Write atom parity

Writes the atom stereo parity for MDLV2000 format
cdk · Feb 19, 2012 · c7aa428 · c7aa428
1 parent 8ff4584
commit c7aa428
Show file tree

Hide file tree

Showing 2 changed files with 21 additions and 2 deletions.
diff --git a/src/main/org/openscience/cdk/io/MDLV2000Writer.java b/src/main/org/openscience/cdk/io/MDLV2000Writer.java
@@ -322,7 +322,7 @@ public void writeMolecule(IAtomContainer container) throws Exception {
         	}else{
         		line += formatMDLString(container.getAtom(f).getSymbol(), 3);
         	}
-        	line += " 0  0  0  0  0";
+        	line += String.format(" 0  0  %d  0  0", atom.getStereoParity() == null ? 0 : atom.getStereoParity());
         	if (writeQueryFormatValencies.isSet() &&
         	    atom.getValency() != (Integer)CDKConstants.UNSET) {
         	    // valence 0 is defined as 15 in mol files - but this writer

diff --git a/src/test/org/openscience/cdk/io/MDLV2000WriterTest.java b/src/test/org/openscience/cdk/io/MDLV2000WriterTest.java
@@ -23,7 +23,7 @@
  */
 package org.openscience.cdk.io;
 
-
+import java.io.IOException;
 import java.io.InputStream;
 import java.io.StringWriter;
 import java.util.Properties;
@@ -359,6 +359,25 @@ public void testUnsupportedBondOrder() throws Exception {
         mdlWriter.write(benzene);
         Assert.assertTrue(writer.toString().indexOf("2  1  4  0  0  0  0") != -1);
     }
+
+    @Test
+    public void testAtomParity() throws CDKException, IOException{
+
+        InputStream in = ClassLoader.getSystemResourceAsStream("data/mdl/mol_testAtomParity.mol");
+        MDLV2000Reader reader = new MDLV2000Reader(in);
+        IAtomContainer molecule = DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainer.class);
+        reader.read(molecule);
+        reader.close();
+
+        StringWriter sw =new StringWriter();
+        MDLV2000Writer writer = new MDLV2000Writer(sw);
+        writer.write(molecule);
+        writer.close();
+
+        Assert.assertTrue(writer.toString().contains("   -1.1749    0.1436    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0"));              
+
+
+    }
 
     @Test
     public void testWritePseudoAtoms() throws Exception {