diff --git a/base/test-standard/src/test/java/org/openscience/cdk/fingerprint/AbstractFixedLengthFingerprinterTest.java b/base/test-standard/src/test/java/org/openscience/cdk/fingerprint/AbstractFixedLengthFingerprinterTest.java index fd24b78123..8339efd001 100644 --- a/base/test-standard/src/test/java/org/openscience/cdk/fingerprint/AbstractFixedLengthFingerprinterTest.java +++ b/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 diff --git a/legacy/pom.xml b/legacy/pom.xml index faeb322c6f..620c4fc1fa 100644 --- a/legacy/pom.xml +++ b/legacy/pom.xml @@ -104,7 +104,6 @@ org.openscience.cdk cdk-smiles ${project.version} - test org.openscience.cdk diff --git a/misc/extra/src/main/java/org/openscience/cdk/tools/CDKUtilities.java b/legacy/src/main/java/org/openscience/cdk/normalize/CDKUtilities.java similarity index 92% rename from misc/extra/src/main/java/org/openscience/cdk/tools/CDKUtilities.java rename to legacy/src/main/java/org/openscience/cdk/normalize/CDKUtilities.java index 66dfb86de6..a2c8d4a3c6 100644 --- a/misc/extra/src/main/java/org/openscience/cdk/tools/CDKUtilities.java +++ b/legacy/src/main/java/org/openscience/cdk/normalize/CDKUtilities.java @@ -2,23 +2,24 @@ * * 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. + * 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) { diff --git a/storage/smiles/src/main/java/org/openscience/cdk/normalize/Normalizer.java b/legacy/src/main/java/org/openscience/cdk/normalize/Normalizer.java similarity index 77% rename from storage/smiles/src/main/java/org/openscience/cdk/normalize/Normalizer.java rename to legacy/src/main/java/org/openscience/cdk/normalize/Normalizer.java index 226b3e55a1..8630388aa7 100644 --- a/storage/smiles/src/main/java/org/openscience/cdk/normalize/Normalizer.java +++ b/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: cdk-devel@lists.sourceforge.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 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; @@ -40,6 +35,9 @@ 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. * @@ -47,7 +45,9 @@ * @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 { /** diff --git a/storage/smiles/src/main/resources/org/openscience/cdk/smiles/normalize/fixsmiles.xml b/legacy/src/main/resources/org/openscience/cdk/normalize/fixsmiles.xml similarity index 100% rename from storage/smiles/src/main/resources/org/openscience/cdk/smiles/normalize/fixsmiles.xml rename to legacy/src/main/resources/org/openscience/cdk/normalize/fixsmiles.xml diff --git a/storage/smiles/src/test/java/org/openscience/cdk/normalize/NormalizerTest.java b/legacy/src/test/java/org/openscience/cdk/normalize/NormalizerTest.java similarity index 74% rename from storage/smiles/src/test/java/org/openscience/cdk/normalize/NormalizerTest.java rename to legacy/src/test/java/org/openscience/cdk/normalize/NormalizerTest.java index d4a3d4809b..3b63d3dd34 100644 --- a/storage/smiles/src/test/java/org/openscience/cdk/normalize/NormalizerTest.java +++ b/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: 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. + * 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