Test case and fix misaligned (when at end of line) MDL int parsing.

johnmay · johnmay · commit ca0ccf541b44 · 2019-07-03T22:25:59.000+01:00
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
@@ -1519,6 +1519,8 @@ private static int readMolfileInt(final String line, final int index) {
             default:
                 return 0;
         }
+        if (index+1 == line.length())
+            return sign * result;
         switch ((c = line.charAt(index + 1))) {
             case ' ':
                 if (result > 0) return sign * result;
@@ -1542,14 +1544,12 @@ private static int readMolfileInt(final String line, final int index) {
             default:
                 return sign * result;
         }
+        if (index+2 == line.length())
+            return sign * result;
         switch ((c = line.charAt(index + 2))) {
             case ' ':
                 if (result > 0) return sign * result;
                 break;
-            case '-':
-                if (result > 0) return sign * result;
-                sign = -1;
-                break;
             case '0':
             case '1':
             case '2':
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
@@ -24,6 +24,7 @@
  *  */
 package org.openscience.cdk.io;
 
+import org.hamcrest.CoreMatchers;
 import org.junit.Assert;
 import org.junit.BeforeClass;
 import org.junit.Test;
@@ -40,6 +41,8 @@
 import org.openscience.cdk.interfaces.IBond;
 import org.openscience.cdk.interfaces.IBond.Order;
 import org.openscience.cdk.interfaces.IChemFile;
+import org.openscience.cdk.interfaces.IChemObject;
+import org.openscience.cdk.interfaces.IChemObjectBuilder;
 import org.openscience.cdk.interfaces.IPseudoAtom;
 import org.openscience.cdk.interfaces.IStereoElement;
 import org.openscience.cdk.interfaces.ITetrahedralChirality;
@@ -51,6 +54,7 @@
 import org.openscience.cdk.sgroup.SgroupBracket;
 import org.openscience.cdk.sgroup.SgroupKey;
 import org.openscience.cdk.sgroup.SgroupType;
+import org.openscience.cdk.silent.SilentChemObjectBuilder;
 import org.openscience.cdk.tools.ILoggingTool;
 import org.openscience.cdk.tools.LoggingToolFactory;
 import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
@@ -1790,4 +1794,23 @@ public void testBadAtomCoordinateFormat() throws Exception {
         final org.openscience.cdk.silent.AtomContainer atomContainer = mdlv2000Reader.read(new org.openscience.cdk.silent.AtomContainer());
         Assert.assertEquals(17, atomContainer.getAtomCount());
     }
+
+    @Test public void test() throws Exception {
+        String input = "\n" +
+                       "Structure query\n" +
+                       "\n" +
+                       "  1  0  0  0  0  0  0  0  0  0999 V2000\n" +
+                       " 2430.7100 2427.0000    0.0000 C   0  0  0  0  0  0\n" +
+                       "A   1\n" +
+                       "Blah\n" +
+                       "M  END";
+        IChemObjectBuilder bldr = SilentChemObjectBuilder.getInstance();
+        try (MDLV2000Reader mdlr = new MDLV2000Reader(new StringReader(input))) {
+            IAtomContainer mol = mdlr.read(bldr.newAtomContainer());
+            assertThat(mol.getAtom(0),
+                       instanceOf(IPseudoAtom.class));
+            assertThat(((IPseudoAtom)mol.getAtom(0)).getLabel(),
+                       is("Blah"));
+        }
+    }
 }
