Still quite slow but improved API to allow InChI options to be passed…

… in. We can't remove the old method that forces slow execution but it has now be deprecated. New tests added to demonstrate correct exectution.

tool/tautomer/src/main/java/org/openscience/cdk/tautomers/InChITautomerGenerator.java

@@ -31,7 +31,6 @@
 import org.openscience.cdk.graph.invariant.InChINumbersTools;
 import org.openscience.cdk.inchi.InChIGenerator;
 import org.openscience.cdk.inchi.InChIGeneratorFactory;
-import org.openscience.cdk.inchi.InChIToStructure;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IAtomType;
@@ -56,12 +55,43 @@
  * @cdk.module tautomer
  * @cdk.githash
  */
-public class InChITautomerGenerator {
+public final class InChITautomerGenerator {
 
     private final static ILoggingTool LOGGER = LoggingToolFactory.createLoggingTool(InChITautomerGenerator.class);
 
     private static final SmilesGenerator CANSMI = new SmilesGenerator(SmiFlavor.Canonical);
 
+    /** Generate InChI with -KET (keto-enol tautomers) option. */
+    public static final int KETO_ENOL      = 0x1;
+
+    /** Generate InChI with -15T (1,5-shift tautomers) option. */
+    public static final int ONE_FIVE_SHIFT = 0x2;
+
+    private final int flags;
+
+    /**
+     * Create a tautomer generator specifygin whether to enable, keto-enol (-KET) and 1,5-shifts (-15T).
+     *
+     * <pre>{@code
+     * // enabled -KET option
+     * InChITautomerGenerator tautgen = new InChITautomerGenerator(InChITautomerGenerator.KETO_ENOL);
+     * // enabled both -KET and -15T
+     * InChITautomerGenerator tautgen = new InChITautomerGenerator(InChITautomerGenerator.KETO_ENOL | InChITautomerGenerator.ONE_FIVE_SHIFT);
+     * }</pre>
+     *
+     * @param flags the options
+     */
+    public InChITautomerGenerator(int flags) {
+        this.flags = flags;
+    }
+
+    /**
+     * Create a tautomer generator, keto-enol (-KET) and 1,5-shifts (-15T) are disabled.
+     */
+    public InChITautomerGenerator() {
+        this(0);
+    }
+
     /**
      * Public method to get tautomers for an input molecule, based on the InChI which will be calculated by JNI-InChI.
      * @param mol molecule for which to generate tautomers
@@ -71,7 +101,13 @@ public class InChITautomerGenerator {
      */
     public List<IAtomContainer> getTautomers(IAtomContainer mol) throws CDKException, CloneNotSupportedException {
 
-        InChIGenerator gen   = InChIGeneratorFactory.getInstance().getInChIGenerator(mol, "");
+        String opt = "";
+        if ((flags & KETO_ENOL) != 0)
+            opt += " -KET";
+        if ((flags & ONE_FIVE_SHIFT) != 0)
+            opt += " -15T";
+
+        InChIGenerator gen   = InChIGeneratorFactory.getInstance().getInChIGenerator(mol, opt);
         String         inchi = gen.getInchi();
         String         aux   = gen.getAuxInfo();
 
@@ -84,6 +120,18 @@ public List<IAtomContainer> getTautomers(IAtomContainer mol) throws CDKException
         return getTautomers(mol, inchi, amap);
     }
 
+    /**
+     * This method is slower than recalculating the InChI with {@link #getTautomers(IAtomContainer)} as the mapping
+     * between the two can be found more efficiently.
+     *
+     * @param mol
+     * @param inchi
+     * @return
+     * @throws CDKException
+     * @throws CloneNotSupportedException
+     * @deprecated use {@link #getTautomers(IAtomContainer)} directly
+     */
+    @Deprecated
     public List<IAtomContainer> getTautomers(IAtomContainer mol, String inchi) throws CDKException, CloneNotSupportedException {
         return getTautomers(mol, inchi, null);
     }

tool/tautomer/src/test/java/org/openscience/cdk/tautomers/InChITautomerGeneratorTest.java

@@ -71,6 +71,16 @@ private List<IAtomContainer> unitTestWithInchiProvided(String smiles, String inc
         return tautomers;
     }
 
+    private List<IAtomContainer> unitTestWithoutInchiProvided(String smiles, int flags, int tautCountExpected)
+            throws Exception {
+        IAtomContainer container = smilesParser.parseSmiles(smiles);
+        AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(container);
+        InChITautomerGenerator tautegen = new InChITautomerGenerator(flags);
+        List<IAtomContainer> tautomers = tautegen.getTautomers(container);
+        Assert.assertEquals(tautCountExpected, tautomers.size());
+        return tautomers;
+    }
+
     @Test
     public void test1() throws Exception {
         unitTestWithInchiProvided("NC1=CC(N)=NC(O)=N1", "InChI=1S/C4H6N4O/c5-2-1-3(6)8-4(9)7-2/h1H,(H5,5,6,7,8,9)", 5);
@@ -108,6 +118,37 @@ public void test6() throws Exception {
                         + "h2-10,15H,1H3,(H2,11,20)(H,17,21,22)", 6);
     }
 
+    @Test
+    public void test1_fast() throws Exception {
+        unitTestWithoutInchiProvided("NC1=CC(N)=NC(O)=N1", 0, 5);
+    }
+
+    @Test
+    public void test2_fast() throws Exception {
+        unitTestWithoutInchiProvided("CCCN1C2=C(NC=N2)C(=O)NC1=O", 0, 8);
+    }
+
+    @Test
+    public void test3_fast() throws Exception {
+        unitTestWithoutInchiProvided("CCNC(=N)NC", 0, 3);
+    }
+
+    @Test
+    public void test4_fast() throws Exception {
+        unitTestWithoutInchiProvided("O=C1NC=CC(=O)N1", 0, 6);
+    }
+
+    @Test
+    public void test5_fast() throws Exception {
+        unitTestWithoutInchiProvided("CCN1CCOC2=CC(NC3=NCCN3)=CC=C12", 0, 2);
+    }
+
+    @Test
+    public void test6_fast() throws Exception {
+        //Warfarin: not you need to create the InChI with option KET to get the ketone/hydroxyl tautomerism
+        unitTestWithoutInchiProvided("CC(=O)CC(C1=CC=CC=C1)C1=C(O)C2=C(OC1=O)C=CC=C2", InChITautomerGenerator.KETO_ENOL,  6);
+    }
+
     @Test(expected = CDKException.class)
     // bail out on dots in formula
     public void testFail1() throws Exception {