some small issues

Author: thsa

src/main/java/org/openmolecules/fx/viewer3d/V3DMolecule.java

@@ -199,11 +199,15 @@ public V3DMolecule(StereoMolecule mol, int constructionMode, int hydrogenMode, i
 	 * @param hydrogenMode one of MoleculeArchitect.HYDROGEN_MODE_ options
 	 * @param ribbonMode one of Ribbon.MODE_ options
 	 * @param surfaceMode SURFACE_NONE, SURFACE_WIRES, or SURFACE_FILLED
+	 * @param surfaceColorMode one of SurfaceMesh.SURFACE_COLOR_...
+	 * @param surfaceColor null or color to be used for color modes PLAIN or ATOMIC_NO
+	 * @param surfaceTransparency SURFACE_NONE, SURFACE_WIRES, or SURFACE_FILLED
 	 * @param id
 	 */
-	public V3DMolecule(StereoMolecule protein, ArrayList<StereoMolecule> ligands, int constructionMode, int hydrogenMode, int ribbonMode, int surfaceMode, int id) {
-		this(protein, constructionMode, hydrogenMode, ribbonMode, surfaceMode,
-				DEFAULT_SURFACE_COLOR_MODE, null, DEFAULT_SURFACE_TRANSPARENCY, id, MoleculeRole.MACROMOLECULE, true, false, ligands);
+	public V3DMolecule(StereoMolecule protein, ArrayList<StereoMolecule> ligands, int constructionMode, int hydrogenMode,
+					   int ribbonMode, int surfaceMode, int surfaceColorMode, Color surfaceColor, double surfaceTransparency, int id) {
+		this(protein, constructionMode, hydrogenMode, ribbonMode, surfaceMode, surfaceColorMode, surfaceColor, surfaceTransparency,
+				id, MoleculeRole.MACROMOLECULE, true, false, ligands);
 	}
 
 	public V3DMolecule(StereoMolecule mol, int constructionMode, int hydrogenMode, int id, MoleculeRole role, boolean overrideHydrogen, boolean splitAllBonds) {
@@ -220,14 +224,14 @@ public V3DMolecule(StereoMolecule mol, int constructionMode, int hydrogenMode, i
 	 * @param surfaceMode SURFACE_NONE, SURFACE_WIRES, or SURFACE_FILLED
 	 * @param surfaceColorMode DEFAULT_SURFACE_COLOR_MODE or one of the SurfaceMesh.SURFACE_COLOR_xxx modes
 	 * @param surfaceColor null or explicit surface color used for some color modes
-	 * @param transparency
+	 * @param surfaceTransparency
 	 * @param id
 	 * @param role
 	 * @param overrideHydrogens whether hydrogen atoms are drawn in the molecule override color
 	 * @param splitAllBonds whether all bonds shall be constructed from two cylinders (allowing better selection coloring)
 	 */
-	public V3DMolecule(StereoMolecule mol, int constructionMode, int  hydrogenMode, int ribbonMode, int surfaceMode,
-					   int surfaceColorMode, Color surfaceColor, double transparency,
+	public V3DMolecule(StereoMolecule mol, int constructionMode, int  hydrogenMode, int ribbonMode,
+					   int surfaceMode, int surfaceColorMode, Color surfaceColor, double surfaceTransparency,
 					   int id, MoleculeRole role, boolean overrideHydrogens, boolean splitAllBonds, ArrayList<StereoMolecule> ligands) {
 		super(mol.getName());
 		mMol = mol;
@@ -257,7 +261,7 @@ public V3DMolecule(StereoMolecule mol, int constructionMode, int  hydrogenMode,
 		mSurfaceMode[0] = surfaceMode;
 		mSurfaceColor[0] = (surfaceColor == null) ? DEFAULT_SURFACE_COLOR : surfaceColor;
 		mSurfaceColorMode[0] = surfaceColorMode;
-		mSurfaceTransparency[0] = transparency;
+		mSurfaceTransparency[0] = surfaceTransparency;
 		mInitialCoordinates = new Coordinates[mol.getAllAtoms()];
 		IntStream.range(0,mol.getAllAtoms()).forEach(i -> {
 			mInitialCoordinates[i] = new Coordinates(mol.getCoordinates(i));
@@ -285,7 +289,7 @@ public V3DMolecule(StereoMolecule mol, int constructionMode, int  hydrogenMode,
 
 		if (surfaceMode != SURFACE_MODE_NONE) {
 			SurfaceCutter cutter = (role == MoleculeRole.MACROMOLECULE) ? createSurfaceCutter() : null;
-			mSurfaceMesh[0] = new SurfaceMesh(mMol, 0, surfaceColorMode, getNeutralColor(0), 1.0 - transparency, cutter);
+			mSurfaceMesh[0] = new SurfaceMesh(mMol, 0, surfaceColorMode, getNeutralColor(0), 1.0 - surfaceTransparency, cutter);
 			updateSurfaceFromMesh(0);
 		}
 	}

src/main/java/org/openmolecules/fx/viewer3d/V3DMouseHandler.java

@@ -475,9 +475,7 @@ private void rotate(double dx, double dy, boolean aroundZAxis) {
 			}
 			else {
 				// world center of gravity:
-				Point3D cog = mScene.getCOGInGroup(mScene.getWorld());
-				mScene.rotateWorld(new Rotate(d, cog.getX(), cog.getY(), cog.getZ(), p1));
-//				mScene.rotateWorld(new Rotate(d, p1), mScene.getCOGInGroup(mScene.getWorld()));
+				mScene.rotateWorld(new Rotate(d, p1), mScene.getCOGInGroup(mScene.getWorld()));
 			}
 
 			if (!aroundZAxis)

src/main/java/org/openmolecules/fx/viewer3d/V3DScene.java

@@ -702,7 +702,8 @@ private void startAnimation() {
 		value.addListener((observable, oldValue, newValue) -> {
 			double angle = 0.5 * Math.cos(newValue.doubleValue());
 			Point3D cog = getCOGInGroup(mWorld);
-			mWorld.rotate(new Rotate(angle, cog.getX(), cog.getY(), cog.getZ(), new Point3D(0, 1, 0)));
+//			mWorld.rotate(new Rotate(angle, cog.getX(), cog.getY(), cog.getZ(), new Point3D(0, 1, 0)));
+			rotateWorldInternal(new Rotate(angle, new Point3D(0, 1, 0)), cog);
 		});
 		mAnimation = new Timeline(new KeyFrame(Duration.seconds(5), new KeyValue(value, 2*Math.PI)));
 		mAnimation.setCycleCount(Animation.INDEFINITE);
@@ -726,17 +727,36 @@ public void rotateWorld(Rotate r) {
 				mAnimationRevivalThread.start();
 			}
 		}
-
 		mPreviousManualRotationMillis = System.currentTimeMillis();
+
 		mWorld.rotate(r);
 	}
 
-/*	public void rotateWorld(Rotate r, Point3D cog) {	// we now put the pivot point into the Rotate
-		if (mAnimation != null) {
+	public void rotateWorld(Rotate r, Point3D cog) {    // we now put the pivot point into the Rotate
+		if (mAnimation != null && mAnimation.getStatus() != Animation.Status.STOPPED) {
 			mAnimation.stop();
-			// on manual rotate stop animation, but keep object for isAnimate() to return true
+			if (mAnimationRevivalThread == null) {
+				mAnimationRevivalThread = new Thread(() -> {
+					while (System.currentTimeMillis()<mPreviousManualRotationMillis + 1500)
+						try {
+							Thread.sleep(200);
+						} catch (InterruptedException ie) {
+						}
+
+					if (Thread.currentThread() == mAnimationRevivalThread) {
+						Platform.runLater(() -> reviveAnimation());
+						mAnimationRevivalThread = null;
+					}
+				});
+				mAnimationRevivalThread.start();
+			}
 		}
+		mPreviousManualRotationMillis = System.currentTimeMillis();
+
+		rotateWorldInternal(r, cog);
+	}
 
+	private void rotateWorldInternal(Rotate r, Point3D cog) {	// we now put the pivot point into the Rotate
 		Point3D p1 = mWorld.getRotation().transform(cog);
 		Point3D p2 = r.transform(p1.getX(), p1.getY(), p1.getZ());
 
@@ -745,7 +765,7 @@ public void rotateWorld(Rotate r) {
 		mWorld.setTranslateX(mWorld.getTranslateX()+p1.getX()-p2.getX());
 		mWorld.setTranslateY(mWorld.getTranslateY()+p1.getY()-p2.getY());
 		mWorld.setTranslateZ(mWorld.getTranslateZ()+p1.getZ()-p2.getZ());
-	}	*/
+	}
 
 	/**
 	 * @param polygon