Merge pull request #179 from cdk/patch/smiles-fixup

Looks good.
cdk · Nov 27, 2015 · 460b001 · 460b001
2 parents f199800 + 21d138e
commit 460b001
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Showing 4 changed files with 14 additions and 3 deletions.
diff --git a/pom.xml b/pom.xml
@@ -371,12 +371,12 @@
             <dependency>
                 <groupId>uk.ac.ebi.beam</groupId>
                 <artifactId>beam-core</artifactId>
-                <version>0.9</version>
+                <version>0.9.1</version>
             </dependency>
             <dependency>
                 <groupId>uk.ac.ebi.beam</groupId>
                 <artifactId>beam-func</artifactId>
-                <version>0.9</version>
+                <version>0.9.1</version>
             </dependency>
             <dependency>
                 <groupId>com.google.guava</groupId>

diff --git a/storage/smiles/src/main/java/org/openscience/cdk/smiles/SmilesParser.java b/storage/smiles/src/main/java/org/openscience/cdk/smiles/SmilesParser.java
@@ -207,6 +207,8 @@ public IAtomContainer parseSmiles(String smiles) throws InvalidSmilesException {
             return beamToCDK.toAtomContainer(kekulise ? g.kekule() : g);
         } catch (IOException e) {
             throw new InvalidSmilesException("could not parse '" + smiles + "', " + e.getMessage());
+        } catch (Exception e) {
+            throw new InvalidSmilesException("could not parse '" + smiles + "'");
         }
     }
 

diff --git a/storage/smiles/src/test/java/org/openscience/cdk/smiles/SmilesGeneratorTest.java b/storage/smiles/src/test/java/org/openscience/cdk/smiles/SmilesGeneratorTest.java
@@ -1208,7 +1208,7 @@ public void assignDbStereo() throws Exception {
         String in = "C(/N)=C\\C=C\\1/N=C1";
         SmilesParser smipar = new SmilesParser(SilentChemObjectBuilder.getInstance());
         IAtomContainer mol = smipar.parseSmiles(in);
-        Assert.assertEquals("C(/N)=C\\C=C\\1/N=C1", SmilesGenerator.isomeric().create(mol));
+        Assert.assertEquals("C(\\N)=C/C=C/1\\N=C1", SmilesGenerator.isomeric().create(mol));
     }
 
     static ITetrahedralChirality anticlockwise(IAtomContainer container, int central, int a1, int a2, int a3, int a4) {

diff --git a/storage/smiles/src/test/java/org/openscience/cdk/smiles/SmilesParserTest.java b/storage/smiles/src/test/java/org/openscience/cdk/smiles/SmilesParserTest.java
@@ -2491,6 +2491,15 @@ public void testDiBorane() throws Exception {
         Assert.assertEquals(2, mol.getConnectedAtomsCount(mol.getAtom(5)));
     }
 
+    /**
+     * Okay exception for a non-SMILES string.
+     * @cdk.bug 1375
+     */
+    @Test(expected = InvalidSmilesException.class)
+    public void idNumber() throws Exception {
+        load("50-00-0");
+    }
+
     /**
      * Counts aromatic atoms in a molecule.
      * @param mol molecule for which to count aromatic atoms.