Ensure double bonds are laid out correctly.

johnmay · Nov 26, 2016 · d03343d · d03343d
1 parent 15e2c81
commit d03343d
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Showing 2 changed files with 26 additions and 3 deletions.
diff --git a/tool/sdg/src/main/java/org/openscience/cdk/layout/StructureDiagramGenerator.java b/tool/sdg/src/main/java/org/openscience/cdk/layout/StructureDiagramGenerator.java
@@ -1071,8 +1071,8 @@ private void generateFragmentCoordinates(IAtomContainer mol, List<IAtomContainer
 
         // correct double-bond stereo, this changes the layout and in reality
         // should be done during the initial placement
-        if (molecule.stereoElements().iterator().hasNext())
-            CorrectGeometricConfiguration.correct(molecule);
+        if (mol.stereoElements().iterator().hasNext())
+            CorrectGeometricConfiguration.correct(mol);
 
         // finalize
         assignStereochem(mol);

diff --git a/tool/sdg/src/test/java/org/openscience/cdk/layout/StructureDiagramGeneratorTest.java b/tool/sdg/src/test/java/org/openscience/cdk/layout/StructureDiagramGeneratorTest.java
@@ -37,6 +37,8 @@
 import org.openscience.cdk.interfaces.IBond;
 import org.openscience.cdk.interfaces.IChemModel;
 import org.openscience.cdk.interfaces.IChemSequence;
+import org.openscience.cdk.interfaces.IDoubleBondStereochemistry;
+import org.openscience.cdk.interfaces.IStereoElement;
 import org.openscience.cdk.io.CMLReader;
 import org.openscience.cdk.io.IChemObjectReader.Mode;
 import org.openscience.cdk.io.ISimpleChemObjectReader;
@@ -50,6 +52,7 @@
 import org.openscience.cdk.sgroup.SgroupType;
 import org.openscience.cdk.silent.SilentChemObjectBuilder;
 import org.openscience.cdk.smiles.SmilesParser;
+import org.openscience.cdk.stereo.StereoElementFactory;
 import org.openscience.cdk.templates.TestMoleculeFactory;
 
 import javax.vecmath.Point2d;
@@ -85,7 +88,7 @@
 public class StructureDiagramGeneratorTest extends CDKTestCase {
 
     private static final StructureDiagramGenerator SDG = new StructureDiagramGenerator();
-    
+
     static {
         SDG.setUseIdentityTemplates(true);
     }
@@ -1243,4 +1246,24 @@ public void NH4OH() throws Exception {
                    is(greaterThan(SDG.getBondLength())));
 
     }
+
+    @Test public void fragmentDoubleBondConfiguration() throws Exception {
+        SmilesParser smipar = new SmilesParser(SilentChemObjectBuilder.getInstance());
+        IAtomContainer mol = smipar.parseSmiles("C(\\C)=C/C.C(\\C)=C\\C.C(\\C)=C/C.C(\\C)=C\\C");
+        layout(mol);
+        List<IStereoElement> elements = StereoElementFactory.using2DCoordinates(mol).createAll();
+        int numCis = 0;
+        int numTrans = 0;
+        for (IStereoElement se : elements) {
+            if (se instanceof IDoubleBondStereochemistry) {
+                IDoubleBondStereochemistry.Conformation config = ((IDoubleBondStereochemistry) se).getStereo();
+                if (config == IDoubleBondStereochemistry.Conformation.TOGETHER)
+                    numCis++;
+                else if (config == IDoubleBondStereochemistry.Conformation.OPPOSITE)
+                    numTrans++;
+            }
+        }
+        assertThat(numCis, is(2));
+        assertThat(numTrans, is(2));
+    }
 }