Added ability to read atom parity from Mol files (inc. junit test).

cdk · Feb 19, 2012 · 07bbbb2 · 07bbbb2
1 parent fb47c57
commit 07bbbb2
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diff --git a/src/main/org/openscience/cdk/io/MDLV2000Reader.java b/src/main/org/openscience/cdk/io/MDLV2000Reader.java
@@ -518,6 +518,11 @@ private IMolecule readMolecule(IMolecule molecule) throws CDKException {
                     logger.error("Cannot set mass difference for a non-element!");
                 }
 
+
+                // set the stereo partiy
+                Integer parity = line.length() > 41 ? Character.digit(line.charAt(41), 10) : 0;                                
+                atom.setStereoParity(parity);
+
                 if (line.length() >= 51) {
                     String valenceString = removeNonDigits(line.substring(48,51));
                     logger.debug("Valence: ", valenceString);

diff --git a/src/test/data/mdl/mol_testAtomParity.mol b/src/test/data/mdl/mol_testAtomParity.mol
@@ -0,0 +1,16 @@
+
+  Mrv0541 01311217092D          
+
+  6  5  0  0  0  0            999 V2000
+   -1.1749    0.1436    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
+   -0.7624    0.8581    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.7624   -0.5709    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.1749    1.5726    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0626    0.8581    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.9999    0.1436    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0  0  0  0
+  1  3  1  1  0  0  0
+  2  4  2  0  0  0  0
+  2  5  1  0  0  0  0
+  1  6  1  0  0  0  0
+M  END
diff --git a/src/test/org/openscience/cdk/io/MDLV2000ReaderTest.java b/src/test/org/openscience/cdk/io/MDLV2000ReaderTest.java
@@ -919,4 +919,25 @@ public void testPseudoAtomLabels() throws Exception {
         Assert.assertEquals("Gln", pa.getLabel());
     }
 
+    @Test
+    public void testAtomParity() throws CDKException{
+
+        InputStream in = ClassLoader.getSystemResourceAsStream("data/mdl/mol_testAtomParity.mol");
+        MDLV2000Reader reader = new MDLV2000Reader(in);
+        IAtomContainer molecule = DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainer.class);
+        reader.read(molecule);
+
+        boolean chiralCentre = false;
+        IAtom[] atoms = AtomContainerManipulator.getAtomArray(molecule);
+        for (IAtom atom : atoms) {
+            Integer parity = atom.getStereoParity();
+            if(parity == 1){
+                chiralCentre = true;
+            }
+        }
+
+        Assert.assertTrue(chiralCentre);
+
+    }
+
 }