fixed inconsistent bond types when parsing smiles with multiple, comm…

…a-separated bond types
Actelion · Jan 14, 2025 · 14198e4 · 14198e4
1 parent 8aeee28
commit 14198e4
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Showing 3 changed files with 65 additions and 43 deletions.
diff --git a/src/main/java/com/actelion/research/chem/Molecule.java b/src/main/java/com/actelion/research/chem/Molecule.java
@@ -3498,6 +3498,55 @@ public void setBondQueryFeature(int bond, int feature, boolean value) {
 		}
 
 
+	/**
+	 * If a molecule is a substructure fragment, and if multiple allowed bond types
+	 * are defined in a bond's query features, then the explicit bond type must match
+	 * the lowest order of the allowed query feature bond types.
+	 * Call this function after setting bond type and query features to make sure,
+	 * the correct bond type is used.
+	 * @param bond
+	 */
+	public void adaptBondTypeToQueryFeatures(int bond) {
+		int bondType = -1;
+		int selectionCount = 0;
+
+		if ((mBondQueryFeatures[bond] & Molecule.cBondTypeMetalLigand) != 0) {
+			bondType = Molecule.cBondTypeMetalLigand;
+			selectionCount++;
+		}
+		if ((mBondQueryFeatures[bond] & Molecule.cBondTypeQuintuple) != 0) {
+			bondType = Molecule.cBondTypeQuintuple;
+			selectionCount++;
+		}
+		if ((mBondQueryFeatures[bond] & Molecule.cBondTypeQuadruple) != 0) {
+			bondType = Molecule.cBondTypeQuadruple;
+			selectionCount++;
+		}
+		if ((mBondQueryFeatures[bond] & Molecule.cBondTypeTriple) != 0) {
+			bondType = Molecule.cBondTypeTriple;
+			selectionCount++;
+		}
+		if ((mBondQueryFeatures[bond] & Molecule.cBondTypeDouble) != 0) {
+			bondType = Molecule.cBondTypeDouble;
+			selectionCount++;
+		}
+		if ((mBondQueryFeatures[bond] & Molecule.cBondTypeDelocalized) != 0) {
+			bondType = Molecule.cBondTypeDelocalized;
+			selectionCount++;
+		}
+		if ((mBondQueryFeatures[bond] & Molecule.cBondTypeSingle) != 0) {
+			bondType = Molecule.cBondTypeSingle;
+			selectionCount++;
+		}
+
+		if (bondType != -1 && bondType != (mBondType[bond] & cBondTypeMaskSimple))
+			mBondType[bond] = bondType;	// set to the lowest bond order of query options
+
+		if (selectionCount < 2)
+			mBondQueryFeatures[bond] &= ~(cBondQFBondTypes + cBondQFRareBondTypes);
+	}
+
+
 	/**
 	 * Sets the bond type based on bond order without stereo orientation.
 	 * @param bond

diff --git a/src/main/java/com/actelion/research/chem/SmilesParser.java b/src/main/java/com/actelion/research/chem/SmilesParser.java
@@ -432,6 +432,7 @@ public void parse(StereoMolecule mol, byte[] smiles, int position, int endIndex,
 						if (bondQueryFeatures != 0) {
 							mSmartsFeatureFound = true;
 							mMol.setBondQueryFeature(bond, bondQueryFeatures, true);
+							mMol.adaptBondTypeToQueryFeatures(bond);
 						}
 					}
 
@@ -462,6 +463,7 @@ public void parse(StereoMolecule mol, byte[] smiles, int position, int endIndex,
 					if (bondQueryFeatures != 0) {
 						mSmartsFeatureFound = true;
 						mMol.setBondQueryFeature(bond, bondQueryFeatures, true);
+						mMol.adaptBondTypeToQueryFeatures(bond);
 					}
 				}
 
@@ -667,6 +669,7 @@ else if (bondType == Molecule.cBondTypeDown)
 						if (bondQueryFeatures != 0) {
 							mSmartsFeatureFound = true;
 							mMol.setBondQueryFeature(bond, ringClosureBondQueryFeatures[number], true);
+							mMol.adaptBondTypeToQueryFeatures(bond);
 						}
 						ringClosureAtom[number] = -1; // for number re-usage
 					}

diff --git a/src/main/java/com/actelion/research/gui/editor/BondQueryFeatureDialogBuilder.java b/src/main/java/com/actelion/research/gui/editor/BondQueryFeatureDialogBuilder.java
@@ -296,51 +296,20 @@ private void setQueryFeatures(int bond) {
 			mMol.setBondType(bond, Molecule.cBondTypeSingle);
             }
         else {
-        	// priority in order of bond orders (except 0)
-            int bondType = -1;
-			int selectionCount = 0;
-
-			if (mCBMetalLigand.isSelected()) {
-				bondType = Molecule.cBondTypeMetalLigand;
-				queryFeatures |= Molecule.cBondTypeMetalLigand;
-				selectionCount++;
-				}
-			if (mCBQuintuple.isSelected()) {
-				bondType = Molecule.cBondTypeQuintuple;
-				queryFeatures |= Molecule.cBondTypeQuintuple;
-				selectionCount++;
-				}
-			if (mCBQuadruple.isSelected()) {
-				bondType = Molecule.cBondTypeQuadruple;
-				queryFeatures |= Molecule.cBondTypeQuadruple;
-				selectionCount++;
-				}
-			if (mCBTriple.isSelected()) {
-				bondType = Molecule.cBondTypeTriple;
-				queryFeatures |= Molecule.cBondTypeTriple;
-				selectionCount++;
-				}
-			if (mCBDouble.isSelected()) {
-				bondType = Molecule.cBondTypeDouble;
+			if (mCBSingle.isSelected())
+				queryFeatures |= Molecule.cBondTypeSingle;
+			if (mCBDouble.isSelected())
 				queryFeatures |= Molecule.cBondTypeDouble;
-				selectionCount++;
-				}
-			if (mCBDelocalized.isSelected()) {
-				bondType = Molecule.cBondTypeDelocalized;
+			if (mCBTriple.isSelected())
+				queryFeatures |= Molecule.cBondTypeTriple;
+			if (mCBQuadruple.isSelected())
+				queryFeatures |= Molecule.cBondTypeQuadruple;
+			if (mCBQuintuple.isSelected())
+				queryFeatures |= Molecule.cBondTypeQuintuple;
+			if (mCBDelocalized.isSelected())
 				queryFeatures |= Molecule.cBondTypeDelocalized;
-				selectionCount++;
-				}
-			if (mCBSingle.isSelected()) {
-				bondType = Molecule.cBondTypeSingle;
-				queryFeatures |= Molecule.cBondTypeSingle;
-				selectionCount++;
-				}
-
-			if (bondType != -1)
-				mMol.setBondType(bond, bondType);	// set to the lowest bond order of query options
-
-			if (selectionCount < 2)
-				queryFeatures = 0;
+			if (mCBMetalLigand.isSelected())
+				queryFeatures |= Molecule.cBondTypeMetalLigand;
 
 			if (mComboBoxRing.getSelectedIndex() != 0) {
 				if (mComboBoxRing.getSelectedIndex() == 1) {
@@ -374,6 +343,7 @@ else if (mComboBoxRing.getSelectedIndex() == 4) {
 
 		mMol.setBondQueryFeature(bond, Molecule.cBondQFAllFeatures, false);
 		mMol.setBondQueryFeature(bond, queryFeatures, true);
+		mMol.adaptBondTypeToQueryFeatures(bond);
 		}
 
     private boolean isSelectedBond(int bond) {