Move deprecated classes out of cdk-smiles.

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

@@ -22,9 +22,6 @@
  */
 package org.openscience.cdk.fingerprint;
 
-import java.io.InputStream;
-import java.util.BitSet;
-
 import org.junit.Assert;
 import org.junit.Test;
 import org.openscience.cdk.AtomContainer;
@@ -39,10 +36,12 @@
 import org.openscience.cdk.interfaces.IChemObjectBuilder;
 import org.openscience.cdk.io.IChemObjectReader.Mode;
 import org.openscience.cdk.io.MDLV2000Reader;
-import org.openscience.cdk.smiles.FixBondOrdersTool;
 import org.openscience.cdk.tools.CDKHydrogenAdder;
 import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
 
+import java.io.InputStream;
+import java.util.BitSet;
+
 import static org.hamcrest.CoreMatchers.is;
 
 /**

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

@@ -1,20 +1,24 @@
-/* Copyright (C) 2006-2007  Rajarshi Guha <rajarshi@users.sf.net>
+/*
+ * Copyright (c) 2017 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.
+ * 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.smiles;
 
@@ -29,13 +33,13 @@
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IAtomType.Hybridization;
-import org.openscience.cdk.interfaces.IBond.Order;
 import org.openscience.cdk.interfaces.IBond;
+import org.openscience.cdk.interfaces.IBond.Order;
 import org.openscience.cdk.ringsearch.AllRingsFinder;
-import org.openscience.cdk.silent.SilentChemObjectBuilder;
 import org.openscience.cdk.silent.Atom;
 import org.openscience.cdk.silent.AtomContainer;
 import org.openscience.cdk.silent.Bond;
+import org.openscience.cdk.silent.SilentChemObjectBuilder;
 import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
 
 /**