Keep atomic number of alias elements in molfile.

johnmay · johnmay · commit fdce829e4a65 · 2019-11-26T18:46:08.000Z
diff --git a/base/testdata/src/test/resources/data/mdl/element-with-alias.mol b/base/testdata/src/test/resources/data/mdl/element-with-alias.mol
@@ -0,0 +1,21 @@
+
+  MAYFIELD12221314372D
+
+  7  7  0  0  0  0            999 V2000
+    7.8089   -1.3194    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    7.0944   -1.7319    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    7.0944   -2.5569    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    7.8089   -2.9694    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    8.5233   -2.5569    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    8.5233   -1.7319    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    7.8089   -0.4944    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0  0  0  0
+  2  3  2  0  0  0  0
+  3  4  1  0  0  0  0
+  4  5  2  0  0  0  0
+  5  6  1  0  0  0  0
+  1  6  2  0  0  0  0
+  1  7  1  0  0  0  0
+A    7
+N1
+M  END
diff --git a/storage/ctab/src/main/java/org/openscience/cdk/io/MDLV2000Reader.java b/storage/ctab/src/main/java/org/openscience/cdk/io/MDLV2000Reader.java
@@ -1585,7 +1585,7 @@ static void label(final IAtomContainer container, final int index, final String
             pseudoAtom.setLabel(label);
         } else {
             pseudoAtom.setSymbol(label);
-            pseudoAtom.setAtomicNumber(0);
+            pseudoAtom.setAtomicNumber(atom.getAtomicNumber());
             pseudoAtom.setPoint2d(atom.getPoint2d());
             pseudoAtom.setPoint3d(atom.getPoint3d());
             pseudoAtom.setMassNumber(atom.getMassNumber());
@@ -1922,6 +1922,7 @@ private void readPropertiesSlow(BufferedReader input, IAtomContainer container,
                 }
 
                 IAtom newPseudoAtom = container.getBuilder().newInstance(IPseudoAtom.class, alias);
+                newPseudoAtom.setAtomicNumber(aliasAtom.getAtomicNumber());
                 if (aliasAtom.getPoint2d() != null) newPseudoAtom.setPoint2d(aliasAtom.getPoint2d());
                 if (aliasAtom.getPoint3d() != null) newPseudoAtom.setPoint3d(aliasAtom.getPoint3d());
                 AtomContainerManipulator.replaceAtomByAtom(container, aliasAtom, newPseudoAtom);
diff --git a/storage/ctab/src/test/java/org/openscience/cdk/io/MDLV2000ReaderTest.java b/storage/ctab/src/test/java/org/openscience/cdk/io/MDLV2000ReaderTest.java
@@ -1012,7 +1012,9 @@ public void testRGroupHighAtomNumber() throws Exception {
         IAtomContainer molecule = DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainer.class);
         reader.read(molecule);
         reader.close();
-        Assert.assertEquals("R", molecule.getAtom(55).getSymbol());
+        IAtom atom = molecule.getAtom(55);
+        Assert.assertThat(atom, CoreMatchers.<IAtom>instanceOf(IPseudoAtom.class));
+        Assert.assertEquals("R", ((IPseudoAtom)atom).getLabel());
     }
 
     @Test
@@ -1370,6 +1372,17 @@ public void testAliasAfterRgroup() throws Exception {
         assertThat(((IPseudoAtom) container.getAtom(7)).getLabel(), is("Protein"));
     }
 
+    @Test
+    public void keepAtomicNumberOfAlias() throws Exception {
+        InputStream in = getClass().getResourceAsStream("/data/mdl/element-with-alias.mol");
+        MDLV2000Reader reader = new MDLV2000Reader(in);
+        IAtomContainer container = reader.read(new AtomContainer());
+        reader.close();
+        assertThat(container.getAtom(6), is(instanceOf(IPseudoAtom.class)));
+        assertThat(((IPseudoAtom) container.getAtom(6)).getLabel(), is("N1"));
+        assertThat(((IPseudoAtom) container.getAtom(6)).getAtomicNumber(), is(7));
+    }
+
     @Test
     public void v2000Version() throws Exception {
         assertThat(MDLV2000Reader.CTabVersion.ofHeader("  5  5  0  0  0  0            999 V2000"),
