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46 import java.applet.Applet  ;
47 import java.awt.Image ;
48 import java.awt.Event ;
49 import java.awt.Graphics ;
50 import java.awt.Dimension ;
51 import java.io.*;
52 import java.net.URL ;
53 import java.util.Hashtable ;
54 import java.awt.image.IndexColorModel ;
55 import java.awt.image.ColorModel ;
56 import java.awt.image.MemoryImageSource ;
57 import java.awt.event.*;
58
59
60 class XYZChemModel {
61 float vert[];
62 Atom atoms[];
63 int tvert[];
64 int ZsortMap[];
65 int nvert, maxvert;
66
67 static Hashtable atomTable = new Hashtable ();
68 static Atom defaultAtom;
69 static {
70 atomTable.put("c", new Atom(0, 0, 0));
71 atomTable.put("h", new Atom(210, 210, 210));
72 atomTable.put("n", new Atom(0, 0, 255));
73 atomTable.put("o", new Atom(255, 0, 0));
74 atomTable.put("p", new Atom(255, 0, 255));
75 atomTable.put("s", new Atom(255, 255, 0));
76 atomTable.put("hn", new Atom(150, 255, 150));
77 defaultAtom = new Atom(255, 100, 200);
78 }
79
80 boolean transformed;
81 Matrix3D mat;
82
83 float xmin, xmax, ymin, ymax, zmin, zmax;
84
85
86 XYZChemModel () {
87 mat = new Matrix3D();
88 mat.xrot(20);
89 mat.yrot(30);
90 }
91
92
93
94 XYZChemModel (InputStream is) throws Exception
95 {
96 this();
97 StreamTokenizer st = new StreamTokenizer(
98 new BufferedReader(new InputStreamReader(is, "UTF-8")));
99 st.eolIsSignificant(true);
100 st.commentChar('#');
101 int slot = 0;
102
103 try
104 {
105 scan:
106 while (true)
107 {
108 switch ( st.nextToken() )
109 {
110 case StreamTokenizer.TT_EOF:
111 break scan;
112 default:
113 break;
114 case StreamTokenizer.TT_WORD:
115 String name = st.sval;
116 double x = 0, y = 0, z = 0;
117 if (st.nextToken() == StreamTokenizer.TT_NUMBER)
118 {
119 x = st.nval;
120 if (st.nextToken() == StreamTokenizer.TT_NUMBER)
121 {
122 y = st.nval;
123 if (st.nextToken() == StreamTokenizer.TT_NUMBER)
124 z = st.nval;
125 }
126 }
127 addVert(name, (float) x, (float) y, (float) z);
128 while( st.ttype != StreamTokenizer.TT_EOL &&
129 st.ttype != StreamTokenizer.TT_EOF )
130 st.nextToken();
131
132 }
134 }
136 is.close();
137
138 } catch( IOException e) {}
140
141 if (st.ttype != StreamTokenizer.TT_EOF)
142 throw new Exception (st.toString());
143
144 }
146
147 int addVert(String name, float x, float y, float z) {
148 int i = nvert;
149 if (i >= maxvert)
150 if (vert == null) {
151 maxvert = 100;
152 vert = new float[maxvert * 3];
153 atoms = new Atom[maxvert];
154 } else {
155 maxvert *= 2;
156 float nv[] = new float[maxvert * 3];
157 System.arraycopy(vert, 0, nv, 0, vert.length);
158 vert = nv;
159 Atom na[] = new Atom[maxvert];
160 System.arraycopy(atoms, 0, na, 0, atoms.length);
161 atoms = na;
162 }
163 Atom a = (Atom) atomTable.get(name.toLowerCase());
164 if (a == null) a = defaultAtom;
165 atoms[i] = a;
166 i *= 3;
167 vert[i] = x;
168 vert[i + 1] = y;
169 vert[i + 2] = z;
170 return nvert++;
171 }
172
173
174 void transform() {
175 if (transformed || nvert <= 0)
176 return;
177 if (tvert == null || tvert.length < nvert * 3)
178 tvert = new int[nvert * 3];
179 mat.transform(vert, tvert, nvert);
180 transformed = true;
181 }
182
183
184
188 void paint(Graphics g) {
189 if (vert == null || nvert <= 0)
190 return;
191 transform();
192 int v[] = tvert;
193 int zs[] = ZsortMap;
194 if (zs == null) {
195 ZsortMap = zs = new int[nvert];
196 for (int i = nvert; --i >= 0;)
197 zs[i] = i * 3;
198 }
199
200
206
207 for (int i = nvert - 1; --i >= 0;) {
208 boolean flipped = false;
209 for (int j = 0; j <= i; j++) {
210 int a = zs[j];
211 int b = zs[j + 1];
212 if (v[a + 2] > v[b + 2]) {
213 zs[j + 1] = a;
214 zs[j] = b;
215 flipped = true;
216 }
217 }
218 if (!flipped)
219 break;
220 }
221
222 int lg = 0;
223 int lim = nvert;
224 Atom ls[] = atoms;
225 if (lim <= 0 || nvert <= 0)
226 return;
227 for (int i = 0; i < lim; i++) {
228 int j = zs[i];
229 int grey = v[j + 2];
230 if (grey < 0)
231 grey = 0;
232 if (grey > 15)
233 grey = 15;
234 atoms[j/3].paint(g, v[j], v[j + 1], grey);
236 }
239 }
240
241
242 void findBB() {
243 if (nvert <= 0)
244 return;
245 float v[] = vert;
246 float xmin = v[0], xmax = xmin;
247 float ymin = v[1], ymax = ymin;
248 float zmin = v[2], zmax = zmin;
249 for (int i = nvert * 3; (i -= 3) > 0;) {
250 float x = v[i];
251 if (x < xmin)
252 xmin = x;
253 if (x > xmax)
254 xmax = x;
255 float y = v[i + 1];
256 if (y < ymin)
257 ymin = y;
258 if (y > ymax)
259 ymax = y;
260 float z = v[i + 2];
261 if (z < zmin)
262 zmin = z;
263 if (z > zmax)
264 zmax = z;
265 }
266 this.xmax = xmax;
267 this.xmin = xmin;
268 this.ymax = ymax;
269 this.ymin = ymin;
270 this.zmax = zmax;
271 this.zmin = zmin;
272 }
273 }
274
275
276 public class XYZApp
277 extends Applet
278 implements Runnable , MouseListener, MouseMotionListener {
279 XYZChemModel md;
280 boolean painted = true;
281 float xfac;
282 int prevx, prevy;
283 float xtheta, ytheta;
284 float scalefudge = 1;
285 Matrix3D amat = new Matrix3D(), tmat = new Matrix3D();
286 String mdname = null;
287 String message = null;
288 Image backBuffer;
289 Graphics backGC;
290 Dimension backSize;
291
292
293 private synchronized void newBackBuffer() {
294 backBuffer = createImage(getSize().width, getSize().height);
295 if (backGC != null) {
296 backGC.dispose();
297 }
298 backGC = backBuffer.getGraphics();
299 backSize = getSize();
300 }
301
302 public void init() {
303 mdname = getParameter("model");
304 try {
305 scalefudge = Float.valueOf(getParameter("scale")).floatValue();
306 } catch(Exception e) {
307 };
308 amat.yrot(20);
309 amat.xrot(20);
310 if (mdname == null)
311 mdname = "model.obj";
312 resize(getSize().width <= 20 ? 400 : getSize().width,
313 getSize().height <= 20 ? 400 : getSize().height);
314 newBackBuffer();
315 addMouseListener(this);
316 addMouseMotionListener(this);
317 }
318
319 public void destroy() {
320 removeMouseListener(this);
321 removeMouseMotionListener(this);
322 }
323
324 public void run() {
325 InputStream is = null;
326 try {
327 Thread.currentThread().setPriority(Thread.MIN_PRIORITY);
328 is = new URL (getDocumentBase(), mdname).openStream();
329 XYZChemModel m = new XYZChemModel (is);
330 Atom.setApplet(this);
331 md = m;
332 m.findBB();
333 float xw = m.xmax - m.xmin;
334 float yw = m.ymax - m.ymin;
335 float zw = m.zmax - m.zmin;
336 if (yw > xw)
337 xw = yw;
338 if (zw > xw)
339 xw = zw;
340 float f1 = getSize().width / xw;
341 float f2 = getSize().height / xw;
342 xfac = 0.7f * (f1 < f2 ? f1 : f2) * scalefudge;
343 } catch(Exception e) {
344 e.printStackTrace();
345 md = null;
346 message = e.toString();
347 }
348 try {
349 if (is != null)
350 is.close();
351 } catch(Exception e) {
352 }
353 repaint();
354 }
355 public void start() {
356 if (md == null && message == null)
357 new Thread (this).start();
358 }
359 public void stop() {
360 }
361
362 public void mouseClicked(MouseEvent e) {
363 }
364 public void mousePressed(MouseEvent e) {
365 prevx = e.getX();
366 prevy = e.getY();
367 e.consume();
368 }
369 public void mouseReleased(MouseEvent e) {
370 }
371 public void mouseEntered(MouseEvent e) {
372 }
373 public void mouseExited(MouseEvent e) {
374 }
375 public void mouseDragged(MouseEvent e) {
376 int x = e.getX();
377 int y = e.getY();
378 tmat.unit();
379 float xtheta = (prevy - y) * (360.0f / getSize().width);
380 float ytheta = (x - prevx) * (360.0f / getSize().height);
381 tmat.xrot(xtheta);
382 tmat.yrot(ytheta);
383 amat.mult(tmat);
384 if (painted) {
385 painted = false;
386 repaint();
387 }
388 prevx = x;
389 prevy = y;
390 e.consume();
391 }
392 public void mouseMoved(MouseEvent e) {
393 }
394
395 public void update(Graphics g) {
396 if (backBuffer == null)
397 g.clearRect(0, 0, getSize().width, getSize().height);
398 paint(g);
399 }
400
401 public void paint(Graphics g) {
402 if (md != null) {
403 md.mat.unit();
404 md.mat.translate(-(md.xmin + md.xmax) / 2,
405 -(md.ymin + md.ymax) / 2,
406 -(md.zmin + md.zmax) / 2);
407 md.mat.mult(amat);
408 md.mat.scale(xfac, -xfac, 16 * xfac / getSize().width);
410 md.mat.translate(getSize().width / 2, getSize().height / 2, 8);
411 md.transformed = false;
412 if (backBuffer != null) {
413 if (!backSize.equals(getSize()))
414 newBackBuffer();
415 backGC.setColor(getBackground());
416 backGC.fillRect(0,0,getSize().width,getSize().height);
417 md.paint(backGC);
418 g.drawImage(backBuffer, 0, 0, this);
419 }
420 else
421 md.paint(g);
422 setPainted();
423 } else if (message != null) {
424 g.drawString("Error in model:", 3, 20);
425 g.drawString(message, 10, 40);
426 }
427 }
428 private synchronized void setPainted() {
429 painted = true;
430 notifyAll();
431 }
432
433 private synchronized void waitPainted()
434 {
435 while (!painted)
436 {
437 try
438 {
439 wait();
440 }
441 catch (InterruptedException e) {}
442 }
443 painted = false;
444 }
445
446 public String getAppletInfo() {
447 return "Title: XYZApp \nAuthor: James Gosling \nAn applet to put a Chemical model into a page.";
448 }
449
450 public String [][] getParameterInfo() {
451 String [][] info = {
452 {"model", "path string", "The path to the model to be displayed in .xyz format (see http://chem.leeds.ac.uk/Project/MIME.html). Default is model.obj."},
453 {"scale", "float", "Scale factor. Default is 1 (i.e. no scale)."}
454 };
455 return info;
456 }
457 }
459 class Atom {
460 private static Applet applet;
461 private static byte[] data;
462 private final static int R = 40;
463 private final static int hx = 15;
464 private final static int hy = 15;
465 private final static int bgGrey = 192;
466 private final static int nBalls = 16;
467 private static int maxr;
468
469 private int Rl;
470 private int Gl;
471 private int Bl;
472 private Image balls[];
473
474 static {
475 data = new byte[R * 2 * R * 2];
476 int mr = 0;
477 for (int Y = 2 * R; --Y >= 0;) {
478 int x0 = (int) (Math.sqrt(R * R - (Y - R) * (Y - R)) + 0.5);
479 int p = Y * (R * 2) + R - x0;
480 for (int X = -x0; X < x0; X++) {
481 int x = X + hx;
482 int y = Y - R + hy;
483 int r = (int) (Math.sqrt(x * x + y * y) + 0.5);
484 if (r > mr)
485 mr = r;
486 data[p++] = r <= 0 ? 1 : (byte) r;
487 }
488 }
489 maxr = mr;
490 }
491 static void setApplet(Applet app) {
492 applet = app;
493 }
494 Atom(int Rl, int Gl, int Bl) {
495 this.Rl = Rl;
496 this.Gl = Gl;
497 this.Bl = Bl;
498 }
499 private final int blend(int fg, int bg, float fgfactor) {
500 return (int) (bg + (fg - bg) * fgfactor);
501 }
502 private void Setup() {
503 balls = new Image [nBalls];
504 byte red[] = new byte[256];
505 red[0] = (byte) bgGrey;
506 byte green[] = new byte[256];
507 green[0] = (byte) bgGrey;
508 byte blue[] = new byte[256];
509 blue[0] = (byte) bgGrey;
510 for (int r = 0; r < nBalls; r++) {
511 float b = (float) (r+1) / nBalls;
512 for (int i = maxr; i >= 1; --i) {
513 float d = (float) i / maxr;
514 red[i] = (byte) blend(blend(Rl, 255, d), bgGrey, b);
515 green[i] = (byte) blend(blend(Gl, 255, d), bgGrey, b);
516 blue[i] = (byte) blend(blend(Bl, 255, d), bgGrey, b);
517 }
518 IndexColorModel model = new IndexColorModel (8, maxr + 1,
519 red, green, blue, 0);
520 balls[r] = applet.createImage(
521 new MemoryImageSource (R*2, R*2, model, data, 0, R*2));
522 }
523 }
524 void paint(Graphics gc, int x, int y, int r) {
525 Image ba[] = balls;
526 if (ba == null) {
527 Setup();
528 ba = balls;
529 }
530 Image i = ba[r];
531 int size = 10 + r;
532 gc.drawImage(i, x - (size >> 1), y - (size >> 1), size, size, applet);
533 }
534 }
535 |
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