Spotted in previous commit - we should add H to extended tetrahedral …

…also.
cdk · Jun 17, 2017 · 253820a · 253820a
1 parent 1dc567b
commit 253820a
Showing 1 changed file with 29 additions and 12 deletions.
diff --git a/...tandard/src/main/java/org/openscience/cdk/tools/manipulator/AtomContainerManipulator.java b/...tandard/src/main/java/org/openscience/cdk/tools/manipulator/AtomContainerManipulator.java
@@ -444,6 +444,13 @@ public static int countExplicitHydrogens(IAtomContainer atomContainer, IAtom ato
         return hCount;
     }
 
+    private static final void replaceAtom(IAtom[] atoms, IAtom org, IAtom rep) {
+        for (int i = 0; i < atoms.length; i++) {
+            if (atoms[i].equals(org))
+                atoms[i] = rep;
+        }
+    }
+
     /**
      * Adds explicit hydrogens (without coordinates) to the IAtomContainer,
      * equaling the number of set implicit hydrogens.
@@ -483,28 +490,38 @@ public static void convertImplicitToExplicitHydrogens(IAtomContainer atomContain
         for (IBond bond : newBonds)
             atomContainer.addBond(bond);
 
-        // update tetrahedral elements with an implicit part
+        // update stereo elements with an implicit part
         List<IStereoElement> stereos = new ArrayList<>();
         for (IStereoElement stereo : atomContainer.stereoElements()) {
             if (stereo instanceof ITetrahedralChirality) {
                 ITetrahedralChirality tc = (ITetrahedralChirality) stereo;
 
-                IAtom focus = tc.getChiralAtom();
-                IAtom[] neighbors = tc.getLigands();
-                IAtom hydrogen = hNeighbor.get(focus);
+                IAtom   focus    = tc.getFocus();
+                IAtom[] carriers = tc.getCarriers().toArray(new IAtom[4]);
+                IAtom   hydrogen = hNeighbor.get(focus);
 
                 // in sulfoxide - the implicit part of the tetrahedral centre
                 // is a lone pair
 
                 if (hydrogen != null) {
-                    for (int i = 0; i < 4; i++) {
-                        if (neighbors[i] == focus) {
-                            neighbors[i] = hydrogen;
-                            break;
-                        }
-                    }
-                    // neighbors is a copy so need to create a new stereocenter
-                    stereos.add(new TetrahedralChirality(focus, neighbors, tc.getStereo()));
+                    replaceAtom(carriers, focus, hydrogen);
+                    stereos.add(new TetrahedralChirality(focus, carriers, tc.getStereo()));
+                } else {
+                    stereos.add(stereo);
+                }
+            } else if (stereo instanceof ExtendedTetrahedral) {
+                ExtendedTetrahedral tc = (ExtendedTetrahedral) stereo;
+
+                IAtom   focus    = tc.getFocus();
+                IAtom[] carriers = tc.getCarriers().toArray(new IAtom[4]);
+                IAtom   hydrogen = hNeighbor.get(focus);
+
+                // in sulfoxide - the implicit part of the tetrahedral centre
+                // is a lone pair
+
+                if (hydrogen != null) {
+                    replaceAtom(carriers, focus, hydrogen);
+                    stereos.add(new TetrahedralChirality(focus, carriers, tc.getConfig()));
                 } else {
                     stereos.add(stereo);
                 }