Additional test for converting "Molecules" to queries using the useful SMARTS therom: D=X+h.

johnmay · egonw · commit 064b0a3caa94 · 2021-12-16T07:24:25.000+01:00
diff --git a/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/QueryAtomContainer.java b/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/QueryAtomContainer.java
@@ -1794,7 +1794,14 @@ public static void create(IAtomContainer dst,
                 if (optset.contains(IS_IN_CHAIN) && !atom.isInRing())
                     expr.and(new Expr(IS_IN_CHAIN));
                 if (optset.contains(IMPL_H_COUNT))
-                    expr.and(new Expr(IMPL_H_COUNT));
+                    expr.and(new Expr(IMPL_H_COUNT, atom.getImplicitHydrogenCount()));
+                if (optset.contains(TOTAL_H_COUNT)) {
+                    int hcount = atom.getImplicitHydrogenCount();
+                    for (IBond bond : src.getConnectedBondsList(atom))
+                        if (bond.getOther(atom).getAtomicNumber() == AtomRef.H)
+                            hcount++;
+                    expr.and(new Expr(TOTAL_H_COUNT, hcount));
+                }
                 if (optset.contains(RING_BOND_COUNT)) {
                     int rbonds = 0;
                     for (IBond bond : src.getConnectedBondsList(atom))
diff --git a/tool/smarts/src/test/java/org/openscience/cdk/smarts/MolToQueryTest.java b/tool/smarts/src/test/java/org/openscience/cdk/smarts/MolToQueryTest.java
@@ -94,6 +94,18 @@ public void elementAndConnectivityDegree() throws InvalidSmilesException {
                 Expr.Type.ELEMENT, Expr.Type.TOTAL_DEGREE);
     }
 
+    @Test
+    public void elementAndConnectivityAndTotHydrogenCount() throws InvalidSmilesException {
+        test("[#6X3H1]1~[#6X3H1]~[#6X3H1]~[#6X3H1]~[#7X2H0]~[#6X3H0]~1~[#6X4H3]", "c1cccnc1C",
+                Expr.Type.ELEMENT, Expr.Type.TOTAL_DEGREE, Expr.Type.TOTAL_H_COUNT);
+    }
+
+    @Test
+    public void elementAndConnectivityAndImplHydrogenCount() throws InvalidSmilesException {
+        test("[#6X3h1]1~[#6X3h1]~[#6X3h1]~[#6X3h1]~[#7X2h0]~[#6X3h0]~1~[#6X4h3]", "c1cccnc1C",
+                Expr.Type.ELEMENT, Expr.Type.TOTAL_DEGREE, Expr.Type.IMPL_H_COUNT);
+    }
+
     @Test
     public void complexDocExample() throws InvalidSmilesException {
         test("[nx2+0]1:[cx2+0]:[cx2+0]:[cx2+0](=[O&x0+0]):[cx2+0]:[cx2+0]:1",
