Improved behaviour of badly specified isotopes, we can do a bit better than returning 0.

johnmay · johnmay · commit edb39b09dfd7 · 2021-04-29T11:24:29.000+01:00
diff --git a/base/core/src/main/java/org/openscience/cdk/config/IsotopeFactory.java b/base/core/src/main/java/org/openscience/cdk/config/IsotopeFactory.java
@@ -230,7 +230,7 @@ public IIsotope getMajorIsotope(int elem) {
 
     /**
      * Get the mass of the most abundant (major) isotope, if there is no
-     * major isotopes 0 is returned.
+     * major isotopes 2*elem is returned.
      *
      * @param elem the atomic number
      * @return the major isotope mass
@@ -239,11 +239,17 @@ public double getMajorIsotopeMass(int elem) {
         if (this.majorIsotope[elem] != null)
             return this.majorIsotope[elem].getExactMass();
         IIsotope major = getMajorIsotope(elem);
-        return major != null ? major.getExactMass() : 0;
+        if (major == null) {
+            logger.warn("No major isotope for elem" + elem);
+            return 2*elem;
+        }
+        return major.getExactMass();
     }
 
     /**
-     * Get the exact mass of a specified isotope for an atom.
+     * Get the exact mass of a specified isotope for an atom. If there is no isotope with that
+     * mass number then it is returned.
+     *
      * @param atomicNumber atomic number
      * @param massNumber the mass number
      * @return the exact mass
@@ -255,7 +261,7 @@ public double getExactMass(Integer atomicNumber, Integer massNumber) {
             if (isotope.getMassNumber().equals(massNumber))
                 return isotope.getExactMass();
         }
-        return 0;
+        return massNumber;
     }
 
     private IIsotope clone(IIsotope isotope) {
diff --git a/base/test-standard/src/test/java/org/openscience/cdk/tools/manipulator/AtomContainerManipulatorTest.java b/base/test-standard/src/test/java/org/openscience/cdk/tools/manipulator/AtomContainerManipulatorTest.java
@@ -1387,6 +1387,19 @@ static void assertAddH(String smiIn, String smiExp) throws Exception {
                    closeTo(4729.147, 0.001));
     }
 
+    @Test public void getMassBadIsotopes() throws InvalidSmilesException {
+        IChemObjectBuilder bldr = SilentChemObjectBuilder.getInstance();
+        IAtomContainer mol = new SmilesParser(bldr).parseSmiles("[24cH]1[24cH][24cH][24cH][24cH][24cH]1");
+        assertThat(AtomContainerManipulator.getMass(mol, MolWeight),
+                closeTo(150.0476, 0.001));
+        assertThat(AtomContainerManipulator.getMass(mol, MolWeightIgnoreSpecified),
+                closeTo(78.1120, 0.001));
+        assertThat(AtomContainerManipulator.getMass(mol, MonoIsotopic),
+                closeTo(150.0469, 0.001));
+        assertThat(AtomContainerManipulator.getMass(mol, MostAbundant),
+                closeTo(150.0469, 0.001));
+    }
+
     @Test public void getMassCranbinSpecIsotopes() {
         IChemObjectBuilder bldr = SilentChemObjectBuilder.getInstance();
         IAtomContainer mol =
