Atom values were omitted from output.

cdk · Aug 16, 2016 · c494b38 · c494b38
1 parent 2dffeff
commit c494b38
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diff --git a/storage/smiles/src/main/java/org/openscience/cdk/smiles/CxSmilesGenerator.java b/storage/smiles/src/main/java/org/openscience/cdk/smiles/CxSmilesGenerator.java
@@ -161,6 +161,27 @@ public int compare(List<Integer> a, List<Integer> b) {
             sb.append('$');
         }
 
+        // Atom Values
+        if (SmiFlavour.isSet(opts, SmiFlavour.CxAtomValue) &&
+            state.atomValues != null && !state.atomValues.isEmpty()) {
+
+            if (sb.length() > 2)
+                sb.append(',');
+            sb.append("$_AV:");
+            int nonempty_cnt = 0;
+            for (int idx : invorder) {
+                String label = state.atomValues.get(idx);
+                if (label == null || label.isEmpty()) label = "";
+                else nonempty_cnt++;
+                sb.append(encode_alias(label));
+                // don't need to write anymore more ';'
+                if (nonempty_cnt == state.atomValues.size())
+                    break;
+                sb.append(";");
+            }
+            sb.append('$');
+        }
+
         // 2D/3D Coordinates
         if (SmiFlavour.isSet(opts, SmiFlavour.CxCoordinates) &&
             state.atomCoords != null && !state.atomCoords.isEmpty()) {

diff --git a/storage/smiles/src/test/java/org/openscience/cdk/smiles/CxSmilesTest.java b/storage/smiles/src/test/java/org/openscience/cdk/smiles/CxSmilesTest.java
@@ -370,4 +370,12 @@ public void atomValues() throws InvalidSmilesException {
                    is(smigen.create(rxn2)));
     }
 
+    @Test public void canonAtomLabels() throws CDKException {
+        IChemObjectBuilder bldr = SilentChemObjectBuilder.getInstance();
+        SmilesParser smipar = new SmilesParser(bldr);
+        IAtomContainer mol = smipar.parseSmiles("c1ccccc1O |$_AV:0;1;2;3;4;5;6$|");
+        SmilesGenerator smigen = new SmilesGenerator(SmiFlavour.Canonical | SmiFlavour.CxAtomValue);
+        assertThat(smigen.create(mol), is("OC=1C=CC=CC1 |$_AV:6;5;0;1;2;3;4$|"));
+    }
+
 }