Merge pull request #164 from cdk/patch/pathfplimit

Looks good.
cdk · Oct 6, 2015 · ae42093 · ae42093
2 parents 055c1dd + 73371fb
commit ae42093
Show file tree

Hide file tree

Showing 2 changed files with 12 additions and 3 deletions.
diff --git a/base/standard/src/main/java/org/openscience/cdk/fingerprint/Fingerprinter.java b/base/standard/src/main/java/org/openscience/cdk/fingerprint/Fingerprinter.java
@@ -93,7 +93,7 @@
 public class Fingerprinter implements IFingerprinter {
 
     /** Throw an exception if too many paths (per atom) are generated. */
-    private final static int                 PATH_LIMIT           = 150;
+    private final static int                 DEFAULT_PATH_LIMIT   = 1500;
 
     /** The default length of created fingerprints. */
     public final static int                  DEFAULT_SIZE         = 1024;
@@ -102,9 +102,11 @@ public class Fingerprinter implements IFingerprinter {
 
     private int                              size;
     private int                              searchDepth;
+    private int                              pathLimit = DEFAULT_PATH_LIMIT;
 
     static int                               debugCounter         = 0;
 
+
     private static ILoggingTool              logger               = LoggingToolFactory
                                                                           .createLoggingTool(Fingerprinter.class);
 
@@ -216,7 +218,7 @@ protected int[] findPathes(IAtomContainer container, int searchDepth) throws CDK
         Map<IAtom, Map<IAtom, IBond>> cache = new HashMap<IAtom, Map<IAtom, IBond>>();
 
         for (IAtom startAtom : container.atoms()) {
-            List<List<IAtom>> p = PathTools.getLimitedPathsOfLengthUpto(container, startAtom, searchDepth, PATH_LIMIT);
+            List<List<IAtom>> p = PathTools.getLimitedPathsOfLengthUpto(container, startAtom, searchDepth, pathLimit);
             for (List<IAtom> path : p) {
                 StringBuffer sb = new StringBuffer();
                 IAtom x = path.get(0);
@@ -309,6 +311,10 @@ protected String getBondSymbol(IBond bond) {
         return bondSymbol;
     }
 
+    public void setPathLimit(int limit) {
+        this.pathLimit = limit;
+    }
+
     public int getSearchDepth() {
         return searchDepth;
     }

diff --git a/base/test-standard/src/test/java/org/openscience/cdk/fingerprint/FingerprinterTest.java b/base/test-standard/src/test/java/org/openscience/cdk/fingerprint/FingerprinterTest.java
@@ -28,10 +28,12 @@
 
 import org.junit.Assert;
 import org.junit.Test;
+import org.junit.experimental.categories.Category;
 import org.openscience.cdk.Atom;
 import org.openscience.cdk.ChemFile;
 import org.openscience.cdk.DefaultChemObjectBuilder;
 import org.openscience.cdk.Reaction;
+import org.openscience.cdk.SlowTest;
 import org.openscience.cdk.exception.CDKException;
 import org.openscience.cdk.graph.AtomContainerAtomPermutor;
 import org.openscience.cdk.graph.AtomContainerBondPermutor;
@@ -165,7 +167,8 @@ public void testBug1851202() throws Exception {
         Assert.assertNotNull(fingerprinter.getBitFingerprint(product));
     }
 
-    @Test(timeout = 500, expected = CDKException.class)
+    @Test(expected = CDKException.class)
+    @Category(SlowTest.class)
     public void testbug2917084() throws Exception {
         String filename1 = "data/mdl/boronBuckyBall.mol";
         logger.info("Testing: " + filename1);