Merge pull request #300 from cdk/patch/wedgebondpriority

Slight tweak to assign wedge bonds.
cdk · Apr 20, 2017 · c05eac4 · c05eac4
2 parents 385c145 + c0db57f
commit c05eac4
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Showing 2 changed files with 34 additions and 3 deletions.
diff --git a/tool/sdg/src/main/java/org/openscience/cdk/layout/NonplanarBonds.java b/tool/sdg/src/main/java/org/openscience/cdk/layout/NonplanarBonds.java
@@ -36,7 +36,6 @@
 import org.openscience.cdk.ringsearch.RingSearch;
 import org.openscience.cdk.stereo.ExtendedTetrahedral;
 import org.openscience.cdk.tools.LoggingToolFactory;
-import uk.ac.ebi.beam.Bond;
 
 import javax.vecmath.Point2d;
 import java.util.ArrayList;
@@ -338,7 +337,8 @@ private void label(final ITetrahedralChirality element) {
         }
 
         // set the label for the highest priority and available bond
-        IBond.Stereo firstlabel = null;
+        IBond.Stereo firstlabel      = null;
+        boolean      assignTwoLabels = assignTwoLabels(bonds, labels);
         for (int v : priority(atomToIndex.get(focus), atoms, n)) {
             IBond bond = bonds[v];
             if (bond.getStereo() != NONE || bond.getOrder() != SINGLE)
@@ -349,7 +349,7 @@ private void label(final ITetrahedralChirality element) {
                 bond.setStereo(labels[v]);
                 firstlabel = labels[v];
                 // don't assign a second label when there are only three ligands
-                if (labels.length == 3)
+                if (!assignTwoLabels)
                     break;
             }
             // second label
@@ -365,6 +365,19 @@ else if (labels[v] != firstlabel) {
             throw new IllegalArgumentException("could not assign non-planar (up/down) labels");
     }
 
+    private boolean assignTwoLabels(IBond[] bonds, IBond.Stereo[] labels) {
+        return labels.length == 4 && countRingBonds(bonds) != 3;
+    }
+
+    private int countRingBonds(IBond[] bonds) {
+        int rbonds = 0;
+        for (IBond bond : bonds) {
+            if (bond != null && bond.isInRing())
+                rbonds++;
+        }
+        return rbonds;
+    }
+
     /**
      * Obtain the parity of a value x. The parity is -1 if the value is odd or
      * +1 if the value is even.

diff --git a/tool/sdg/src/test/java/org/openscience/cdk/layout/NonPlanarBondsTest.java b/tool/sdg/src/test/java/org/openscience/cdk/layout/NonPlanarBondsTest.java
@@ -33,6 +33,8 @@
 import org.openscience.cdk.interfaces.ITetrahedralChirality;
 import org.openscience.cdk.silent.Atom;
 import org.openscience.cdk.silent.AtomContainer;
+import org.openscience.cdk.silent.SilentChemObjectBuilder;
+import org.openscience.cdk.smiles.SmilesParser;
 import org.openscience.cdk.stereo.DoubleBondStereochemistry;
 import org.openscience.cdk.stereo.ExtendedTetrahedral;
 import org.openscience.cdk.stereo.TetrahedralChirality;
@@ -595,6 +597,22 @@ public void unspecifiedMarkedOnDifferentLigands() {
         assertThat(wavyCount, is(1));
     }
 
+    /**
+     * {@code SMILES: O=C4C=C2[C@]([C@@]1([H])CC[C@@]3([C@@]([H])(O)CC[C@@]3([H])[C@]1([H])CC2)C)(C)CC4}
+     */
+    @Test
+    public void testosterone() throws CDKException {
+        SmilesParser smipar = new SmilesParser(SilentChemObjectBuilder.getInstance());
+        IAtomContainer mol = smipar.parseSmiles("O=C4C=C2[C@]([C@@]1([H])CC[C@@]3([C@@]([H])(O)CC[C@@]3([H])[C@]1([H])CC2)C)(C)CC4");
+        StructureDiagramGenerator sdg = new StructureDiagramGenerator();
+        sdg.generateCoordinates(mol);
+        int wedgeCount = 0;
+        for (IBond bond : mol.bonds())
+            if (bond.getStereo() == IBond.Stereo.UP || bond.getStereo() == IBond.Stereo.DOWN)
+                wedgeCount++;
+        assertThat(wedgeCount, is(7));
+    }
+
     static IAtom atom(String symbol, int hCount, double x, double y) {
         IAtom a = new Atom(symbol);
         a.setImplicitHydrogenCount(hCount);