XYZChemModelpublic class XYZChemModel extends Object | The representation of a Chemical .xyz model |
| Fields Summary |
|---|
| float[] | vert | | Atom[] | atoms | | int[] | tvert | | int[] | ZsortMap | | int | nvert | | int | maxvert | | static Map | atomTable | | static Atom | defaultAtom | | boolean | transformed | | Matrix3D | mat | | float | xmin | | float | xmax | | float | ymin | | float | ymax | | float | zmin | | float | zmax |
| Constructors Summary |
|---|
XYZChemModel()
mat = new Matrix3D();
mat.xrot(20);
mat.yrot(30);
| XYZChemModel(InputStream is)Create a Chemical model by parsing an input stream
this();
try {
StreamTokenizer st = new StreamTokenizer(
new BufferedReader(new InputStreamReader(is)));
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 Error(st.toString());
} catch (Exception ex) {
throw new Error("Input error: " + ex);
}
|
| Methods Summary |
|---|
| int | addVert(java.lang.String name, float x, float y, float z)Add a vertex to this model
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++;
| | void | findBB()Find the bounding box of this model
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;
| | synchronized void | paint(java.awt.Graphics g)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
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 radius = v[j + 2];
if (radius < 0) {
radius = 0;
} else if (radius > 15) {
radius = 15;
}
atoms[j/3].paint(g, v[j], v[j + 1], radius);
}
| | void | transform()Transform all the points in this model
if (transformed || nvert <= 0)
return;
if (tvert == null || tvert.length < nvert * 3)
tvert = new int[nvert * 3];
mat.transform(vert, tvert, nvert);
transformed = true;
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