only clear wedge bond flags after normalization

Author: Tosco, Paolo

org.rdkit.knime.types/rdkit-chemsrc/org/rdkit/knime/types/RDKitMolValueRenderer.java

@@ -67,6 +67,7 @@
 import org.RDKit.RDKFuncs;
 import org.RDKit.ROMol;
 import org.RDKit.RWMol;
+import org.RDKit.Bond;
 import org.apache.batik.anim.dom.SAXSVGDocumentFactory;
 import org.apache.batik.util.XMLResourceDescriptor;
 import org.knime.base.data.xml.SvgProvider;
@@ -568,6 +569,37 @@ public static int compute2DCoords(ROMol mol, boolean bUseCoordGen, boolean bNorm
 return compute2DCoords(mol, (Int_Point2D_Map)null, bUseCoordGen, bNormalize);
 }
 
+/**
+ * Clears the single bond direction flags of the passed in molecule.
+ * If bOnlyWedgeFlags is true, only the wedge flags are cleared, otherwise
+ * all single bond direction flags are cleared.
+ * FIXME: This method can be replaced with the native clearSingleBondDirFlags
+ * method once the RDKit version is updated to 2025_03_4 or later
+ * @param mol Molecule to clear the single bond direction flags for. Can be null to do nothing.
+ * @param bOnlyWedgeFlags If true, only the wedge flags are cleared, otherwise
+ * all single bond direction flags are cleared.
+ */
+public static void clearSingleBondDirFlags(ROMol mol, boolean bOnlyWedgeFlags) {
+if (mol == null) {
+return;
+}
+for (int i = 0; i < mol.getNumBonds(); ++i) {
+final Bond bond = mol.getBondWithIdx(i);
+if (bond.getBondType() == Bond.BondType.SINGLE) {
+if (bond.getBondDir() == Bond.BondDir.UNKNOWN) {
+bond.setProp("_UnknownStereo", "1");
+}
+
+if (!bOnlyWedgeFlags ||
+(bond.getBondDir() != Bond.BondDir.ENDDOWNRIGHT &&
+bond.getBondDir() != Bond.BondDir.ENDUPRIGHT)) {
+bond.setBondDir(Bond.BondDir.NONE);
+}
+}
+}
+}
+
+
 /**
  * Calls the compute2DCoords method on the passed in ROMol object (if not null)
  * and passes default parameters except for the last boolean parameter, which
@@ -608,7 +640,7 @@ public static int compute2DCoords(ROMol mol, Int_Point2D_Map mapTemplate, boolea
 // canonicalization may flip the molecule around the Z axis,
 // so we recompute bond wedging to make sure the stereochemistry
 // is depicted correctly (KNIME-1692)
-mol.ClearSingleBondDirFlags();
+clearSingleBondDirFlags(mol, true);
 mol.WedgeMolBonds(mol.getConformer());
 }
 }