SMARTS mass matching semantics, 0 = unspecified. Attempting to update…

… the grammar was not successful.
cdk · Mar 30, 2017 · 5728eea · 5728eea
1 parent dec3e14
commit 5728eea
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Showing 2 changed files with 35 additions and 3 deletions.
diff --git a/tool/smarts/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/MassAtom.java b/tool/smarts/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/MassAtom.java
@@ -34,14 +34,17 @@
  */
 public class MassAtom extends SMARTSAtom {
 
+    private final int mass;
+
     /**
      * Creates a new instance
      *
      * @param mass
      */
     public MassAtom(int mass, IChemObjectBuilder builder) {
         super(builder);
-        this.setMassNumber(mass);
+        setMassNumber(mass);
+        this.mass = mass;
     }
 
     /*
@@ -52,7 +55,10 @@ public MassAtom(int mass, IChemObjectBuilder builder) {
      */
     @Override
     public boolean matches(IAtom atom) {
-        return atom.getMassNumber() == this.getMassNumber();
+        if (mass == 0)
+            return atom.getMassNumber() == null;
+        else
+            return atom.getMassNumber() != null && mass == atom.getMassNumber();
     }
 
     /*
@@ -61,7 +67,7 @@ public boolean matches(IAtom atom) {
      */
     @Override
     public String toString() {
-        return ("(MassAtom(" + this.getMassNumber() + ")");
+        return ("(MassAtom(" + mass + ")");
     }
 
 }
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
@@ -86,6 +86,32 @@ public void ringSizeOrNumber_ringSize() throws Exception {
         assertTrue(SmartsPattern.ringSizeOrNumber("[r5]"));
     }
 
+    @Test
+    public void isotopes() throws Exception {
+        // FIXME SMARTS Grammar needs fixing/replacing [12] is not considered valid
+
+        assertFalse(SmartsPattern.create("[12*]", bldr).matches(smi("C")));
+        assertFalse(SmartsPattern.create("[12*]", bldr).matches(smi("[CH4]")));
+        assertTrue(SmartsPattern.create("[12*]", bldr).matches(smi("[12CH4]")));
+        assertFalse(SmartsPattern.create("[12*]", bldr).matches(smi("[13CH4]")));
+
+        assertFalse(SmartsPattern.create("[13*]", bldr).matches(smi("C")));
+        assertFalse(SmartsPattern.create("[13*]", bldr).matches(smi("[CH4]")));
+        assertFalse(SmartsPattern.create("[13*]", bldr).matches(smi("[12CH4]")));
+        assertTrue(SmartsPattern.create("[13*]", bldr).matches(smi("[13CH4]")));
+
+        assertTrue(SmartsPattern.create("[0*]", bldr).matches(smi("C")));
+        assertTrue(SmartsPattern.create("[0*]", bldr).matches(smi("[CH4]")));
+        assertFalse(SmartsPattern.create("[0*]", bldr).matches(smi("[12CH4]")));
+        assertFalse(SmartsPattern.create("[0*]", bldr).matches(smi("[13CH4]")));
+
+//      Not possible with current grammar
+//        assertFalse(SmartsPattern.create("[!0*]", bldr).matches(smi("C")));
+//        assertFalse(SmartsPattern.create("[!0*]", bldr).matches(smi("[CH4]")));
+//        assertTrue(SmartsPattern.create("[!0*]", bldr).matches(smi("[12CH4]")));
+//        assertTrue(SmartsPattern.create("[!0*]", bldr).matches(smi("[13CH4]")));
+    }
+
     @Test
     public void components() throws Exception {
         assertTrue(SmartsPattern.create("(O).(O)", bldr).matches(smi("O.O")));