Better error handling in non-strict mode.

cdk · Aug 26, 2017 · d98a113 · d98a113
1 parent 11473ec
commit d98a113
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Showing 2 changed files with 6 additions and 4 deletions.
diff --git a/storage/ctab/src/main/java/org/openscience/cdk/io/MDLV2000Reader.java b/storage/ctab/src/main/java/org/openscience/cdk/io/MDLV2000Reader.java
@@ -1197,8 +1197,10 @@ void readPropertiesFast(final BufferedReader input, final IAtomContainer contain
 
         // check of ill specified atomic mass
         for (IAtom atom : container.atoms()) {
-            if (atom.getMassNumber() != null && atom.getMassNumber() < 0)
-                throw new CDKException("Unstable use of mass delta on " + atom.getSymbol() + " please use M  ISO");
+            if (atom.getMassNumber() != null && atom.getMassNumber() < 0) {
+              handleError("Unstable use of mass delta on " + atom.getSymbol() + " please use M  ISO");
+              atom.setMassNumber(null);
+            }
         }
 
 

diff --git a/storage/ctab/src/test/java/org/openscience/cdk/io/MDLV2000ReaderTest.java b/storage/ctab/src/test/java/org/openscience/cdk/io/MDLV2000ReaderTest.java
@@ -1701,15 +1701,15 @@ public void testSgroupBracketStyle() throws Exception {
     @Test(expected = CDKException.class)
     public void seaborgiumMassDelta() throws Exception {
         try (InputStream in = getClass().getResourceAsStream("seaborgium.mol");
-             MDLV2000Reader mdlr = new MDLV2000Reader(in)) {
+             MDLV2000Reader mdlr = new MDLV2000Reader(in, Mode.STRICT)) {
             IAtomContainer mol = mdlr.read(new AtomContainer());
         }
     }
 
     @Test
     public void seaborgiumAbsMass() throws Exception {
         try (InputStream in = getClass().getResourceAsStream("seaborgium_abs.mol");
-             MDLV2000Reader mdlr = new MDLV2000Reader(in)) {
+             MDLV2000Reader mdlr = new MDLV2000Reader(in, Mode.STRICT)) {
             IAtomContainer mol = mdlr.read(new AtomContainer());
             assertThat(mol.getAtom(0).getMassNumber(), is(261));
         }