Mask hydrogens in canonical labelling.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
cdk · Jul 15, 2014 · 17a518e · 17a518e
1 parent 5b4c073
commit 17a518e
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diff --git a/base/standard/src/main/java/org/openscience/cdk/graph/invariant/Canon.java b/base/standard/src/main/java/org/openscience/cdk/graph/invariant/Canon.java
@@ -354,6 +354,25 @@ private static int charge(IAtom atom) {
         return 0;
     }
 
+    /**
+     * Locate explicit hydrogens that are attached to exactly one other atom.
+     *
+     * @param ac a structure
+     * @return binary set of terminal hydrogens
+     */
+    static boolean[] terminalHydrogens(final IAtomContainer ac, final int[][] g) {
+
+        final boolean[] hydrogens = new boolean[ac.getAtomCount()];
+
+        // we specifically don't check for null atomic number, this must be set.
+        // if not, something major is wrong
+        for (int i = 0; i < ac.getAtomCount(); i++) {
+            hydrogens[i] = ac.getAtom(i).getAtomicNumber() == 1 && g[i].length == 1;
+        }
+
+        return hydrogens;
+    }
+
     /** The first 2229 primes. */
     private static final int[] PRIMES = {2, 3, 5, 7, 11, 13, 17, 19, 23, 29, 31, 37, 41, 43, 47, 53, 59, 61, 67, 71, 73,
                                          79, 83, 89, 97, 101, 103, 107, 109, 113, 127, 131, 137, 139, 149, 151, 157, 163,

diff --git a/base/test-standard/src/test/java/org/openscience/cdk/graph/invariant/CanonTest.java b/base/test-standard/src/test/java/org/openscience/cdk/graph/invariant/CanonTest.java
@@ -82,6 +82,31 @@ public class CanonTest {
         assertThat(act, is(exp));
     }
 
+    @Test public void terminalExplicitHydrogensAreNotIncluded() throws Exception {
+        IAtomContainer m    = smi("C/C=C(/C)C[H]");
+        boolean[]      mask = Canon.terminalHydrogens(m, GraphUtil.toAdjList(m));
+        assertThat(mask, is(new boolean[]{false, false, false, false, false, true}));
+    }
+
+    @Test public void bridgingExplicitHydrogensAreIncluded() throws Exception {
+        IAtomContainer m    = smi("B1[H]B[H]1");
+        boolean[]      mask = Canon.terminalHydrogens(m, GraphUtil.toAdjList(m));
+        assertThat(mask, is(new boolean[]{false, false, false, false}));
+    }
+
+    @Test public void explicitHydrogensIonsAreIncluded() throws Exception {
+        IAtomContainer m    = smi("[H+]");
+        boolean[]      mask = Canon.terminalHydrogens(m, GraphUtil.toAdjList(m));
+        assertThat(mask, is(new boolean[]{false}));
+    }
+
+    @Test public void molecularHydrogensAreNotIncluded() throws Exception {
+        IAtomContainer m    = smi("[H][H]");
+        boolean[]      mask = Canon.terminalHydrogens(m, GraphUtil.toAdjList(m));
+        assertThat(mask, is(new boolean[]{true, true}));
+    }
+
+
     static final SmilesParser sp = new SmilesParser(SilentChemObjectBuilder.getInstance());
 
     static IAtomContainer smi(String smi) throws Exception {