Extend standard-substructure for countable MACCS

- Remove static modifier for the smarts pattern, to allow reuse of classe.
- Countable MACCS fingerprints are supported now as well, following the
  SMARTS list structure given before.

descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/StandardSubstructureSets.java

@@ -16,19 +16,46 @@
  * @cdk.githash
  */
 public class StandardSubstructureSets {
-
-    private static String[] smarts = null;
-
     /**
      * The functional groups.
      *
      * @return A set of the functional groups.
      * @throws Exception if there is an error parsing SMILES for the functional groups
      */
     public static String[] getFunctionalGroupSMARTS() throws Exception {
-        if (smarts != null) return smarts;
+        return readSMARTSPattern("org/openscience/cdk/fingerprint/data/SMARTS_InteLigand.txt");
+    }
+
+    /**
+     * Subset of the MACCS fingerprint definitions. The subset encompasses the pattern
+     * that are countable:
+     * <ul>
+     *     <li>Patterns have obvious counting nature, <i>e.g., 6-Ring, C=O, etc.</i></li>
+     *     <li>Patterns like <i>"Is there at least 1 of this and that?", "Are there at least 2 ..."</i> etc. are merged</li>
+     *     <li>Patterns clearly corresponding to binary properties, <i>e.g., actinide group ([Ac,Th,Pa,...]), isotope, etc.,</i> have been removed.</li>
+     * </ul>
+     *
+     *
+     * @return Countable subset of the MACCS fingerprint definition
+     * @throws Exception if there is an error parsing SMILES patterns
+     */
+    public static String[] getCountableMACCSSMARTS() throws Exception {
+        return readSMARTSPattern("org/openscience/cdk/fingerprint/data/SMARTS_countable_MACCS_keys.txt");
+    }
 
-        String filename = "org/openscience/cdk/fingerprint/data/SMARTS_InteLigand.txt";
+    /**
+     * Load a list of SMARTS patterns from the specified file.
+     *
+     * Each line in the file corresponds to a pattern with the following structure:
+     * PATTERN_DESCRIPTION: SMARTS_PATTERN, <i>e.g., Thioketone: [#6][CX3](=[SX1])[#6]</i>
+     *
+     * Empty lines and lines starting with a "#" are skipped.
+     *
+     * @param filename list of the SMARTS pattern to be loaded
+     * @return list of strings containing the loaded SMARTS pattern
+     * @throws Exception if there is an error parsing SMILES patterns
+     */
+    private static String[] readSMARTSPattern(String filename) throws Exception {
         InputStream ins = StandardSubstructureSets.class.getClassLoader().getResourceAsStream(filename);
         BufferedReader reader = new BufferedReader(new InputStreamReader(ins));
 
@@ -43,9 +70,6 @@ public static String[] getFunctionalGroupSMARTS() throws Exception {
             s.append(toks[toks.length - 1]);
             tmp.add(s.toString().trim());
         }
-        smarts = tmp.toArray(new String[]{});
-        return smarts;
-
+        return tmp.toArray(new String[]{});
     }
-
 }

descriptor/fingerprint/src/test/java/org/openscience/cdk/fingerprint/StandardSubstructureSetsTest.java

@@ -39,4 +39,12 @@ public void testGetFunctionalGroupSubstructureSet() throws Exception {
         Assert.assertEquals(307, smarts.length);
     }
 
+    @Test
+    public void testGetCountableMACCSSMARTSSubstructureSet() throws Exception {
+        String[] smarts = null;
+        smarts = StandardSubstructureSets.getCountableMACCSSMARTS();
+        Assert.assertNotNull(smarts);
+        Assert.assertEquals(141, smarts.length); // currently two smarts are ignored!
+    }
+
 }