Make sure we have correct storage order in a bond when reading from InChI.

johnmay · johnmay · commit 60a559e0bac1 · 2022-01-11T10:04:42.000Z
diff --git a/storage/inchi/src/main/java/org/openscience/cdk/inchi/InChIToStructure.java b/storage/inchi/src/main/java/org/openscience/cdk/inchi/InChIToStructure.java
@@ -23,14 +23,14 @@
 import io.github.dan2097.jnainchi.InchiBondStereo;
 import io.github.dan2097.jnainchi.InchiBondType;
 import io.github.dan2097.jnainchi.InchiInput;
+import io.github.dan2097.jnainchi.InchiInputFromInchiOutput;
+import io.github.dan2097.jnainchi.InchiOptions;
 import io.github.dan2097.jnainchi.InchiStatus;
 import io.github.dan2097.jnainchi.InchiStereo;
 import io.github.dan2097.jnainchi.InchiStereoParity;
 import io.github.dan2097.jnainchi.InchiStereoType;
-import net.sf.jniinchi.INCHI_RET;
-import io.github.dan2097.jnainchi.InchiInputFromInchiOutput;
-import io.github.dan2097.jnainchi.InchiOptions;
 import io.github.dan2097.jnainchi.JnaInchi;
+import net.sf.jniinchi.INCHI_RET;
 import org.openscience.cdk.config.Elements;
 import org.openscience.cdk.config.Isotopes;
 import org.openscience.cdk.exception.CDKException;
@@ -362,7 +362,8 @@ protected void generateAtomContainerFromInchi(IChemObjectBuilder builder) throws
                     if (ends[0] != a)
                         flip(stereoBond);
                 } else {
-                    flip(stereoBond);
+                    if (!stereoBond.getBegin().equals(a))
+                        flip(stereoBond);
                 }
 
                 int config = IStereoElement.TOGETHER;
diff --git a/storage/inchi/src/test/java/org/openscience/cdk/inchi/InChIToStructureTest.java b/storage/inchi/src/test/java/org/openscience/cdk/inchi/InChIToStructureTest.java
@@ -22,6 +22,7 @@
 
 import org.junit.Assert;
 import org.junit.Test;
+import org.openscience.cdk.interfaces.IBond;
 import org.openscience.cdk.test.CDKTestCase;
 import org.openscience.cdk.DefaultChemObjectBuilder;
 import org.openscience.cdk.exception.CDKException;
@@ -35,6 +36,7 @@
 import org.openscience.cdk.stereo.ExtendedTetrahedral;
 
 import java.util.Iterator;
+import java.util.List;
 
 import static org.hamcrest.CoreMatchers.instanceOf;
 import static org.hamcrest.CoreMatchers.is;
@@ -272,12 +274,39 @@ public void testExtendedCisTrans() throws Exception {
                         SilentChemObjectBuilder.getInstance()).getAtomContainer();
         assertNotNull(mol);
         int nExtendedCisTrans = 0;
-        for (IStereoElement se : mol.stereoElements()) {
-            if (se.getConfig() != IStereoElement.CU)
+        for (IStereoElement<?,?> se : mol.stereoElements()) {
+            if (se.getConfigClass() == IStereoElement.CU)
                 nExtendedCisTrans++;
             else
                 Assert.fail("Expected onl extended cis/trans");
         }
         Assert.assertEquals(1, nExtendedCisTrans);
     }
+
+    /**
+     * Make sure the IBond{beg,end} storage order is correct for the
+     * IStereoElement
+     * @throws Exception
+     */
+    @Test
+    @SuppressWarnings("unchecked")
+    public void ensureBondStorageOrder() throws Exception {
+        IAtomContainer mol = InChIGeneratorFactory.getInstance()
+                                                  .getInChIToStructure("InChI=1S/C16H25NO/c1-14(2)8-6-9-15(3)10-7-11-16(18)17-12-4-5-13-17/h7-8,10-11H,4-6,9,12-13H2,1-3H3/b11-7+,15-10+",
+                                                          SilentChemObjectBuilder.getInstance()).getAtomContainer();
+        assertNotNull(mol);
+        int nCisTrans = 0;
+        for (IStereoElement<?,?> se : mol.stereoElements()) {
+            if (se.getConfigClass() == IStereoElement.CisTrans) {
+                nCisTrans++;
+                IStereoElement<IBond,IBond> ctse = (IStereoElement<IBond,IBond>)se;
+                IBond bond = ctse.getFocus();
+                List<IBond> carriers = ctse.getCarriers();
+                Assert.assertEquals(2, carriers.size());
+                Assert.assertTrue(carriers.get(0).contains(bond.getBegin()));
+                Assert.assertTrue(carriers.get(1).contains(bond.getEnd()));
+            }
+        }
+        Assert.assertEquals(2, nCisTrans);
+    }
 }
