Improve alignment of mapped reaction layout (don't crash).

cdk · Jul 20, 2018 · c5c4567 · c5c4567
1 parent dd41d4c
commit c5c4567
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Showing 2 changed files with 67 additions and 1 deletion.
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
@@ -63,11 +63,13 @@
 import javax.vecmath.Point2d;
 import javax.vecmath.Vector2d;
 import java.util.AbstractMap.SimpleImmutableEntry;
+import java.util.ArrayDeque;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
 import java.util.Collections;
 import java.util.Comparator;
+import java.util.Deque;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Iterator;
@@ -288,12 +290,58 @@ public final void generateCoordinates(final IReaction reaction) throws CDKExcept
                                 }
                             }
                         }
-                        // XXX: can do better
+
                         afix.clear();
                         for (IBond bond : bfix) {
                             afix.put(bond.getBegin(), null);
                             afix.put(bond.getEnd(), null);
                         }
+
+                        int[] parts2 = new int[mol.getAtomCount()];
+                        int numParts = 0;
+                        Deque<IAtom> queue = new ArrayDeque<>();
+                        for (IAtom atom : afix.keySet()) {
+                            if (parts2[mol.indexOf(atom)] != 0)
+                                continue;
+                            parts2[mol.indexOf(atom)] = ++numParts;
+                            for (IBond bond : mol.getConnectedBondsList(atom)) {
+                                if (bfix.contains(bond))
+                                    queue.add(bond.getOther(atom));
+                            }
+                            while (!queue.isEmpty()) {
+                                atom = queue.poll();
+                                if (parts2[mol.indexOf(atom)] != 0)
+                                    continue;
+                                parts2[mol.indexOf(atom)] = numParts;
+                                for (IBond bond : mol.getConnectedBondsList(atom)) {
+                                    if (bfix.contains(bond))
+                                        queue.add(bond.getOther(atom));
+                                }
+                            }
+                        }
+
+                        if (numParts > 1) {
+                            int best     = 0;
+                            int bestSize = 0;
+                            for (int part = 1; part <= numParts; part++) {
+                                int size = 0;
+                                for (int i = 0; i < parts2.length; i++) {
+                                    if (parts2[i] == part)
+                                        ++size;
+                                }
+                                if (size > bestSize) {
+                                    bestSize = size;
+                                    best = part;
+                                }
+                            }
+
+                            for (IAtom atom : new ArrayList<>(afix.keySet())) {
+                                if (parts2[mol.indexOf(atom)] != best) {
+                                    afix.remove(atom);
+                                    bfix.removeAll(mol.getConnectedBondsList(atom));
+                                }
+                            }
+                        }
                     }
                 }
 

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 +37,7 @@
 import org.openscience.cdk.interfaces.IChemModel;
 import org.openscience.cdk.interfaces.IChemSequence;
 import org.openscience.cdk.interfaces.IDoubleBondStereochemistry;
+import org.openscience.cdk.interfaces.IReaction;
 import org.openscience.cdk.interfaces.IStereoElement;
 import org.openscience.cdk.io.CMLReader;
 import org.openscience.cdk.io.IChemObjectReader.Mode;
@@ -52,6 +53,7 @@
 import org.openscience.cdk.smiles.SmilesParser;
 import org.openscience.cdk.stereo.StereoElementFactory;
 import org.openscience.cdk.templates.TestMoleculeFactory;
+import org.openscience.cdk.tools.manipulator.ReactionManipulator;
 
 import javax.vecmath.Point2d;
 import javax.vecmath.Vector2d;
@@ -1270,4 +1272,20 @@ public void setBondLength() {
         StructureDiagramGenerator sdg = new StructureDiagramGenerator();
         sdg.setBondLength(2);
     }
+
+    /**
+     * Reaction from US20050272744A1 [0195], a bond is broken and made. The
+     * reaction layout should not crash.
+     */
+    @Test
+    public void alignReactionBondBrokenAndMade() throws CDKException {
+        String smiles = "[CH3:18][NH:19][CH3:20].[cH:14]1[cH:13][cH:12][c:11]([cH:16][cH:15]1)[CH2:10][O:9][C:1](=[O:17])[NH:2][C@H:3]2[CH2:8][C:6](=[O:7])[O:5][CH2:4]2>C1CCOC1>[CH3:18][N:19]([CH3:20])[C:6](=[O:7])[CH2:8][C@H:3]([CH2:4][OH:5])[NH:2][C:1](=[O:17])[O:9][CH2:10][c:11]1[cH:12][cH:13][cH:14][cH:15][cH:16]1";
+        SmilesParser smipar = new SmilesParser(SilentChemObjectBuilder.getInstance());
+        IReaction reaction =  smipar.parseReactionSmiles(smiles);
+        StructureDiagramGenerator sdg = new StructureDiagramGenerator();
+        sdg.setAlignMappedReaction(true);
+        sdg.generateCoordinates(reaction);
+        for (IAtom atom : ReactionManipulator.toMolecule(reaction).atoms())
+            assertNotNull(atom.getPoint2d());
+    }
 }