Report a version/param description for fingerprints.

cdk · Apr 30, 2017 · 5995e07 · 5995e07
1 parent 05d316d
commit 5995e07
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Showing 9 changed files with 123 additions and 15 deletions.
diff --git a/base/core/src/main/java/org/openscience/cdk/fingerprint/IFingerprinter.java b/base/core/src/main/java/org/openscience/cdk/fingerprint/IFingerprinter.java
@@ -39,6 +39,24 @@
  */
 public interface IFingerprinter {
 
+    /**
+     * Generate a fingerprint type version description in chemfp's FPS format. We
+     * report the library version rather than an individual version per fingerprint,
+     * although this is awkward as many fingerprint's don't/won't change between releases
+     * and we can not keep comptability we guarantee we document how the fingerprint was
+     * encoded.
+     *
+     * <br>
+     * Examples:
+     * <pre>
+     * #type=CDK-Fingerprinter/2.0 searchDepth=7 pathLimit=2000 hashPseudoAtoms=true
+     * #type=CDK-CircularFingerprint/2.0 classType=ECFP4
+     * </pre>
+     *
+     * @return version description.
+     */
+    String getVersionDescription();
+
     /**
      * Generate a binary fingerprint as a bit. This method will usually delegate to
      * {@link #getBitFingerprint(IAtomContainer)} and invoke

diff --git a/base/standard/src/main/java/org/openscience/cdk/fingerprint/AbstractFingerprinter.java b/base/standard/src/main/java/org/openscience/cdk/fingerprint/AbstractFingerprinter.java
@@ -23,13 +23,40 @@
 
 package org.openscience.cdk.fingerprint;
 
+import org.openscience.cdk.CDK;
 import org.openscience.cdk.exception.CDKException;
 import org.openscience.cdk.interfaces.IAtomContainer;
 
 import java.util.BitSet;
+import java.util.Collections;
+import java.util.List;
+import java.util.Map;
 
 public abstract class AbstractFingerprinter implements IFingerprinter {
 
+    /**
+     * Base classes should override this method to report the parameters they
+     * are configured with.
+     *
+     * @return The key=value pairs of configured parameters
+     */
+    protected List<Map.Entry<String,String>> getParameters() {
+        return Collections.emptyList();
+    }
+
+    @Override
+    public final String getVersionDescription() {
+        StringBuilder sb = new StringBuilder();
+        sb.append("CDK-")
+          .append(getClass().getSimpleName())
+          .append("/")
+          .append(CDK.getVersion()); // could version fingerprints separetely
+        for (Map.Entry<String,String> param : getParameters()) {
+            sb.append(' ').append(param.getKey()).append('=').append(param.getValue());
+        }
+        return sb.toString();
+    }
+
     /** {@inheritDoc} */
     @Override
     public BitSet getFingerprint(IAtomContainer mol) throws CDKException {

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
@@ -35,7 +35,10 @@
 import org.openscience.cdk.tools.LoggingToolFactory;
 import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
 
+import java.util.AbstractMap;
+import java.util.AbstractMap.SimpleImmutableEntry;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.BitSet;
 import java.util.Collections;
 import java.util.HashMap;
@@ -142,6 +145,15 @@ public Fingerprinter(int size, int searchDepth) {
 
     }
 
+    @Override
+    protected List<Map.Entry<String, String>> getParameters() {
+        return Arrays.<Map.Entry<String,String>>asList(
+            new SimpleImmutableEntry<>("searchDepth", Integer.toString(searchDepth)),
+            new SimpleImmutableEntry<>("pathLimit", Integer.toString(pathLimit)),
+            new SimpleImmutableEntry<>("hashPseudoAtoms", Boolean.toString(hashPseudoAtoms))
+        );
+    }
+
     /**
      * Generates a fingerprint of the default size for the given AtomContainer.
      *

diff --git a/base/standard/src/main/java/org/openscience/cdk/fingerprint/HybridizationFingerprinter.java b/base/standard/src/main/java/org/openscience/cdk/fingerprint/HybridizationFingerprinter.java
@@ -23,23 +23,9 @@
  */
 package org.openscience.cdk.fingerprint;
 
-import java.util.ArrayList;
-import java.util.BitSet;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Random;
-import java.util.Set;
-
-import org.openscience.cdk.exception.CDKException;
-import org.openscience.cdk.graph.PathTools;
-import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IAtomType.Hybridization;
 import org.openscience.cdk.interfaces.IBond;
-import org.openscience.cdk.interfaces.IPseudoAtom;
-import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
 import org.openscience.cdk.tools.periodictable.PeriodicTable;
 
 /**

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
@@ -26,16 +26,17 @@
 import java.math.BigInteger;
 import java.util.BitSet;
 
+import org.hamcrest.CoreMatchers;
 import org.junit.Assert;
 import org.junit.Test;
 import org.junit.experimental.categories.Category;
 import org.openscience.cdk.Atom;
+import org.openscience.cdk.CDK;
 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.exception.InvalidSmilesException;
 import org.openscience.cdk.graph.AtomContainerAtomPermutor;
 import org.openscience.cdk.graph.AtomContainerBondPermutor;
 import org.openscience.cdk.interfaces.IAtomContainer;
@@ -53,6 +54,7 @@
 import org.openscience.cdk.tools.manipulator.ChemFileManipulator;
 
 import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertThat;
 import static org.junit.Assert.assertTrue;
 
 /**
@@ -407,4 +409,13 @@ public static void main(String[] args) throws Exception {
         assertFalse(FingerprinterTool.isSubset(fp4, fp3));
         assertFalse(FingerprinterTool.isSubset(fp3, fp4));
     }
+
+    @Test public void testVersion() {
+        Fingerprinter fpr = new Fingerprinter(1024, 7);
+        fpr.setPathLimit(2000);
+        fpr.setHashPseudoAtoms(true);
+        String expected = "CDK-Fingerprinter/" + CDK.getVersion() + " searchDepth=7 pathLimit=2000 hashPseudoAtoms=true";
+        assertThat(fpr.getVersionDescription(),
+                   CoreMatchers.is(expected));
+    }
 }
diff --git a/...ptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/CircularFingerprinter.java b/...ptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/CircularFingerprinter.java
@@ -28,8 +28,11 @@
 
 package org.openscience.cdk.fingerprint;
 
+import java.util.AbstractMap;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.BitSet;
+import java.util.Collections;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
@@ -188,6 +191,24 @@ public CircularFingerprinter(int classType, int len) {
         this.length = len;
     }
 
+    @Override
+    protected List<Map.Entry<String, String>> getParameters() {
+        String type = null;
+        switch (classType) {
+            case CLASS_ECFP0: type = "ECFP0"; break;
+            case CLASS_ECFP2: type = "ECFP2"; break;
+            case CLASS_ECFP4: type = "ECFP4"; break;
+            case CLASS_ECFP6: type = "ECFP6"; break;
+            case CLASS_FCFP0: type = "FCFP0"; break;
+            case CLASS_FCFP2: type = "FCFP2"; break;
+            case CLASS_FCFP4: type = "FCFP4"; break;
+            case CLASS_FCFP6: type = "FCFP6"; break;
+        }
+        return Collections.<Map.Entry<String,String>>singletonList(
+            new AbstractMap.SimpleImmutableEntry<>("classType", type)
+        );
+    }
+
     /**
      * Calculates the fingerprints for the given {@link IAtomContainer}, and stores them for subsequent retrieval.
      *

diff --git a/.../fingerprint/src/test/java/org/openscience/cdk/fingerprint/CircularFingerprinterTest.java b/.../fingerprint/src/test/java/org/openscience/cdk/fingerprint/CircularFingerprinterTest.java
@@ -42,7 +42,10 @@
 import java.util.zip.ZipEntry;
 import java.util.zip.ZipInputStream;
 
+import org.hamcrest.CoreMatchers;
+import org.junit.Assert;
 import org.openscience.cdk.AtomContainer;
+import org.openscience.cdk.CDK;
 import org.openscience.cdk.CDKTestCase;
 import org.openscience.cdk.SlowTest;
 import org.openscience.cdk.exception.CDKException;
@@ -336,4 +339,11 @@ static IAtom atom(String symbol, int h, double x, double y) {
         return a;
     }
 
+    @Test public void testVersion() {
+        IFingerprinter fpr = new CircularFingerprinter(CircularFingerprinter.CLASS_ECFP4);
+        String expected = "CDK-CircularFingerprinter/" + CDK.getVersion() + " classType=ECFP4";
+        Assert.assertThat(fpr.getVersionDescription(),
+                          CoreMatchers.is(expected));
+    }
+
 }
diff --git a/...iptor/signature/src/main/java/org/openscience/cdk/fingerprint/SignatureFingerprinter.java b/...iptor/signature/src/main/java/org/openscience/cdk/fingerprint/SignatureFingerprinter.java
@@ -22,7 +22,11 @@
  */
 package org.openscience.cdk.fingerprint;
 
+import java.util.AbstractMap;
+import java.util.Arrays;
+import java.util.Collections;
 import java.util.HashMap;
+import java.util.List;
 import java.util.Map;
 
 import org.openscience.cdk.exception.CDKException;
@@ -57,6 +61,14 @@ public SignatureFingerprinter(int depth) {
         this.signatureDepth = depth;
     }
 
+
+    @Override
+    protected List<Map.Entry<String, String>> getParameters() {
+        return Collections.<Map.Entry<String,String>>singletonList(
+            new AbstractMap.SimpleImmutableEntry<>("signatureDepth", Integer.toString(signatureDepth))
+        );
+    }
+
     @Override
     public IBitFingerprint getBitFingerprint(IAtomContainer atomContainer) throws CDKException {
         return new IntArrayFingerprint(getRawFingerprint(atomContainer));

diff --git a/storage/smiles/src/main/java/org/openscience/cdk/fingerprint/LingoFingerprinter.java b/storage/smiles/src/main/java/org/openscience/cdk/fingerprint/LingoFingerprinter.java
@@ -30,7 +30,11 @@
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.smiles.SmilesGenerator;
 
+import java.util.AbstractMap;
+import java.util.Arrays;
+import java.util.Collections;
 import java.util.HashMap;
+import java.util.List;
 import java.util.Map;
 import java.util.regex.Pattern;
 
@@ -74,6 +78,13 @@ public LingoFingerprinter(int n) {
         this.n = n;
     }
 
+    @Override
+    protected List<Map.Entry<String, String>> getParameters() {
+        return Collections.<Map.Entry<String,String>>singletonList(
+            new AbstractMap.SimpleImmutableEntry<>("ngramLength", Integer.toString(n))
+        );
+    }
+
     @Override
     public IBitFingerprint getBitFingerprint(IAtomContainer iAtomContainer) throws CDKException {
         return FingerprinterTool.makeBitFingerprint(getRawFingerprint(iAtomContainer));