From 32cdc48811dd96a11d264921a654b23f694fb39f Mon Sep 17 00:00:00 2001
From: Egon Willighagen <egonw@users.sourceforge.net>
Date: Fri, 13 Aug 2010 14:38:35 +0200
Subject: [PATCH] Throw a CDKException when a QUADRUPLE bond order is in the
 input, which is not supported by the MDL/Symyx molfile format (fixes
 #3029352)

Signed-off-by: Rajarshi  Guha <rajarshi.guha@gmail.com>
---
 src/main/org/openscience/cdk/io/MDLWriter.java |  6 +++---
 .../org/openscience/cdk/io/MDLWriterTest.java  | 18 ++++++++++++++++++
 2 files changed, 21 insertions(+), 3 deletions(-)

diff --git a/src/main/org/openscience/cdk/io/MDLWriter.java b/src/main/org/openscience/cdk/io/MDLWriter.java
index 0dffa57f3bf..7d184f6a876 100644
--- a/src/main/org/openscience/cdk/io/MDLWriter.java
+++ b/src/main/org/openscience/cdk/io/MDLWriter.java
@@ -35,12 +35,9 @@
 import java.text.NumberFormat;
 import java.text.SimpleDateFormat;
 import java.util.ArrayList;
-import java.util.Calendar;
 import java.util.Iterator;
 import java.util.List;
 import java.util.Locale;
-import java.util.StringTokenizer;
-import java.util.TimeZone;
 
 import org.openscience.cdk.CDKConstants;
 import org.openscience.cdk.annotations.TestClass;
@@ -50,6 +47,7 @@
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IBond;
+import org.openscience.cdk.interfaces.IBond.Order;
 import org.openscience.cdk.interfaces.IChemFile;
 import org.openscience.cdk.interfaces.IChemModel;
 import org.openscience.cdk.interfaces.IChemObject;
@@ -345,6 +343,8 @@ else if(atom.getValency()==0)
                         int bondType;
                         if (writeAromaticBondTypes.isSet() && bond.getFlag(CDKConstants.ISAROMATIC))
                             bondType=4;
+                        else if (Order.QUADRUPLE  == bond.getOrder())
+                            throw new CDKException("MDL molfiles do not support quadruple bonds.");
                         else
                             bondType=(int)bond.getOrder().ordinal()+1;
                         line += formatMDLInt(bondType,3);
diff --git a/src/test/org/openscience/cdk/io/MDLWriterTest.java b/src/test/org/openscience/cdk/io/MDLWriterTest.java
index 2cc0cad7efa..5ad42503181 100644
--- a/src/test/org/openscience/cdk/io/MDLWriterTest.java
+++ b/src/test/org/openscience/cdk/io/MDLWriterTest.java
@@ -36,6 +36,7 @@
 
 import org.openscience.cdk.Atom;
 import org.openscience.cdk.AtomContainer;
+import org.openscience.cdk.Bond;
 import org.openscience.cdk.CDKConstants;
 import org.openscience.cdk.ChemFile;
 import org.openscience.cdk.ChemModel;
@@ -45,6 +46,7 @@
 import org.openscience.cdk.exception.CDKException;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IBond;
+import org.openscience.cdk.interfaces.IBond.Order;
 import org.openscience.cdk.interfaces.IChemModel;
 import org.openscience.cdk.interfaces.IChemObjectBuilder;
 import org.openscience.cdk.interfaces.IMolecule;
@@ -235,6 +237,22 @@ public class MDLWriterTest extends ChemObjectIOTest {
         Assert.assertTrue(output.indexOf("2  3  1  3  0  0  0")>-1);
     }
 
+    @Test(expected=CDKException.class)
+    public void testUnsupportedBondOrder() throws Exception {
+        Molecule molecule = new Molecule();
+        molecule.addAtom(new Atom("C"));
+        molecule.addAtom(new Atom("C"));
+        molecule.addBond(
+            new Bond(
+                molecule.getAtom(0),
+                molecule.getAtom(1),
+                Order.QUADRUPLE
+            )
+        );
+        MDLWriter mdlWriter = new MDLWriter(new StringWriter());
+        mdlWriter.write(molecule);
+    }
+
     @Test public void testTwoFragmentsWithTitle() throws CDKException{
         IMolecule mol1 = MoleculeFactory.makeAlphaPinene();
         mol1.setProperty(CDKConstants.TITLE,"title1");