Utility to methods to clear any mass numbers that are determined to t…

…he be the major isotope.
cdk · May 29, 2018 · 0b19b79 · 0b19b79
1 parent 21a0f5b
commit 0b19b79
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Showing 3 changed files with 80 additions and 3 deletions.
diff --git a/base/core/src/main/java/org/openscience/cdk/config/Isotopes.java b/base/core/src/main/java/org/openscience/cdk/config/Isotopes.java
@@ -32,7 +32,13 @@
 import java.util.HashMap;
 import java.util.List;
 
+import com.google.common.collect.FluentIterable;
+import org.openscience.cdk.interfaces.IAtom;
+import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IIsotope;
+import org.openscience.cdk.interfaces.IMolecularFormula;
+import org.openscience.cdk.tools.ILoggingTool;
+import org.openscience.cdk.tools.LoggingToolFactory;
 import org.openscience.cdk.tools.periodictable.PeriodicTable;
 
 /**
@@ -51,6 +57,9 @@
  */
 public class Isotopes extends IsotopeFactory {
 
+    private static final ILoggingTool logger =
+        LoggingToolFactory.createLoggingTool(Isotopes.class);
+
     private static Isotopes myself = null;
 
     /**
@@ -85,4 +94,56 @@ private Isotopes() throws IOException {
             add(isotope);
         }
     }
+
+    private static boolean isMajor(IIsotope atom) {
+        Integer mass = atom.getMassNumber();
+        if (mass == null)
+            return false;
+        try {
+            Isotopes instance = Isotopes.getInstance();
+            IIsotope major = instance.getMajorIsotope(atom.getAtomicNumber());
+            if (major == null)
+                return false; // no major isotope
+            return major.getMassNumber().equals(mass);
+        } catch (IOException e) {
+            logger.error("Could not load Isotope data: ", e.getMessage());
+            return false;
+        }
+    }
+
+    /**
+     * Clear the isotope information from atoms that are major isotopes (e.g.
+     * 12C, 1H, etc).
+     * @param mol the molecule
+     */
+    public static void clearMajorIsotopes(IAtomContainer mol) {
+        for (IAtom atom : mol.atoms())
+            if (isMajor(atom)) {
+                atom.setMassNumber(null);
+                atom.setExactMass(null);
+                atom.setNaturalAbundance(null);
+            }
+    }
+
+    /**
+     * Clear the isotope information from istopes that are major (e.g.
+     * 12C, 1H, etc).
+     * @param formula the formula
+     */
+    public static void clearMajorIsotopes(IMolecularFormula formula) {
+        for (IIsotope iso : FluentIterable.from(formula.isotopes()).toList())
+            if (isMajor(iso)) {
+                int count = formula.getIsotopeCount(iso);
+                formula.removeIsotope(iso);
+                iso.setMassNumber(null);
+                // may be immutable
+                if (iso.getMassNumber() != null) {
+                    iso = formula.getBuilder().newInstance(IIsotope.class, iso.getSymbol());
+                    iso.setAtomicNumber(iso.getAtomicNumber());
+                }
+                iso.setExactMass(null);
+                iso.setNaturalAbundance(null);
+                formula.addIsotope(iso, count);
+            }
+    }
 }
diff --git a/...mula/src/main/java/org/openscience/cdk/tools/manipulator/MolecularFormulaManipulator.java b/...mula/src/main/java/org/openscience/cdk/tools/manipulator/MolecularFormulaManipulator.java
@@ -201,8 +201,8 @@ private static void appendElement(StringBuilder sb, Integer mass, int elem, int
         if (mass != null)
             sb.append('[')
               .append(mass)
-              .append(Elements.ofNumber(elem).symbol())
-              .append(']');
+              .append(']')
+              .append(Elements.ofNumber(elem).symbol());
         else
             sb.append(Elements.ofNumber(elem).symbol());
         if (count != 0)

diff --git a/.../src/test/java/org/openscience/cdk/tools/manipulator/MolecularFormulaManipulatorTest.java b/.../src/test/java/org/openscience/cdk/tools/manipulator/MolecularFormulaManipulatorTest.java
@@ -1336,7 +1336,23 @@ public void testImplicitH() throws Exception {
         mf.addIsotope(ifac.getIsotope("Br", 81), 1);
 
         assertThat(MolecularFormulaManipulator.getString(mf, false, false), is("C7H3Br2O3"));
-        assertThat(MolecularFormulaManipulator.getString(mf, false, true), is("C7H3[81Br]BrO3"));
+        assertThat(MolecularFormulaManipulator.getString(mf, false, true), is("C7H3[81]BrBrO3"));
     }
 
+    @Test
+    public void testMassNumberDisplayWithDefinedIsotopes() throws Exception {
+        IsotopeFactory ifac = Isotopes.getInstance();
+
+        IChemObjectBuilder bldr = SilentChemObjectBuilder.getInstance();
+        IMolecularFormula mf = bldr.newInstance(IMolecularFormula.class);
+
+        mf.addIsotope(ifac.getMajorIsotope("C"), 7);
+        mf.addIsotope(ifac.getMajorIsotope("O"), 3);
+        mf.addIsotope(ifac.getMajorIsotope("H"), 3);
+        mf.addIsotope(ifac.getMajorIsotope("Br"), 1);
+        mf.addIsotope(ifac.getIsotope("Br", 81), 1);
+        Isotopes.clearMajorIsotopes(mf);
+        assertThat(MolecularFormulaManipulator.getString(mf, false, false), is("C7H3Br2O3"));
+        assertThat(MolecularFormulaManipulator.getString(mf, false, true), is("C7H3Br[81]BrO3"));
+    }
 }