public void centerResidues() {
double globalCenterX = 0d;
double globalCenterY = 0d;
double globalCenterZ = 0d;
int count = 0;
for (Residue res : residueList) {
for (Atom atom : res.getAtomList()) {
globalCenterX += atom.getCoordinates()[0];
globalCenterY += atom.getCoordinates()[1];
globalCenterZ += atom.getCoordinates()[2];
}
count += res.getAtomList().size();
}
globalCenterX /= count;
globalCenterY /= count;
globalCenterZ /= count;
for (Node node : root.pdbObjects.getChildren()) {
node.setTranslateX(node.getTranslateX() - globalCenterX);
node.setTranslateY(node.getTranslateY() - globalCenterY);
node.setTranslateZ(node.getTranslateZ() - globalCenterZ);
}
}
private static SubScene createSubScene(
String title, Node node, Paint fillPaint, Camera camera, boolean msaa) {
Group root = new Group();
PointLight light = new PointLight(Color.WHITE);
light.setTranslateX(50);
light.setTranslateY(-300);
light.setTranslateZ(-400);
PointLight light2 = new PointLight(Color.color(0.6, 0.3, 0.4));
light2.setTranslateX(400);
light2.setTranslateY(0);
light2.setTranslateZ(-400);
AmbientLight ambientLight = new AmbientLight(Color.color(0.2, 0.2, 0.2));
node.setRotationAxis(new Point3D(2, 1, 0).normalize());
node.setTranslateX(180);
node.setTranslateY(180);
root.getChildren().addAll(setTitle(title), ambientLight, light, light2, node);
SubScene subScene =
new SubScene(
root, 500, 400, true, msaa ? SceneAntialiasing.BALANCED : SceneAntialiasing.DISABLED);
subScene.setFill(fillPaint);
subScene.setCamera(camera);
return subScene;
}