return the matching isotope closest to the provided exact mass

Change-Id: I842af6599bc25ebfab9b6f1f7a150973c8e253c3 Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
cdk · Mar 24, 2013 · e69c387 · e69c387
1 parent 8e9243e
commit e69c387
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Showing 2 changed files with 17 additions and 6 deletions.
diff --git a/src/main/org/openscience/cdk/config/IsotopeFactory.java b/src/main/org/openscience/cdk/config/IsotopeFactory.java
@@ -196,26 +196,29 @@ public IIsotope getIsotope(String symbol, int massNumber) {
     /**
      * Get an isotope based on the element symbol and exact mass.
      *
-     * @param symbol the element symbol
-     * @param massNumber the mass number
+     * @param symbol    the element symbol
+     * @param exactMass the mass number
+     * @param tolerance allowed difference from provided exact mass
      * @return the corresponding isotope
      */
     @TestMethod("testGetIsotopeFromExactMass")
     public IIsotope getIsotope(String symbol, double exactMass, double tolerance) {
-        IIsotope ret = null;
+        IIsotope ret     = null;
+        double   minDiff = Double.MAX_VALUE;
         for (IIsotope isotope : isotopes) {
+            double diff = Math.abs(isotope.getExactMass() - exactMass);
             if (isotope.getSymbol().equals(symbol) &&
-            	Math.abs(isotope.getExactMass() - exactMass) <= tolerance) {
+            	diff <= tolerance && diff < minDiff) {
                 try {
                     ret = (IIsotope) isotope.clone();
+                    minDiff = diff;
                 } catch (CloneNotSupportedException e) {
                     logger.error("Could not clone IIsotope: ", e.getMessage());
                     logger.debug(e);
                 }
-                return ret;
             }
         }
-        return null;
+        return ret;
     }
 
     /**

diff --git a/src/test/org/openscience/cdk/config/IsotopeFactoryTest.java b/src/test/org/openscience/cdk/config/IsotopeFactoryTest.java
@@ -318,6 +318,14 @@ public void warning(SAXParseException arg0) throws SAXException {
         Assert.assertNull(match);
     }
 
+    @Test public void testGetIsotopeFromExactMass_LargeTolerance() throws Exception {
+        IsotopeFactory isofac = IsotopeFactory.getInstance(new ChemObject().getBuilder());
+        IIsotope carbon13 = isofac.getIsotope("C", 13);
+        IIsotope match = isofac.getIsotope(carbon13.getSymbol(), carbon13.getExactMass(), 2.0);
+        Assert.assertNotNull(match);
+        Assert.assertEquals(13, match.getMassNumber().intValue());
+    }
+
     /**
      * @cdk.bug 3534288
      */