Let's look at the Benzene model in the "XYZApp.Mak" project
from your "\Cafe\Sample\Java\MoleculeViewer" directory:
(click and drag the molecule to rotate)
Let's look at the Benzene model in the "XYZApp.Mak" project
from your "\Cafe\Sample\Java\MoleculeViewer" directory:
(click and drag the molecule to rotate)
In order to understand how this program works, we could either
go through the follow two .java files....
| XYZApp.java | /* * 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.io.StreamTokenizer; import java.io.InputStream; import java.io.BufferedInputStream; 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 = new StreamTokenizer(new BufferedInputStream(is, 4000)); st.eolIsSignificant(true); st.commentChar('#'); int slot = 0; 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(); } is.close(); if (st.ttype != StreamTokenizer.TT_EOF) throw new Exception(st.toString()); } /** 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; 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); } 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; backBuffer = createImage(size().width, size().height); backGC = backBuffer.getGraphics(); } 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) { 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 (Exception e) {} painted = false; } } 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); } } |
|---|---|
| Matrix3D.java | /** A fairly conventional 3D matrix object that can
transform sets of 3D points and perform a variety of manipulations on the
transform */ class Matrix3D { float xx, xy, xz, xo; float yx, yy, yz, yo;
float zx, zy, zz, zo; static final double pi = 3.14159265; /** Create a
new unit matrix */ Matrix3D () { xx = 1.0f; yy = 1.0f; zz = 1.0f; } /**
Scale by f in all dimensions */ void scale(float f) { xx *= f; xy *= f;
xz *= f; xo *= f; yx *= f; yy *= f; yz *= f; yo *= f; zx *= f; zy *= f;
zz *= f; zo *= f; } /** Scale along each axis independently */ void scale(float
xf, float yf, float zf) { xx *= xf; xy *= xf; xz *= xf; xo *= xf; yx *=
yf; yy *= yf; yz *= yf; yo *= yf; zx *= zf; zy *= zf; zz *= zf; zo *= zf;
} /** Translate the origin */ void translate(float x, float y, float z)
{ xo += x; yo += y; zo += z; } /** rotate theta degrees about the y axis
*/ void yrot(double theta) { theta *= (pi / 180); double ct = Math.cos(theta);
double st = Math.sin(theta);
float Nxx = (float) (xx * ct + zx * st); float Nxy = (float) (xy * ct + zy * st); float Nxz = (float) (xz * ct + zz * st); float Nxo = (float) (xo * ct + zo * st); float Nzx = (float) (zx * ct - xx * st); float Nzy = (float) (zy * ct - xy * st); float Nzz = (float) (zz * ct - xz * st); float Nzo = (float) (zo * ct - xo * st); xo = Nxo; xx = Nxx; xy = Nxy; xz = Nxz; zo = Nzo; zx = Nzx; zy = Nzy; zz = Nzz; } /** rotate theta degrees about the x axis */ void xrot(double theta) { theta *= (pi / 180); double ct = Math.cos(theta); double st = Math.sin(theta); float Nyx = (float) (yx * ct + zx * st); float Nyy = (float) (yy * ct + zy * st); float Nyz = (float) (yz * ct + zz * st); float Nyo = (float) (yo * ct + zo * st); float Nzx = (float) (zx * ct - yx * st); float Nzy = (float) (zy * ct - yy * st); float Nzz = (float) (zz * ct - yz * st); float Nzo = (float) (zo * ct - yo * st); yo = Nyo; yx = Nyx; yy = Nyy; yz = Nyz; zo = Nzo; zx = Nzx; zy = Nzy; zz = Nzz; } /** rotate theta degrees about the z axis */ void zrot(double theta) { theta *= (pi / 180); double ct = Math.cos(theta); double st = Math.sin(theta); float Nyx = (float) (yx * ct + xx * st); float Nyy = (float) (yy * ct + xy * st); float Nyz = (float) (yz * ct + xz * st); float Nyo = (float) (yo * ct + xo * st); float Nxx = (float) (xx * ct - yx * st); float Nxy = (float) (xy * ct - yy * st); float Nxz = (float) (xz * ct - yz * st); float Nxo = (float) (xo * ct - yo * st); yo = Nyo; yx = Nyx; yy = Nyy; yz = Nyz; xo = Nxo; xx = Nxx; xy = Nxy; xz = Nxz; } /** Multiply this matrix by a second: M = M*R */ void mult(Matrix3D rhs) { float lxx = xx * rhs.xx + yx * rhs.xy + zx * rhs.xz; float lxy = xy * rhs.xx + yy * rhs.xy + zy * rhs.xz; float lxz = xz * rhs.xx + yz * rhs.xy + zz * rhs.xz; float lxo = xo * rhs.xx + yo * rhs.xy + zo * rhs.xz + rhs.xo; float lyx = xx * rhs.yx + yx * rhs.yy + zx * rhs.yz; float lyy = xy * rhs.yx + yy * rhs.yy + zy * rhs.yz; float lyz = xz * rhs.yx + yz * rhs.yy + zz * rhs.yz; float lyo = xo * rhs.yx + yo * rhs.yy + zo * rhs.yz + rhs.yo; float lzx = xx * rhs.zx + yx * rhs.zy + zx * rhs.zz; float lzy = xy * rhs.zx + yy * rhs.zy + zy * rhs.zz; float lzz = xz * rhs.zx + yz * rhs.zy + zz * rhs.zz; float lzo = xo * rhs.zx + yo * rhs.zy + zo * rhs.zz + rhs.zo; xx = lxx; xy = lxy; xz = lxz; xo = lxo; yx = lyx; yy = lyy; yz = lyz; yo = lyo; zx = lzx; zy = lzy; zz = lzz; zo = lzo; } /** Reinitialize to the unit matrix */ void unit() { xo = 0; xx = 1; xy = 0; xz = 0; yo = 0; yx = 0; yy = 1; yz = 0; zo = 0; zx = 0; zy = 0; zz = 1; } /** Transform nvert points from v into tv. v contains the input coordinates in floating point. Three successive entries in the array constitute a point. tv ends up holding the transformed points as integers; three successive entries per point */ void transform(float v[], int tv[], int nvert) { float lxx = xx, lxy = xy, lxz = xz, lxo = xo; float lyx = yx, lyy = yy, lyz = yz, lyo = yo; float lzx = zx, lzy = zy, lzz = zz, lzo = zo; for (int i = nvert * 3; (i -= 3) >= 0;) { float x = v[i]; float y = v[i + 1]; float z = v[i + 2]; tv[i ] = (int) (x * lxx + y * lxy + z * lxz + lxo); tv[i + 1] = (int) (x * lyx + y * lyy + z * lyz + lyo); tv[i + 2] = (int) (x * lzx + y * lzy + z * lzz + lzo); } } public String toString() { return ("[" + xo + "," + xx + "," + xy + "," + xz + ";" + yo + "," + yx + "," + yy + "," + yz + ";" + zo + "," + zx + "," + zy + "," + zz + "]"); } } |
Or... we could have a clear overview of the program's underlying object structure in 3 easy steps using With Class 3.1!
#1: In With Class, we set our preference to Java
#2: Now we use With Class's utility to reverse entire directory of the project.
#3: Then we choose we aspects of the program's structure we would like to illustrate...
And in just seconds, we have a clear picture of the whole program's structure! (represented here in UML format).
.
As you can see, each class with it's methods, properties, has been clearly laid out - along with it's relationships to all of the other classes defined in the program! Now, you can interact with this diagram, changes relations, structure, and code; or simply use the diagram for documentation purposes. And when you're done, you can use With Class's powerful scripting language to generate new code from the changes you've made!
