Merge branch 'master' of ssh://cdk.git.sourceforge.net/gitroot/cdk/cdk

src/main/org/openscience/cdk/io/MDLWriter.java

@@ -86,6 +86,9 @@ public class MDLWriter extends DefaultChemObjectWriter {
         LoggingToolFactory.createLoggingTool(MDLWriter.class);
 
     private BooleanIOSetting forceWriteAs2DCoords;
+
+    /* Should aromatic bonds be written as bond type 4? If true, this makes the output a query file. */
+    private BooleanIOSetting writeAromaticBondTypes;
 
     private BufferedWriter writer;
 
@@ -324,7 +327,7 @@ else if(atom.getValency()==0)
         // write Bond block
         Iterator<IBond> bonds = container.bonds().iterator();
         while (bonds.hasNext()) {
-            IBond bond = (IBond) bonds.next();
+            IBond bond = bonds.next();
 
         	if (bond.getAtomCount() != 2) {
         		logger.warn("Skipping bond with more/less than two atoms: " + bond);
@@ -339,7 +342,13 @@ else if(atom.getValency()==0)
         			line = formatMDLInt(container.getAtomNumber(bond.getAtom(0)) + 1,3);
         			line += formatMDLInt(container.getAtomNumber(bond.getAtom(1)) + 1,3);
         		}
-        		line += formatMDLInt((int)bond.getOrder().ordinal()+1,3);
+                        int bondType;
+                        if (writeAromaticBondTypes.isSet() && bond.getFlag(CDKConstants.ISAROMATIC))
+                            bondType=4;
+                        else
+                            bondType=(int)bond.getOrder().ordinal()+1;
+                        line += formatMDLInt(bondType,3);
+
         		line += "  ";
         		switch(bond.getStereo()){
         		case UP:
@@ -513,26 +522,39 @@ protected static String formatMDLString(String s, int le) {
             s += " ";
         return s;
     }
-
+
+    /**
+     * Initializes IO settings.<br>
+     * Please note with regards to "writeAromaticBondTypes": bond type values 4 through 8 are for SSS queries only,
+     * so a 'query file' is created if the container has aromatic bonds and this settings is true.
+     */
     private void initIOSettings() {
         forceWriteAs2DCoords = new BooleanIOSetting(
             "ForceWriteAs2DCoordinates",
             IOSetting.LOW,
             "Should coordinates always be written as 2D?",
             "false"
         );
+        writeAromaticBondTypes = new BooleanIOSetting(
+            "WriteAromaticBondTypes",
+            IOSetting.LOW,
+            "Should aromatic bonds be written as bond type 4?",
+            "false"
+        );
     }
 
     public void customizeJob() {
         fireIOSettingQuestion(forceWriteAs2DCoords);
+        fireIOSettingQuestion(writeAromaticBondTypes);
+
     }
 
     public IOSetting[] getIOSettings() {
-        IOSetting[] settings = new IOSetting[1];
+        IOSetting[] settings = new IOSetting[2];
         settings[0] = forceWriteAs2DCoords;
+        settings[1] = writeAromaticBondTypes;
         return settings;
     }
-
 }
 
 

src/test/org/openscience/cdk/io/MDLWriterTest.java

@@ -24,6 +24,7 @@
 package org.openscience.cdk.io;
 
 import java.io.StringWriter;
+
 import java.util.Properties;
 
 import javax.vecmath.Point2d;
@@ -32,6 +33,7 @@
 import org.junit.Assert;
 import org.junit.BeforeClass;
 import org.junit.Test;
+
 import org.openscience.cdk.Atom;
 import org.openscience.cdk.AtomContainer;
 import org.openscience.cdk.CDKConstants;
@@ -49,8 +51,11 @@
 import org.openscience.cdk.interfaces.IMoleculeSet;
 import org.openscience.cdk.interfaces.IPseudoAtom;
 import org.openscience.cdk.io.listener.PropertiesListener;
+import org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder;
+import org.openscience.cdk.smiles.SmilesParser;
 import org.openscience.cdk.templates.MoleculeFactory;
 
+
 /**
  * TestCase for the writer MDL mol files using one test file.
  *
@@ -297,11 +302,38 @@ public class MDLWriterTest extends ChemObjectIOTest {
         StringWriter writer = new StringWriter();
         MDLWriter mdlWriter = new MDLWriter(writer);
         mdlWriter.write(molecule);
-        System.out.println(writer.toString());
 
         Assert.assertTrue(writer.toString().indexOf("V    1 Oxygen comment") != -1);
         Assert.assertTrue(writer.toString().indexOf("V    2 Carbon comment") != -1);
 
     }
+
+    /**
+     * Test option to write aromatic bonds with bond type "4".
+     * Please note: bond type values 4 through 8 are for SSS queries only.
+     * @throws Exception
+     */
+    @Test public void testAromaticBondType4() throws Exception {
+        SmilesParser sp = new SmilesParser(NoNotificationChemObjectBuilder.getInstance());
+        String smiles = "c1ccccc1";
+        IMolecule benzene = sp.parseSmiles(smiles);
+
 
+        StringWriter writer = new StringWriter();
+        MDLWriter mdlWriter = new MDLWriter(writer);
+        mdlWriter.write(benzene);
+        Assert.assertTrue(writer.toString().indexOf("2  1  1  0  0  0  0") != -1);
+
+
+        writer = new StringWriter();
+        mdlWriter = new MDLWriter(writer);
+        Properties prop = new Properties();
+        prop.setProperty("WriteAromaticBondTypes","true");
+        PropertiesListener listener = new PropertiesListener(prop);
+        mdlWriter.addChemObjectIOListener(listener);
+        mdlWriter.customizeJob();
+        mdlWriter.write(benzene);
+        Assert.assertTrue(writer.toString().indexOf("2  1  4  0  0  0  0") != -1);
+    }
+
 }