Fix labelling of protons.

cdk · Jun 22, 2017 · cdc1ec1 · cdc1ec1
1 parent 801b108
commit cdc1ec1
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Showing 2 changed files with 8 additions and 3 deletions.
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
@@ -137,7 +137,6 @@ static long[] parseUSmilesNumbers(String aux, IAtomContainer container) {
             if ((index = aux.indexOf("/F:")) >= 0) {
                 String[] fixedHNumbers = aux.substring(index + 3, aux.indexOf('/', index + 3)).split(";");
                 for (int i = 0; i < fixedHNumbers.length; i++) {
-
                     String component = fixedHNumbers[i];
 
                     // m, 2m, 3m ... need to lookup number in the base numbering
@@ -152,9 +151,8 @@ static long[] parseUSmilesNumbers(String aux, IAtomContainer container) {
                         }
                     } else {
                         String[] numbering = component.split(",");
-                        first[i] = Integer.parseInt(numbering[0]) - 1;
                         for (String number : numbering)
-                            numbers[Integer.parseInt(number) - 1] = label++;
+                            numbers[Integer.parseInt(number)-1] = label++;
                     }
                 }
             } else {

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
@@ -171,6 +171,13 @@ public void bug1370() throws Exception {
         assertThat(InChINumbersTools.getUSmilesNumbers(container), is(new long[]{3, 1, 2}));
     }
 
+    @Test
+    public void protons() throws Exception {
+        IAtomContainer container = new SmilesParser(SilentChemObjectBuilder.getInstance())
+            .parseSmiles("[H+].[H+].F[Si-2](F)(F)(F)(F)F");
+        assertThat(InChINumbersTools.getUSmilesNumbers(container), is(new long[]{8, 9, 1, 7, 2, 3, 4, 5, 6}));
+    }
+
     static IAtomContainer mock(int nAtoms) {
         IAtomContainer container = Mockito.mock(IAtomContainer.class);
         when(container.getAtomCount()).thenReturn(nAtoms);