fix: update OCL to master branch (#247)

Refs: Actelion/openchemlib#128

__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);
+});

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;
                         }
                     }

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

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;
+	}
 
 	/**
 	 *

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
 {
 

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;

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;

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,

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)

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<>();

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);

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);
     }

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
 {
     /**

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;

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;

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
 {
 

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
 {
 

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
 {