Deprecate move legacy normlizer classes - functionality better met wi…

…th SMIRKS (via AMBIT atm)

base/test-standard/src/test/java/org/openscience/cdk/fingerprint/AbstractFixedLengthFingerprinterTest.java

@@ -31,6 +31,7 @@
 import org.openscience.cdk.CDKConstants;
 import org.openscience.cdk.DefaultChemObjectBuilder;
 import org.openscience.cdk.aromaticity.Aromaticity;
+import org.openscience.cdk.aromaticity.Kekulization;
 import org.openscience.cdk.exception.CDKException;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
@@ -160,9 +161,8 @@ public void testBug771485() throws Exception {
         addImplicitHydrogens(structure1);
         addImplicitHydrogens(structure2);
 
-        FixBondOrdersTool fbot = new FixBondOrdersTool();
-        structure1 = fbot.kekuliseAromaticRings(structure1);
-        structure2 = fbot.kekuliseAromaticRings(structure2);
+        Kekulization.kekulize(structure1);
+        Kekulization.kekulize(structure2);
 
         // hydrogens loaded from MDL mol files if non-query. Structure 2 has
         // query aromatic bonds and the hydrogen counts are not assigned - ensure

legacy/pom.xml

@@ -104,7 +104,6 @@
             <groupId>org.openscience.cdk</groupId>
             <artifactId>cdk-smiles</artifactId>
             <version>${project.version}</version>
-            <scope>test</scope>
         </dependency>
         <dependency>
             <groupId>org.openscience.cdk</groupId>

misc/extra/src/main/java/org/openscience/cdk/tools/CDKUtilities.java → legacy/src/main/java/org/openscience/cdk/normalize/CDKUtilities.java

@@ -2,23 +2,24 @@
  *
  * Contact: [email protected]
  *
- * 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.
+ * 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.
+ * 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 USA.
+ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 U
  */
-package org.openscience.cdk.tools;
-
-import java.util.List;
+package org.openscience.cdk.normalize;
 
 import org.openscience.cdk.CDKConstants;
 import org.openscience.cdk.aromaticity.Aromaticity;
@@ -31,6 +32,8 @@
 import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
 import org.openscience.cdk.tools.manipulator.RingSetManipulator;
 
+import java.util.List;
+
 /**
  * Utility class written by Todd Martin, for help in his QSAR descriptors and SMILES
  * parser. Seems to have overlap with, at least, cdk.normalize.Normalizer.
@@ -41,8 +44,10 @@
  * @cdk.module extra
  * @cdk.githash
  *
- * @see        org.openscience.cdk.normalize.Normalizer
+ * @see        Normalizer
+ * @deprecated better accomplished with SMARTS patterns or simple REGEX
  */
+@Deprecated
 public class CDKUtilities {
 
     public static String fixSmiles(String Smiles) {

storage/smiles/src/main/java/org/openscience/cdk/normalize/Normalizer.java → legacy/src/main/java/org/openscience/cdk/normalize/Normalizer.java

@@ -1,33 +1,28 @@
 /*  
- *  Copyright (C) 2004-2010  The Chemistry Development Kit (CDK) project
- *                     2014  Mark B Vine (orcid:0000-0002-7794-0426)
+ * Copyright (C) 2004-2010  The Chemistry Development Kit (CDK) project
+ *                    2014  Mark B Vine (orcid:0000-0002-7794-0426)
  *
- *  Contact: [email protected]
+ * Contact: [email protected]
  *
- *  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 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 USA.
+ * 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.normalize;
 
-import java.util.Iterator;
-import java.util.List;
-
 import org.openscience.cdk.exception.CDKException;
 import org.openscience.cdk.exception.InvalidSmilesException;
 import org.openscience.cdk.interfaces.IAtom;
@@ -40,14 +35,19 @@
 import org.w3c.dom.Element;
 import org.w3c.dom.NodeList;
 
+import java.util.Iterator;
+import java.util.List;
+
 /**
  * Adjusts parts of an AtomContainer to the configuration of a fragment.
  *
  * @author        shk3
  * @cdk.created   2004-03-04
  * @cdk.module    smiles
  * @cdk.githash
+ * @deprecated The functionality provided by with class is better suited to SMIRKS
  */
+@Deprecated
 public class Normalizer {
 
     /**

storage/smiles/src/test/java/org/openscience/cdk/normalize/NormalizerTest.java → legacy/src/test/java/org/openscience/cdk/normalize/NormalizerTest.java

@@ -1,26 +1,27 @@
-/* Copyright (C) 1997-2010  The Chemistry Development Kit (CDK) project
+/*
+ * Copyright (C) 1997-2010  The Chemistry Development Kit (CDK) project
  *
  * Contact: [email protected]
  *
- * 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.
+ * 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.
+ * 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 USA.
+ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 U
  */
 package org.openscience.cdk.normalize;
 
-import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
-
 import org.junit.Assert;
 import org.junit.Test;
 import org.openscience.cdk.Atom;
@@ -32,9 +33,9 @@
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
 
-/**
- * @cdk.module test-smiles
- */
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+
 public class NormalizerTest extends CDKTestCase {
 
     @Test