fix: update OCL to v2025.11.2

__tests__/__snapshots__/reaction.test.ts.snap

@@ -152,3 +152,167 @@ OCL_RXN_V1.0:!####
   0  0
 "
 `;
+
+exports[`Reaction class > toRXN options keepIdCode one product 1`] = `
+"$RXN
+
+
+
+  0  1
+$MOL
+
+Actelion Java MolfileCreator 1.0
+
+  3  2  0  0  0  0  0  0  0  0999 V2000
+    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    1.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  2  0  0  0  0
+  2  3  2  0  0  0  0
+M  END
+"
+`;
+
+exports[`Reaction class > toRXN options keepIdCode one product 2`] = `
+"$RXN
+Hello world!
+
+OCL_RXN_V1.0:!eMDARU@##!R_?y??kH@@@##
+  0  1
+$MOL
+
+Actelion Java MolfileCreator 1.0
+
+  3  2  0  0  0  0  0  0  0  0999 V2000
+    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    1.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  2  0  0  0  0
+  2  3  2  0  0  0  0
+M  END
+"
+`;
+
+exports[`Reaction class > toRXN options keepIdCode one reagent 1`] = `
+"$RXN
+
+
+
+  1  0
+$MOL
+
+Actelion Java MolfileCreator 1.0
+
+  1  0  0  0  0  0  0  0  0  0999 V2000
+    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+M  END
+"
+`;
+
+exports[`Reaction class > toRXN options keepIdCode one reagent 2`] = `
+"$RXN
+Hello world!
+
+OCL_RXN_V1.0:fH@@!##!RGP@@##
+  1  0
+$MOL
+
+Actelion Java MolfileCreator 1.0
+
+  1  0  0  0  0  0  0  0  0  0999 V2000
+    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+M  END
+"
+`;
+
+exports[`Reaction class > toRXN options keepIdCode two products 1`] = `
+"$RXN
+
+
+
+  0  2
+$MOL
+
+Actelion Java MolfileCreator 1.0
+
+  1  0  0  0  0  0  0  0  0  0999 V2000
+    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+M  END
+$MOL
+
+Actelion Java MolfileCreator 1.0
+
+  1  0  0  0  0  0  0  0  0  0999 V2000
+    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+M  END
+"
+`;
+
+exports[`Reaction class > toRXN options keepIdCode two products 2`] = `
+"$RXN
+Hello world!
+
+OCL_RXN_V1.0:!fH@@ fI@@##!RGP@@ !RGP@@##
+  0  2
+$MOL
+
+Actelion Java MolfileCreator 1.0
+
+  1  0  0  0  0  0  0  0  0  0999 V2000
+    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+M  END
+$MOL
+
+Actelion Java MolfileCreator 1.0
+
+  1  0  0  0  0  0  0  0  0  0999 V2000
+    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+M  END
+"
+`;
+
+exports[`Reaction class > toRXN options keepIdCode two reagents 1`] = `
+"$RXN
+
+
+
+  2  0
+$MOL
+
+Actelion Java MolfileCreator 1.0
+
+  1  0  0  0  0  0  0  0  0  0999 V2000
+    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+M  END
+$MOL
+
+Actelion Java MolfileCreator 1.0
+
+  1  0  0  0  0  0  0  0  0  0999 V2000
+    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+M  END
+"
+`;
+
+exports[`Reaction class > toRXN options keepIdCode two reagents 2`] = `
+"$RXN
+Hello world!
+
+OCL_RXN_V1.0:fH@@ fI@@!##!RGP@@ !RGP@@##
+  2  0
+$MOL
+
+Actelion Java MolfileCreator 1.0
+
+  1  0  0  0  0  0  0  0  0  0999 V2000
+    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+M  END
+$MOL
+
+Actelion Java MolfileCreator 1.0
+
+  1  0  0  0  0  0  0  0  0  0999 V2000
+    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+M  END
+"
+`;

__tests__/reaction.test.ts

@@ -43,7 +43,90 @@ describe('Reaction class', () => {
       keepIdCode: true,
       programName: 'Hello world!',
     });
-    // this test could fail once this bug is fixed: https://github.com/Actelion/openchemlib/issues/158
+    expect(rxn2).toMatchSnapshot();
+  });
+
+  it('toRXN options keepIdCode one reagent', () => {
+    const reaction = Reaction.create();
+    const methane = Molecule.fromSmiles('C');
+    reaction.addReactant(methane);
+    expect(reaction.getReactants()).toBe(1);
+    expect(reaction.getProducts()).toBe(0);
+    expect(reaction.getCatalysts()).toBe(0);
+    const rxn = reaction.toRxn();
+    expect(rxn).toMatchSnapshot();
+    const reaction2 = Reaction.fromRxn(rxn);
+    expect(reaction2.getReactants()).toBe(1);
+    expect(reaction2.getProducts()).toBe(0);
+    expect(reaction2.getCatalysts()).toBe(0);
+    const rxn2 = reaction2.toRxn({
+      keepIdCode: true,
+      programName: 'Hello world!',
+    });
+    expect(rxn2).toMatchSnapshot();
+  });
+
+  it('toRXN options keepIdCode two reagents', () => {
+    const reaction = Reaction.create();
+    const methane = Molecule.fromSmiles('C');
+    const oxygen = Molecule.fromSmiles('O');
+    reaction.addReactant(methane);
+    reaction.addReactant(oxygen);
+    expect(reaction.getReactants()).toBe(2);
+    expect(reaction.getProducts()).toBe(0);
+    expect(reaction.getCatalysts()).toBe(0);
+    const rxn = reaction.toRxn();
+    expect(rxn).toMatchSnapshot();
+    const reaction2 = Reaction.fromRxn(rxn);
+    expect(reaction2.getReactants()).toBe(2);
+    expect(reaction2.getProducts()).toBe(0);
+    expect(reaction2.getCatalysts()).toBe(0);
+    const rxn2 = reaction2.toRxn({
+      keepIdCode: true,
+      programName: 'Hello world!',
+    });
+    expect(rxn2).toMatchSnapshot();
+  });
+
+  it('toRXN options keepIdCode one product', () => {
+    const reaction = Reaction.create();
+    const carbonDioxide = Molecule.fromSmiles('O=C=O');
+    reaction.addProduct(carbonDioxide);
+    expect(reaction.getReactants()).toBe(0);
+    expect(reaction.getProducts()).toBe(1);
+    expect(reaction.getCatalysts()).toBe(0);
+    const rxn = reaction.toRxn();
+    expect(rxn).toMatchSnapshot();
+    const reaction2 = Reaction.fromRxn(rxn);
+    expect(reaction2.getReactants()).toBe(0);
+    expect(reaction2.getProducts()).toBe(1);
+    expect(reaction2.getCatalysts()).toBe(0);
+    const rxn2 = reaction2.toRxn({
+      keepIdCode: true,
+      programName: 'Hello world!',
+    });
+    expect(rxn2).toMatchSnapshot();
+  });
+
+  it('toRXN options keepIdCode two products', () => {
+    const reaction = Reaction.create();
+    const carbon = Molecule.fromSmiles('C');
+    reaction.addProduct(carbon);
+    const oxygen = Molecule.fromSmiles('O');
+    reaction.addProduct(oxygen);
+    expect(reaction.getReactants()).toBe(0);
+    expect(reaction.getProducts()).toBe(2);
+    expect(reaction.getCatalysts()).toBe(0);
+    const rxn = reaction.toRxn();
+    expect(rxn).toMatchSnapshot();
+    const reaction2 = Reaction.fromRxn(rxn);
+    expect(reaction2.getReactants()).toBe(0);
+    expect(reaction2.getProducts()).toBe(2);
+    expect(reaction2.getCatalysts()).toBe(0);
+    const rxn2 = reaction2.toRxn({
+      keepIdCode: true,
+      programName: 'Hello world!',
+    });
     expect(rxn2).toMatchSnapshot();
   });
 

src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/IDCodeParserWithoutCoordinateInvention.java

@@ -99,7 +99,7 @@ public StereoMolecule getCompactMolecule(byte[] idcode) {
 	/**
 	 * Creates and returns a molecule from the idcode with its atom and bond arrays being
 	 * just as large as needed to hold the molecule. Use this to conserve memory if no
-	 * atoms or bonds are added to the molecule afterwards.
+	 * atoms or bonds are added to the molecule afterward.
 	 * @param idcode may be null
 	 * @param coordinates may be null
 	 * @return
@@ -112,7 +112,7 @@ public StereoMolecule getCompactMolecule(String idcode, String coordinates) {
 	/**
 	 * Creates and returns a molecule from the idcode with its atom and bond arrays being
 	 * just as large as needed to hold the molecule. Use this to conserve memory if no
-	 * atoms or bonds are added to the molecule afterwards.
+	 * atoms or bonds are added to the molecule afterward.
 	 * @param idcode may be null
 	 * @param coordinates may be null
 	 * @return

src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/io/pdb/calc/AminoAcids.java

@@ -101,7 +101,7 @@ public static Molecule3D createResidue(String label, Map<String,AtomRecord> atom
         if (mol != null) {
             Molecule3D aminoAcid = new Molecule3D(mol);
 
-            for (int atom=0; atom<aminoAcid.getAllAtoms(); atom++) {
+            for (int atom=0; atom<mol.getAllAtoms(); atom++) {
                 String atomName = mol.getAtomLabel(atom);
                 String customLabel = mol.getAtomCustomLabel(atom);
                 if (customLabel != null && customLabel.startsWith("]"))
@@ -119,6 +119,17 @@ public static Molecule3D createResidue(String label, Map<String,AtomRecord> atom
                     aminoAcid.setAtomX(atom, coords3d.x);
                     aminoAcid.setAtomY(atom, coords3d.y);
                     aminoAcid.setAtomZ(atom, coords3d.z);
+
+                    AtomRecord bridgeRecord = record.getCovalentBridgeAtom();
+                    if (bridgeRecord != null) {
+                        int bridgeAtom = aminoAcid.addAtom(0);
+                        aminoAcid.setAtomCustomLabel(bridgeAtom,"]cov");
+                        aminoAcid.setAtomX(bridgeAtom, (bridgeRecord.getX() + record.getX()) / 2);
+                        aminoAcid.setAtomY(bridgeAtom, (bridgeRecord.getY() + record.getY()) / 2);
+                        aminoAcid.setAtomZ(bridgeAtom, (bridgeRecord.getZ() + record.getZ()) / 2);
+                        aminoAcid.addBond(atom, bridgeAtom, Molecule.cBondTypeSingle);
+                        aminoAcid.setCovalentLigand(true);
+                    }
                 }
             };
 

src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/io/pdb/parser/AtomRecord.java

@@ -43,7 +43,6 @@
 public class AtomRecord implements Comparable<AtomRecord> {
 
 	private boolean isHetAtom;
-
 	private int serialId;
 
     // From field atom name
@@ -53,30 +52,19 @@ public class AtomRecord implements Comparable<AtomRecord> {
 
     // Alternate location indicator.
     private String labelAltID;
-
 	private int labelSeqID;
-
 	private String authCompID;
-
     private String authAsymId;
-
     private String insertionCode;
-
     private int authSeqID;
-
     private double x,y,z;
-
     private double occupancy;
-
     private double tempFactor;
-
     private String element;
-
     private String charge;
-
     private String anisou;
-
     private boolean isTerminalC;
+	private AtomRecord covalentBridgeAtom;
 
 	public AtomRecord() {}
 
@@ -204,6 +192,14 @@ public void setTerminalC(boolean isTerminalC) {
     	this.isTerminalC = isTerminalC;
     }
 
+	public void setCovalentBridgeAtom(AtomRecord atom) {
+		covalentBridgeAtom = atom;
+	}
+
+	public AtomRecord getCovalentBridgeAtom() {
+		return covalentBridgeAtom;
+	}
+
 	@Override
 	public int compareTo(AtomRecord o) {
 		return Integer.compare(serialId, o.serialId);

src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/io/pdb/parser/Residue.java

@@ -136,6 +136,16 @@ else if (!altLoc.equals(record.getLabelAltID()))
 			fragment.setAtomX(atom,record.getX());
 			fragment.setAtomY(atom,record.getY());
 			fragment.setAtomZ(atom,record.getZ());
+			AtomRecord bridgeRecord = record.getCovalentBridgeAtom();
+			if (bridgeRecord != null) {
+				int bridgeAtom = fragment.addAtom(0);
+				fragment.setAtomCustomLabel(bridgeAtom,"]cov");
+				fragment.setAtomX(bridgeAtom, (bridgeRecord.getX() + record.getX()) / 2);
+				fragment.setAtomY(bridgeAtom, (bridgeRecord.getY() + record.getY()) / 2);
+				fragment.setAtomZ(bridgeAtom, (bridgeRecord.getZ() + record.getZ()) / 2);
+				fragment.addBond(atom, bridgeAtom, Molecule.cBondTypeSingle);
+				fragment.setCovalentLigand(true);
+			}
 		}
 
 		if (mAddBonds) {