@Override
public void setAtomClickability() {
if (atomEllipsoids.isEmpty()) return;
for (Ellipsoid e : atomEllipsoids.values()) {
int i = e.tensor.atomIndex1;
Atom atom = ms.at[i];
if ((atom.shapeVisibilityFlags & vf) == 0 || ms.isAtomHidden(i)) continue;
atom.setClickable(vf);
}
}
protected void render() {
Stars stars = (Stars) shape;
if (stars.mads == null) return;
Atom[] atoms = modelSet.atoms;
for (int i = modelSet.getAtomCount(); --i >= 0; ) {
Atom atom = atoms[i];
if (!atom.isShapeVisible(myVisibilityFlag) || modelSet.isAtomHidden(i)) continue;
colix = Shape.getColix(stars.colixes, i, atom);
if (!g3d.setColix(colix)) continue;
render1(atom, stars.mads[i]);
}
}
protected void render() {
Vectors vectors = (Vectors) shape;
if (!vectors.isActive) return;
short[] mads = vectors.mads;
if (mads == null) return;
Atom[] atoms = vectors.atoms;
short[] colixes = vectors.colixes;
for (int i = modelSet.getAtomCount(); --i >= 0; ) {
Atom atom = atoms[i];
if (!atom.isShapeVisible(myVisibilityFlag) || modelSet.isAtomHidden(i)) continue;
Vector3f vibrationVector = viewer.getVibrationVector(i);
if (vibrationVector == null) continue;
vectorScale = viewer.getVectorScale();
if (transform(mads[i], atom, vibrationVector)
&& g3d.setColix(Shape.getColix(colixes, i, atom))) renderVector(atom);
}
}
private void drawSegment(Atom atomA, Atom atomB, short colixA, short colixB, float max) {
if (atomA.getNBackbonesDisplayed() == 0
|| atomB.getNBackbonesDisplayed() == 0
|| ms.isAtomHidden(atomB.i)
|| !isDataFrame && atomA.distanceSquared(atomB) > max) return;
colixA = C.getColixInherited(colixA, atomA.colixAtom);
colixB = C.getColixInherited(colixB, atomB.colixAtom);
if (!isExport && !isPass2 && !setBioColix(colixA) && !setBioColix(colixB)) return;
int xA = atomA.sX, yA = atomA.sY, zA = atomA.sZ;
int xB = atomB.sX, yB = atomB.sY, zB = atomB.sZ;
int mad = this.mad;
if (max == 1000) mad = mad >> 1;
if (mad < 0) {
g3d.drawLine(colixA, colixB, xA, yA, zA, xB, yB, zB);
} else {
int width =
(int)
(exportType == GData.EXPORT_CARTESIAN
? mad
: vwr.tm.scaleToScreen((zA + zB) / 2, mad));
g3d.fillCylinderXYZ(colixA, colixB, GData.ENDCAPS_SPHERICAL, width, xA, yA, zA, xB, yB, zB);
}
}