Option to enable/disable mapped reaction alignment.

app/depict/src/main/java/org/openscience/cdk/depict/DepictionGenerator.java

@@ -194,6 +194,11 @@ public final class DepictionGenerator {
      */
     private Color[] atomMapColors = null;
 
+    /**
+     * Reactions are aligned such that mapped atoms have the same coordinates on the left/right.
+     */
+    private boolean alignMappedReactions = true;
+
     /**
      * Object that should be highlighted
      */
@@ -681,6 +686,7 @@ private boolean ensure2dLayout(IAtomContainer container) throws CDKException {
      */
     private void ensure2dLayout(IReaction rxn) throws CDKException {
         StructureDiagramGenerator sdg = new StructureDiagramGenerator();
+        sdg.setAlignMappedReaction(alignMappedReactions);
         sdg.generateCoordinates(rxn);
     }
 
@@ -853,6 +859,19 @@ public DepictionGenerator withRxnTitle() {
                          true);
     }
 
+    /**
+     * Specifies that reactions with atom-atom mappings should have their reactants/product
+     * coordinates aligned. Default: true.
+     *
+     * @param val setting value
+     * @return new generator for method chaining
+     */
+    public DepictionGenerator withMappedRxnAlign(boolean val) {
+        DepictionGenerator copy = new DepictionGenerator();
+        copy.alignMappedReactions = val;
+        return copy;
+    }
+
     /**
      * Set the color annotations (e.g. atom-numbers) will appear in.
      *

tool/sdg/src/main/java/org/openscience/cdk/layout/StructureDiagramGenerator.java

@@ -111,19 +111,19 @@ public class StructureDiagramGenerator {
     private IRingSet       sssr;
     private double bondLength = DEFAULT_BOND_LENGTH;
     private Vector2d firstBondVector;
-    private RingPlacer       ringPlacer        = new RingPlacer();
-    private AtomPlacer       atomPlacer        = new AtomPlacer();
-    private MacroCycleLayout macroPlacer       = null;
-    private List<IRingSet>   ringSystems       = null;
-    private Set<IAtom>       afix              = null;
-    private Set<IBond>       bfix              = null;
-    private boolean          useIdentTemplates = true;
+    private RingPlacer       ringPlacer          = new RingPlacer();
+    private AtomPlacer       atomPlacer          = new AtomPlacer();
+    private MacroCycleLayout macroPlacer         = null;
+    private List<IRingSet>   ringSystems         = null;
+    private Set<IAtom>       afix                = null;
+    private Set<IBond>       bfix                = null;
+    private boolean          useIdentTemplates   = true;
+    private boolean          alignMappedReaction = true;
 
     // show we orient the structure (false: keep de facto ring systems drawn
     // the right way up)
     private boolean selectOrientation = true;
 
-
     /**
      * Identity templates - for laying out primary ring system.
      */
@@ -176,6 +176,7 @@ public final void generateCoordinates(IAtomContainer mol) throws CDKException {
     /**
      * <p>Convenience method to generate 2D coordinates for a reaction. If atom-atom
      * maps are present on a reaction, the substructures are automatically aligned.</p>
+     * <p>This feature can be disabled by changing the {@link #setAlignMappedReaction(boolean)}</p>
      *
      * @param reaction reaction to layout
      * @throws CDKException problem with layout
@@ -186,6 +187,8 @@ public final void generateCoordinates(final IReaction reaction) throws CDKExcept
         for (IAtomContainer product : reaction.getProducts().atomContainers()) {
             setMolecule(product, false);
             generateCoordinates();
+            if (!alignMappedReaction)
+                continue;
             for (IBond bond : product.bonds()) {
                 Integer begidx = bond.getAtom(0).getProperty(CDKConstants.ATOM_ATOM_MAPPING);
                 Integer endidx = bond.getAtom(1).getProperty(CDKConstants.ATOM_ATOM_MAPPING);
@@ -375,6 +378,15 @@ public void setMolecule(IAtomContainer molecule) {
         setMolecule(molecule, true);
     }
 
+    /**
+     * Set whether reaction reactants should be allignned to their product.
+     *
+     * @param align align setting
+     */
+    public void setAlignMappedReaction(boolean align) {
+        this.alignMappedReaction = align;
+    }
+
     /**
      * Returns the molecule, usually used after a call of generateCoordinates()
      *