Support for @sp,@tb, and @oh configurations.

core/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <artifactId>beam</artifactId>
         <groupId>uk.ac.ebi.beam</groupId>
-        <version>1.0</version>
+        <version>1.1-SNAPSHOT</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 

core/src/main/java/uk/ac/ebi/beam/Graph.java

@@ -342,7 +342,7 @@ void replace(Edge org, Edge rep) {
      * @return whether the topology replaced an existing configuration
      */
     void addTopology(Topology t) {
-        if (t != Topology.unknown())
+        if (t != null && t != Topology.unknown())
             topologies[t.atom()] = t;
     }
 
@@ -357,7 +357,7 @@ void clearTopology(int v) {
      * @param u a vertex to access the topology of
      * @return the topology of vertex 'u'
      */
-    Topology topologyOf(int u) {
+    public Topology topologyOf(int u) {
         if (topologies[u] == null)
             return Topology.unknown();
         return topologies[u];

core/src/test/java/uk/ac/ebi/beam/GraphTest.java

@@ -491,4 +491,49 @@ public void invalidPermutation() {
         assertThat(Graph.fromSmiles("C1C[N@2]2CC[C@H]1C2").toSmiles(),
                    containsString("C1C[N@@]2CC[C@H]1C2"));
     }
+
+    @Test public void cisplatin() throws InvalidSmilesException {
+        Graph g = Graph.fromSmiles("[NH3][Pt@SP1]([NH3])(Cl)Cl");
+        assertThat(g.topologyOf(1).type(),
+                   is(Configuration.Type.SquarePlanar));
+        assertThat(g.toSmiles(), is("[NH3][Pt@SP1]([NH3])(Cl)Cl"));
+        assertThat(g.permute(new int[]{0, 1, 2, 4, 3}).toSmiles(),
+                   is("[NH3][Pt@SP3]([NH3])(Cl)Cl"));
+    }
+
+    @Test public void trigonalBipyramidal() throws InvalidSmilesException {
+        Graph g = Graph.fromSmiles("S[As@TB1](F)(Cl)(Br)N");
+        assertThat(g.topologyOf(1).type(),
+                   is(Configuration.Type.TrigonalBipyramidal));
+        assertThat(g.toSmiles(), is("S[As@](F)(Cl)(Br)N"));
+        assertThat(g.permute(new int[]{0, 1, 2, 4, 3, 5}).toSmiles(),
+                   is("S[As@@](F)(Br)(Cl)N"));
+    }
+
+    @Test public void trigonalBipyramidal2() throws InvalidSmilesException {
+        Graph g = Graph.fromSmiles("S[As@TB2](F)(Cl)(Br)N");
+        assertThat(g.topologyOf(1).type(),
+                   is(Configuration.Type.TrigonalBipyramidal));
+        assertThat(g.toSmiles(), is("S[As@@](F)(Cl)(Br)N"));
+        assertThat(g.permute(new int[]{0, 1, 2, 4, 3, 5}).toSmiles(),
+                   is("S[As@](F)(Br)(Cl)N"));
+    }
+
+    @Test public void trigonalBipyramidal15() throws InvalidSmilesException {
+        Graph g = Graph.fromSmiles("F[As@TB15](Cl)(S)(Br)N");
+        assertThat(g.topologyOf(1).type(),
+                   is(Configuration.Type.TrigonalBipyramidal));
+        assertThat(g.toSmiles(), is("F[As@TB15](Cl)(S)(Br)N"));
+        assertThat(g.permute(new int[]{0, 1, 2, 4, 3, 5}).toSmiles(),
+                   is("F[As@TB17](Cl)(Br)(S)N"));
+    }
+
+    @Test public void octahedral1() throws InvalidSmilesException {
+        Graph g = Graph.fromSmiles("C[Co@](F)(Cl)(Br)(I)S");
+        assertThat(g.topologyOf(1).type(),
+                   is(Configuration.Type.Octahedral));
+        assertThat(g.toSmiles(), is("C[Co@](F)(Cl)(Br)(I)S"));
+        assertThat(g.permute(new int[]{0, 1, 2, 4, 3, 5, 6}).toSmiles(),
+                   is("C[Co@OH8](F)(Br)(Cl)(I)S"));
+    }
 }

core/src/test/java/uk/ac/ebi/beam/TopologyTest.java

@@ -312,20 +312,41 @@ public void create_Clockwise() {
 
     @Test
     public void create_tb() {
-        assertThat(Topology.create(0, new int[0], Collections
-                .<Edge>emptyList(), Configuration.TB1), is(Topology.unknown()));
+        int[] vs = new int[]{1, 2, 3, 4, 5};
+        List<Edge> es = Arrays.asList(new Edge(0, 1, Bond.IMPLICIT),
+                                      new Edge(0, 2, Bond.IMPLICIT),
+                                      new Edge(0, 3, Bond.IMPLICIT),
+                                      new Edge(0, 4, Bond.IMPLICIT),
+                                      new Edge(0, 5, Bond.IMPLICIT));
+        Topology t = Topology.create(0, vs, es, Configuration.TB5);
+        assertThat(t.configuration(), is(Configuration.TB5));
+        assertThat(t.atom(), is(0));
     }
 
     @Test
     public void create_sp() {
-        assertThat(Topology.create(0, new int[0], Collections
-                .<Edge>emptyList(), Configuration.SP1), is(Topology.unknown()));
+        int[] vs = new int[]{1, 2, 3, 4};
+        List<Edge> es = Arrays.asList(new Edge(0, 1, Bond.IMPLICIT),
+                                      new Edge(0, 2, Bond.IMPLICIT),
+                                      new Edge(0, 3, Bond.IMPLICIT),
+                                      new Edge(0, 4, Bond.IMPLICIT));
+        Topology t = Topology.create(0, vs, es, Configuration.SP1);
+        assertThat(t.configuration(), is(Configuration.SP1));
+        assertThat(t.atom(), is(0));
     }
 
     @Test
     public void create_oh() {
-        assertThat(Topology.create(0, new int[0], Collections
-                .<Edge>emptyList(), Configuration.OH1), is(Topology.unknown()));
+        int[] vs = new int[]{1, 2, 3, 4, 5, 6};
+        List<Edge> es = Arrays.asList(new Edge(0, 1, Bond.IMPLICIT),
+                                      new Edge(0, 2, Bond.IMPLICIT),
+                                      new Edge(0, 3, Bond.IMPLICIT),
+                                      new Edge(0, 4, Bond.IMPLICIT),
+                                      new Edge(0, 5, Bond.IMPLICIT),
+                                      new Edge(0, 6, Bond.IMPLICIT));
+        Topology t = Topology.create(0, vs, es, Configuration.OH1);
+        assertThat(t.configuration(), is(Configuration.OH1));
+        assertThat(t.atom(), is(0));
     }
 
     @Test(expected = IllegalArgumentException.class)

exec/pom.xml

@@ -9,7 +9,7 @@
   <parent>
     <artifactId>beam</artifactId>
     <groupId>uk.ac.ebi.beam</groupId>
-    <version>1.0</version>
+    <version>1.1-SNAPSHOT</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
 

func/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <artifactId>beam</artifactId>
         <groupId>uk.ac.ebi.beam</groupId>
-        <version>1.0</version>
+        <version>1.1-SNAPSHOT</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 

pom.xml

@@ -7,7 +7,7 @@
     <description>SMILES parsing and generation library for cheminformatics</description>
     <url>http://www.github.com/johnmay/beam/</url>
     <packaging>pom</packaging>
-    <version>1.0</version>
+    <version>1.1-SNAPSHOT</version>
     <modules>
         <module>core</module>
         <module>func</module>