Correct MDL V3000 reading, CFG=2 should be wavy bond. Also ensure passing null to setStereo doesn't cause an error.

johnmay · johnmay · commit 58849f65924f · 2019-11-21T12:56:38.000Z
diff --git a/base/data/src/main/java/org/openscience/cdk/Bond.java b/base/data/src/main/java/org/openscience/cdk/Bond.java
@@ -409,24 +409,27 @@ public IBond.Stereo getStereo() {
      */
     @Override
     public void setStereo(IBond.Stereo stereo) {
-        this.stereo = stereo;
-        switch (stereo) {
-            case UP:
-                display = Display.WedgeBegin;
-                break;
-            case DOWN:
-                display = Display.WedgedHashBegin;
-                break;
-            case UP_INVERTED:
-                display = Display.WedgeEnd;
-                break;
-            case DOWN_INVERTED:
-                display = Display.WedgedHashEnd;
-                break;
-            case UP_OR_DOWN:
-            case UP_OR_DOWN_INVERTED:
-                display = Display.Wavy;
-                break;
+        if (stereo == null) {
+            this.display = Display.Solid;
+        } else {
+            switch (stereo) {
+                case UP:
+                    display = Display.WedgeBegin;
+                    break;
+                case DOWN:
+                    display = Display.WedgedHashBegin;
+                    break;
+                case UP_INVERTED:
+                    display = Display.WedgeEnd;
+                    break;
+                case DOWN_INVERTED:
+                    display = Display.WedgedHashEnd;
+                    break;
+                case UP_OR_DOWN:
+                case UP_OR_DOWN_INVERTED:
+                    display = Display.Wavy;
+                    break;
+            }
         }
         notifyChanged();
     }
diff --git a/base/silent/src/main/java/org/openscience/cdk/silent/Bond.java b/base/silent/src/main/java/org/openscience/cdk/silent/Bond.java
@@ -404,23 +404,27 @@ public IBond.Stereo getStereo() {
     @Override
     public void setStereo(IBond.Stereo stereo) {
         this.stereo = stereo;
-        switch (stereo) {
-            case UP:
-                display = Display.WedgeBegin;
-                break;
-            case DOWN:
-                display = Display.WedgedHashBegin;
-                break;
-            case UP_INVERTED:
-                display = Display.WedgeEnd;
-                break;
-            case DOWN_INVERTED:
-                display = Display.WedgedHashEnd;
-                break;
-            case UP_OR_DOWN:
-            case UP_OR_DOWN_INVERTED:
-                display = Display.Wavy;
-                break;
+        if (stereo == null) {
+            this.display = Display.Solid;
+        } else {
+            switch (stereo) {
+                case UP:
+                    display = Display.WedgeBegin;
+                    break;
+                case DOWN:
+                    display = Display.WedgedHashBegin;
+                    break;
+                case UP_INVERTED:
+                    display = Display.WedgeEnd;
+                    break;
+                case DOWN_INVERTED:
+                    display = Display.WedgedHashEnd;
+                    break;
+                case UP_OR_DOWN:
+                case UP_OR_DOWN_INVERTED:
+                    display = Display.Wavy;
+                    break;
+            }
         }
     }
 
diff --git a/storage/ctab/src/main/java/org/openscience/cdk/io/MDLV3000Reader.java b/storage/ctab/src/main/java/org/openscience/cdk/io/MDLV3000Reader.java
@@ -469,7 +469,7 @@ public void readBondBlock(IAtomContainer readData) throws CDKException {
                                     } else if (configuration == 1) {
                                         bond.setStereo(IBond.Stereo.UP);
                                     } else if (configuration == 2) {
-                                        bond.setStereo((IBond.Stereo) CDKConstants.UNSET);
+                                        bond.setStereo(IBond.Stereo.UP_OR_DOWN);
                                     } else if (configuration == 3) {
                                         bond.setStereo(IBond.Stereo.DOWN);
                                     }
diff --git a/storage/ctab/src/test/java/org/openscience/cdk/io/MDLV3000ReaderTest.java b/storage/ctab/src/test/java/org/openscience/cdk/io/MDLV3000ReaderTest.java
@@ -22,6 +22,7 @@
  *  */
 package org.openscience.cdk.io;
 
+import org.hamcrest.CoreMatchers;
 import org.junit.Assert;
 import org.junit.BeforeClass;
 import org.junit.Test;
@@ -30,10 +31,12 @@
 import org.openscience.cdk.exception.CDKException;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.io.iterator.IteratingSDFReader;
 import org.openscience.cdk.sgroup.Sgroup;
 import org.openscience.cdk.sgroup.SgroupType;
 import org.openscience.cdk.silent.AtomContainer;
 import org.openscience.cdk.interfaces.IPseudoAtom;
+import org.openscience.cdk.silent.SilentChemObjectBuilder;
 import org.openscience.cdk.tools.ILoggingTool;
 import org.openscience.cdk.tools.LoggingToolFactory;
 
@@ -144,4 +147,11 @@ public void testPseudoAtomLabels() throws Exception {
             assertThat(container.getAtom(0).getImplicitHydrogenCount(), is(3));
         }
     }
+
+    @Test public void issue602() throws Exception {
+        try (MDLV3000Reader reader = new MDLV3000Reader(getClass().getResourceAsStream("issue602.mol"))) {
+            IAtomContainer mol = reader.read(SilentChemObjectBuilder.getInstance().newAtomContainer());
+            assertThat(mol.getAtomCount(), CoreMatchers.is(31));
+        }
+    }
 }

Original file line number	Diff line number	Diff line change
`@@ -469,7 +469,7 @@ public void readBondBlock(IAtomContainer readData) throws CDKException {`
`469`	`469`	`} else if (configuration == 1) {`
`470`	`470`	`bond.setStereo(IBond.Stereo.UP);`
`471`	`471`	`} else if (configuration == 2) {`
`472`		`- bond.setStereo((IBond.Stereo) CDKConstants.UNSET);`
	`472`	`+ bond.setStereo(IBond.Stereo.UP_OR_DOWN);`
`473`	`473`	`} else if (configuration == 3) {`
`474`	`474`	`bond.setStereo(IBond.Stereo.DOWN);`
`475`	`475`	`}`