Use SMSD path fingerprints in ReactionFingerprinter and ReactionContainer

Replace CDK CircularFingerprinter/Fingerprinter with SMSD SearchEngine.pathFingerprint
in ReactionFingerprinter and ReactionContainer for lighter CDK dependency.
GameTheoryEngine and StandardizeReaction retain CDK ECFP4 where threshold-sensitive
similarity and deterministic cache keys are required. All 163 tests pass.

Author: asad

pom.xml

@@ -151,11 +151,6 @@
             <artifactId>cdk-isomorphism</artifactId>
             <version>${cdk.version}</version>
         </dependency>
-        <dependency>
-            <groupId>org.openscience.cdk</groupId>
-            <artifactId>cdk-fingerprint</artifactId>
-            <version>${cdk.version}</version>
-        </dependency>
         <dependency>
             <groupId>org.openscience.cdk</groupId>
             <artifactId>cdk-atomtype</artifactId>
@@ -186,6 +181,11 @@
             <artifactId>cdk-inchi</artifactId>
             <version>${cdk.version}</version>
         </dependency>
+        <dependency>
+            <groupId>org.openscience.cdk</groupId>
+            <artifactId>cdk-fingerprint</artifactId>
+            <version>${cdk.version}</version>
+        </dependency>
 
         <dependency>
             <groupId>com.bioinceptionlabs</groupId>

src/main/java/com/bioinceptionlabs/reactionblast/fingerprints/ReactionFingerprinter.java

@@ -22,7 +22,7 @@
 import java.util.BitSet;
 import org.openscience.cdk.Reaction;
 import org.openscience.cdk.exception.CDKException;
-import org.openscience.cdk.fingerprint.CircularFingerprinter;
+import com.bioinception.smsd.core.SearchEngine;
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IAtomContainerSet;
 import org.openscience.cdk.interfaces.IReaction;
@@ -34,7 +34,6 @@
 import static java.lang.String.valueOf;
 import static java.lang.System.currentTimeMillis;
 import static java.util.logging.Level.SEVERE;
-import static org.openscience.cdk.fingerprint.CircularFingerprinter.CLASS_ECFP4;
 import static org.openscience.cdk.geometry.GeometryUtil.has2DCoordinates;
 import static org.openscience.cdk.graph.ConnectivityChecker.isConnected;
 import static org.openscience.cdk.tools.LoggingToolFactory.createLoggingTool;
@@ -212,6 +211,9 @@ public static interface IFingerprintGenerator {
      */
     public static class FingerprintGenerator implements IFingerprintGenerator {
 
+        private static final int FP_PATH_LENGTH = 7;
+        private static final int FP_SIZE = 1024;
+
         private final static ILoggingTool LOGGER
                 = createLoggingTool(FingerprintGenerator.class);
 
@@ -221,20 +223,13 @@ public static class FingerprintGenerator implements IFingerprintGenerator {
          * @return
          */
         public static int getFingerprinterSize() {
-            return new CircularFingerprinter(CLASS_ECFP4).getSize();
+            return FP_SIZE;
         }
 
-        //define the FINGERPRINT_SIZE of the fingerprint
-        //NOTE: this should be a multiple of 64 and preferably not 1024 or 2048
-        //as for these values we often get the random numbers for one-atom or
-        //two-atom paths the same!
-        final CircularFingerprinter fingerprinter;
-
         /**
          *
          */
         public FingerprintGenerator() {
-            fingerprinter = new CircularFingerprinter(CLASS_ECFP4);
         }
 
         /**
@@ -255,11 +250,28 @@ public BitSet getFingerprint(IAtomContainer mol) throws CDKException {
                     LOGGER.debug("Disconnected components needs to be layout separately");
                 }
             }
-            return fingerprinter.getBitFingerprint(mol).asBitSet();
+            long[] fp = SearchEngine.pathFingerprint(mol, FP_PATH_LENGTH, FP_SIZE);
+            return longArrayToBitSet(fp);
         }
 
     }
 
+    /**
+     * Convert SMSD long[] fingerprint to BitSet
+     */
+    public static BitSet longArrayToBitSet(long[] fp) {
+        BitSet bs = new BitSet(fp.length * 64);
+        for (int i = 0; i < fp.length; i++) {
+            long word = fp[i];
+            for (int bit = 0; bit < 64; bit++) {
+                if ((word & (1L << bit)) != 0) {
+                    bs.set(i * 64 + bit);
+                }
+            }
+        }
+        return bs;
+    }
+
 
 
     /**

src/main/java/com/bioinceptionlabs/reactionblast/mapping/ReactionContainer.java

@@ -22,8 +22,8 @@
 import java.util.Objects;
 import java.util.Set;
 import java.util.TreeMap;
+import com.bioinception.smsd.core.SearchEngine;
 import org.openscience.cdk.exception.CDKException;
-import org.openscience.cdk.fingerprint.Fingerprinter;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IReaction;
@@ -1144,8 +1144,8 @@ private IAtomContainer setProperty(IAtomContainer molecule) throws Exception {
                         Single Atom fingerprints
                          */
                         if (fingerprint_Present_Mol.isEmpty()) {
-                            Fingerprinter fingerprinter = new Fingerprinter();
-                            fingerprint_Present_Mol = fingerprinter.getBitFingerprint(molecule).asBitSet();
+                            long[] fp = SearchEngine.pathFingerprint(molecule, 7, 1024);
+                            fingerprint_Present_Mol = com.bioinceptionlabs.reactionblast.fingerprints.ReactionFingerprinter.longArrayToBitSet(fp);
                         }
                         //Loop for Unique Mol ID Creation
                         if (!fingerprint_Present_Mol.isEmpty()) {