Output the chiral flag as absolute in V2000 molfiles if there is tetr…

…ahedral centres present.
cdk · Aug 8, 2017 · cfd5802 · cfd5802
1 parent 5851070
commit cfd5802
Showing 1 changed file with 12 additions and 9 deletions.
diff --git a/storage/ctab/src/main/java/org/openscience/cdk/io/MDLV2000Writer.java b/storage/ctab/src/main/java/org/openscience/cdk/io/MDLV2000Writer.java
@@ -360,22 +360,25 @@ public void writeMolecule(IAtomContainer container) throws Exception {
         writer.write(comment);
         writer.newLine();
 
-        // write Counts line
-        line += formatMDLInt(container.getAtomCount(), 3);
-        line += formatMDLInt(container.getBondCount(), 3);
-        line += "  0  0  0  0  0  0  0  0999 V2000";
-        writer.write(line);
-        writer.newLine();
-
         // index stereo elements for setting atom parity values
         Map<IAtom,ITetrahedralChirality> atomstereo = new HashMap<>();
         Map<IAtom,Integer> atomindex = new HashMap<>();
         for (IStereoElement element : container.stereoElements())
-                if (element instanceof ITetrahedralChirality)
-                    atomstereo.put(((ITetrahedralChirality) element).getChiralAtom(), (ITetrahedralChirality) element);
+            if (element instanceof ITetrahedralChirality)
+                atomstereo.put(((ITetrahedralChirality) element).getChiralAtom(), (ITetrahedralChirality) element);
         for (IAtom atom : container.atoms())
             atomindex.put(atom, atomindex.size());
 
+        // write Counts line
+        line += formatMDLInt(container.getAtomCount(), 3);
+        line += formatMDLInt(container.getBondCount(), 3);
+        line += "  0  0";
+        // we mark all stereochemistry to absolute for now
+        line += atomstereo.isEmpty() ? "  0" : "  1";
+        line += "0  0  0  0  0999 V2000";
+        writer.write(line);
+        writer.newLine();
+
         // write Atom block
         for (int f = 0; f < container.getAtomCount(); f++) {
             IAtom atom = container.getAtom(f);