(sep);
}
public static void postAddGlobal(SB sb, String key, String val) {
sb.append("GLOBAL ").append(key).append(" ").append(val).append(sep);
}
public static SB postAddCmd(SB sb, String cmd) {
return sb.append("CMD ").append(cmd).append(sep);
}
/**
* Creates the title blocks with background color for headers.
*
* @param title
* - title for the section
* @param rightSideComponent
* help button, for example
* @return Box formatted title box
*/
public static Box createTitleBox(String title, Component rightSideComponent) {
Box box = Box.createVerticalBox();
JLabel label = new JLabel(title);
label.setAlignmentX(0);
label.setBackground(NBOConfig.titleColor);
label.setForeground(Color.white);
label.setFont(NBOConfig.titleFont);
label.setOpaque(true);
if (rightSideComponent != null) {
JPanel box2 = new JPanel(new BorderLayout());
box2.setAlignmentX(0);
box2.add(label, BorderLayout.WEST);
box2.add(rightSideComponent, BorderLayout.EAST);
box2.setMaximumSize(new Dimension(360, 25));
box.add(box2);
} else
box.add(label);
box.setAlignmentX(0.0f);
return box;
}
/**
* create a bordered box, either vertical or horizontal
*
* @param isVertical
* @return a box
*/
public static Box createBorderBox(boolean isVertical) {
Box box = isVertical ? Box.createVerticalBox() : Box.createHorizontalBox();
box.setAlignmentX(0.0f);
box.setBorder(BorderFactory.createLineBorder(Color.black));
return box;
}
public static final String sep = System.getProperty("line.separator");
public static String round(double value, int places) {
return PT.formatD(value, places, -1 - places, false, false, true);
// if (places < 0)
// throw new IllegalArgumentException();
// BigDecimal bd = new BigDecimal(value);
// bd = bd.setScale(places, RoundingMode.HALF_UP);
// return bd.doubleValue();
}
/**
* Get the listing of the atoms picked -- in order of picking, if a bond
* @param data
* @return [atom1, Integer.MIN_VALUE] (atom) or [atom1, atom2] (bond) or [Integer.MIN_VALUE, 0] (other)
*/
public static int[] getAtomsPicked(Object[] data) {
int atom1 = ((Integer) data[2]).intValue();
//System.out.println("----" + type.toString() + ": " + atomIndex);
if (atom1 >= 0)
return new int[] { atom1 + 1, Integer.MIN_VALUE };
if (atom1 != -3)
return new int[] { Integer.MIN_VALUE, 0 };
String[] sdata = PT.getTokens(data[1].toString().replace('"', ' '));
atom1 = PT.parseInt(sdata[3]);
int atom2 = PT.parseInt(sdata[4]);
System.out.println(atom1 + " picked " + atom2);
return new int[] { atom1 + 1, atom2 + 1};
}
public static String addNBOKeyword(String tmp, String s) {
int pt;
if ((pt = findKeyword(tmp, s, false)) >= 0)
return tmp.substring(0, pt) + tmp.substring(pt + 1);
if (findKeyword(tmp, s, true) >= 0)
return tmp;
if (tmp.length() + s.length() - tmp.lastIndexOf(NBOUtil.sep) >= 80)
tmp += NBOUtil.sep + " ";
if (tmp.length() == 0)
tmp = " ";
tmp += s.toUpperCase() + " ";
return tmp;
}
/**
* check for a full keyword; all must be caps
* @param keywords
* @param s
* @param ifPresent true for is in the list; false for is not in the list
* @return point of " " or KEYWORD_NEGATE PRIOR TO KEYWORD or -1 if not present
*/
public static int findKeyword(String keywords, String s, boolean ifPresent) {
int pt;
if (!keywords.startsWith(" "))
keywords = " " + keywords + " ";
String prefix = (ifPresent ? " " : KEYWORD_IGNORE);
return ((pt = keywords.indexOf(prefix + s + " ")) >= 0 ? pt
: (pt = keywords.indexOf(prefix + s + "=")) >= 0 ? pt : -1);
}
private static String KEYWORD_IGNORE = "_";
public static String removeNBOKeyword(String keywords, String name) {
// look for "_NAME " or "_NAME="
int pt = findKeyword(keywords, name, false);
if (pt >= 0)
return keywords;
// look for " NAME " or " NAME="
pt = findKeyword(keywords, name, true);
if (pt < 0)
return keywords;
// found that -- must negate
return keywords.substring(0, pt) + " " + KEYWORD_IGNORE + keywords.substring(pt + 1);
}
public static String removeNBOFileKeyword(String nboKeywords, String[] fnameRet) {
// TODO Q: what about "FILE xxxx" ?
String[] tokens = PT.getTokens(nboKeywords);
nboKeywords = "";
for (int i = 0; i < tokens.length; i++)
if (tokens[i].indexOf("=") < 0 || tokens[i].toUpperCase().indexOf("FILE=") < 0)
nboKeywords += " " + tokens[i].toUpperCase();
else if (fnameRet != null)
fnameRet[0] = tokens[i].substring(5);
return nboKeywords.trim();
}
public static boolean lineContainsUncommented(String line, String key) {
int ptComment;
int ptKey = line.indexOf(key);
return (ptKey >= 0 && ((ptComment = line.indexOf("!")) < 0 || ptComment > ptKey));
}
public static String removeNBOComment(String line) {
int ptComment = line.indexOf("!");
return (ptComment < 0 ? line : line.substring(0, ptComment));
}
/**
* Read a file reducing lines to
*
* @param inputFile
* @param data
* @param doAll set false to only read through $NBO keyword
* @return true if successful; false if not
*/
public static boolean read47FileBuffered(File inputFile, SB data, boolean doAll) {
try {
boolean have$NBO = false, haveNBO$END = false;
BufferedReader b = null;
b = new BufferedReader(new FileReader(inputFile));
String line;
while ((line = b.readLine()) != null && (doAll || !line.contains("$COORD"))) {
if (have$NBO && !haveNBO$END || !have$NBO && (have$NBO = lineContainsUncommented(line, "$NBO")) == true) {
line = removeNBOComment(line);
if (line.indexOf("$END") >= 0) {
haveNBO$END = true;
}
}
data.append(line + NBOFileHandler.sep);
}
b.close();
return true;
} catch (IOException e) {
}
return false;
}
public static String getExt(File newFile) {
String fname = newFile.toString();
return fname.substring(fname.lastIndexOf(".") + 1);
}
public static String getJobStem(File inputFile) {
String fname = inputFile.getName();
return fname.substring(0, fname.lastIndexOf("."));
}
public static String pathWithoutExtension(String fname) {
int pt = fname.lastIndexOf(".");
return (pt < 0 ? fname : fname.substring(0, pt));
}
public static File newNBOFile(File f, String ext) {
return new File(pathWithoutExtension(NBOUtil.fixPath(f.toString())) + "." + ext);
}
public static String fix47File(String data) {
return PT.rep(data, "FORMAT=PRECISE", "");
}
/**
* change \ to /
*
* @param path
* @return fixed path
*/
public static String fixPath(String path) {
return path.replace('\\', '/');
}
/**
* Windows-centric elaboration of path to default to C: drive
*
* @param folder
* @param fullFilePath
* @return full file path, using "C:/" for the default.
*/
public static String getWindowsFolderFor(String folder, String fullFilePath) {
return (folder.equals("") ? new File(fullFilePath).getParent()
: !folder.contains(":") ? folder = "C:/" + folder : folder);
}
/**
* if folder is not blank, create a full path name to the designated file
* @param folder
* @param name root name or root.ext
* @param ext ext or null if name already contains it
* @return full Windows path to file
*/
public static String getWindowsFullNameFor(String folder, String name,
String ext) {
if (!folder.equals("")) {
if (!folder.contains(":"))
folder = "C:/" + folder;
folder = folder + "/" + (name.equals("") ? "" : name + (ext == null ? "" : "." + ext));
}
return folder;
}
///**
//* Centers the dialog on the screen.
//*
//* @param d
//*/
//public void centerDialog(JDialog d) {
// int x = getWidth() / 2 - d.getWidth() / 2 + this.getX();
// int y = getHeight() / 2 - d.getHeight() / 2;
// d.setLocation(x, y);
//}
//
}
class StyledComboBoxUI extends MetalComboBoxUI {
public int height;
public int width;
public StyledComboBoxUI(int h, int w) {
super();
height = h;
width = w;
}
@Override
public ComboPopup createPopup() {
BasicComboPopup popup = new BasicComboPopup(comboBox) {
@Override
public Rectangle computePopupBounds(int px, int py, int pw, int ph) {
return super.computePopupBounds(px, py, Math.max(width, pw), height);
}
};
popup.getAccessibleContext().setAccessibleParent(comboBox);
return popup;
}
}