Check string length of AuxInfo - resolve bug1370.

cdk · Sep 3, 2015 · 4eb0299 · 4eb0299
1 parent 282550d
commit 4eb0299
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diff --git a/storage/inchi/src/main/java/org/openscience/cdk/graph/invariant/InChINumbersTools.java b/storage/inchi/src/main/java/org/openscience/cdk/graph/invariant/InChINumbersTools.java
@@ -104,7 +104,10 @@ static long[] parseUSmilesNumbers(String aux, IAtomContainer container) {
         int label = 1;
 
         if ((index = aux.indexOf("/R:")) >= 0) { // reconnected metal numbers
-            String[] baseNumbers = aux.substring(index + 8, aux.indexOf('/', index + 8)).split(";");
+            int endIndex = aux.indexOf('/', index + 8);
+            if (endIndex<0)
+                endIndex = aux.length();
+            String[] baseNumbers = aux.substring(index + 8, endIndex).split(";");
             first = new int[baseNumbers.length];
             Arrays.fill(first, -1);
             for (int i = 0; i < baseNumbers.length; i++) {

diff --git a/storage/inchi/src/test/java/org/openscience/cdk/graph/invariant/InChINumbersToolsTest.java b/storage/inchi/src/test/java/org/openscience/cdk/graph/invariant/InChINumbersToolsTest.java
@@ -164,6 +164,13 @@ public void unlabelledHydrogens() throws Exception {
         assertThat(InChINumbersTools.getUSmilesNumbers(container), is(new long[]{2, 1, 3, 4, 5}));
     }
 
+    @Test
+    public void bug1370() throws Exception {
+        IAtomContainer container = new SmilesParser(SilentChemObjectBuilder.getInstance())
+                .parseSmiles("O=[Bi]Cl");
+        assertThat(InChINumbersTools.getUSmilesNumbers(container), is(new long[]{3, 1, 2}));
+    }
+
     static IAtomContainer mock(int nAtoms) {
         IAtomContainer container = Mockito.mock(IAtomContainer.class);
         when(container.getAtomCount()).thenReturn(nAtoms);