Some restructuring requiring to resolve failing unit tests.

cdk · May 9, 2018 · 99e888a · 99e888a
1 parent a58bdd5
commit 99e888a
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Showing 3 changed files with 27 additions and 10 deletions.
diff --git a/base/standard/src/main/java/org/openscience/cdk/stereo/StereoElementFactory.java b/base/standard/src/main/java/org/openscience/cdk/stereo/StereoElementFactory.java
@@ -38,7 +38,6 @@
 import javax.vecmath.Vector2d;
 import javax.vecmath.Vector3d;
 import java.util.ArrayList;
-import java.util.Arrays;
 import java.util.Collections;
 import java.util.EnumSet;
 import java.util.List;
@@ -241,7 +240,8 @@ public List<IStereoElement> createAll() {
                                 if (element != null) elements.add(element);
                             } else {
                                 // extended cis-trans
-                                IStereoElement element = createExtendedCisTrans(dbs);
+                                IStereoElement element = createExtendedCisTrans(dbs,
+                                                                                centers);
                                 if (element != null) elements.add(element);
                             }
                             break;
@@ -441,9 +441,11 @@ public List<IStereoElement> createAll() {
      * </pre>
      *
      * @param bonds cumulated double bonds
+     * @param centers discovered stereocentres
      * @return the extended cis/trans geometry if one could be created
      */
-    abstract ExtendedCisTrans createExtendedCisTrans(List<IBond> bonds);
+    abstract ExtendedCisTrans createExtendedCisTrans(List<IBond> bonds,
+                                                     Stereocenters centers);
 
     /**
      * Indicate that stereochemistry drawn as a certain projection should be
@@ -775,6 +777,11 @@ ExtendedTetrahedral createExtendedTetrahedral(int v, Stereocenters stereocenters
             int t0 = container.indexOf(terminals[0]);
             int t1 = container.indexOf(terminals[1]);
 
+            if (stereocenters.isSymmetryChecked() &&
+                (!stereocenters.isStereocenter(t0) ||
+                 !stereocenters.isStereocenter(t1)))
+                return null;
+
             IAtom[] neighbors = new IAtom[4];
             int[] elevation = new int[4];
 
@@ -817,8 +824,7 @@ ExtendedTetrahedral createExtendedTetrahedral(int v, Stereocenters stereocenters
             return new ExtendedTetrahedral(focus, neighbors, winding);
         }
 
-        @Override
-        ExtendedCisTrans createExtendedCisTrans(List<IBond> dbs) {
+        ExtendedCisTrans createExtendedCisTrans(List<IBond> dbs, Stereocenters stereocenters) {
 
             // only applies to odd-counts
             if ((dbs.size() & 0x1) == 0)
@@ -834,6 +840,11 @@ ExtendedCisTrans createExtendedCisTrans(List<IBond> dbs) {
             List<IBond> begBonds = container.getConnectedBondsList(begAtom);
             List<IBond> endBonds = container.getConnectedBondsList(endAtom);
 
+            if (stereocenters.isSymmetryChecked() &&
+                (!stereocenters.isStereocenter(container.indexOf(begAtom)) ||
+                 !stereocenters.isStereocenter(container.indexOf(endAtom))))
+                return null;
+
             if (begBonds.size() < 2 || endBonds.size() < 2)
                 return null;
 
@@ -1235,7 +1246,8 @@ ExtendedTetrahedral createExtendedTetrahedral(int v, Stereocenters stereocenters
         }
 
         @Override
-        ExtendedCisTrans createExtendedCisTrans(List<IBond> dbs) {
+        ExtendedCisTrans createExtendedCisTrans(List<IBond> dbs,
+                                                Stereocenters centers) {
 
             // only applies to odd-counts
             if ((dbs.size() & 0x1) == 0)

diff --git a/base/standard/src/main/java/org/openscience/cdk/stereo/Stereocenters.java b/base/standard/src/main/java/org/openscience/cdk/stereo/Stereocenters.java
@@ -210,6 +210,10 @@ public Type elementType(final int v) {
             return elements[v].type;
     }
 
+    boolean isSymmetryChecked() {
+        return checkSymmetry;
+    }
+
     /**
      * Is the atom be a stereocenter (i.e. True or Para).
      *

diff --git a/base/test-standard/src/test/java/org/openscience/cdk/stereo/StereoElementFactoryTest.java b/base/test-standard/src/test/java/org/openscience/cdk/stereo/StereoElementFactoryTest.java
@@ -26,6 +26,7 @@
 
 import com.google.common.collect.Iterables;
 import org.junit.Test;
+import org.openscience.cdk.CDKConstants;
 import org.openscience.cdk.exception.CDKException;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
@@ -224,7 +225,7 @@ public void e_hexa234triene() {
         dbs.add(mol.getBond(0));
         dbs.add(mol.getBond(1));
         dbs.add(mol.getBond(2));
-        ExtendedCisTrans element = factory.createExtendedCisTrans(dbs);
+        ExtendedCisTrans element = factory.createExtendedCisTrans(dbs, Stereocenters.of(mol));
         assertNotNull(element);
         assertThat(element.getConfigOrder(), is(IStereoElement.OPPOSITE));
     }
@@ -252,7 +253,7 @@ public void z_hexa234triene() {
         dbs.add(mol.getBond(0));
         dbs.add(mol.getBond(1));
         dbs.add(mol.getBond(2));
-        ExtendedCisTrans element = factory.createExtendedCisTrans(dbs);
+        ExtendedCisTrans element = factory.createExtendedCisTrans(dbs, Stereocenters.of(mol));
         assertNotNull(element);
         assertThat(element.getConfigOrder(), is(IStereoElement.TOGETHER));
     }
@@ -280,7 +281,7 @@ public void e_hexa234triene_3D() {
         dbs.add(mol.getBond(0));
         dbs.add(mol.getBond(1));
         dbs.add(mol.getBond(2));
-        ExtendedCisTrans element = factory.createExtendedCisTrans(dbs);
+        ExtendedCisTrans element = factory.createExtendedCisTrans(dbs, Stereocenters.of(mol));
         assertNotNull(element);
         assertThat(element.getConfigOrder(), is(IStereoElement.OPPOSITE));
     }
@@ -308,7 +309,7 @@ public void z_hexa234triene_3D() {
         dbs.add(mol.getBond(0));
         dbs.add(mol.getBond(1));
         dbs.add(mol.getBond(2));
-        ExtendedCisTrans element = factory.createExtendedCisTrans(dbs);
+        ExtendedCisTrans element = factory.createExtendedCisTrans(dbs, Stereocenters.of(mol));
         assertNotNull(element);
         assertThat(element.getConfigOrder(), is(IStereoElement.TOGETHER));
     }