diff --git a/__tests__/copyMoleculeByAtoms.test.js b/__tests__/copyMoleculeByAtoms.test.js
deleted file mode 100644
index 660d7c67..00000000
--- a/__tests__/copyMoleculeByAtoms.test.js
+++ /dev/null
@@ -1,26 +0,0 @@
-import { expect, test } from 'vitest';
-
-import { Molecule } from '../full.pretty.js';
-
-// idCode debug view: https://www.cheminfo.org/?viewURL=https%3A%2F%2Fcouch.cheminfo.org%2Fcheminfo-public%2F1cc9e892242664b1d5a37312bda159ef%2Fview.json&loadversion=true&fillsearch=Display+OCLcode+oclID
-test.fails('copyMoleculeByAtoms and keep aromaticity', () => {
-  const molecule = Molecule.fromSmiles('c1ccccc1');
-  const fragment = new Molecule(0, 0);
-
-  expect(molecule.getBondOrder(0)).toBe(2);
-  expect(molecule.isDelocalizedBond(0)).toBe(true);
-  expect(molecule.getBondOrder(1)).toBe(1);
-  expect(molecule.isDelocalizedBond(1)).toBe(true);
-
-  const atomMask = [true, true, true, false, false, false];
-  molecule.copyMoleculeByAtoms(fragment, atomMask, true, null);
-  fragment.ensureHelperArrays(Molecule.cHelperBitRings); // would crash without Helper
-
-  expect(fragment.getAllAtoms()).toBe(3);
-  expect(fragment.getAllBonds()).toBe(2);
-
-  expect(fragment.getBondOrder(0)).toBe(2);
-  expect(fragment.isDelocalizedBond(0)).toBe(true);
-  expect(fragment.getBondOrder(1)).toBe(1);
-  expect(fragment.isDelocalizedBond(1)).toBe(true);
-});
diff --git a/__tests__/copy_molecule_by_atoms.test.js b/__tests__/copy_molecule_by_atoms.test.js
new file mode 100644
index 00000000..27eaa5f3
--- /dev/null
+++ b/__tests__/copy_molecule_by_atoms.test.js
@@ -0,0 +1,70 @@
+import { expect, test } from 'vitest';
+
+import { Molecule } from '../minimal.js';
+
+// idCode debug view: https://www.cheminfo.org/?viewURL=https%3A%2F%2Fcouch.cheminfo.org%2Fcheminfo-public%2F1cc9e892242664b1d5a37312bda159ef%2Fview.json&loadversion=true&fillsearch=Display+OCLcode+oclID
+test('copyMoleculeByAtoms and keep aromaticity. We copy only 3 atoms', () => {
+  const molecule = Molecule.fromSmiles('c1ccccc1');
+  const fragment = new Molecule(0, 0);
+
+  expect(molecule.getBondOrder(0)).toBe(2);
+  expect(molecule.isDelocalizedBond(0)).toBe(true);
+  expect(molecule.getBondOrder(1)).toBe(1);
+  expect(molecule.isDelocalizedBond(1)).toBe(true);
+
+  const atomMask = [true, true, true, false, false, false];
+  molecule.copyMoleculeByAtoms(fragment, atomMask, true, null);
+  fragment.ensureHelperArrays(Molecule.cHelperRings); // would crash without Helper
+
+  expect(fragment.getAllAtoms()).toBe(3);
+  expect(fragment.getAllBonds()).toBe(2);
+
+  expect(fragment.getBondOrder(0)).toBe(1);
+  expect(fragment.isDelocalizedBond(0)).toBe(true);
+  expect(fragment.getBondOrder(1)).toBe(1);
+  expect(fragment.isDelocalizedBond(1)).toBe(true);
+});
+
+test('copyMoleculeByAtoms and keep aromaticity, we copy 5 atoms', () => {
+  const molecule = Molecule.fromSmiles('c1ccccc1');
+  const fragment = new Molecule(0, 0);
+
+  expect(molecule.getBondOrder(0)).toBe(2);
+  expect(molecule.isDelocalizedBond(0)).toBe(true);
+  expect(molecule.getBondOrder(1)).toBe(1);
+  expect(molecule.isDelocalizedBond(1)).toBe(true);
+
+  const atomMask = [true, true, true, true, true, false];
+  molecule.copyMoleculeByAtoms(fragment, atomMask, true, null);
+  fragment.ensureHelperArrays(Molecule.cHelperRings); // would crash without Helper
+
+  expect(fragment.getAllAtoms()).toBe(5);
+  expect(fragment.getAllBonds()).toBe(4);
+
+  expect(fragment.getBondOrder(0)).toBe(1);
+  expect(fragment.isDelocalizedBond(0)).toBe(true);
+  expect(fragment.getBondOrder(1)).toBe(1);
+  expect(fragment.isDelocalizedBond(1)).toBe(true);
+});
+
+test('copyMoleculeByAtoms and keep aromaticity, we copy all atoms', () => {
+  const molecule = Molecule.fromSmiles('c1ccccc1');
+  const fragment = new Molecule(0, 0);
+
+  expect(molecule.getBondOrder(0)).toBe(2);
+  expect(molecule.isDelocalizedBond(0)).toBe(true);
+  expect(molecule.getBondOrder(1)).toBe(1);
+  expect(molecule.isDelocalizedBond(1)).toBe(true);
+
+  const atomMask = [true, true, true, true, true, true];
+  molecule.copyMoleculeByAtoms(fragment, atomMask, true, null);
+  fragment.ensureHelperArrays(Molecule.cHelperRings); // would crash without Helper
+
+  expect(fragment.getAllAtoms()).toBe(6);
+  expect(fragment.getAllBonds()).toBe(6);
+
+  expect(fragment.getBondOrder(0)).toBe(2);
+  expect(fragment.isDelocalizedBond(0)).toBe(true);
+  expect(fragment.getBondOrder(1)).toBe(1);
+  expect(fragment.isDelocalizedBond(1)).toBe(true);
+});
diff --git a/openchemlib b/openchemlib
index c5fed7c4..371e35aa 160000
--- a/openchemlib
+++ b/openchemlib
@@ -1 +1 @@
-Subproject commit c5fed7c434f83a9ac8df7bade5177e0daafce42d
+Subproject commit 371e35aaeec16e3b7eeda4087580f0b95e52f87d
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/AromaticityResolver.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/AromaticityResolver.java
index 2f40fe7a..24da5cd5 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/AromaticityResolver.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/AromaticityResolver.java
@@ -450,6 +450,7 @@ private void promoteDelocalizedChains() {
                         int terminalBond = bond;
                         int bridgeAtom = mMol.getBondAtom(1-i, bond);
                         while (terminalBond != -1) {
+							mIsDelocalizedAtom[terminalAtom] = false;
                             mIsDelocalizedBond[terminalBond] = false;
                             mDelocalizedBonds--;
                             mMol.setBondType(terminalBond, Molecule.cBondTypeDelocalized);
@@ -462,13 +463,15 @@ private void promoteDelocalizedChains() {
                                         bridgeAtom = mMol.getConnAtom(terminalAtom, j);
                                         }
                                     else {
-                                        terminalAtom = -1;
+                                        terminalAtom = -1;	// Stop here! We have hit an aromatic branch.
                                         terminalBond = -1;
                                         break;
                                         }
                                     }
                                 }
                             }
+						if (terminalAtom != -1)		// Regular end of aromatic chain (no branch).
+							mIsDelocalizedAtom[bridgeAtom] = false;
                         break;
                         }
                     }
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 00062cf5..4729ae17 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
@@ -1634,6 +1634,9 @@ public boolean isPseudoRotatableBond(int bond) {
 		return false;
 		}
 
+	/**
+	 * @return number of distinct aromatic rings in the molecule
+	 */
 	public int getAromaticRingCount() {
 		ensureHelperArrays(cHelperRings);
 		int count = 0;
@@ -1775,6 +1778,7 @@ public boolean isHeteroAromaticAtom(int atom) {
 
 
 	/**
+	 * Requires helper arrays state cHelperRings.
 	 * @param atom
 	 * @return whether the atom is a member of a delocalized ring (subset of aromatic rings)
 	 */
@@ -1783,11 +1787,21 @@ public boolean isDelocalizedAtom(int atom) {
 	}
 
 
+	/**
+	 * Requires helper arrays state cHelperRings.
+	 * @param bond
+	 * @return whether the bond is a member of an aromatic ring
+	 */
 	public boolean isAromaticBond(int bond) {
 		return bond<mBonds && mRingSet.isAromaticBond(bond);
 	}
 
 
+	/**
+	 * Requires helper arrays state cHelperRings.
+	 * @param bond
+	 * @return whether the bond is a member of an aromatic ring that contains at least one hetero atom
+	 */
 	public boolean isHeteroAromaticBond(int bond) {
 		return bond<mBonds && mRingSet.isHeteroAromaticBond(bond);
 	}
@@ -1800,26 +1814,38 @@ public boolean isHeteroAromaticBond(int bond) {
 	 * Indole has 6 delocalized bonds.
 	 * This method also returns true, if the molecule is a fragment and if the bond is explicitly
 	 * defined to be delocalized.
+	 * Requires helper arrays state cHelperRings.
 	 * @param bond
 	 * @return
 	 */
 	@Override
 	public boolean isDelocalizedBond(int bond) {
-		return (bond < mBonds) ? mRingSet.isDelocalizedBond(bond) || mBondType[bond] == cBondTypeDelocalized : false;
+		return bond<mBonds && (mRingSet.isDelocalizedBond(bond) || mBondType[bond] == cBondTypeDelocalized);
 		}
 
 
+	/**
+	 * Requires helper arrays state cHelperRings.
+	 * @param atom
+	 * @return whether the atom is a member of ring of any size
+	 */
 	public boolean isRingAtom(int atom) {
 		return (mAtomFlags[atom] & cAtomFlagsRingBonds) != 0;
 		}
 
 
-	public boolean isRingBond(int bnd) {
-		return (mBondFlags[bnd] & cBondFlagRing) != 0;
+	/**
+	 * Requires helper arrays state cHelperRings.
+	 * @param bond
+	 * @return whether the bond is a member of ring of any size
+	 */
+	public boolean isRingBond(int bond) {
+		return (mBondFlags[bond] & cBondFlagRing) != 0;
 		}
 
 
 	/**
+	 * Requires helper arrays state cHelperRings.
 	 * @param atom
 	 * @return whether atom is a member of a ring not larger than 7 atoms
 	 */
@@ -1829,6 +1855,7 @@ public boolean isSmallRingAtom(int atom) {
 
 
 	/**
+	 * Requires helper arrays state cHelperRings.
 	 * @param bond
 	 * @return whether bond is a member of a ring not larger than 7 atoms
 	 */
@@ -1838,6 +1865,7 @@ public boolean isSmallRingBond(int bond) {
 
 
 	/**
+	 * Requires helper arrays state cHelperNeighbours.
 	 * @param atom
 	 * @return whether atom has a neighbor that is connected through a double/triple bond to a hetero atom
 	 */
@@ -1846,6 +1874,11 @@ public boolean isStabilizedAtom(int atom) {
 		}
 
 
+	/**
+	 * Requires helper arrays state cHelperRings.
+	 * @param atom
+	 * @return number of connected bonds, which are member of a ring
+	 */
 	public int getAtomRingBondCount(int atom) {
 		int flags = (mAtomFlags[atom] & cAtomFlagsRingBonds);
 		return (flags == 0) ? 0
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/ExtendedMoleculeFunctions.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/ExtendedMoleculeFunctions.java
index bc760d99..61b6eb0a 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/ExtendedMoleculeFunctions.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/ExtendedMoleculeFunctions.java
@@ -1096,12 +1096,36 @@ public static boolean containsFiveBindingCarbon(StereoMolecule mol) {
 					int bo = mol.getConnBondOrder(i,j);
 					sumBO+=bo;
 				}
-				five=(sumBO>4)?true:false;
+				if(sumBO>4){
+					five=true;
+					break;
+				}
 			}
 		}
 
 		return five;
 	}
+	public static boolean containsFiveBindingNitrogenWithoutCharge(StereoMolecule mol) {
+
+		boolean fiveBindingNNoPositiveCharge=false;
+		for (int i = 0; i < mol.getAtoms(); i++) {
+			if(mol.getAtomicNo(i)==5){
+				int sumBO=0;
+				for (int j = 0; j < mol.getConnAtoms(i); j++) {
+					int bo = mol.getConnBondOrder(i,j);
+					sumBO+=bo;
+				}
+				if(sumBO==5){
+					if(mol.getAtomCharge(i)!=1) {
+						fiveBindingNNoPositiveCharge = true;
+						break;
+					}
+				}
+			}
+		}
+
+		return fiveBindingNNoPositiveCharge;
+	}
 
 	/**
 	 *
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/Arrow.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/Arrow.java
index 3601d3b4..d42d25f6 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/Arrow.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/Arrow.java
@@ -38,6 +38,7 @@
 import com.actelion.research.share.gui.editor.chem.IDrawingObject;
 import com.actelion.research.share.gui.editor.geom.IDrawContext;
 
+@Deprecated
 public class Arrow implements IDrawingObject
 {
 
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/ChemistryGeometryHelper.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/ChemistryGeometryHelper.java
index dcceb26b..80dbf86f 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/ChemistryGeometryHelper.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/ChemistryGeometryHelper.java
@@ -43,6 +43,7 @@
 import java.awt.*;
 
 
+@Deprecated
 public class ChemistryGeometryHelper
 {
     public static final int REACTION_TYPE_NOMOLS = 0;
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/Delegator.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/Delegator.java
index 37c575f0..de16573b 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/Delegator.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/Delegator.java
@@ -33,6 +33,7 @@
 
 package com.actelion.research.share.gui;
 
+@Deprecated
 public class Delegator<T>
 {
     T delegate;
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/DialogResult.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/DialogResult.java
index 5355039c..b1e55b02 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/DialogResult.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/DialogResult.java
@@ -36,6 +36,7 @@
 /**
  * Return values from Dialog calls
  */
+@Deprecated
 public enum DialogResult
 {
     IDOK, IDCANCEL, IDYES, IDNO, IDABORT, IDRETRY,
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/DrawConfig.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/DrawConfig.java
index a49a997d..e2fb3868 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/DrawConfig.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/DrawConfig.java
@@ -4,6 +4,7 @@
  * User: rufenec
  * Creation Date: 8/24/2016
  */
+@Deprecated
 public abstract class DrawConfig
 {
     public final long createColor(double r, double g, double b, double alpha)
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/Polygon.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/Polygon.java
index 6c80e5ca..1a4b2f89 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/Polygon.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/Polygon.java
@@ -41,6 +41,7 @@
 import java.util.List;
 
 
+@Deprecated
 public class Polygon implements IPolygon
 {
     List<GenericPoint> list = new ArrayList<>();
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/ImageProvider.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/ImageProvider.java
index e279a843..71756d7c 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/ImageProvider.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/ImageProvider.java
@@ -36,6 +36,7 @@
 /**
  * Created by rufenec on 08/05/15.
  */
+@Deprecated
 public abstract class ImageProvider<T>
 {
     public abstract T getESRImage(boolean up);
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/Model.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/Model.java
index 853b0488..0952c48f 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/Model.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/Model.java
@@ -60,14 +60,17 @@
  * Date: 1/24/13
  * Time: 5:02 PM
  */
+@Deprecated
 public abstract class Model
 {
-    public interface AtomHighlightCallback
+    @Deprecated
+public interface AtomHighlightCallback
     {
         void onHighlight(int atom, boolean selected);
     }
 
-    public interface BondHighlightCallback
+    @Deprecated
+public interface BondHighlightCallback
     {
         void onHighlight(int atom, boolean selected);
     }
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/Action.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/Action.java
index 82008593..169b2be0 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/Action.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/Action.java
@@ -44,6 +44,7 @@
 /**
  * Basic Interface for all editor actions
  */
+@Deprecated
 public interface Action
 {
     /**
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/AddRingAction.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/AddRingAction.java
index dc7403a7..b9951f31 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/AddRingAction.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/AddRingAction.java
@@ -45,6 +45,7 @@
  * Date: 2/1/13
  * Time: 4:03 PM
  */
+@Deprecated
 public class AddRingAction extends BondHighlightAction
 {
     Model model;
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/ArrowAction.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/ArrowAction.java
index 5c75ed5e..788200a1 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/ArrowAction.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/ArrowAction.java
@@ -47,6 +47,7 @@
  * Date: 5/16/13
  * Time: 3:46 PM
  */
+@Deprecated
 public class ArrowAction extends DrawAction
 {
     GenericPoint origin,last;
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/AtomHighlightAction.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/AtomHighlightAction.java
index 62ad80af..abc7241b 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/AtomHighlightAction.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/AtomHighlightAction.java
@@ -54,6 +54,7 @@
  * Date: 2/1/13
  * Time: 4:13 PM
  */
+@Deprecated
 public abstract class AtomHighlightAction extends DrawAction
 {
 
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/AtomMapAction.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/AtomMapAction.java
index 6022d1b8..4dbc740a 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/AtomMapAction.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/AtomMapAction.java
@@ -48,6 +48,7 @@
  * Date: 5/22/13
  * Time: 4:00 PM
  */
+@Deprecated
 public class AtomMapAction extends AtomHighlightAction
 {
 
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/BondBaseAction.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/BondBaseAction.java
index 27a80056..069c81fb 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/BondBaseAction.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/BondBaseAction.java
@@ -46,6 +46,7 @@
  * Date: 1/28/13
  * Time: 1:07 PM
  */
+@Deprecated
 public abstract class BondBaseAction extends BondHighlightAction
 {
 
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/BondHighlightAction.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/BondHighlightAction.java
index 7b63d6f2..a837c190 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/BondHighlightAction.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/BondHighlightAction.java
@@ -52,6 +52,7 @@
  * Date: 1/28/13
  * Time: 1:07 PM
  */
+@Deprecated
 public abstract class BondHighlightAction extends AtomHighlightAction
 {
     GenericPoint origin = null;
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/ChangeAtomAction.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/ChangeAtomAction.java
index 1dfabc65..d6ab6c8f 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/ChangeAtomAction.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/ChangeAtomAction.java
@@ -44,6 +44,7 @@
  * Date: 2/1/13
  * Time: 4:13 PM
  */
+@Deprecated
 public class ChangeAtomAction extends AtomHighlightAction {
 
     int theAtomNo = 6;
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/ChangeAtomPropertiesAction.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/ChangeAtomPropertiesAction.java
index d98666f8..f9f4ad46 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/ChangeAtomPropertiesAction.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/ChangeAtomPropertiesAction.java
@@ -48,6 +48,7 @@
  * Date: 2/1/13
  * Time: 4:13 PM
  */
+@Deprecated
 public class ChangeAtomPropertiesAction extends AtomHighlightAction
 {
 
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/ChangeChargeAction.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/ChangeChargeAction.java
index a31df2f2..178a57ce 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/ChangeChargeAction.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/ChangeChargeAction.java
@@ -44,6 +44,7 @@
  * Date: 2/1/13
  * Time: 4:13 PM
  */
+@Deprecated
 public class ChangeChargeAction extends AtomHighlightAction
 {
 
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/CleanAction.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/CleanAction.java
index 0bdb8a82..9cde549f 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/CleanAction.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/CleanAction.java
@@ -42,6 +42,7 @@
  * Date: 1/28/13
  * Time: 10:09 AM
  */
+@Deprecated
 public class CleanAction extends CommandAction
 {
 
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/ClearAction.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/ClearAction.java
index 0f71739e..2f077410 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/ClearAction.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/ClearAction.java
@@ -41,6 +41,7 @@
  * Date: 1/24/13
  * Time: 5:09 PM
  */
+@Deprecated
 public class ClearAction extends CommandAction
 {
 
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/CommandAction.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/CommandAction.java
index d4a99553..a51de40f 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/CommandAction.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/CommandAction.java
@@ -44,6 +44,7 @@
  * handle single type of actions: the action is executed when
  * pressing the button and the current drawing action will remain unchanged
  */
+@Deprecated
 public abstract class CommandAction implements Action
 {
     protected Model model;
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/CopyAction.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/CopyAction.java
index a013b4d0..54b68968 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/CopyAction.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/CopyAction.java
@@ -42,6 +42,7 @@
  * Date: 5/16/13
  * Time: 3:31 PM
  */
+@Deprecated
 public abstract class CopyAction extends CommandAction
 {
     public CopyAction(Model model)
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/CutAction.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/CutAction.java
index 0186495b..e61b03b3 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/CutAction.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/CutAction.java
@@ -41,6 +41,7 @@
  * Date: 5/16/13
  * Time: 3:43 PM
  */
+@Deprecated
 public class CutAction extends CommandAction
 {
     public CutAction(Model model)
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/DeleteAction.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/DeleteAction.java
index 20d3643b..03c5e590 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/DeleteAction.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/DeleteAction.java
@@ -45,6 +45,7 @@
  * Date: 3/26/13
  * Time: 4:15 PM
  */
+@Deprecated
 public class DeleteAction extends BondHighlightAction
 {
     public DeleteAction(Model model)
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/DownBondAction.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/DownBondAction.java
index e4a67661..f4e45f4e 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/DownBondAction.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/DownBondAction.java
@@ -1,32 +1 @@
-/*
-* Copyright (c) 1997 - 2016
-* Actelion Pharmaceuticals Ltd.
-* Gewerbestrasse 16
-* CH-4123 Allschwil, Switzerland
-*
-* All rights reserved.
-*
-* Redistribution and use in source and binary forms, with or without
-* modification, are permitted provided that the following conditions are met:
-*
-* 1. Redistributions of source code must retain the above copyright notice, this
-*    list of conditions and the following disclaimer.
-* 2. Redistributions in binary form must reproduce the above copyright notice,
-*    this list of conditions and the following disclaimer in the documentation
-*    and/or other materials provided with the distribution.
-* 3. Neither the name of the the copyright holder nor the
-*    names of its contributors may be used to endorse or promote products
-*    derived from this software without specific prior written permission.
-*
-* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
-* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-* DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
-* ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
-* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
-* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
-* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-*
-*/

package com.actelion.research.share.gui.editor.actions;

import com.actelion.research.chem.Molecule;
import com.actelion.research.chem.StereoMolecule;
import com.actelion.research.share.gui.editor.Model;

/**
 * Project:
 * User: rufenec
 * Date: 1/28/13
 * Time: 1:51 PM
 */
public class DownBondAction extends NewBondAction
{
    public DownBondAction(Model model)
    {
        super(model);
    }

    public int getBondType()
    {
        return Molecule.cBondTypeDown;
    }


    public void onChangeBond(int bond)
     {
       StereoMolecule mol = model.getMolecule();
       if (mol != null) {
           mol.changeBond(bond,Molecule.cBondTypeDown);
           mol.ensureHelperArrays(Molecule.cHelperNeighbours);
       }
     }
}
\ No newline at end of file
+/*
* Copyright (c) 1997 - 2016
* Actelion Pharmaceuticals Ltd.
* Gewerbestrasse 16
* CH-4123 Allschwil, Switzerland
*
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice, this
*    list of conditions and the following disclaimer.
* 2. Redistributions in binary form must reproduce the above copyright notice,
*    this list of conditions and the following disclaimer in the documentation
*    and/or other materials provided with the distribution.
* 3. Neither the name of the the copyright holder nor the
*    names of its contributors may be used to endorse or promote products
*    derived from this software without specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
* ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*
*/

package com.actelion.research.share.gui.editor.actions;

import com.actelion.research.chem.Molecule;
import com.actelion.research.chem.StereoMolecule;
import com.actelion.research.share.gui.editor.Model;

/**
 * Project:
 * User: rufenec
 * Date: 1/28/13
 * Time: 1:51 PM
 */
@Deprecated
public class DownBondAction extends NewBondAction
{
    public DownBondAction(Model model)
    {
        super(model);
    }

    public int getBondType()
    {
        return Molecule.cBondTypeDown;
    }


    public void onChangeBond(int bond)
     {
       StereoMolecule mol = model.getMolecule();
       if (mol != null) {
           mol.changeBond(bond,Molecule.cBondTypeDown);
           mol.ensureHelperArrays(Molecule.cHelperNeighbours);
       }
     }
}
\ No newline at end of file
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/DrawAction.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/DrawAction.java
index cae69edd..22b1081d 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/DrawAction.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/DrawAction.java
@@ -47,6 +47,7 @@
 /**
  * Basic class which handles all actions which interact with the drawing surface
  */
+@Deprecated
 public abstract class DrawAction implements Action
 {
     public static final double HIGHLIGHT_ATOM_RADIUS = 5;
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/NewBondAction.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/NewBondAction.java
index 2f025f02..6218438a 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/NewBondAction.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/NewBondAction.java
@@ -29,4 +29,31 @@
 * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 *
-*/

package com.actelion.research.share.gui.editor.actions;

import com.actelion.research.chem.Molecule;
import com.actelion.research.share.gui.editor.Model;

/**
 * Project:
 * User: rufenec
 * Date: 1/28/13
 * Time: 1:28 PM
 */
public class NewBondAction extends BondBaseAction
{
    public NewBondAction(Model model)
    {
        super(model);
    }

    public int getBondType()
    {
        return Molecule.cBondTypeSingle;
    }


}
\ No newline at end of file
+*/
+
+package com.actelion.research.share.gui.editor.actions;
+
+import com.actelion.research.chem.Molecule;
+import com.actelion.research.share.gui.editor.Model;
+
+/**
+ * Project:
+ * User: rufenec
+ * Date: 1/28/13
+ * Time: 1:28 PM
+ */
+@Deprecated
+public class NewBondAction extends BondBaseAction
+{
+    public NewBondAction(Model model)
+    {
+        super(model);
+    }
+
+    public int getBondType()
+    {
+        return Molecule.cBondTypeSingle;
+    }
+
+
+}
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/NewChainAction.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/NewChainAction.java
index 7bc17feb..9fec54e1 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/NewChainAction.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/NewChainAction.java
@@ -47,6 +47,7 @@
  * Date: 3/26/13
  * Time: 3:42 PM
  */
+@Deprecated
 public class NewChainAction extends BondHighlightAction {
 
     private int sourceAtom = -1;
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/PasteAction.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/PasteAction.java
index f17c3b03..45b19412 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/PasteAction.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/PasteAction.java
@@ -44,6 +44,7 @@
  * Date: 5/16/13
  * Time: 3:39 PM
  */
+@Deprecated
 public abstract class PasteAction extends CommandAction
 {
     java.awt.Dimension bounds;
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/SelectionAction.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/SelectionAction.java
index 5757a169..8f89b847 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/SelectionAction.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/SelectionAction.java
@@ -58,6 +58,7 @@
  * Date: 1/24/13
  * Time: 5:57 PM
  */
+@Deprecated
 public class SelectionAction extends BondHighlightAction//DrawAction
 {
 
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/ToolbarSelectionChange.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/ToolbarSelectionChange.java
index 52d2945d..7e4b5202 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/ToolbarSelectionChange.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/ToolbarSelectionChange.java
@@ -38,6 +38,7 @@
 /**
  * Created by rufenec on 5/3/16.
  */
+@Deprecated
 public interface ToolbarSelectionChange {
     void changed(Action a);
 }
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/UndoAction.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/UndoAction.java
index c8f8e470..e5201cab 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/UndoAction.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/UndoAction.java
@@ -42,6 +42,7 @@
  * Date: 3/26/13
  * Time: 4:39 PM
  */
+@Deprecated
 public class UndoAction extends CommandAction
 {
 
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/UnknownParityAction.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/UnknownParityAction.java
index 4203050b..e4a62d67 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/UnknownParityAction.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/UnknownParityAction.java
@@ -44,6 +44,7 @@
  * Date: 3/26/13
  * Time: 4:33 PM
  */
+@Deprecated
 public class UnknownParityAction extends AtomHighlightAction
 {
 
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/UpBondAction.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/UpBondAction.java
index 144a00b5..8643fbff 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/UpBondAction.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/UpBondAction.java
@@ -1,32 +1 @@
-/*
-* Copyright (c) 1997 - 2016
-* Actelion Pharmaceuticals Ltd.
-* Gewerbestrasse 16
-* CH-4123 Allschwil, Switzerland
-*
-* All rights reserved.
-*
-* Redistribution and use in source and binary forms, with or without
-* modification, are permitted provided that the following conditions are met:
-*
-* 1. Redistributions of source code must retain the above copyright notice, this
-*    list of conditions and the following disclaimer.
-* 2. Redistributions in binary form must reproduce the above copyright notice,
-*    this list of conditions and the following disclaimer in the documentation
-*    and/or other materials provided with the distribution.
-* 3. Neither the name of the the copyright holder nor the
-*    names of its contributors may be used to endorse or promote products
-*    derived from this software without specific prior written permission.
-*
-* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
-* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-* DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
-* ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
-* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
-* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
-* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-*
-*/
package com.actelion.research.share.gui.editor.actions;

import com.actelion.research.chem.Molecule;
import com.actelion.research.chem.StereoMolecule;
import com.actelion.research.share.gui.editor.Model;
/**
 * Project:
 * User: rufenec
 * Date: 1/28/13
 * Time: 1:49 PM
 */
public class UpBondAction extends NewBondAction
{
    public UpBondAction(Model model)
    {
        super(model);
    }

    public int getBondType()
    {
        return Molecule.cBondTypeUp;
    }

    public void onChangeBond(int bond)
    {
        StereoMolecule mol = model.getMolecule();
        if (mol != null) {
            mol.changeBond(bond, Molecule.cBondTypeUp);
            mol.ensureHelperArrays(Molecule.cHelperNeighbours);
        }
    }


}
\ No newline at end of file
+/*
* Copyright (c) 1997 - 2016
* Actelion Pharmaceuticals Ltd.
* Gewerbestrasse 16
* CH-4123 Allschwil, Switzerland
*
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice, this
*    list of conditions and the following disclaimer.
* 2. Redistributions in binary form must reproduce the above copyright notice,
*    this list of conditions and the following disclaimer in the documentation
*    and/or other materials provided with the distribution.
* 3. Neither the name of the the copyright holder nor the
*    names of its contributors may be used to endorse or promote products
*    derived from this software without specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
* ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*
*/
package com.actelion.research.share.gui.editor.actions;

import com.actelion.research.chem.Molecule;
import com.actelion.research.chem.StereoMolecule;
import com.actelion.research.share.gui.editor.Model;
/**
 * Project:
 * User: rufenec
 * Date: 1/28/13
 * Time: 1:49 PM
 */
@Deprecated
public class UpBondAction extends NewBondAction
{
    public UpBondAction(Model model)
    {
        super(model);
    }

    public int getBondType()
    {
        return Molecule.cBondTypeUp;
    }

    public void onChangeBond(int bond)
    {
        StereoMolecule mol = model.getMolecule();
        if (mol != null) {
            mol.changeBond(bond, Molecule.cBondTypeUp);
            mol.ensureHelperArrays(Molecule.cHelperNeighbours);
        }
    }


}
\ No newline at end of file
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/ZoomRotateAction.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/ZoomRotateAction.java
index c836a991..9d4ce32e 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/ZoomRotateAction.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/actions/ZoomRotateAction.java
@@ -47,6 +47,7 @@
  * Date: 4/28/2014
  * Time: 12:39 PM
  */
+@Deprecated
 public class ZoomRotateAction extends DrawAction {
     private java.awt.geom.Point2D origin = null;
 
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/chem/AbstractExtendedDepictor.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/chem/AbstractExtendedDepictor.java
index 6cc7d3ea..61eccddb 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/chem/AbstractExtendedDepictor.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/chem/AbstractExtendedDepictor.java
@@ -47,6 +47,7 @@
 import java.util.List;
 
 
+@Deprecated
 public abstract class AbstractExtendedDepictor<T, C>
 {
     protected StereoMolecule[] mMolecule;
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/chem/IArrow.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/chem/IArrow.java
index 1122ced3..d9abab6d 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/chem/IArrow.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/chem/IArrow.java
@@ -39,6 +39,7 @@
  * Date: 11/24/2014
  * Time: 3:28 PM
  */
+@Deprecated
 public interface IArrow extends IDrawingObject
 {
     int getLength();
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/chem/IDepictor.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/chem/IDepictor.java
index 9e8ee7b6..f5a7ad92 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/chem/IDepictor.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/chem/IDepictor.java
@@ -44,6 +44,7 @@
  * Date: 11/24/2014
  * Time: 3:26 PM
  */
+@Deprecated
 public interface IDepictor<T>
 {
     DepictorTransformation updateCoords(IDrawContext<T> g, GenericRectangle aFloat, int cModeInflateToMaxAVBL);
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/chem/IDrawingObject.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/chem/IDrawingObject.java
index b668e7b4..3250807c 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/chem/IDrawingObject.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/chem/IDrawingObject.java
@@ -43,6 +43,7 @@
  * Date: 11/24/2014
  * Time: 3:28 PM
  */
+@Deprecated
 public interface IDrawingObject
 {
     void setSelected(boolean b);
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/chem/IReactionArrow.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/chem/IReactionArrow.java
index 7bb0a3df..4fd14d37 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/chem/IReactionArrow.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/chem/IReactionArrow.java
@@ -39,6 +39,7 @@
  * Date: 11/24/2014
  * Time: 5:49 PM
  */
+@Deprecated
 public interface IReactionArrow
 {
 }
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/dialogs/IAtomPropertiesDialog.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/dialogs/IAtomPropertiesDialog.java
index 9d0e1b4d..4ea2ebed 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/dialogs/IAtomPropertiesDialog.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/dialogs/IAtomPropertiesDialog.java
@@ -39,6 +39,7 @@
  * Date: 11/24/2014
  * Time: 5:03 PM
  */
+@Deprecated
 public interface IAtomPropertiesDialog extends IDialog
 {
 }
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/dialogs/IAtomQueryFeaturesDialog.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/dialogs/IAtomQueryFeaturesDialog.java
index 9a08ccc8..a103b8b9 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/dialogs/IAtomQueryFeaturesDialog.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/dialogs/IAtomQueryFeaturesDialog.java
@@ -39,6 +39,7 @@
  * Date: 11/24/2014
  * Time: 4:53 PM
  */
+@Deprecated
 public interface IAtomQueryFeaturesDialog extends IDialog
 {
 }
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/dialogs/IBondQueryFeaturesDialog.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/dialogs/IBondQueryFeaturesDialog.java
index 1838d595..73ceb444 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/dialogs/IBondQueryFeaturesDialog.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/dialogs/IBondQueryFeaturesDialog.java
@@ -39,6 +39,7 @@
  * Date: 11/24/2014
  * Time: 4:57 PM
  */
+@Deprecated
 public interface IBondQueryFeaturesDialog extends IDialog
 {
 }
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/dialogs/IDialog.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/dialogs/IDialog.java
index 8003adaa..8e80efcc 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/dialogs/IDialog.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/dialogs/IDialog.java
@@ -37,6 +37,7 @@
 
 import java.util.function.Consumer;
 
+@Deprecated
 public interface IDialog
 {
     DialogResult doModal();
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/geom/GeomFactory.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/geom/GeomFactory.java
index 24681e34..443d2dfe 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/geom/GeomFactory.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/geom/GeomFactory.java
@@ -50,6 +50,7 @@
  * Date: 11/24/2014
  * Time: 3:15 PM
  */
+@Deprecated
 public abstract class GeomFactory
 {
 
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/geom/IColor.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/geom/IColor.java
index 7304744d..a08b07c2 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/geom/IColor.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/geom/IColor.java
@@ -39,14 +39,15 @@
  * Date: 11/24/2014
  * Time: 3:21 PM
  */
+@Deprecated
 public interface IColor
 {
-    public static final long BLACK = 0x000000FFl;
-    public static final long WHITE = 0xFFFFFFFFl;
-    public static final long RED = 0xFF00000FFl;
-    public static final long BLUE = 0x0000FFFFl;
-    public static final long GREEN = 0x00FF00FFl;
-    public static final long GRAY = 0xAAAAAAFFl;
-    public static final long TRANSPARENT = 0x00000000l;
+    public static final long BLACK = 0x000000FFL;
+    public static final long WHITE = 0xFFFFFFFFL;
+    public static final long RED = 0xFF0000FFL;
+    public static final long BLUE = 0x0000FFFFL;
+    public static final long GREEN = 0x00FF00FFL;
+    public static final long GRAY = 0xAAAAAAFFL;
+    public static final long TRANSPARENT = 0x00000000L;
 
 }
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/geom/ICursor.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/geom/ICursor.java
index c7b4780e..5f550593 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/geom/ICursor.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/geom/ICursor.java
@@ -41,6 +41,7 @@
  * Date: 11/24/2014
  * Time: 3:21 PM
  */
+@Deprecated
 public interface ICursor
 {
 
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/geom/IDrawContext.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/geom/IDrawContext.java
index 33432e51..6a15ac33 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/geom/IDrawContext.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/geom/IDrawContext.java
@@ -40,6 +40,7 @@
  * Date: 11/24/2014
  * Time: 3:22 PM
  */
+@Deprecated
 public interface IDrawContext<T>
 {
 
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/geom/IPolygon.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/geom/IPolygon.java
index bc62e4c0..b02260fb 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/geom/IPolygon.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/geom/IPolygon.java
@@ -41,6 +41,7 @@
  * Date: 11/24/2014
  * Time: 4:45 PM
  */
+@Deprecated
 public interface IPolygon
 {
     void add(GenericPoint pt);
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/geom/IRectangle2D.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/geom/IRectangle2D.java
index 3afd98ce..cdcbbca6 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/geom/IRectangle2D.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/geom/IRectangle2D.java
@@ -39,6 +39,7 @@
  * Date: 11/24/2014
  * Time: 3:17 PM
  */
+@Deprecated
 public interface IRectangle2D
 {
     boolean contains(double x, double y);
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/geom/StrokeLineCap.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/geom/StrokeLineCap.java
index 5cfb57f9..80b349b2 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/geom/StrokeLineCap.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/geom/StrokeLineCap.java
@@ -39,6 +39,7 @@
  * Date: 11/24/2014
  * Time: 4:20 PM
  */
+@Deprecated
 public interface StrokeLineCap<T>
 {
     T getNative();
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/geom/StrokeLineJoin.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/geom/StrokeLineJoin.java
index a2fe16e9..0e34cc13 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/geom/StrokeLineJoin.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/geom/StrokeLineJoin.java
@@ -39,6 +39,7 @@
  * Date: 11/24/2014
  * Time: 4:20 PM
  */
+@Deprecated
 public interface StrokeLineJoin
 {
 }
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/io/IKeyCode.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/io/IKeyCode.java
index cdca2042..ba722083 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/io/IKeyCode.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/io/IKeyCode.java
@@ -39,6 +39,7 @@
  * Date: 11/24/2014
  * Time: 4:17 PM
  */
+@Deprecated
 public interface IKeyCode
 {
 }
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/io/IKeyEvent.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/io/IKeyEvent.java
index c944073f..6743a3c8 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/io/IKeyEvent.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/io/IKeyEvent.java
@@ -40,6 +40,7 @@
  * Date: 11/24/2014
  * Time: 3:20 PM
  */
+@Deprecated
 public interface IKeyEvent
 {
     IKeyCode getCode();
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/io/IMouseEvent.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/io/IMouseEvent.java
index 9ccab4c4..ab11d067 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/io/IMouseEvent.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/io/IMouseEvent.java
@@ -39,6 +39,7 @@
  * Date: 11/24/2014
  * Time: 3:19 PM
  */
+@Deprecated
 public interface IMouseEvent
 {
     double getX();
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/listeners/IChangeListener.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/listeners/IChangeListener.java
index 27275341..30be67db 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/listeners/IChangeListener.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/listeners/IChangeListener.java
@@ -39,6 +39,7 @@
  * Date: 11/24/2014
  * Time: 3:25 PM
  */
+@Deprecated
 public interface IChangeListener
 {
     void onChange();
diff --git a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/listeners/IValidationListener.java b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/listeners/IValidationListener.java
index 6c5efba2..78057b27 100644
--- a/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/listeners/IValidationListener.java
+++ b/src/com/actelion/research/gwt/chemlib/com/actelion/research/share/gui/editor/listeners/IValidationListener.java
@@ -39,6 +39,7 @@
  * Date: 11/24/2014
  * Time: 3:27 PM
  */
+@Deprecated
 public interface IValidationListener
 {
     void valueInvalidated();