MDLV3000Reader throws NPE when query bond is present Issue #664

marois · marois · commit 8977dcc1be6d · 2020-08-24T10:55:43.000-07:00
When an order &gt;= 4 set the bond order to IBond.Order.UNSET to avoid the NPE in valence calculation.
diff --git a/storage/ctab/src/main/java/org/openscience/cdk/io/MDLV3000Reader.java b/storage/ctab/src/main/java/org/openscience/cdk/io/MDLV3000Reader.java
@@ -417,6 +417,7 @@ public void readBondBlock(IAtomContainer readData) throws CDKException {
                     String orderString = tokenizer.nextToken();
                     int order = Integer.parseInt(orderString);
                     if (order >= 4) {
+                        bond.setOrder(IBond.Order.UNSET);
                         logger.warn("Query order types are not supported (yet). File a bug if you need it");
                     } else {
                         bond.setOrder(BondManipulator.createBondOrder((double) order));
diff --git a/storage/ctab/src/test/java/org/openscience/cdk/io/MDLV3000ReaderTest.java b/storage/ctab/src/test/java/org/openscience/cdk/io/MDLV3000ReaderTest.java
@@ -31,7 +31,7 @@
 import org.openscience.cdk.exception.CDKException;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
-import org.openscience.cdk.io.iterator.IteratingSDFReader;
+import org.openscience.cdk.interfaces.IBond;
 import org.openscience.cdk.sgroup.Sgroup;
 import org.openscience.cdk.sgroup.SgroupType;
 import org.openscience.cdk.silent.AtomContainer;
@@ -154,4 +154,20 @@ public void testPseudoAtomLabels() throws Exception {
             assertThat(mol.getAtomCount(), CoreMatchers.is(31));
         }
     }
+
+    /**
+     * @cdk.bug https://github.com/cdk/cdk/issues/664
+     *
+     * MDLV3000Reader does not yet support queries. Parsed query bonds (order >= 4) should be set to IBond.Order.UNSET
+     * to avoid NPE in valence calculation.
+     */
+    @Test public void reading_query_bond_should_not_npe() throws Exception {
+        try (MDLV3000Reader reader = new MDLV3000Reader(getClass().getResourceAsStream("v3000Query.mol"))) {
+            IAtomContainer container = reader.read(SilentChemObjectBuilder.getInstance().newAtomContainer());
+            for (IBond bond: container.bonds()) {
+                assertNotNull(bond.getOrder());
+            }
+            assertThat(container.getBond(4).getOrder(), is(IBond.Order.UNSET));
+        }
+    }
 }
diff --git a/storage/ctab/src/test/resources/org/openscience/cdk/io/v3000Query.mol b/storage/ctab/src/test/resources/org/openscience/cdk/io/v3000Query.mol
@@ -0,0 +1,24 @@
+
+
+
+  0  0  0     0  0            999 V3000
+M  V30 BEGIN CTAB
+M  V30 COUNTS 6 6 0 0 0
+M  V30 BEGIN ATOM
+M  V30 1 C -4.5418 1.0401 0 0
+M  V30 2 C -5.8753 0.2701 0 0
+M  V30 3 C -5.8753 -1.2701 0 0
+M  V30 4 C -4.5418 -2.0401 0 0
+M  V30 5 C -3.208 -1.2701 0 0
+M  V30 6 C -3.208 0.2701 0 0
+M  V30 END ATOM
+M  V30 BEGIN BOND
+M  V30 1 2 1 2
+M  V30 2 1 2 3
+M  V30 3 2 3 4
+M  V30 4 1 4 5
+M  V30 5 4 5 6
+M  V30 6 1 6 1
+M  V30 END BOND
+M  V30 END CTAB
+M  END
