/*
 * @(#)XYZApp.java	1.3 96/12/06
 *
 * Copyright (c) 1994-1996 Sun Microsystems, Inc. All Rights Reserved.
 *
 * Sun grants you ("Licensee") a non-exclusive, royalty free, license to use,
 * modify and redistribute this software in source and binary code form,
 * provided that i) this copyright notice and license appear on all copies of
 * the software; and ii) Licensee does not utilize the software in a manner
 * which is disparaging to Sun.
 *
 * This software is provided "AS IS," without a warranty of any kind. ALL
 * EXPRESS OR IMPLIED CONDITIONS, REPRESENTATIONS AND WARRANTIES, INCLUDING ANY
 * IMPLIED WARRANTY OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE OR
 * NON-INFRINGEMENT, ARE HEREBY EXCLUDED. SUN AND ITS LICENSORS SHALL NOT BE
 * LIABLE FOR ANY DAMAGES SUFFERED BY LICENSEE AS A RESULT OF USING, MODIFYING
 * OR DISTRIBUTING THE SOFTWARE OR ITS DERIVATIVES. IN NO EVENT WILL SUN OR ITS
 * LICENSORS BE LIABLE FOR ANY LOST REVENUE, PROFIT OR DATA, OR FOR DIRECT,
 * INDIRECT, SPECIAL, CONSEQUENTIAL, INCIDENTAL OR PUNITIVE DAMAGES, HOWEVER
 * CAUSED AND REGARDLESS OF THE THEORY OF LIABILITY, ARISING OUT OF THE USE OF
 * OR INABILITY TO USE SOFTWARE, EVEN IF SUN HAS BEEN ADVISED OF THE
 * POSSIBILITY OF SUCH DAMAGES.
 *
 * This software is not designed or intended for use in on-line control of
 * aircraft, air traffic, aircraft navigation or aircraft communications; or in
 * the design, construction, operation or maintenance of any nuclear
 * facility. Licensee represents and warrants that it will not use or
 * redistribute the Software for such purposes.
 */

/*
 * A set of classes to parse, represent and display Chemical compounds in
 * .xyz format (see http://chem.leeds.ac.uk/Project/MIME.html)
 */

import java.applet.Applet;
import java.awt.Image;
import java.awt.Event;
import java.awt.Graphics;
import java.awt.Dimension;
import java.io.StreamTokenizer;
import java.io.InputStream;
import java.io.BufferedInputStream;
import java.io.IOException;
import java.net.URL;
import java.util.Hashtable;
import java.awt.image.IndexColorModel;
import java.awt.image.ColorModel;
import java.awt.image.MemoryImageSource;


/** The representation of a Chemical .xyz model */
class XYZChemModel {
    float vert[];
    Atom atoms[];
    int tvert[];
    int ZsortMap[];
    int nvert, maxvert;

    static Hashtable atomTable = new Hashtable();
    static Atom defaultAtom;
    static {
	atomTable.put("c", new Atom(0, 0, 0));
	atomTable.put("h", new Atom(210, 210, 210));
	atomTable.put("n", new Atom(0, 0, 255));
	atomTable.put("o", new Atom(255, 0, 0));
	atomTable.put("p", new Atom(255, 0, 255));
	atomTable.put("s", new Atom(255, 255, 0));
	atomTable.put("hn", new Atom(150, 255, 150)); /* !!*/
	defaultAtom = new Atom(255, 100, 200);
    }

    boolean transformed;
    Matrix3D mat;

    float xmin, xmax, ymin, ymax, zmin, zmax;


    XYZChemModel () {
	mat = new Matrix3D();
	mat.xrot(20);
	mat.yrot(30);
    }


    /** Create a Cehmical model by parsing an input stream */
    XYZChemModel (InputStream is) throws Exception
    {
       this();
       StreamTokenizer st;
       st = new StreamTokenizer(new BufferedInputStream(is, 4000));
       st.eolIsSignificant(true);
       st.commentChar('#');
       int slot = 0;
      
       try
       {
scan:
          while (true)
          {
             switch ( st.nextToken() ) 
             {
                case StreamTokenizer.TT_EOF:
                   break scan;
                default:
                   break;
                case StreamTokenizer.TT_WORD:
                   String name = st.sval;
                   double x = 0, y = 0, z = 0;
                   if (st.nextToken() == StreamTokenizer.TT_NUMBER) 
                   {
                      x = st.nval;
                      if (st.nextToken() == StreamTokenizer.TT_NUMBER) 
                      {
                         y = st.nval;
                         if (st.nextToken() == StreamTokenizer.TT_NUMBER)
                            z = st.nval;
                      }
                   }
                   addVert(name, (float) x, (float) y, (float) z);
                   while( st.ttype != StreamTokenizer.TT_EOL &&
                          st.ttype != StreamTokenizer.TT_EOF )
                      st.nextToken();

             }   // end Switch

          }  // end while

          is.close();

       }  // end Try
       catch( IOException e) {}

       if (st.ttype != StreamTokenizer.TT_EOF)
          throw new Exception(st.toString());

    }  // end XYZChemModel()

    /** Add a vertex to this model */
    int addVert(String name, float x, float y, float z) {
	int i = nvert;
	if (i >= maxvert)
	    if (vert == null) {
		maxvert = 100;
		vert = new float[maxvert * 3];
		atoms = new Atom[maxvert];
	    } else {
		maxvert *= 2;
		float nv[] = new float[maxvert * 3];
		System.arraycopy(vert, 0, nv, 0, vert.length);
		vert = nv;
		Atom na[] = new Atom[maxvert];
		System.arraycopy(atoms, 0, na, 0, atoms.length);
		atoms = na;
	    }
	Atom a = (Atom) atomTable.get(name.toLowerCase());
	if (a == null) a = defaultAtom;
	atoms[i] = a;
	i *= 3;
	vert[i] = x;
	vert[i + 1] = y;
	vert[i + 2] = z;
	return nvert++;
    }

    /** Transform all the points in this model */
    void transform() {
	if (transformed || nvert <= 0)
	    return;
	if (tvert == null || tvert.length < nvert * 3)
	    tvert = new int[nvert * 3];
	mat.transform(vert, tvert, nvert);
	transformed = true;
    }


    /** Paint this model to a graphics context.  It uses the matrix associated
	with this model to map from model space to screen space.
	The next version of the browser should have double buffering,
	which will make this *much* nicer */
    void paint(Graphics g) {
	if (vert == null || nvert <= 0)
	    return;
	transform();
	int v[] = tvert;
	int zs[] = ZsortMap;
	if (zs == null) {
	    ZsortMap = zs = new int[nvert];
	    for (int i = nvert; --i >= 0;)
		zs[i] = i * 3;
	}

	/*
	 * I use a bubble sort since from one iteration to the next, the sort
	 * order is pretty stable, so I just use what I had last time as a
	 * "guess" of the sorted order.  With luck, this reduces O(N log N)
	 * to O(N)
	 */

	for (int i = nvert - 1; --i >= 0;) {
	    boolean flipped = false;
	    for (int j = 0; j <= i; j++) {
		int a = zs[j];
		int b = zs[j + 1];
		if (v[a + 2] > v[b + 2]) {
		    zs[j + 1] = a;
		    zs[j] = b;
		    flipped = true;
		}
	    }
	    if (!flipped)
		break;
	}

	int lg = 0;
	int lim = nvert;
	Atom ls[] = atoms;
	if (lim <= 0 || nvert <= 0)
	    return;
	for (int i = 0; i < lim; i++) {
	    int j = zs[i];
	    int grey = v[j + 2];
	    if (grey < 0)
		grey = 0;
	    if (grey > 15)
		grey = 15;
	    // g.drawString(names[i], v[j], v[j+1]);
	    atoms[j/3].paint(g, v[j], v[j + 1], grey);
	    // g.drawImage(iBall, v[j] - (iBall.width >> 1), v[j + 1] -
	    // (iBall.height >> 1));
	}
    }

    /** Find the bounding box of this model */
    void findBB() {
	if (nvert <= 0)
	    return;
	float v[] = vert;
	float xmin = v[0], xmax = xmin;
	float ymin = v[1], ymax = ymin;
	float zmin = v[2], zmax = zmin;
	for (int i = nvert * 3; (i -= 3) > 0;) {
	    float x = v[i];
	    if (x < xmin)
		xmin = x;
	    if (x > xmax)
		xmax = x;
	    float y = v[i + 1];
	    if (y < ymin)
		ymin = y;
	    if (y > ymax)
		ymax = y;
	    float z = v[i + 2];
	    if (z < zmin)
		zmin = z;
	    if (z > zmax)
		zmax = z;
	}
	this.xmax = xmax;
	this.xmin = xmin;
	this.ymax = ymax;
	this.ymin = ymin;
	this.zmax = zmax;
	this.zmin = zmin;
    }
}

/** An applet to put a Cehmical model into a page */
public class XYZApp extends Applet implements Runnable {
    XYZChemModel md;
    boolean painted = true;
    float xfac;
    int prevx, prevy;
    float xtheta, ytheta;
    float scalefudge = 1;
    Matrix3D amat = new Matrix3D(), tmat = new Matrix3D();
    String mdname = null;
    String message = null;
    Image backBuffer;
    Graphics backGC;
    Dimension backSize;


    private synchronized void newBackBuffer() {
	backBuffer = createImage(size().width, size().height);
	backGC = backBuffer.getGraphics();
	backSize = size();
    }

    public void init() {
	mdname = getParameter("model");
	try {
	    scalefudge = Float.valueOf(getParameter("scale")).floatValue();
	} catch(Exception e) {
	};
	amat.yrot(20);
	amat.xrot(20);
	if (mdname == null)
	    mdname = "model.obj";
	resize(size().width <= 20 ? 400 : size().width,
	       size().height <= 20 ? 400 : size().height);
	newBackBuffer();
    }
    public void run() {
	InputStream is = null;
	try {
	    Thread.currentThread().setPriority(Thread.MIN_PRIORITY);
	    is = new URL(getDocumentBase(), mdname).openStream();
	    XYZChemModel m = new XYZChemModel (is);
	    Atom.setApplet(this);
	    md = m;
	    m.findBB();
	    float xw = m.xmax - m.xmin;
	    float yw = m.ymax - m.ymin;
	    float zw = m.zmax - m.zmin;
	    if (yw > xw)
		xw = yw;
	    if (zw > xw)
		xw = zw;
	    float f1 = size().width / xw;
	    float f2 = size().height / xw;
	    xfac = 0.7f * (f1 < f2 ? f1 : f2) * scalefudge;
	} catch(Exception e) {
	    e.printStackTrace();
	    md = null;
	    message = e.toString();
	}
	try {
	    if (is != null)
		is.close();
	} catch(Exception e) {
	}
	repaint();
    }
    public void start() {
	if (md == null && message == null)
	    new Thread(this).start();
    }
    public void stop() {
    }
    public boolean mouseDown(Event e, int x, int y) {
	prevx = x;
	prevy = y;
	return true;
    }
    public boolean mouseDrag(Event e, int x, int y) {
	tmat.unit();
	float xtheta = (prevy - y) * (360.0f / size().width);
	float ytheta = (x - prevx) * (360.0f / size().height);
	tmat.xrot(xtheta);
	tmat.yrot(ytheta);
	amat.mult(tmat);
	if (painted) {
	    painted = false;
	    repaint();
	}
	prevx = x;
	prevy = y;
	return true;
    }
    public void update(Graphics g) {
	if (backBuffer == null)
	    g.clearRect(0, 0, size().width, size().height);
	paint(g);
    }

    public void paint(Graphics g) {
	if (md != null) {
	    md.mat.unit();
	    md.mat.translate(-(md.xmin + md.xmax) / 2,
			     -(md.ymin + md.ymax) / 2,
			     -(md.zmin + md.zmax) / 2);
	    md.mat.mult(amat);
	    // md.mat.scale(xfac, -xfac, 8 * xfac / size().width);
	    md.mat.scale(xfac, -xfac, 16 * xfac / size().width);
	    md.mat.translate(size().width / 2, size().height / 2, 8);
	    md.transformed = false;
	    if (backBuffer != null) {
		if (!backSize.equals(size()))
		    newBackBuffer();
		backGC.setColor(getBackground());
		backGC.fillRect(0,0,size().width,size().height);
		md.paint(backGC);
		g.drawImage(backBuffer, 0, 0, this);
	    }
	    else
		md.paint(g);
	    setPainted();
	} else if (message != null) {
	    g.drawString("Error in model:", 3, 20);
	    g.drawString(message, 10, 40);
	}
    }
    private synchronized void setPainted() {
	painted = true;
	notifyAll();
    }

    private synchronized void waitPainted() 
    {
       while (!painted)
       {
          try
          {
             wait();
          }
          catch (InterruptedException e) {}
       }
       painted = false;
    }
}   // end class XYZApp

class Atom {
    private static Applet applet;
    private static byte[] data;
    private final static int R = 40;
    private final static int hx = 15;
    private final static int hy = 15;
    private final static int bgGrey = 192;
    private final static int nBalls = 16;
    private static int maxr;

    private int Rl;
    private int Gl;
    private int Bl;
    private Image balls[];

    static {
	data = new byte[R * 2 * R * 2];
	int mr = 0;
	for (int Y = 2 * R; --Y >= 0;) {
	    int x0 = (int) (Math.sqrt(R * R - (Y - R) * (Y - R)) + 0.5);
	    int p = Y * (R * 2) + R - x0;
	    for (int X = -x0; X < x0; X++) {
		int x = X + hx;
		int y = Y - R + hy;
		int r = (int) (Math.sqrt(x * x + y * y) + 0.5);
		if (r > mr)
		    mr = r;
		data[p++] = r <= 0 ? 1 : (byte) r;
	    }
	}
	maxr = mr;
    }
    static void setApplet(Applet app) {
	applet = app;
    }
    Atom(int Rl, int Gl, int Bl) {
	this.Rl = Rl;
	this.Gl = Gl;
	this.Bl = Bl;
    }
    private final int blend(int fg, int bg, float fgfactor) {
	return (int) (bg + (fg - bg) * fgfactor);
    }
    private void Setup() {
	balls = new Image[nBalls];
	byte red[] = new byte[256];
	red[0] = (byte) bgGrey;
	byte green[] = new byte[256];
	green[0] = (byte) bgGrey;
	byte blue[] = new byte[256];
	blue[0] = (byte) bgGrey;
	for (int r = 0; r < nBalls; r++) {
	    float b = (float) (r+1) / nBalls;
	    for (int i = maxr; i >= 1; --i) {
		float d = (float) i / maxr;
		red[i] = (byte) blend(blend(Rl, 255, d), bgGrey, b);
		green[i] = (byte) blend(blend(Gl, 255, d), bgGrey, b);
		blue[i] = (byte) blend(blend(Bl, 255, d), bgGrey, b);
	    }
	    IndexColorModel model = new IndexColorModel(8, maxr + 1,
							red, green, blue, 0);
	    balls[r] = applet.createImage(
		new MemoryImageSource(R*2, R*2, model, data, 0, R*2));
	}
    }
    void paint(Graphics gc, int x, int y, int r) {
	Image ba[] = balls;
	if (ba == null) {
	    Setup();
	    ba = balls;
	}
	Image i = ba[r];
	int size = 10 + r;
	gc.drawImage(i, x - (size >> 1), y - (size >> 1), size, size, applet);
    }
}
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atag.href=template.replace('_MYURL_', window.location.href.replace('http://', '')).replace('_MYTITLE_','Check%20out%20this%20Tripod%20Member%20site!'); 
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                        else if (n.childNodes[i].nodeType === 1)
                        {
                            getNodesThatHaveComments(n.childNodes[i], pattern);
                        }
                    }
                }
            }(document.body, regexPattern));

            for (var i in preferredNodesList)
            {
                if (nodes[preferredNodesList[i]])
                {
                    if( isTrellix && nodes[preferredNodesList[i]].parentNode.parentNode.parentNode.parentNode )
                    {
                        nodesA.push(nodes[preferredNodesList[i]].parentNode.parentNode.parentNode.parentNode);
                    }
                    else
                    {
                        nodesA.push( nodes[preferredNodesList[i]] );
                    }
                }
            }
            return nodesA;
        }
        
        
        var properNode = null;
        var areaNodes = getCommentNodes( new RegExp( '^area Type="area_(\\w+)"' ) );

        for (var i = 0; i < areaNodes.length; i++)
        {
            var a = parseInt(getComputedStyle(areaNodes[i]).width);
            if ((a >= 300) && (a <= 400))
            {
                properNode = areaNodes[i];
                break;
            }
        }


        var propertyName = getMetaContent("property") || false;
        if( isTrellix && (properNode) )
        {
            e.src = '/adm/ad/injectAd.iframe.html';
            properNode.insertBefore(e, properNode.firstChild);
        }
        else if( isTrellix && !( properNode ) ) // Slap the ad eventhought there is no alocated slot
        {
            e.src = '/adm/ad/injectAd.iframe.html';
            e.style.cssFloat = 'none';
            var cdiv = document.createElement('div');
            cdiv.style = "width:300px;margin:10px auto;";
            cdiv.appendChild( e );
            b.insertBefore(cdiv, b.lastChild);
        }
        else if( !isBlokedByDomain( location.href ) )
        {
            var injF = document.createElement('iframe');
            injF.style.border = '0';
            injF.style.margin = 0;
            injF.style.display = 'block';
            injF.style.cssFloat = 'none';
            injF.style.height = '254px';
            injF.style.overflow = 'hidden';
            injF.style.padding = 0;
            injF.style.width = '300px';
            injF.src = '/adm/ad/injectAd.iframe.html';

            if( b && ( !isTrellix || ( typeof isTrellix == "undefined" ) ) ) // All other tripod props
            {
                var cdiv = document.createElement('div');
                cdiv.style = "width:300px;margin:10px auto;";
                cdiv.appendChild( injF );
                b.insertBefore(cdiv, b.lastChild);
            } 
        }
  }( document.isTrellix ));
}

</script>

<div id="tb_container" style="background:#DFDCCF; border-bottom:1px solid #393939; position:relative; z-index:999999999!important">
<!--form name="search" onSubmit="return searchit()" id='header_search' >
<input type="text" placeholder="Search" size=30 name="search2" value="">
<input type="button" value="Go!" onClick="searchit()">
</form>
<style>
form#header_search {
    width: 916px;
    margin: 0 auto 8px;
    position: relative;
}


form#header_search input {
    height: 40px;
    font-size: 14px;
    line-height: 40px;
    padding: 0 8px;
    box-sizing: border-box;
    background: #F4F2E9;
    border: 1px solid #BBB8B8;
    transition: background-color 300ms ease-out,
                color 300ms ease;
}

form#header_search input[type="text"] {
    width: 100%;
}
form#header_search input[type="text"]:focus {
    border-color: #A2D054;
    background-color: #fff;
    box-shadow: 0 0px 12px -4px #A2D054;
}



form#header_search input[type="button"] {
    position: absolute;
    top: 1px;
    right: 1px;
    opacity: 1;
    background: #DFDCCF;
    color: #463734;
    width: 125px;
    cursor: pointer;
    height: 38px;
    border: none;
}
form#header_search input[type="text"]:focus ~ input[type='button']:hover,
form#header_search input[type='button']:hover {
    background-color: #A5CE56;
    color: #fff;
}
form#header_search input[type="text"]:focus ~ input[type='button'] {
    background-color: #52AEDF;
    color: #fff;
}

</style>

<script>
function searchit(){
    
    // determine environment 
    var search_env 
    if (lycos_ad_www_server.indexOf(".pd.") > -1) {
       search_env = 'http://search51.pd.lycos.com/a/';
    } else if (lycos_ad_www_server.indexOf(".qa.") > -1) {
       search_env = 'http://search51.qa.lycos.com/a/';
    } else {
       search_env = 'http://search51.lycos.com/a/';
    }

var search_term = encodeURIComponent(document.search.search2.value)
var search_url = search_env+search_term;
window.open(search_url);

return false
}
</script-->
<style>
    .adCenterClass{margin:0 auto}
</style>
<div id="tb_ad" class="adCenterClass" style="display:block!important; overflow:hidden; width:916px;">

<div id="ad_container" style="display:block!important; float:left; width:728px ">
<script type="text/javascript">
if (typeof lycos_ad !== "undefined" && "leaderboard" in lycos_ad) {
  document.write(lycos_ad['leaderboard']);
}
</script>
</div>
</div>
</div>
<script type="text/javascript">
if (typeof lycos_ad !== "undefined" && "slider" in lycos_ad) {
  document.write(lycos_ad['slider']);
}
</script> <!-- added 7/22 -->
<div id="FooterAd" style="background:#DFDCCF; border-top:1px solid #393939; clear:both; display:none; width:100%!important; position:relative; z-index:999999!important; height:90px!important"> 
<div class="adCenterClass" style="display:block!important; overflow:hidden; width:916px;">
<div id="footerAd_container" style="display:block!important; float:left; width:728px">
<iframe id="lycosFooterAdiFrame" style="border:0; display:block; float:left; height:96px; overflow:hidden; padding:0; width:750px"></iframe>
</div>
</div>
</div>