Merge pull request #231 from cdk/patch/smarts-ecfp

extracting the substructure patterns of CircularFingerprint.

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

@@ -30,18 +30,23 @@
 
 import java.util.ArrayList;
 import java.util.BitSet;
+import java.util.HashMap;
+import java.util.List;
 import java.util.Map;
 import java.util.TreeMap;
 import java.util.zip.CRC32;
 
 import javax.vecmath.Point2d;
 import javax.vecmath.Point3d;
 
+import com.google.common.primitives.Ints;
 import org.openscience.cdk.exception.CDKException;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IBond;
 
+
+
 /**
  *  <p>Circular fingerprints: for generating fingerprints that are functionally equivalent to ECFP-2/4/6 and FCFP-2/4/6
  *  fingerprints, which are partially described by Rogers et al. {@cdk.cite Rogers2010}.
@@ -112,6 +117,7 @@ public FP(int hashCode, int iteration, int[] atoms) {
             this.atoms = atoms;
         }
     }
+
 
     // ------------ private members ------------
 
@@ -1238,7 +1244,7 @@ private int findBond(int a1, int a2) {
             if (atomAdj[a1][n] == a2) return bondAdj[a1][n];
         return -1;
     }
-
+    
     /*
      * for debugging convenience: revive if necessary private void wr(String
      * str) {System.out.println(str);} private String arrayStr(int[] val) { if

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

@@ -0,0 +1,148 @@
+/*
+ * Copyright (c) 2016 John May <jwmay@users.sf.net>
+ *
+ * Contact: cdk-devel@lists.sourceforge.net
+ *
+ * This program is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation; either version 2.1 of the License, or (at
+ * your option) any later version. All we ask is that proper credit is given
+ * for our work, which includes - but is not limited to - adding the above
+ * copyright notice to the beginning of your source code files, and to any
+ * copyright notice that you may distribute with programs based on this work.
+ *
+ * This program is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ * FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
+ * License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 U
+ */
+package org.openscience.cdk.fingerprint;
+
+import org.junit.Test;
+import org.openscience.cdk.CDKTestCase;
+import org.openscience.cdk.fingerprint.CircularFingerprinter.FP;
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.silent.SilentChemObjectBuilder;
+import org.openscience.cdk.smarts.SmartsFragmentExtractor;
+import org.openscience.cdk.smiles.SmilesParser;
+import org.openscience.cdk.tools.ILoggingTool;
+import org.openscience.cdk.tools.LoggingToolFactory;
+
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.Set;
+
+import static org.hamcrest.CoreMatchers.everyItem;
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.hamcrest.collection.IsIn.isIn;
+
+/**
+ * @cdk.module test-standard
+ */
+public class CircularFingerprintSmartsTest extends CDKTestCase {
+
+	private static ILoggingTool logger = LoggingToolFactory
+			.createLoggingTool(CircularFingerprintSmartsTest.class);
+
+	public static SmilesParser parser = new SmilesParser(
+			SilentChemObjectBuilder.getInstance());
+
+	@Test
+	public void testMol1() throws Exception {
+		String molSmiles = "CC";
+		String expectedFPSmarts[][] = { { "C*" }, { "CC" } };
+		checkFPSmartsForMolecule(molSmiles, expectedFPSmarts);
+	}
+
+	@Test
+	public void testMol2() throws Exception {
+		String molSmiles = "CCC";
+		String expectedFPSmarts[][] = { { "C*" }, { "C(*)*" },
+				{ "CC*", "C(*)C" }, { "CCC" }, };
+		checkFPSmartsForMolecule(molSmiles, expectedFPSmarts);
+	}
+
+	@Test
+	public void testMol3() throws Exception {
+		String molSmiles = "CCN";
+		String expectedFPSmarts[][] = { { "C*" }, { "C(*)*" }, { "N*" },
+				{ "CC*", "C(*)C" }, { "C(*)N", "NC*" },
+				{ "CCN", "NCC", "C(C)N", "C(N)C" }, };
+		checkFPSmartsForMolecule(molSmiles, expectedFPSmarts);
+	}
+
+	@Test
+	public void testMol4() throws Exception {
+		String molSmiles = "C1CC1";
+		String expectedFPSmarts[][] = {
+
+		{ "C(*)*" }, { "C1CC1", "C(C1)C1" } };
+		checkFPSmartsForMolecule(molSmiles, expectedFPSmarts);
+	}
+
+	@Test
+	public void testMol5() throws Exception {
+		String molSmiles = "C1CCC1";
+		String expectedFPSmarts[][] = {
+
+		{ "C(*)*" }, { "C(C*)C*", "C(CC*)*", "C(*)CC*" },
+				{ "C1CCC1", "C(CC1)C1", "C(C1)CC1" } };
+		checkFPSmartsForMolecule(molSmiles, expectedFPSmarts);
+	}
+
+	@Test
+	public void testMol6() throws Exception {
+		String molSmiles = "CC[C-]";
+		String expectedFPSmarts[][] = {
+
+		{ "C*" }, { "C(*)*" }, { "[C-]*" }, { "CC*", "C(*)C" },
+				{ "[C-]C*", "C(*)[C-]" },
+				{ "CC[C-]", "C(C)[C-]", "[C-]CC", "C([C-])C" } };
+		checkFPSmartsForMolecule(molSmiles, expectedFPSmarts);
+	}
+
+	@Test
+	public void testMol7() throws Exception {
+		String molSmiles = "c1ccccc1";
+		String expectedFPSmarts[][] = {
+
+				{ "c(a)a" },
+				{ "c(a)cca", "c(ca)ca", "c(cca)a" },
+				{ "c(a)cccca", "c(ca)ccca", "c(cca)cca", "c(ccca)ca",
+						"c(cccca)a" },
+				{ "c1ccccc1", "c(c1)cccc1", "c(cc1)ccc1", "c(ccc1)cc1",
+						"c(cccc1)c1" } };
+		checkFPSmartsForMolecule(molSmiles, expectedFPSmarts);
+	}
+
+	private void checkFPSmartsForMolecule(String moleculeSmiles,
+			String expectedFPSmarts[][]) throws Exception {
+
+        Set<String> expected = new HashSet<>();
+        for (String[] strs : expectedFPSmarts)
+            Collections.addAll(expected, strs);
+
+		// expectedFPSmarts[][] is a double array because for each smarts
+		// several equivalent variants
+		// of the smarts are given e.g. CCC C(C)C
+		IAtomContainer mol = parser.parseSmiles(moleculeSmiles);
+
+		CircularFingerprinter circ = new CircularFingerprinter();
+		circ.calculate(mol);
+        SmartsFragmentExtractor subsmarts = new SmartsFragmentExtractor(mol);
+        subsmarts.setMode(SmartsFragmentExtractor.MODE_JCOMPOUNDMAPPER);
+		int numFP = circ.getFPCount();
+
+        Set<String> actual = new HashSet<>();
+		for (int i = 0; i < numFP; i++) {
+			FP fp = circ.getFP(i);
+            actual.add(subsmarts.generate(fp.atoms));
+		}
+
+		assertThat(actual, everyItem(isIn(expected)));
+	}
+}