diff --git a/openchemlib b/openchemlib
index 1c3edb12..a0042e2a 160000
--- a/openchemlib
+++ b/openchemlib
@@ -1 +1 @@
-Subproject commit 1c3edb1264f14575430c6c57504c9ee3cb644809
+Subproject commit a0042e2aa41bf4d111281e5eabe40e7ee963a1e5
diff --git a/scripts/openchemlib/classes.js b/scripts/openchemlib/classes.js
index 4bd13053..873aa963 100644
--- a/scripts/openchemlib/classes.js
+++ b/scripts/openchemlib/classes.js
@@ -94,7 +94,6 @@ const removed = [
   'chem/AtomTypeList.java',
   'chem/chemicalspaces',
   'chem/Clusterer.java',
-  'chem/combinatorialspace',
   'chem/conf/BondRotationHelper.java',
   'chem/conf/ConformerSetGenerator.java',
   'chem/conf/MolecularFlexibilityCalculator.java',
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/AbstractDepictor.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/AbstractDepictor.java
index 868b932f..2dbce4fe 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/AbstractDepictor.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/AbstractDepictor.java
@@ -203,7 +203,7 @@ public void setAtomText(String[] atomText) {
 
 	/**
 	 * If the foreground color is set (!=0), then molecule is drawn in the foreground
-	 * color except for non carbon atoms, which are drawn in atomicNo specific
+	 * color except for non-carbon atoms, which are drawn in atomicNo specific
 	 * colors. If a background color is given (!=0), then atom coloring and highlighting
 	 * is optimized to achieve good contrasts.
 	 * @param foreground null (black) or color to be used for molecule drawing
@@ -217,7 +217,7 @@ public void setForegroundColor(Color foreground, Color background) {
 
 	/**
 	 * If the foreground color is set (!=0), then molecule is drawn in the foreground
-	 * color except for non carbon atoms, which are drawn in atomicNo specific
+	 * color except for non-carbon atoms, which are drawn in atomicNo specific
 	 * colors. If a background color is given (!=0), then atom coloring and highlighting
 	 * is optimized to achieve good contrasts.
 	 * @param foreground 0 or ARGB values of color to be used for molecule drawing
@@ -628,7 +628,7 @@ public synchronized void paint(T context) {
 				mAtomColor[atom] = Molecule.cAtomColorMagenta;
 			}
 
-		setColor_(COLOR_INITIALIZE);	// to initialize the color tracking mechanism
+		setColorCode(COLOR_INITIALIZE);	// to initialize the color tracking mechanism
 
 		if (mAtomHiliteColor != null && (mAtomHiliteColor.length >= mMol.getAtoms()))
 			hiliteAtomBackgrounds(mAtomHiliteColor, mAtomHiliteRadius);
@@ -641,7 +641,7 @@ public synchronized void paint(T context) {
 		mpSetNormalLabelSize();
 		setLineWidth(mpLineWidth);
 
-		setColor_(mStandardForegroundColor);
+		setColorCode(mStandardForegroundColor);
 		markIsolatedAtoms();
 
 		mpDot.clear();
@@ -656,14 +656,14 @@ public synchronized void paint(T context) {
 
 		for (int i=0; i<mMol.getAllAtoms(); i++) {
 			if (isHighlightedAtom(i)) {
-				setColor_(COLOR_HILITE_BOND_FG);
+				setColorCode(COLOR_HILITE_BOND_FG);
 	    		mpDrawAtom(i, esrGroupMemberCount);
-				setColor_(mStandardForegroundColor);
+				setColorCode(mStandardForegroundColor);
 				}
 			else if (mAtomColor[i] != 0) {
-				setColor_(mAtomColor[i]);
+				setColorCode(mAtomColor[i]);
 	    		mpDrawAtom(i, esrGroupMemberCount);
-				setColor_(mStandardForegroundColor);
+				setColorCode(mStandardForegroundColor);
 				}
 			else if (!explicitAtomColors
 				  && mMol.getMoleculeColor() != Molecule.cMoleculeColorNeutral
@@ -671,10 +671,12 @@ else if (!explicitAtomColors
 				  && mMol.getAtomicNo(i) != 6
 				  && ((mDisplayMode & cDModeNoImplicitAtomLabelColors) == 0)
 				  && mMol.getAtomList(i) == null
-				  && mMol.getAtomicNo(i) < ATOM_LABEL_COLOR.length) {
-				setRGBColor(getContrastColor(ATOM_LABEL_COLOR[mMol.getAtomicNo(i)], i));
+				  && mMol.getAtomicNo(i) < ATOM_LABEL_COLOR.length
+				  && ATOM_LABEL_COLOR[mMol.getAtomicNo(i)] != 0) {
+				int rgb = ATOM_LABEL_COLOR[mMol.getAtomicNo(i)];
+				setRGBColor(getContrastColor(rgb, i));
 	    		mpDrawAtom(i, esrGroupMemberCount);
-				setColor_(mStandardForegroundColor);
+				setColorCode(mStandardForegroundColor);
 				}
 			else {
 	    		mpDrawAtom(i, esrGroupMemberCount);
@@ -751,7 +753,7 @@ private void addChiralInfo() {
 
 			setTextSize((int)mChiralTextSize);
 			if (mMol.getMoleculeColor() != Molecule.cMoleculeColorNeutral)
-				setColor_(COLOR_CHIRALITY_TEXT);
+				setColorCode(COLOR_CHIRALITY_TEXT);
 			drawString(chiralText, mChiralTextLocation.x, mChiralTextLocation.y+0.3f*mChiralTextSize);
 			}
 		}
@@ -792,7 +794,7 @@ private void hiliteBondBackgrounds() {
 	        	line.y1 = getAtomY(atom1);
 	            line.x2 = getAtomX(atom2);
 	            line.y2 = getAtomY(atom2);
-				setColor_(COLOR_HILITE_BOND_BG);
+				setColorCode(COLOR_HILITE_BOND_BG);
 	            drawBlackLine(line);
         		}
         	}
@@ -802,7 +804,7 @@ private void hiliteBondBackgrounds() {
 	private void hiliteExcludeGroups() {
 		if (mMol.isFragment()) {
 			double radius = mpExcludeGroupRadius;
-			setColor_(COLOR_EXCLUDE_GROUP_BG);
+			setColorCode(COLOR_EXCLUDE_GROUP_BG);
 			for (int atom = 0; atom < mMol.getAtoms(); atom++)
 				if ((mMol.getAtomQueryFeatures(atom) & Molecule.cAtomQFExcludeGroup) != 0)
 					fillCircle(getAtomX(atom)-radius, getAtomY(atom)-radius, 2*radius);
@@ -827,7 +829,7 @@ private void hiliteExcludeGroups() {
 
 	private void indicateQueryFeatures() {
 		if (mMol.isFragment()) {
-			setColor_(Molecule.cAtomColorOrange);
+			setColorCode(Molecule.cAtomColorOrange);
 			if (((mDisplayMode & cDModeHiliteAllQueryFeatures) != 0))
 				for (int atom=0; atom<mMol.getAtoms(); atom++)
 					if ((mMol.getAtomQueryFeatures(atom) & ~Molecule.cAtomQFExcludeGroup) != 0)
@@ -853,7 +855,7 @@ private void mpDrawAllBonds(int[][] esrGroupMemberCount) {
 		if ((mDisplayMode & cDModeDrawBondsInGray) != 0) {
 			mStandardForegroundColor = COLOR_CUSTOM_FOREGROUND;
 			mCustomForeground = 0xFF808080;
-			setColor_(cColorGray);
+			setColorCode(cColorGray);
 			}
 
 		mAlternativeCoords = new GenericPoint[mMol.getAllAtoms()];
@@ -894,7 +896,7 @@ private void mpDrawAllBonds(int[][] esrGroupMemberCount) {
 
 					if (cipStr != null) {
 						mpSetSmallLabelSize();
-						setColor_(mMol.isBondForegroundHilited(i) ? COLOR_HILITE_BOND_FG :
+						setColorCode(mMol.isBondForegroundHilited(i) ? COLOR_HILITE_BOND_FG :
 								(mMol.getMoleculeColor() == Molecule.cMoleculeColorNeutral || (mDisplayMode & cDModeNoColorOnESRAndCIP) != 0) ?
 										mStandardForegroundColor : COLOR_CIP_LETTER);
 						int atom1 = mMol.getBondAtom(0,i);
@@ -904,7 +906,7 @@ private void mpDrawAllBonds(int[][] esrGroupMemberCount) {
 						double dx = (getAtomX(atom1) - getAtomX(atom2)) / 3;
 						double dy = (getAtomY(atom1) - getAtomY(atom2)) / 3;
 						mpDrawString(x+dy,y-dx, cipStr,true);
-						setColor_(mStandardForegroundColor);
+						setColorCode(mStandardForegroundColor);
 						mpSetNormalLabelSize();
 						}
 					}
@@ -913,7 +915,7 @@ private void mpDrawAllBonds(int[][] esrGroupMemberCount) {
 
 		if ((mDisplayMode & cDModeBondNo) != 0) {
 			mpSetSmallLabelSize();
-			setColor_(Molecule.cAtomColorDarkGreen);
+			setColorCode(Molecule.cAtomColorDarkGreen);
 			for (int i=0; i<mMol.getAllBonds(); i++) {
 				int atom1 = mMol.getBondAtom(0,i);
 				int atom2 = mMol.getBondAtom(1,i);
@@ -923,7 +925,7 @@ private void mpDrawAllBonds(int[][] esrGroupMemberCount) {
 				double y = (getAtomY(atom1) + getAtomY(atom2)) / 2;
 				mpDrawString(x,y,type+String.valueOf(i),true);
 				}
-			setColor_(mStandardForegroundColor);
+			setColorCode(mStandardForegroundColor);
 			mpSetNormalLabelSize();
 			}
 
@@ -951,7 +953,7 @@ private void mpDrawBond(int bnd) {
 		 && !mMol.isSelectedAtom(atom2)
 		 && ((mMol.getAtomQueryFeatures(atom1)
 			| mMol.getAtomQueryFeatures(atom2)) & Molecule.cAtomQFExcludeGroup) != 0)
-			setColor_(COLOR_EXCLUDE_GROUP_FG);
+			setColorCode(COLOR_EXCLUDE_GROUP_FG);
 
 		if (mAlternativeCoords[atom1] == null) {
 			theLine.x1 = getAtomX(atom1);
@@ -973,7 +975,7 @@ private void mpDrawBond(int bnd) {
 
         if ((mMol.getBondQueryFeatures(bnd) & Molecule.cBondQFBridge) != 0) {
             mpHandleDottedLine(theLine, atom1, atom2);
-			setColor_(COLOR_RESTORE_PREVIOUS);
+			setColorCode(COLOR_RESTORE_PREVIOUS);
             return;
             }
 
@@ -1028,9 +1030,9 @@ private void mpDrawBond(int bnd) {
 					aLine.x2 = theLine.x1 + i*xdiff/17 + i*ydiff/128;
 					aLine.y2 = theLine.y1 + i*ydiff/17 - i*xdiff/128;
 					if (mpProperLine(aLine)) {
-						setColor_((i<9) ? color1 : color2);
+						setColorCode((i<9) ? color1 : color2);
 						drawBlackLine(aLine);
-						setColor_(mStandardForegroundColor);
+						setColorCode(mStandardForegroundColor);
 						}
 					}
 				break;
@@ -1178,7 +1180,7 @@ else if ((mAtomLabelDisplayed[atom1] || mMol.getAtomPi(atom1) == 2)
             }
 
 		if (mCurrentColor == COLOR_EXCLUDE_GROUP_FG)
-			setColor_(COLOR_RESTORE_PREVIOUS);
+			setColorCode(COLOR_RESTORE_PREVIOUS);
 		}
 
 
@@ -1952,7 +1954,7 @@ else if (mMol.getAtomicNo(atom) != 6
 		double labelWidth = 0.0;
 
 		if (!mMol.isSelectedAtom(atom) & (mMol.getAtomQueryFeatures(atom) & Molecule.cAtomQFExcludeGroup) != 0)
-			setColor_(COLOR_EXCLUDE_GROUP_FG);
+			setColorCode(COLOR_EXCLUDE_GROUP_FG);
 
 		if (atomStr != null) {
 			labelWidth = getStringWidth(atomStr);
@@ -1990,9 +1992,9 @@ else if (mpAlleneCenter(atom))
 			y = getAtomY(atom) + ((getTextSize()*4+4)/8);
 			int theColor = mCurrentColor;
 			if (mMol.getMoleculeColor() != Molecule.cMoleculeColorNeutral && (mDisplayMode & cDModeNoColorOnESRAndCIP) == 0)
-				setColor_(COLOR_CIP_LETTER);
+				setColorCode(COLOR_CIP_LETTER);
 			mpDrawString(x,y,cipStr,false);
-			setColor_(theColor);
+			setColorCode(theColor);
 			mpSetNormalLabelSize();
 			}
 
@@ -2001,9 +2003,9 @@ else if (mpAlleneCenter(atom))
 			x = getAtomX(atom) + ((labelWidth + getStringWidth(mapStr)) / 2.0 + 1);
 			y = getAtomY(atom) + ((getTextSize()*4+4)/8);
 			int theColor = mCurrentColor;
-			setColor_(mMol.isAutoMappedAtom(atom) ? Molecule.cAtomColorDarkGreen : Molecule.cAtomColorDarkRed);
+			setColorCode(mMol.isAutoMappedAtom(atom) ? Molecule.cAtomColorDarkGreen : Molecule.cAtomColorDarkRed);
 			mpDrawString(x,y,mapStr,true);
-			setColor_(theColor);
+			setColorCode(theColor);
 			mpSetNormalLabelSize();
 			}
 
@@ -2014,15 +2016,15 @@ else if (mpAlleneCenter(atom))
             y = getAtomY(atom) + 0.7*getTextSize()*Math.cos(angle);
             int theColor = mCurrentColor;
 			if (!mIsValidatingView && mMol.getMoleculeColor() != Molecule.cMoleculeColorNeutral)
-	            setColor_(getESRColor(atom));
+	            setColorCode(getESRColor(atom));
             mpDrawString(x,y,esrStr,false);
-            setColor_(theColor);
+            setColorCode(theColor);
 			mpSetNormalLabelSize();
             }
 
         if (hydrogensToAdd == 0 && unpairedElectrons == 0) {
 			if (mCurrentColor == COLOR_EXCLUDE_GROUP_FG)
-				setColor_(COLOR_RESTORE_PREVIOUS);
+				setColorCode(COLOR_RESTORE_PREVIOUS);
 			return;
 			}
 
@@ -2189,7 +2191,7 @@ else if (hindrance[i] == minHindrance) {
 			}
 
 		if (mCurrentColor == COLOR_EXCLUDE_GROUP_FG)
-			setColor_(COLOR_RESTORE_PREVIOUS);
+			setColorCode(COLOR_RESTORE_PREVIOUS);
 		}
 
 	private String createRingSizeText(long queryFeatures) {
@@ -2307,10 +2309,10 @@ private void mpDrawDot(double x, double y, int atm) {
 
 	private void mpDrawAllDots() {
 		for (DepictorDot dot:mpDot) {
-			setColor_(dot.color);
+			setColorCode(dot.color);
 			drawDot(dot.x, dot.y);
 			}
-		setColor_(mStandardForegroundColor);
+		setColorCode(mStandardForegroundColor);
 		}
 
 
@@ -2375,17 +2377,17 @@ else if ((mMol.getBondQueryFeatures(bond) & Molecule.cBondQFRingState) != 0) {
 
     private void drawLine(DepictorLine theLine, int atom1, int atom2) {
     	if (mMol.isBondForegroundHilited(mMol.getBond(atom1, atom2))) {
-			setColor_(COLOR_HILITE_BOND_FG);
+			setColorCode(COLOR_HILITE_BOND_FG);
 			drawBlackLine(theLine);
-			setColor_(mStandardForegroundColor);
+			setColorCode(mStandardForegroundColor);
     		}
     	else if (mAtomColor[atom1] != mAtomColor[atom2]) {
     		drawColorLine(theLine, atom1, atom2);
     		}
     	else if (mAtomColor[atom1] != Molecule.cAtomColorNone) {
-			setColor_(mAtomColor[atom1]);
+			setColorCode(mAtomColor[atom1]);
 			drawBlackLine(theLine);
-			setColor_(mStandardForegroundColor);
+			setColorCode(mStandardForegroundColor);
     		}
 		else {
 			drawBlackLine(theLine);
@@ -2405,14 +2407,14 @@ private void drawColorLine(DepictorLine theLine,int atm1,int atm2) {
 		line2.x2 = theLine.x2;
 		line2.y2 = theLine.y2;
 		if (mpProperLine(line1)) {
-			setColor_(mAtomColor[atm1]);
+			setColorCode(mAtomColor[atm1]);
 			drawBlackLine(line1);
 			}
 		if (mpProperLine(line2)) {
-			setColor_(mAtomColor[atm2]);
+			setColorCode(mAtomColor[atm2]);
 			drawBlackLine(line2);
 			}
-		setColor_(mStandardForegroundColor);
+		setColorCode(mStandardForegroundColor);
 		}
 
 
@@ -2432,7 +2434,7 @@ private void drawDashedLine(DepictorLine theLine, int atom1, int atom2) {
 			color2 = mAtomColor[atom2];
 			}
 
-		setColor_(color1);
+		setColorCode(color1);
 		aLine.x1 = theLine.x1;
 		aLine.y1 = theLine.y1;
 		aLine.x2 = theLine.x1 + xinc * 2;
@@ -2444,7 +2446,7 @@ private void drawDashedLine(DepictorLine theLine, int atom1, int atom2) {
 		aLine.y2 = theLine.y1 + yinc * 5;
 		drawBlackLine(aLine);
 
-		setColor_(color2);
+		setColorCode(color2);
 		aLine.x1 = theLine.x1 + xinc * 5;
 		aLine.y1 = theLine.y1 + yinc * 5;
 		aLine.x2 = theLine.x1 + xinc * 6;
@@ -2456,7 +2458,7 @@ private void drawDashedLine(DepictorLine theLine, int atom1, int atom2) {
 		aLine.y2 = theLine.y2;
 		drawBlackLine(aLine);
 
-		setColor_(mStandardForegroundColor);
+		setColorCode(mStandardForegroundColor);
 		}
 
 
@@ -2482,21 +2484,21 @@ private void drawShortDashedLine(DepictorLine theLine, int atom1, int atom2) {
 		double x = theLine.x1 - mpLineWidth/2;
 		double y = theLine.y1 - mpLineWidth/2;
 
-		setColor_(color1);
+		setColorCode(color1);
 		for (int i=0; i<points/2; i++) {
 			fillCircle(x, y, mpLineWidth);
 			x += xinc;
 			y += yinc;
 			}
 
-		setColor_(color2);
+		setColorCode(color2);
 		for (int i=0; i<points/2; i++) {
 			fillCircle(x, y, mpLineWidth);
 			x += xinc;
 			y += yinc;
 			}
 
-		setColor_(mStandardForegroundColor);
+		setColorCode(mStandardForegroundColor);
 		}
 
 
@@ -2537,11 +2539,11 @@ private void drawWedge(DepictorLine theWedge,int atom1, int atom2) {
 				}
 			}
 
-        setColor_(color1);
+        setColorCode(color1);
 		drawPolygon(p1);
-		setColor_(color2);
+		setColorCode(color2);
 		drawPolygon(p2);
-		setColor_(mStandardForegroundColor);
+		setColorCode(mStandardForegroundColor);
 		}
 
 
@@ -2565,7 +2567,7 @@ private void setRGBColor(int rgb) {
 		}
 
 
-	private void setColor_(int theColor) {
+	private void setColorCode(int theColor) {
 		if (mIsValidatingView)
 			return;
 
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/ExtendedDepictor.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/ExtendedDepictor.java
index a899e6f0..29e1c24c 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/ExtendedDepictor.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/ExtendedDepictor.java
@@ -41,7 +41,7 @@
 import com.actelion.research.gui.generic.GenericRectangle;
 
 import java.awt.*;
-
+import java.util.PriorityQueue;
 
 
 public class ExtendedDepictor {
@@ -231,7 +231,7 @@ public void paint(GenericDrawContext context) {
 
     public void paintFragmentNumbers(GenericDrawContext context) {
         if (mFragmentNoColor != 0 && mMolecule != null) {
-            double averageBondLength = calculateAverageBondLength();
+            double averageBondLength = calculateMedianBondLength() / mTransformation.getScaling();
             context.setRGB(mFragmentNoColor);
             context.setFont((int)(1.6*averageBondLength), true, false);
             for (int i=0; i<mMolecule.length; i++) {
@@ -267,7 +267,7 @@ public void paintFragmentNumbers(GenericDrawContext context) {
 
     public void paintStructures(GenericDrawContext context) {
         if (mDepictor != null) {
-	        double avbl = calculateAverageBondLength() / mTransformation.getScaling();  // this still contains individual depictor scaling
+	        double avbl = calculateMedianBondLength() / mTransformation.getScaling();  // this still contains individual depictor scaling
             for (GenericDepictor d:mDepictor) {
                 d.setDisplayMode(mDisplayMode);
 				d.setAtomLabelAVBL(avbl);
@@ -367,7 +367,7 @@ public DepictorTransformation validateView(GenericDrawContext context, GenericRe
         if (boundingRect == null)
             return null;
 
-        double avbl = calculateAverageBondLength();
+        double avbl = calculateMedianBondLength();
 
         DepictorTransformation t = new DepictorTransformation(boundingRect, viewRect, avbl, mode);
 
@@ -388,20 +388,72 @@ public DepictorTransformation validateView(GenericDrawContext context, GenericRe
         return null;
         }
 
-    private double calculateAverageBondLength() {
+	private double calculateMedianBondLength() {
+		PriorityQueue<Double> maxHeap = new PriorityQueue<>((a, b) -> (a > b) ? -1 : (a < b) ? 1 : 0);
+		PriorityQueue<Double> minHeap = new PriorityQueue<>();
+
+		if (mMolecule != null) {
+			for (int i=0; i<mMolecule.length; i++) {
+				for (int bond=0; bond<mMolecule[i].getAllBonds(); bond++) {
+					maxHeap.offer(mDepictor[i].getTransformation().getScaling() * mMolecule[i].getBondLength(bond));
+					minHeap.offer(maxHeap.poll());
+					if (maxHeap.size() < minHeap.size())
+						maxHeap.offer(minHeap.poll());
+					}
+				}
+			}
+
+		int bondCount = maxHeap.size() + minHeap.size();
+		return (bondCount == 0) ? calculatePseudoBondLengthFromBounds() : mTransformation.getScaling() *
+			((bondCount % 2 == 0) ? (maxHeap.peek() + minHeap.peek()) / 2.0 : maxHeap.peek());
+		}
+
+	private double calculatePseudoBondLengthFromBounds() {
+		double x1 = Double.MAX_VALUE;
+		double x2 = -Double.MAX_VALUE;
+		double y1 = Double.MAX_VALUE;
+		double y2 = -Double.MAX_VALUE;
+		int count = 0;
+		if (mMolecule != null) {
+			for (int i=0; i<mMolecule.length; i++) {
+				for (int atom=0; atom<mMolecule[i].getAllAtoms(); atom++) {
+					double x = mDepictor[i].getTransformation().transformX(mMolecule[i].getCoordinates(atom).x);
+					double y = mDepictor[i].getTransformation().transformY(mMolecule[i].getCoordinates(atom).y);
+					x1 = Math.min(x1, x);
+					x2 = Math.max(x2, x);
+					y1 = Math.min(y1, y);
+					y2 = Math.max(y2, y);
+					count ++;
+					}
+				}
+			}
+
+		if (count <= 1)
+			return mDefaultAVBL;
+
+		double dx = x2 - x1;
+		double dy = y2 - y1;
+		double meanEdgeLength = (dx + dy) / 2;
+		double targetArea = 3.0 * count;  // we assume 2/3 of empty space
+		double area = dx * dy;
+		double b = meanEdgeLength / (1 - targetArea);
+		return Math.sqrt(b * b - area / (1 - targetArea)) - b;
+		}
+
+	private double calculateAverageBondLength() {
     	float averageBondLength = 0.0f;
         int bondCount = 0;
         if (mMolecule != null) {
             for (int i=0; i<mMolecule.length; i++) {
                 if (mMolecule[i].getAllAtoms() != 0) {
                     if (mMolecule[i].getAllBonds() != 0) {
-                        averageBondLength += mDepictor[i].getTransformation().getScaling()
-                                * mMolecule[i].getAllBonds() * mMolecule[i].getAverageBondLength();
+                        averageBondLength += (float)(mDepictor[i].getTransformation().getScaling()
+			                                * mMolecule[i].getAllBonds() * mMolecule[i].getAverageBondLength());
                         bondCount += mMolecule[i].getAllBonds();
                         }
                     else {
-						averageBondLength += mDepictor[i].getTransformation().getScaling()
-								* mMolecule[i].getAverageBondLength();
+						averageBondLength += (float)(mDepictor[i].getTransformation().getScaling()
+											* mMolecule[i].getAverageBondLength());
 						bondCount ++;
                         }
                     }
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/ExtendedMolecule.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/ExtendedMolecule.java
index 9ff78508..72574ef2 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/ExtendedMolecule.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/ExtendedMolecule.java
@@ -4050,16 +4050,25 @@ public void validateAtomQueryFeatures() {
 		ensureHelperArrays(cHelperRings);
 
 		for (int atom=0; atom<mAtoms; atom++) {
-			if (isRingAtom(atom))
-				mAtomQueryFeatures[atom] &= ~(cAtomQFRingSize0 | cAtomQFNotChain);  // forbidden
+			if (isRingAtom(atom)) {
+				// don't remove cAtomQFNotChain, if it is part of more complex ringstate
+				if ((mAtomQueryFeatures[atom] & cAtomQFRingState) == cAtomQFNotChain)
+					mAtomQueryFeatures[atom] &= ~cAtomQFNotChain;  // redundant
+				mAtomQueryFeatures[atom] &= ~cAtomQFRingSize0;  // forbidden
+				}
 
 			if (isAromaticAtom(atom))
 				mAtomQueryFeatures[atom] &= ~cAtomQFAromState;   // redundant or impossible
 			else if ((mAtomQueryFeatures[atom] & cAtomQFAromatic) != 0)
 				mAtomQueryFeatures[atom] &= ~cAtomQFNotAromatic;
 
-			if ((mAtomQueryFeatures[atom] & cAtomQFSmallRingSize) != 0)
-				mAtomQueryFeatures[atom] &= ~cAtomQFNotChain;   // redundant
+			if ((mAtomQueryFeatures[atom] & cAtomQFSmallRingSize) != 0  // of (legacy) smallest ring size is defined
+			 || ((mAtomQueryFeatures[atom] & cAtomQFNewRingSize) != 0)  // allowed list of ring sizes is provided and doesn't contain 'no-ring'
+			  && ((mAtomQueryFeatures[atom] & cAtomQFRingSize0) == 0)) {
+				// don't remove cAtomQFNotChain, if it is part of more complex ringstate
+				if ((mAtomQueryFeatures[atom] & cAtomQFRingState) == cAtomQFNotChain)
+					mAtomQueryFeatures[atom] &= ~cAtomQFNotChain;  // redundant
+				}
 
 			if (mAtomCharge[atom] != 0)	// explicit charge supersedes query features
 				mAtomQueryFeatures[atom] &= ~cAtomQFCharge;
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/Molecule.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/Molecule.java
index af925054..1348faee 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/Molecule.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/Molecule.java
@@ -2445,8 +2445,8 @@ public double getAverageBondLength(int atoms, int bonds, double defaultBondLengt
 	 * If there are no bonds, then the smallest distance between unconnected atoms is
 	 * determined and a reasonable potential bond length derived from that is returned.
 	 * If we have less than 2 atoms, defaultBondLength is returned.
-	 * @param atoms atom indexes >= this are not considered
-	 * @param bonds bond indexes >= this are not considered
+	 * @param atoms atom indexes >= these are not considered
+	 * @param bonds bond indexes >= these are not considered
 	 * @param defaultBondLength
 	 * @param coords to be used, either the molecule's coordinates, or an alternative, e.g. from a Conformer
 	 * @return
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/StereoMolecule.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/StereoMolecule.java
index eec403c1..f5d95136 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/StereoMolecule.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/StereoMolecule.java
@@ -74,6 +74,12 @@ public StereoMolecule createMolecule(int atoms, int bonds) {
 		}
 
 
+	@Override
+	public void clear() {
+		super.clear();
+		mCanonizer = null;
+		}
+
 	public StereoMolecule getCompactCopy() {
 		StereoMolecule theCopy = new StereoMolecule(mAllAtoms, mAllBonds);
 		copyMolecule(theCopy);
@@ -94,7 +100,7 @@ public void copyMoleculeProperties(Molecule destMol) {
 		// the rare case where we have valid parities and no atom coordinates.
 		// Then mCanonizer is null and the parities were read as part of a persistent
 		// molecule. In this case and parity and CIP validity needs to be copied.
-		// Otherwise parity is a perceived property from up/down bonds or 3D atom coords
+		// Otherwise, parity is a perceived property from up/down bonds or 3D atom coords
 		// and should be freshly calculated. 
 		if (mCanonizer != null)
 			destMol.mValidHelperArrays = cHelperNone;
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/descriptor/DescriptorHelper.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/descriptor/DescriptorHelper.java
index c91b7029..15bf0b90 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/descriptor/DescriptorHelper.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/descriptor/DescriptorHelper.java
@@ -39,7 +39,7 @@
 
 public class DescriptorHelper implements DescriptorConstants {
 	
-	public static final String TAG_SIMILARITY = "Similarity";
+	public static final String TAG_SIMILARITY = "Similarity ";
 	
     public static int getDescriptorType(String shortName) {
         DescriptorInfo descriptorInfo = getDescriptorInfo(unifyShortName(shortName));
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/reaction/Reactor.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/reaction/Reactor.java
index ebc4b3c4..13dcc929 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/reaction/Reactor.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/reaction/Reactor.java
@@ -54,7 +54,7 @@ public class Reactor {
 	private boolean[][]			mIsReactionCenter;	// reaction center flags on product atoms
 	private boolean				mRetainCoordinates,mFullyMapReactions,mUniqueProductsOnly,mAllowChargeCorrections;
 	private int					mMaxGenericMapNo,mMaxCount,mReactantMatchCombinationCount;
-	private ArrayList<int[]>[]	mMatchList;
+	private final ArrayList<int[]>[] mMatchList;
 	private int[][][]			mReactantMapNo;	// Reactant mapNos of the real reactant change with every reactant substructure match
 	private StereoMolecule[][]	mProduct;
 	private String[][]			mIDCode;
@@ -152,7 +152,7 @@ public Reactor(Reaction reaction, int mode, int maxProducts) {
 						for (int l=0; l<product.getAtoms(); l++) {
 							if (product.getAtomMapNo(l) == mapNo) {
 								int dif = reactant.getFreeValence(j) - product.getFreeValence(l);
-								mMinFreeValence[i][j] = (dif > 0) ? dif : 0;
+								mMinFreeValence[i][j] = Math.max(dif, 0);
 								}
 							}
 						}
@@ -475,8 +475,7 @@ private boolean nextMatchListCombination(int[] matchListIndex) {
 	 */
 	private int[] getReactantMapNos(int reactant, int[] matchList, int firstMapNo) {
 		int[] reactantMapNo = new int[mReactant[reactant].getAtoms()];
-		for (int i=0; i<reactantMapNo.length; i++)
-			reactantMapNo[i] = -1;
+		Arrays.fill(reactantMapNo, -1);
 
 		StereoMolecule genericReactant = mGenericReaction.getReactant(reactant);
 		for (int atom=0; atom<genericReactant.getAtoms(); atom++)
@@ -509,14 +508,17 @@ private StereoMolecule generateProduct(ArrayList<int[]>[] matchList, int[] match
 			boolean[] excludeAtom = new boolean[mReactant[i].getAtoms()];
 			boolean[] excludeBond = new boolean[mReactant[i].getBonds()];
 
-			// Exclude atoms from real reactants, which are unmapped in generic reaction
+			// Exclude atoms from real reactants, which exist in generic reactant and are not mapped in generic reaction
 			// (including attached bonds)
 			for (int j=0; j<genericReactant.getAtoms(); j++) {
 				if (matchingAtom[j] != -1) {	// non-exclude-group atoms only
 					if (genericReactant.getAtomMapNo(j) == 0) {
 						int excludedAtom = matchingAtom[j];
 						excludeAtom[excludedAtom] = true;
-						for (int k = 0; k < mReactant[i].getConnAtoms(excludedAtom); k++)
+						for (int k=0; k<mReactant[i].getConnAtoms(excludedAtom); k++)
+							excludeBond[mReactant[i].getConnBond(excludedAtom, k)] = true;
+						// To cover the rare case where we have metal bonded neighbours in generic and real reactants:
+						for (int k=mReactant[i].getAllConnAtoms(excludedAtom); k<mReactant[i].getAllConnAtomsPlusMetalBonds(excludedAtom); k++)
 							excludeBond[mReactant[i].getConnBond(excludedAtom, k)] = true;
 						}
 					else {
@@ -750,8 +752,7 @@ else if (esrType == Molecule.cESRTypeOr)
 
 		// delete all fragments from product which are not connected to generic product
 		boolean[] includeAtom = new boolean[product.getAllAtoms()];
-		for (int i=0; i<newAtomNo.length; i++)
-			includeAtom[newAtomNo[i]] = true;
+		for (int j : newAtomNo) includeAtom[j] = true;
 		boolean found = true;
 		while (found) {
 			found = false;
@@ -845,7 +846,7 @@ private void copyPseudoParitiesFromGenericProduct(StereoMolecule genericProduct,
 				}
 			}
 
-		if (pseudoParityList != null && (!matchingAbsParityFound || !invertedAbsParityFound)) {
+		if (!matchingAbsParityFound || !invertedAbsParityFound) {
 			for (int[] pseudoParity : pseudoParityList) {
 				int ps = pseudoParity[1];
 				if ((ps == Molecule.cAtomParity1 || ps == Molecule.cAtomParity2) && invertedAbsParityFound)