JavaDoc fixes

johnmay · Jul 20, 2024 · 7f8596a · 7f8596a
1 parent badb618
commit 7f8596a
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Showing 3 changed files with 21 additions and 3 deletions.
diff --git a/core/src/main/java/uk/ac/ebi/beam/Bond.java b/core/src/main/java/uk/ac/ebi/beam/Bond.java
@@ -34,7 +34,9 @@
  * valid undirected and directed bond types and {@link #DOT}. Opposed to the
  * other types, {@link #DOT} indicates that two atoms are not connected. <br>
  *
- * <table summary="" style="font-family: Courier, monospace;"> <tr><th>{@link
+ * <table style="font-family: Courier, monospace;"> <caption>
+ *     Bond Types
+ * </caption><tr><th>{@link
  * Bond}</th><th>{@link #token()}</th><th>{@link #order()}</th><th>{@link
  * #inverse()}</th></tr> <tr><td>{@link #DOT}</td><td>.</td><td>0</td><td></td></tr>
  * <tr><td>{@link #IMPLICIT}</td><td></td><td>undefined (2 or

diff --git a/core/src/main/java/uk/ac/ebi/beam/Element.java b/core/src/main/java/uk/ac/ebi/beam/Element.java
@@ -41,7 +41,7 @@
 /**
  * Enumeration of valid OpenSMILES elements.
  *
- * <h1>Organic subsets</h1> Several of the elements belong to the organic
+ * <h2>Organic subsets</h2> Several of the elements belong to the organic
  * subset. Atoms of an organic element type can be written just as their symbol
  * (see. <a href="http://www.opensmiles.org/opensmiles.html#orgsbst">Organic
  * Subset, OpenSMILES Specification</a>).
@@ -52,7 +52,7 @@
  * #Sulfur}</li> <li>{@link #Chlorine}</li> <li>{@link #Bromine}</li> <li>{@link
  * #Iodine}</li> </ul>
  *
- * <h1>Usage</h1>
+ * <h2>Usage</h2>
  *
  * Elements can be created by either using the value directly or by looking up
  * it's symbol. If the element may be aromatic the lower-case symbol can also be

diff --git a/core/src/test/java/uk/ac/ebi/beam/GraphTest.java b/core/src/test/java/uk/ac/ebi/beam/GraphTest.java
@@ -546,6 +546,22 @@ public void invalidPermutation() {
         Assert.assertThat(g.topologyOf(3).configuration(), is(Configuration.AL2));
     }
 
+    @Test public void testDegenerateOctahedral() throws InvalidSmilesException {
+        Graph g = Graph.fromSmiles("O=[V@OH25](Cl)(Cl)(F)F");
+        System.err.println(g.configurationOf(1));
+        for (int nbor : g.neighbors(1)) {
+            System.err.println(nbor);
+        }
+    }
+
+    @Test public void testDegenerateOctahedral2() throws InvalidSmilesException {
+        Graph g = Graph.fromSmiles("O=[V@OH25]12(F)F.Cl1.Cl2");
+        System.err.println(g.configurationOf(1));
+        for (int nbor : g.neighbors(1)) {
+            System.err.println(nbor);
+        }
+    }
+
     @Test public void nofail() throws IOException {
         Graph g = Graph.fromSmiles("CCCO[P@H]1(OC[C@@H]2[C@@H](O1)[C@@]([C@@H](O2)n3cnc4c3nc(nc4OCC)N)(C)F)O CHEMBL1630021");
         assertThat(g.toSmiles(),