Better ringset prioritisation favouring heterocycles

cdk · Jun 26, 2016 · 9401728 · 9401728
1 parent 8675e1b
commit 9401728
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Showing 2 changed files with 85 additions and 30 deletions.
diff --git a/tool/sdg/src/main/java/org/openscience/cdk/layout/RingPlacer.java b/tool/sdg/src/main/java/org/openscience/cdk/layout/RingPlacer.java
@@ -40,6 +40,8 @@
 import javax.vecmath.Tuple2d;
 import javax.vecmath.Vector2d;
 import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Comparator;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
@@ -792,4 +794,67 @@ public AtomPlacer getAtomPlacer() {
     public void setAtomPlacer(AtomPlacer atomPlacer) {
         this.atomPlacer = atomPlacer;
     }
+
+
+    /**
+     * Sorts ring systems prioritising the most complex. To sort correctly,
+     * {@link #countHetero(List)} must first be invoked.
+     */
+    static final Comparator<IRingSet> RING_COMPARATOR = new Comparator<IRingSet>() {
+        @Override
+        public int compare(IRingSet a, IRingSet b) {
+
+            // polycyclic better
+            int cmp = Boolean.compare(a.getAtomContainerCount() == 1, b.getAtomContainerCount() == 1);
+            if (cmp != 0) return cmp;
+
+            // more hetero atoms better
+            Integer numHeteroRingA = a.getProperty(NUM_HETERO_RINGS);
+            Integer numHeteroRingB = b.getProperty(NUM_HETERO_RINGS);
+            if (numHeteroRingA == null) numHeteroRingA = 0;
+            if (numHeteroRingB == null) numHeteroRingB = 0;
+            cmp = -Integer.compare(numHeteroRingA, numHeteroRingB);
+            if (cmp != 0) return cmp;
+
+            // more hetero rings better
+            Integer numHeteroAtomA = a.getProperty(NUM_HETERO_ATOMS);
+            Integer numHeteroAtomB = b.getProperty(NUM_HETERO_ATOMS);
+            if (numHeteroAtomA == null) numHeteroAtomA = 0;
+            if (numHeteroAtomB == null) numHeteroAtomB = 0;
+            cmp = -Integer.compare(numHeteroAtomA, numHeteroAtomB);
+            if (cmp != 0) return cmp;
+
+            // more rings better
+            return -Integer.compare(a.getAtomContainerCount(), b.getAtomContainerCount());
+        }
+    };
+
+    private static final String NUM_HETERO_RINGS = "sdg:numHeteroRings";
+    private static final String NUM_HETERO_ATOMS = "sdg:numHeteroAtoms";
+
+    /**
+     * Counds the number of hetero atoms and hetero rings in a ringset. The
+     * properties {@code sdg:numHeteroRings} and {@code sdg:numHeteroAtoms}
+     * are set.
+     *
+     * @param rsets ring systems
+     */
+    static void countHetero(List<IRingSet> rsets) {
+        for (IRingSet rset : rsets) {
+            int numHeteroAtoms = 0;
+            int numHeteroRings = 0;
+            for (IAtomContainer ring : rset.atomContainers()) {
+                int prevNumHeteroAtoms = numHeteroAtoms;
+                for (IAtom atom : ring.atoms()) {
+                    Integer elem = atom.getAtomicNumber();
+                    if (elem != null && elem != 6 && elem != 1)
+                        numHeteroAtoms++;
+                }
+                if (numHeteroAtoms > prevNumHeteroAtoms)
+                    numHeteroRings++;
+            }
+            rset.setProperty(NUM_HETERO_ATOMS, numHeteroAtoms);
+            rset.setProperty(NUM_HETERO_RINGS, numHeteroRings);
+        }
+    }
 }
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
@@ -629,44 +629,34 @@ private void seedLayout() throws CDKException {
             logger.debug("*** Start of handling rings. ***");
             prepareRingSystems();
 
-            // We got our ring systems now, sort by number of bonds (largest first)
-            Collections.sort(ringSystems, new Comparator<IRingSet>() {
-                @Override
-                public int compare(IRingSet a, IRingSet b) {
-                    return -Integer.compare(AtomContainerSetManipulator.getBondCount(a),
-                                            AtomContainerSetManipulator.getBondCount(b));
-                }
-            });
-
-             // Do the layout for the larges/most complex connected ring system
-            int largest = 0;
-            int numComplex = 0;
-            int largestSize = (ringSystems.get(0)).getAtomContainerCount();
-            if (largestSize > 1)
-                numComplex++;
-            logger.debug("We have " + ringSystems.size() + " ring system(s).");
-            for (int f = 1; f < ringSystems.size(); f++) {
-                logger.debug("RingSet " + f + " has size " + (ringSystems.get(f)).getAtomContainerCount());
-                int size = (ringSystems.get(f)).getAtomContainerCount();
-                if (size > 1)
-                    numComplex++;
-                if (size > largestSize) {
-                    largestSize = (ringSystems.get(f)).getAtomContainerCount();
-                    largest = f;
+            // We got our ring systems now choose the best one based on size and
+            // number of heteroatoms
+            RingPlacer.countHetero(ringSystems);
+            Collections.sort(ringSystems, RingPlacer.RING_COMPARATOR);
+
+            int respect = layoutRingSet(firstBondVector, ringSystems.get(0));
+
+            // rotate monocyclic and when >= 4 polycyclic
+            if (respect == 1) {
+                if (ringSystems.get(0).getAtomContainerCount() == 1) {
+                    respect = 0;
+                } else if (ringSystems.size() >= 4) {
+                    int numPoly = 0;
+                    for (IRingSet rset : ringSystems)
+                        if (rset.getAtomContainerCount() > 1)
+                            numPoly++;
+                    if (numPoly >= 4)
+                        respect = 0;
                 }
             }
-            logger.debug("Largest RingSystem is at RingSet collection's position " + largest);
-            logger.debug("Size of Largest RingSystem: " + largestSize);
-
-            int respect = layoutRingSet(firstBondVector, ringSystems.get(largest));
 
-            if (respect == 1 && numComplex == 1 || respect == 2)
+            if (respect == 1 || respect == 2)
                 selectOrientation = false;
 
             logger.debug("First RingSet placed");
 
             // place of all the directly connected atoms of this ring system
-            ringPlacer.placeRingSubstituents(ringSystems.get(largest), bondLength);
+            ringPlacer.placeRingSubstituents(ringSystems.get(0), bondLength);
         } else {
 
             logger.debug("*** Start of handling purely aliphatic molecules. ***");