Merge pull request #275 from cdk/patch/smilesisotopes

Work around historic CDK idioms with an Smiles Generator option.
johnmay · Mar 5, 2017 · 85cd52f · 85cd52f
2 parents 20c1122 + 31ae0dc
commit 85cd52f
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Showing 3 changed files with 53 additions and 10 deletions.
diff --git a/storage/smiles/src/main/java/org/openscience/cdk/smiles/CDKToBeam.java b/storage/smiles/src/main/java/org/openscience/cdk/smiles/CDKToBeam.java
@@ -162,6 +162,33 @@ static Graph toBeamGraph(IAtomContainer ac, int flavour) throws CDKException {
         return gb.build();
     }
 
+    private static Integer getMajorMassNumber(Element e) {
+        try {
+            switch (e) {
+                case Hydrogen:   return 1;
+                case Boron:      return 11;
+                case Carbon:     return 12;
+                case Nitrogen:   return 14;
+                case Oxygen:     return 16;
+                case Fluorine:   return 19;
+                case Silicon:    return 28;
+                case Phosphorus: return 31;
+                case Sulfur:     return 32;
+                case Chlorine:   return 35;
+                case Iodine:     return 127;
+                default:
+                    IsotopeFactory isotopes = Isotopes.getInstance();
+                    IIsotope       isotope  = isotopes.getMajorIsotope(e.symbol());
+                    if (isotope != null)
+                        return isotope.getMassNumber();
+                    return null;
+            }
+
+        } catch (IOException ex) {
+            throw new InternalError("Isotope factory wouldn't load: " + ex.getMessage());
+        }
+    }
+
     /**
      * Convert an CDK {@link IAtom} to a Beam Atom. The symbol and implicit
      * hydrogen count are not optional. If the symbol is not supported by the
@@ -195,17 +222,12 @@ static Atom toBeamAtom(final IAtom a, final int flavour) {
         if (charge != null) ab.charge(charge);
 
         // use the mass number to specify isotope?
-        if (SmiFlavor.isSet(flavour, SmiFlavor.AtomicMass)) {
+        if (SmiFlavor.isSet(flavour, SmiFlavor.AtomicMass | SmiFlavor.AtomicMassStrict)) {
             Integer massNumber = a.getMassNumber();
             if (massNumber != null) {
-                // XXX: likely causing some overhead but okay for now
-                try {
-                    IsotopeFactory isotopes = Isotopes.getInstance();
-                    IIsotope isotope = isotopes.getMajorIsotope(a.getSymbol());
-                    if (isotope == null || !isotope.getMassNumber().equals(massNumber)) ab.isotope(massNumber);
-                } catch (IOException e) {
-                    throw new InternalError("Isotope factory wouldn't load: " + e.getMessage());
-                }
+                if (SmiFlavor.isSet(flavour, SmiFlavor.AtomicMassStrict) ||
+                        !massNumber.equals(getMajorMassNumber(element)))
+                    ab.isotope(massNumber);
             }
         }
 

diff --git a/storage/smiles/src/main/java/org/openscience/cdk/smiles/SmiFlavor.java b/storage/smiles/src/main/java/org/openscience/cdk/smiles/SmiFlavor.java
@@ -55,7 +55,12 @@ private SmiFlavor() {
     public static final int AtomAtomMap        = 0x004;
 
     /**
-     * Output atomic mass on atoms.
+     * Output atomic mass on atoms. For historical reasons the atomic mass is
+     * often set on all atoms in a CDK molecule. Therefore to avoid SMILES like
+     * {@code [12CH3][12CH2][16OH]} major isotopes are not generated. If you
+     * wish to generate SMILES with the major isotopes please use the flag
+     * {@link #AtomicMassStrict} this will output all mass numbers and only be
+     * omitted when the mass is unset (null).
      */
     public static final int AtomicMass         = 0x008;
 
@@ -88,6 +93,13 @@ private SmiFlavor() {
      */
     public static final int StereoExTetrahedral = 0x400;
 
+    /**
+     * Generate SMILES with the major isotopes, only omit mass numbers when it
+     * is unset.
+     */
+    public static final int AtomicMassStrict   = 0x800;
+
+
     /**
      * Output supported stereochemistry types.
      * @see #StereoTetrahedral

diff --git a/storage/smiles/src/test/java/org/openscience/cdk/smiles/SmilesGeneratorTest.java b/storage/smiles/src/test/java/org/openscience/cdk/smiles/SmilesGeneratorTest.java
@@ -49,6 +49,7 @@
 import org.openscience.cdk.config.Elements;
 import org.openscience.cdk.config.IsotopeFactory;
 import org.openscience.cdk.exception.CDKException;
+import org.openscience.cdk.exception.InvalidSmilesException;
 import org.openscience.cdk.graph.AtomContainerAtomPermutor;
 import org.openscience.cdk.graph.AtomContainerBondPermutor;
 import org.openscience.cdk.graph.Cycles;
@@ -1238,6 +1239,14 @@ public void inconsistentAromaticState() throws Exception {
         smigen.create(mol);
     }
 
+    @Test
+    public void strictIsotopes() throws CDKException {
+        SmilesParser smipar = new SmilesParser(SilentChemObjectBuilder.getInstance());
+        IAtomContainer mol = smipar.parseSmiles("[12CH3]C");
+        assertThat(new SmilesGenerator(SmiFlavor.AtomicMassStrict).create(mol), is("[12CH3]C"));
+        assertThat(new SmilesGenerator(SmiFlavor.AtomicMass).create(mol), is("CC"));
+    }
+
     static ITetrahedralChirality anticlockwise(IAtomContainer container, int central, int a1, int a2, int a3, int a4) {
         return new TetrahedralChirality(container.getAtom(central), new IAtom[]{container.getAtom(a1),
                                                                                 container.getAtom(a2), container.getAtom(a3), container.getAtom(a4)},