Deprecate defunct SMILES flag now the core library invariants are bet…

…ter.
cdk · Jun 7, 2017 · f8e1a80 · f8e1a80
1 parent b197fbf
commit f8e1a80
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Showing 5 changed files with 16 additions and 6 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
@@ -225,9 +225,7 @@ static Atom toBeamAtom(final IAtom a, final int flavour) {
         if (SmiFlavor.isSet(flavour, SmiFlavor.AtomicMass | SmiFlavor.AtomicMassStrict)) {
             Integer massNumber = a.getMassNumber();
             if (massNumber != null) {
-                if (SmiFlavor.isSet(flavour, SmiFlavor.AtomicMassStrict) ||
-                        !massNumber.equals(getMajorMassNumber(element)))
-                    ab.isotope(massNumber);
+                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
@@ -96,7 +96,10 @@ private SmiFlavor() {
     /**
      * Generate SMILES with the major isotopes, only omit mass numbers when it
      * is unset.
+     * @deprecated no longer needed, default CDK behaviour is now to pass
+     *             through mass numbers if non-null
      */
+    @Deprecated
     public static final int AtomicMassStrict   = 0x800;
 
 

diff --git a/storage/smiles/src/test/java/org/openscience/cdk/smiles/CDKToBeamTest.java b/storage/smiles/src/test/java/org/openscience/cdk/smiles/CDKToBeamTest.java
@@ -154,11 +154,11 @@ public void specifiedIsotope() throws Exception {
     }
 
     @Test
-    public void defaultIsotope() throws Exception {
+    public void noDefaultIsotope() throws Exception {
         IAtom a = new Atom("C");
         a.setImplicitHydrogenCount(0);
         a.setMassNumber(12);
-        assertThat(new CDKToBeam().toBeamAtom(a).isotope(), is(-1));
+        assertThat(new CDKToBeam().toBeamAtom(a).isotope(), is(12));
     }
 
     // special check that a CDK pseudo atom will default to 0 hydrogens if

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
@@ -1243,7 +1243,13 @@ 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"));
+    }
+
+    @Test
+    public void isotopes() throws CDKException {
+        SmilesParser smipar = new SmilesParser(SilentChemObjectBuilder.getInstance());
+        IAtomContainer mol = smipar.parseSmiles("[12CH3]C");
+        assertThat(new SmilesGenerator(SmiFlavor.AtomicMass).create(mol), is("[12CH3]C"));
     }
 
     static ITetrahedralChirality anticlockwise(IAtomContainer container, int central, int a1, int a2, int a3, int a4) {

diff --git a/tool/smarts/src/test/java/org/openscience/cdk/smiles/smarts/SmartsPatternTest.java b/tool/smarts/src/test/java/org/openscience/cdk/smiles/smarts/SmartsPatternTest.java
@@ -26,13 +26,16 @@
 
 import org.junit.Ignore;
 import org.junit.Test;
+import org.openscience.cdk.exception.InvalidSmilesException;
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IChemObjectBuilder;
 import org.openscience.cdk.interfaces.IReaction;
 import org.openscience.cdk.isomorphism.Pattern;
 import org.openscience.cdk.silent.SilentChemObjectBuilder;
 import org.openscience.cdk.smiles.SmilesParser;
 
+import java.io.IOException;
+
 import static org.hamcrest.CoreMatchers.is;
 import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertThat;