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/*
 * Copyright (C) 2000-2012  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 USA.
 */
package org.openscience.cdk;

import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.interfaces.ICDKObject;
import org.openscience.cdk.interfaces.IChemObject;
import org.openscience.cdk.tools.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;

import java.lang.reflect.Array;
import java.lang.reflect.Constructor;
import java.lang.reflect.InvocationTargetException;
import java.lang.reflect.Modifier;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.Map;
import java.util.Set;
import java.util.TreeSet;

/**
 * A factory class for constructing {@link ICDKObject} and {@link IChemObject}
 * implementations. Instances can be created by registering a construction key
 * ({@link ConstructorKey}) with a corresponding creator ({@link Creator}). In
 * most cases a class can simply be registered by providing an interface and an
 * implementation {@link #register(Class, Class)}.<p/>
 *
 * Internally the factory stores the object creators in a symbol table which
 * allows near constant time access for all registered classes. <p/>
 *
 * In cases of a non-direct parameter match (e.g. {@code Atom(Atom)} can resolve
 * to {@code Atom(Element)}) the constructor is matched by invoking {@link
 * #find(ConstructorKey)}. If a constructor was found the new key will be
 * registered with cache to avoid the overhead of finding the correct
 * constructor again. <p/>
 *
 * <pre>{@code
 *
 *     // create an instance of the factory
 *     DynamicFactory factory = new DynamicFactory(5);
 *
 *     // register some implementations
 *     factory.register(IAtom.class,          Atom.class);
 *     factory.register(IElement.class,       Element.class);
 *     factory.register(IAtomContainer.class, AtomContainer.class);
 *
 *     // create an instance using the default constructor
 *     IAtom a1 = factory.ofClass(IAtom.class);
 *
 *     // create an instance using a parametrised constructor
 *     IAtom c  = factory.ofClass(IAtom.class, "C");
 *
 *     // using a custom creator to actually invoke a constructor
 *     // import static org.openscience.cdk.DynamicFactory.key;
 *     // import static org.openscience.cdk.DynamicFactory.BasicCreator;
 *     factory.register(key(IBond.class, IAtom[].class),
 *                      new BasicCreator<IAtom>(null) {
 *                          public IAtom create(Object[] objects) {
 *                              return new Bond((IAtom[]) objects);
 *                          }
 *                      });
 *
 * }</pre>
 * <p/> It is not always convenient to specify a custom {@link Creator} for
 * every construction type but the objects may still need some modification
 * directly after creation. The factory provides {@link CreationModifier} which
 * is invoked directly after object creation. This allows changing the default
 * of creation. As an example it is possible to set a non-null charge on all
 * atoms that are created. <p/>
 *
 * <pre>{@code
 *      // import static org.openscience.cdk.DynamicFactory.CreationModifier;
 *     factory.register(IAtom.class, Atom.class,
 *                      new CreationModifier<Atom>() {
 *                          public void modify(Atom atom) {
 *                               atom.setFormalCharge(0);
 *                          }
 *                      }));
 * }</pre>
 *
 * <p/>
 *
 * It is also possible change the object creation based on the input parameters.
 * <p/>
 *
 * <pre>{@code
 * factory.register(key(IAtom.class, String.class),
 *                  new DynamicFactory.BasicCreator<IAtom>() {
 *
 *                      public IAtom create(Object[] objects) {
 *                          String symbol = (String) objects[0];
 *                          return "R".equals(symbol)
 *                                      ? new PseudoAtom(symbol)
 *                                      : new Atom(symbol);
 *                      }
 *                  });
 *
 * factory.ofClass(IAtom.class, "C"); // IAtom
 * factory.ofClass(IAtom.class, "R"); // IPseudoAtom
 * }</pre>
 *
 * @author John May
 * @cdk.module core
 */
@TestClass("org.openscience.cdk.DynamicFactoryTest")
public class DynamicFactory {

    /**
     * logger for use in this class
     */
    private static final ILoggingTool logger
            = LoggingToolFactory.createLoggingTool(DynamicFactory.class);


    /**
     * an empty class array which can be used to avoid object creation in
     * default constructors
     */
    private static final Class<?>[] EMPTY_CLASS_ARRAY = new Class<?>[0];

    /**
     * conversion map of primitives to their boxed equivalents
     */
    private static final Map<Class<?>, Class<?>> BOXED_EQUIVALENT = new HashMap<Class<?>, Class<?>>(20);

    // populates the primitive conversion map
    static {
        BOXED_EQUIVALENT.put(int.class, Integer.class);
        BOXED_EQUIVALENT.put(byte.class, Byte.class);
        BOXED_EQUIVALENT.put(short.class, Short.class);
        BOXED_EQUIVALENT.put(long.class, Long.class);
        BOXED_EQUIVALENT.put(boolean.class, Boolean.class);
        BOXED_EQUIVALENT.put(float.class, Float.class);
        BOXED_EQUIVALENT.put(double.class, Double.class);
        BOXED_EQUIVALENT.put(char.class, Character.class);
    }

    /*
     * direct map of keys to constructors
     */
    private final Map<ConstructorKey, Creator<?>> cache;

    /*
     * lookup to help find non-exact constructors and print suggestions
     */
    private final ConstructorLookup lookup;

    /**
     * provide the interfaces this class implements
     */
    private final InterfaceProvider interfaceProvider;

    /**
     * Create a new default factory with an expected number of registered
     * classes and an interface provider. The interface provider is used when
     * registering an implementation without a specified interface {@link
     * #register(Class)}.
     *
     * @param interfaceProvider provides the interfaces of a given
     *                          implementation class
     * @param n                 the expected number of constructors that will be
     *                          stored.
     * @see #DynamicFactory(int)
     */
    public DynamicFactory(InterfaceProvider interfaceProvider, int n) {

        if (n < 0)
            throw new IllegalArgumentException("cannot create factory with negative size");
        if (interfaceProvider == null)
            throw new IllegalArgumentException("null interface provider");

        this.interfaceProvider = interfaceProvider;

        int size = n > 3 ? n + n / 3 : n + 1;

        // double for the cache to account for subclass constructor caching
        // (e.g. Atom(Atom) -> Atom(Element)
        cache = new HashMap<ConstructorKey, Creator<?>>(size * 2);
        lookup = new ConstructorLookup(size);

    }

    /**
     * Create a new default factory with an expected number of registered
     * classes and a default interface provider. The default interface provider
     * simply invokes {@link Class#getInterfaces()} when registering an
     * implementation without an explicit interface {@link #register(Class)}.
     *
     * @param n the expected number of constructors that will be stored.
     */
    public DynamicFactory(int n) {
        this(new DefaultInterfaceProvider(), n);
    }


    /**
     * Inspects whether the provided class is a {@link ICDKObject} interface.
     *
     * @param c class to test
     * @return whether the class is a CDK interface
     */
    private boolean isCDKInterface(Class<?> c) {
        return ICDKObject.class.isAssignableFrom(c) && c.isInterface();
    }

    /**
     * Inspects whether the provided class is a concrete implementation and thus
     * instantiable.
     *
     * @param c class to test
     * @return whether the class is concrete
     */
    private boolean isConcrete(Class<?> c) {
        return !c.isInterface() && !Modifier.isAbstract(c.getModifiers());
    }

    /**
     * Registers a class with the factory. The interfaces of the class will be
     * checked to see if they are CDK interfaces before they are registered.
     * This method is provided for utility but will register the implementation
     * with all valid interfaces. If a restricted registration is required then
     * the safer {@link #register(Class, Class)} can be used.
     *
     * @param impl a concrete class
     * @throws IllegalArgumentException thrown if a non-concrete class is
     *                                  registered
     * @see #register(Class, Class)
     * @see #register(Class, java.lang.reflect.Constructor)
     * @see #register(org.openscience.cdk.DynamicFactory.ConstructorKey,
     *      org.openscience.cdk.DynamicFactory.Creator)
     */
    @TestMethod("testRegister,testRegister_NonCDKInterface")
    public <T extends ICDKObject> boolean register(Class<? extends T> impl) {

        if (!isConcrete(impl))
            throw new IllegalArgumentException("non-concrete implementation provided");

        boolean registered = Boolean.FALSE;

        // only check direct interfaces,
        //     IPolymer -> Polymer not IAtomContainer -> Polymer
        for (Class<?> c : interfaceProvider.getInterfaces(impl)) {

            // register this implementation with it's direct interfaces
            if (isCDKInterface(c)) {
                @SuppressWarnings("unchecked")
                Class<T> intf = (Class<T>) c;
                registered = register(intf, impl) || registered;
            }

        }

        return registered;

    }

    /**
     * Explicitly register a concrete class with a provided interface. The
     * {@link Creator} will be automatically created for all public
     * constructors.
     *
     * @param intf the interface class to register
     * @param impl the concrete class which should implement the interface
     *             class
     * @return whether registration was successful
     */
    @TestMethod("testRegister_Explicit,testRegister_PrivateConstructor,testRegister_Duplicate")
    public <T extends ICDKObject> boolean register(Class<T> intf, Class<? extends T> impl) {
        return register(intf, impl, null);
    }

    /**
     * Explicitly register a concrete class with a provided interface and a
     * given modifier. The {@link Creator} will be automatically created for all
     * public constructors. The modifier is incorporated into the {@link
     * Creator} and is invoked directly after instantiation. <p/>
     *
     *
     * <pre>{@code
     *      // import static org.openscience.cdk.DynamicFactory.CreationModifier;
     *     factory.register(IAtom.class, Atom.class,
     *                      new CreationModifier<Atom>() {
     *                          public void modify(Atom atom) {
     *                               atom.setFormalCharge(0);
     *                          }
     *                      }));
     * }</pre>
     *
     * @param intf     the interface class to register
     * @param impl     the concrete class which should implement the interface
     *                 class
     * @param modifier modify a instance after creation
     * @param <S>      interface type
     * @param <T>      implementation type (must extend interface)
     * @return whether registration was successful
     */
    @TestMethod("testRegister_WithModifier")
    public <S extends ICDKObject, T extends S> boolean register(Class<S> intf, Class<T> impl,
                                                                CreationModifier<T> modifier) {

        if (!isConcrete(impl))
            throw new IllegalArgumentException("attempt to register non-concrete class");

        if (!intf.isInterface())
            throw new IllegalArgumentException("attempt to register a non-interface interface: " + intf
                    .getSimpleName());

        boolean registered = Boolean.FALSE;
        for (Constructor<?> untyped : impl.getConstructors()) {
            @SuppressWarnings("unchecked")
            Constructor<T> typed = (Constructor<T>) untyped;
            registered = register(intf, typed, modifier) || registered;
        }

        if (registered) {
            logger.debug("registered '" + intf.getSimpleName() + "' with '" + impl
                    .getSimpleName() + "' implementation");
        } else {
            logger.debug("could not registered '" + intf.getSimpleName() + "' with '" + impl
                    .getSimpleName() + "' implementation");
        }

        return registered;

    }

    /**
     * Register a specific constructor with an explicit interface. <p/>
     *
     * <pre>{@code
     *     // only register construction of IAtom using a string - Atom("C")
     *     factory.register(IAtom.class,
     *                      Atom.class.getConstructor(String.class));
     * }</pre>
     *
     * @param intf        the interface
     * @param constructor a constructor which builds the given interface
     * @param <S>         interface type
     * @param <T>         implementation type (must extend interface)
     * @return whether the constructor was registered
     */
    @TestMethod("testRegister_Constructor")
    public <S extends ICDKObject, T extends S> boolean register(Class<S> intf,
                                                                Constructor<T> constructor) {
        return register(intf, constructor, null);
    }

    /**
     * Register a specific constructor with a creation modifier to an explicit
     * interface. <p/>
     *
     * <pre>{@code
     *      // only register construction of IAtom using a string - Atom("C")
     *      factory.register(IAtom.class,
     *                       Atom.class.getConstructor(String.class),
     *                       new DynamicFactory.CreationModifier<Atom>() {
     *
     *                           public void modify(Atom instance) {
     *                              instance.setFormalCharge(0);
     *                           }
     *                       });
     * }</pre>
     *
     * @param intf        the interface
     * @param constructor a constructor which builds the given interface
     * @param <S>         interface type
     * @param <T>         implementation type (must extend interface)
     * @return whether the constructor was registered
     */
    @TestMethod("testRegister_Constructor_Modifier")
    public <S extends ICDKObject, T extends S> boolean register(Class<S> intf,
                                                                Constructor<T> constructor,
                                                                CreationModifier<T> modifier) {

        // do not register private/protected constructors
        if (!Modifier.isPublic(constructor.getModifiers()))
            return Boolean.FALSE;

        return register(key(intf, constructor), constructor, modifier) != null;

    }


    /**
     * Register a constructor key with a public constructor.
     *
     * @param key         the key to register this constructor with
     * @param constructor the constructor to invoke when the key is match
     * @param <T>         the type the constructor will create
     * @return return the constructor passed as the parameter
     */
    private <T> Creator<T> register(ConstructorKey key, Constructor<T> constructor,
                                    CreationModifier<T> modifier) {

        Creator<T> creator = new ReflectionCreator<T>(constructor);

        if (modifier != null)
            creator = new ModifiedCreator<T>(creator, modifier);

        return register(key, creator);
    }


    @TestMethod("testOfClass_Wrapping")
    public <T> Creator<T> register(ConstructorKey key, Creator<T> creator) {

        if (creator == null)
            return null;

        // make sure we don't register a constructor over an existing key
        if (cache.containsKey(key))
            throw new IllegalArgumentException("cannot register " + key
                                                       + " suppressed " + cache.get(key));

        lookup.put(key.intf(), key);
        cache.put(key, creator);

        return creator;

    }

    /**
     * Creates a constructor key for use in accessing constructors. The key
     * combines the interface and types in a single instance which we can then
     * use in a map.
     *
     * @param intf        the interface to build the key for
     * @param constructor the constructor value which this key will be linked
     *                    to
     * @return a constructor key which can be used to lookup a constructor
     */
    private static ConstructorKey key(Class<?> intf, Constructor<?> constructor) {
        return key(intf, constructor.getParameterTypes());
    }

    /**
     * Creates a constructor key for use in accessing constructors. The key
     * combines the interface and types in a single instance which we can then
     * use in a map.
     *
     * @param intf  the interface to build the key for
     * @param types the classes that the the constructor requires
     * @return a constructor key which can be used to lookup a constructor
     */
    @TestMethod("testKey_Default,testKey_Parameters,testKey_ArrayParameters,testKey_Primitives")
    public static ConstructorKey key(Class<?> intf, Class<?>... types) {
        return new ClassBasedKey(intf, convert(types));
    }

    /**
     * Converts the provided array of classes to a version with 'boxed'
     * primitives. This will convert {int, int, int} to {Integer, Interger,
     * Interger}.
     *
     * @param classes converted classes
     * @return converted types
     */
    private static Class<?>[] convert(Class<?>[] classes) {
        Class<?>[] types = new Class<?>[classes.length];
        for (int i = 0; i < types.length; i++) {
            types[i] = convert(classes[i]);
        }
        return types;
    }

    /**
     * Converts primitive types to their boxed equivalent {@link int} converts
     * to {@link Integer}. If not conversion was found the parameter is returned
     * without modification.
     *
     * @param unboxed the type to convert
     * @return the boxed type
     */
    private static Class<?> convert(Class<?> unboxed) {
        Class<?> boxed = BOXED_EQUIVALENT.get(unboxed);
        return boxed == null ? unboxed : boxed;
    }


    /**
     * Construct an implementation using a constructor whose parameters match
     * that of the provided objects.
     *
     * @param intf the interface to construct an instance of
     * @param <T>  the type of the class
     * @return an implementation of provided interface
     * @throws IllegalArgumentException thrown if the implementation can not be
     *                                  constructed
     */
    @TestMethod("testOfClass_WithParams,testOfClass_Wrapping")
    public <T extends ICDKObject> T ofClass(Class<T> intf, Object... objects) {

        try {

            Creator<T> constructor = get(new ObjectBasedKey(intf, objects));
            return constructor.create(objects);

        } catch (InstantiationException e) {
            throw new IllegalArgumentException("unable to instantiate chem object: ", e);
        } catch (IllegalAccessException e) {
            throw new IllegalArgumentException("constructor is not accessible: ", e);
        } catch (InvocationTargetException e) {
            throw new IllegalArgumentException("invocation target exception: ", e);
        }

    }

    /**
     * Construct an implementation using the default constructor. This provides
     * some speed boost over invoking {@link #ofClass(Class, Object...)}.
     *
     * @param intf the interface to construct an instance of
     * @param <T>  the type of the class
     * @return an implementation of provided interface constructed using the
     *         default constructor.
     * @throws IllegalArgumentException thrown if the implementation can not be
     *                                  constructed
     */
    @TestMethod("testOfClass")
    public <T extends ICDKObject> T ofClass(Class<T> intf) {

        try {

            Creator<T> creator = get(new ClassBasedKey(intf, EMPTY_CLASS_ARRAY));
            return creator.create(null); // throws an exception if no impl was found

        } catch (InstantiationException e) {
            throw new IllegalArgumentException("unable to instantiate chem object: ", e);
        } catch (IllegalAccessException e) {
            throw new IllegalArgumentException("constructor is not accessible: ", e);
        } catch (InvocationTargetException e) {
            throw new IllegalArgumentException("invocation target exception: ", e);
        }

    }

    /**
     * Access a constructor for a given constructor key. If the key is not found
     * the {@link #find(ConstructorKey)} is automatically invoked.
     *
     * @param key the constructor key of the interface to find
     * @param <T> the type of the constructor
     * @return a constructor for the given key
     * @throws IllegalArgumentException thrown if a key is provided which cannot
     *                                  be resolved.
     */
    private <T> Creator<T> get(ConstructorKey key) {


        @SuppressWarnings("unchecked")
        Creator<T> creator = (Creator<T>) cache.get(key);


        if (creator != null) {
            return creator;
        } else {
            creator = find(key);
            return register(key, creator); // avoids invoking find again
        }

    }


    /**
     * Find a constructor those parameters are assignable from the provided
     * key.
     *
     * @param key a key to find the constructor for
     * @param <T> type of the constructor
     * @return a constructor compatible with the given key
     * @throws IllegalArgumentException when no constructor is found the given
     *                                  key
     */
    private <T> Creator<T> find(final ConstructorKey key) {


        for (ConstructorKey candidate : lookup.getCandidates(key)) {
            if (key.isAssignable(candidate)) {
                return get(candidate);
            }
        }

        // if the key has uniform parameter types
        if (key.isUniform()) {

            // convert the key parameter types (length doesn't matter)
            Object types = Array.newInstance(key.type(0), 0);
            final ConstructorKey alt = new ObjectBasedKey(key.intf(),
                                                          new Object[]{types});

            // find the creator for the new alternate key
            Creator<T> creator = get(alt);

            // if found -> get/find will return the correct constructor, we then need
            //             to wrap the constructor with an creator that will
            //             wrap the objects in an array
            // if not found -> the method will return an non-null instantor that
            //                 will throw an exception (see. below) - wrapping
            //                 has no harm as the params never get used
            //
            return new ArrayWrapCreator<T>(creator);
        }

        logger.debug("no instance handler found for " + key);

        // return an instance handler that will throw an exception when invoked
        return new Creator<T>() {
            public T create(Object[] objects) {
                throw new IllegalArgumentException(getSuggestionMessage(key));
            }

            @Override
            public Class<T> getDeclaringClass() {
                throw new IllegalArgumentException("missing declaring class");
            }
        };

    }


    /**
     * Access the registered implementations for a given interface.
     *
     * @param intf an interface which has registered implementations in the
     *             factory
     * @param <T>  the type of the interface
     * @return set of implementation classes (empty if none found)
     */
    @TestMethod("testImplementationsOf")
    public <T extends ICDKObject> Set<Class<?>> implmentorsOf(Class<T> intf) {
        Set<Class<?>> implementations = new HashSet<Class<?>>(5);
        for (ConstructorKey key : lookup.getConstructors(intf)) {
            implementations.add(get(key).getDeclaringClass());
        }
        return implementations;
    }

    /**
     * Provides a list of all possible constructor keys for the provided
     * interface.
     *
     * @param intf an interface to find all constructors for
     * @return an iterator of constructor keys
     */
    @TestMethod("testSuggest")
    public Iterator<ConstructorKey> suggest(Class<?> intf) {
        return lookup.getConstructors(intf).iterator();
    }

    /**
     * Provides a message for use with exceptions when no valid constructor is
     * found. The message is built using the suggestions from {@link
     * #suggest(Class)}.
     *
     * @param key the constructor key to build the message for
     * @return a message listing possible constructors
     */
    private String getSuggestionMessage(ConstructorKey key) {

        StringBuilder sb = new StringBuilder(200);

        sb.append("No constructor found for '").append(key);
        sb.append("' candidates are: ");

        Iterator<ConstructorKey> iterator = suggest(key.intf());

        while (iterator.hasNext()) {
            sb.append(iterator.next());
            if (iterator.hasNext()) {
                sb.append(", ");
            }
        }

        return sb.toString();

    }

    /**
     * A simple wrapper class for a HashMap so we can insert and access
     * constructors easier.
     */
    private static class ConstructorLookup {

        private final Map<Class<?>, Map<Integer, Set<ConstructorKey>>> keys;
        private final Set<ConstructorKey> EMPTY_KEY_SET = new HashSet<ConstructorKey>(0);

        /**
         * Create a new lookup with an expected number of entries.
         *
         * @param n size
         */
        public ConstructorLookup(int n) {
            keys = new HashMap<Class<?>, Map<Integer, Set<ConstructorKey>>>(n);
        }

        /**
         * Add a key for a given interface.
         *
         * @param intf an interface
         * @param key  the key to add for the interface
         */
        public void put(Class<?> intf, ConstructorKey key) {

            if (!keys.containsKey(intf)) {
                keys.put(intf, new HashMap<Integer, Set<ConstructorKey>>());
            }

            Map<Integer, Set<ConstructorKey>> map = keys.get(intf);

            int n = key.n();

            if (!map.containsKey(n)) {
                map.put(n, new HashSet<ConstructorKey>(5)); // few constructors per class
            }

            map.get(n).add(key);

        }

        /**
         * Access all constructors for a given interface.
         *
         * @param intf the interface to lookup the constructors of.
         * @return set of constructors
         */
        private Set<ConstructorKey> getConstructors(Class<?> intf) {

            Map<Integer, Set<ConstructorKey>> candidates = keys.get(intf);
            Set<ConstructorKey> keys = new TreeSet<ConstructorKey>();

            if (candidates != null) {
                for (Map.Entry<Integer, Set<ConstructorKey>> e : candidates.entrySet()) {
                    keys.addAll(e.getValue());
                }
            }

            return keys;

        }

        /**
         * Access a set of candidates for a given key. Candidates match the
         * interface an number of parameters for the constructors. A key may
         * match when it's parameters are subclasses.
         *
         * @param key the key to find possible candidates for
         * @return set of constructors which 'could' match the given key
         */
        public Set<ConstructorKey> getCandidates(ConstructorKey key) {
            return getCandidates(key.intf(), key.n());
        }

        /**
         * Find all constructor keys which match the given interface and
         * parameters number.
         *
         * @param intf the interface to lookup
         * @param n    number of parameters
         * @return set of constructors which 'could' match the given key
         */
        public Set<ConstructorKey> getCandidates(Class<?> intf, int n) {

            logger.debug("getting candidates for " + intf + " " + n);

            Map<Integer, Set<ConstructorKey>> map = keys.get(intf);
            if (map == null) {
                logger.debug("no keys for " + intf);
                logger.debug(keys);
                return EMPTY_KEY_SET;
            }

            Set<ConstructorKey> candidates = map.get(n);
            if (candidates == null) {
                logger.debug("no keys for parameter count" + n);
                logger.debug(map);
                return EMPTY_KEY_SET;
            }

            return candidates;

        }

    }

    /**
     * A simple class based key which allows a key to use an object array for
     * it's parameter types.
     */
    private static class ObjectBasedKey extends ConstructorKey {

        private final Class<?> intf;
        private final Object[] params;
        private final int n;

        /**
         * Create the key with an interface and array of parameters.
         *
         * @param intf   interface class
         * @param params the object parameters
         */
        private ObjectBasedKey(Class<?> intf, Object[] params) {
            this.intf = intf;
            this.params = params;
            this.n = params.length;
        }

        /**
         * @inheritDoc
         */
        @Override
        public Class<?> intf() {
            return intf;
        }

        /**
         * @inheritDoc
         */
        @Override
        public Class<?> type(int i) {
            if (params[i] == null)
                throw new IllegalArgumentException("null param type");
            return params[i].getClass();
        }

        /**
         * @inheritDoc
         */
        @Override
        public int n() {
            return n;
        }


    }

    /**
     * A simple class based key which allows a key to use a class array for it's
     * parameter types.
     */
    private static class ClassBasedKey extends ConstructorKey {

        private final Class<?> intf;
        private final Class<?>[] params;
        private final int n;

        /**
         * Create the key with an interface and array of parameters.
         *
         * @param intf   interface class
         * @param params the parameter types
         */
        private ClassBasedKey(Class<?> intf, Class<?>[] params) {
            this.intf = intf;
            this.params = params;
            this.n = params.length;
        }

        /**
         * @inheritDoc
         */
        @Override
        public Class<?> intf() {
            return intf;
        }

        /**
         * @inheritDoc
         */
        @Override
        public Class<?> type(int i) {
            return params[i];
        }

        /**
         * @inheritDoc
         */
        @Override
        public int n() {
            return n;
        }

    }

    /**
     * A class which encapsulates the information about an interface (of this
     * implementation) and the parameter types of the constructor.
     */
    public static abstract class ConstructorKey
            implements Comparable<ConstructorKey> {

        /**
         * Access the interface this key indexes.
         *
         * @return class of the interface
         */
        public abstract Class<?> intf();

        /**
         * Access the type of class at the given parameter index.
         *
         * @param i index of the parameter
         * @return class of the parameter at index
         */
        public abstract Class<?> type(int i);

        /**
         * Access the number of parameters in the constructor.
         *
         * @return number of parameters
         */
        public abstract int n();

        /**
         * @inheritDoc
         */
        @Override
        public boolean equals(Object o) {

            ConstructorKey that = (ConstructorKey) o;

            if (intf() != that.intf() || n() != that.n()) {
                return false;
            }
            for (int i = 0; i < n(); i++) {
                if (!type(i).equals(that.type(i)))
                    return false;
            }
            return true;

        }

        /**
         * Indicates whether this key has multiple parameters and they are of
         * uniform type. If there are less then two types this method will
         * return false. <p/> {@code new Object[]{ Atom, Bond, Atom } } // false
         * {@code new Object[]{ Atom, Atom, Atom } } // true
         *
         * @return whether the key is uniform
         */
        public boolean isUniform() {

            if (n() < 2)
                return false;

            Class<?> base = type(0);
            for (int i = 1; i < n(); i++) {
                if (type(i) != base) {
                    return false;
                }
            }

            return true;

        }

        /**
         * @inheritDoc
         */
        @Override
        public int hashCode() {
            int result = intf().hashCode();

            for (int i = 0; i < n(); i++)
                result = 31 * result + type(i).hashCode();

            return result;
        }

        /**
         * Orders constructor keys by the number of parameters and then this
         * name.
         *
         * @param o another constructor key
         * @return whether the other key is greater than, less than or equal to
         *         this key
         */
        @Override
        public int compareTo(ConstructorKey o) {

            // order by number of params first
            if (n() != o.n()) {
                return n() > o.n() ? 1 :
                        n() < o.n() ? -1 : 0;
            }

            // use the lexicographic order of the toString method
            return toString().compareTo(o.toString());

        }

        /**
         * Checks whether this key is assignable to the candidate.
         *
         * @param candidate another constructor key
         * @return whether the provided candidate is assignable
         */
        public boolean isAssignable(ConstructorKey candidate) {

            for (int i = 0; i < candidate.n(); i++) {
                // check whether the parameters are assignable
                if (!candidate.type(i).isAssignableFrom(type(i))) {
                    return false;
                }
            }

            // no conflicts this constructor is okay
            return true;

        }

        /**
         * @inheritDoc
         */
        @Override
        public String toString() {
            StringBuilder sb = new StringBuilder(n() * 50);
            sb.append(intf().getSimpleName());
            sb.append("(");
            int max = n() - 1;
            for (int i = 0; i <= max; i++) {
                sb.append(type(i).getSimpleName());
                if (i != max)
                    sb.append(", ");
            }
            sb.append(")");
            return sb.toString();
        }

    }

    /**
     * A default interface provider implementation that simply returns the
     * classes from {@link Class#getInterfaces()}.
     */
    protected static class DefaultInterfaceProvider
            implements InterfaceProvider {

        /**
         * @inheritDoc
         */
        @Override
        public Class<?>[] getInterfaces(Class<?> c) {
            return c.getInterfaces();
        }
    }

    /**
     * An interface that can provide which interfaces the given class
     * implements. This interface is constructor injectable allowing us to test
     * the registration using this method.
     */
    public interface InterfaceProvider {

        /**
         * Access the interfaces for a given class
         *
         * @param c the class to access the interfaces of
         * @return a set of interfaces
         */
        public Class<?>[] getInterfaces(Class<?> c);
    }

    /**
     * An interface that allows posterior modification of an instance after it
     * has been created.
     *
     * @param <T>
     */
    public interface CreationModifier<T> {
        public void modify(T instance);
    }

    /**
     * A Creator wrapper which can include a modifier
     *
     * @param <T> the type of object that will be created
     */
    private static class ModifiedCreator<T> implements Creator<T> {

        private final CreationModifier<T> modifier;
        private final Creator<T> parent;

        /**
         * Create a new modified created which delegate instance creation to the
         * given parent and applies the modifier after the instance has been
         * constructed.
         *
         * @param parent   parent creator
         * @param modifier a modify to apply after creation
         */
        private ModifiedCreator(Creator<T> parent,
                                CreationModifier<T> modifier) {
            this.parent = parent;
            this.modifier = modifier;
        }

        /**
         * @inheritDoc
         */
        @Override
        public T create(Object[] objects) throws InvocationTargetException,
                                                 IllegalAccessException,
                                                 InstantiationException {
            T instance = parent.create(objects);
            modifier.modify(instance);
            return instance;
        }

        /**
         * @inheritDoc
         */
        @Override
        public Class<T> getDeclaringClass() {
            return parent.getDeclaringClass();
        }
    }

    /**
     * An interface that wraps object creation via the {@link #create(Object[])}
     * method.
     *
     * @param <T> the type of object that will be created
     */
    public interface Creator<T> {

        /**
         * Create a new instance with the provided object parameters.
         *
         * @param objects parameters for the constructor excluding
         * @return a new instance, created with the provided parameters
         * @throws InvocationTargetException thrown if an error occurred during
         *                                   construction
         * @throws IllegalAccessException    if the constructor can't be
         *                                   accessed (e.g. private)
         * @throws InstantiationException    thrown if class is abstract
         */
        public T create(Object[] objects) throws InvocationTargetException,
                                                 IllegalAccessException,
                                                 InstantiationException;

        /**
         * Access the implementation of this class
         *
         * @return the implementation class to be created
         */
        public Class<T> getDeclaringClass();
    }

    /**
     * A simple creator that helps in creating an anonymous classes for a
     * creator.
     *
     * @param <T> the type of object that will be created
     */
    public static abstract class BasicCreator<T>
            implements Creator<T> {

        private final Class<T> c;

        /**
         * Create a basic constructor with a given declaring class.
         *
         * @param c class to be created
         */
        public BasicCreator(Class<T> c) {
            this.c = c;
        }

        /**
         * @inheritDoc
         */
        @Override
        public Class<T> getDeclaringClass() {
            return c;
        }
    }


    /**
     * A simple creator that wraps the object parameters before invoking {@link
     * #create(Object[])} on the proivded parent.
     *
     * @param <T> the type of object that will be created
     */
    private static class ArrayWrapCreator<T> implements Creator<T> {

        private final Creator<T> parent;

        /**
         * Create a new creator with a given parent. The parent is used to
         * actually create the object, this creator wraps the provided params in
         * another and is required if 'varargs' are 'unpacked'.
         *
         * @param parent the parent creator
         */
        public ArrayWrapCreator(Creator<T> parent) {
            this.parent = parent;
        }

        /**
         * @inheritDoc
         */
        @Override
        public T create(Object[] objects) throws InvocationTargetException,
                                                 IllegalAccessException,
                                                 InstantiationException {
            return parent.create(new Object[]{objects});
        }

        /**
         * @inheritDoc
         */
        @Override
        public Class<T> getDeclaringClass() {
            return parent.getDeclaringClass();
        }

    }

    /**
     * A simple instantiation that uses reflection to create an object.
     *
     * @param <T> type of object that will be created
     */
    private static class ReflectionCreator<T> implements Creator<T> {

        private final Constructor<T> constructor;

        /**
         * Create a reflection creator for a given constructor.
         *
         * @param constructor constructor for a class
         */
        private ReflectionCreator(Constructor<T> constructor) {
            this.constructor = constructor;
        }

        /**
         * @inheritDoc
         */
        public T create(Object[] objects) throws InvocationTargetException,
                                                 IllegalAccessException,
                                                 InstantiationException {
            return constructor.newInstance(objects);
        }

        /**
         * @inheritDoc
         */
        @Override
        public Class<T> getDeclaringClass() {
            return constructor.getDeclaringClass();
        }
    }

}
Sam Adams
Jonathan Alvarsson
Rich Apodaca
Saravanaraj N Ayyampalayam
Ulrich Bauer
Stephan Beisken
Arvid Berg
Ed Cannon
Fabian Dortu
Martin Eklund
Matteo Floris
Dan Gezelter
Uli Fechner
Thorsten Flügel
Nimish Gopal
Rajarshi Guha
Yonquan Han
Thierry Hanser
Kai Hartmann
Tobias Helmus
Christian Hoppe
Oliver Horlacher
Miguel Howard
Nina Jeliazkova
Geert Josten
Dmitry Katsubo
Jules Kerssemakers
Anatoli Krassavine
Stefan Kuhn
Uli Köhler
Violeta Labarta
Jonty Lawson
Kevin Lawson
Daniel Leidert
Edgar Luttmann
Todd Martin
John May
Nathanaël Mazuir
Stephan Michels
Scooter Morris
Peter Murray-Rust
Carl Mäsak
Irilenia Nobeli
Peter Odéus
Niels Out
Jerome Pansanel
Julio Peironcely
Tomáš Pluskal
Chris Pudney
Syed Asad Rahman
Jonathan Rienstra-Kiracofe
Mark Rijnbeek
David Robinson
Miguel Rojas Cherto
Bhupinder Sandhu
Jean-Sebastien Senecal
Onkar Shinde
Sulev Sild
Bradley Smith
Ola Spjuth
Christoph Steinbeck
Ralf Stephan
Daniel Szisz
Aleksey Tarkhov
Stephan Tomkinson
Gilleain Torrance
Andreas Truszkowski
Paul Turner
Joerg Wegner
Yap Chun Wei
Stephane Werner
Egon Willighagen
Lars Willighagen
Yong Zhang 
Daniel Zaharevitz
Please file bugs on the SF website:
http://sourceforge.net/tracker/?group_id=20024&atid=120024
<?xml version="1.0" encoding="UTF-8"?>
<module type="JAVA_MODULE" version="4">
  <component name="NewModuleRootManager" inherit-compiler-output="true">
    <exclude-output />
    <content url="file://$MODULE_DIR$">
      <sourceFolder url="file://$MODULE_DIR$/src/main" isTestSource="false" />
      <sourceFolder url="file://$MODULE_DIR$/src/test" isTestSource="true" />
    </content>
    <orderEntry type="inheritedJdk" />
    <orderEntry type="sourceFolder" forTests="false" />
    <orderEntry type="library" name="junit-4.10" level="project" />
    <orderEntry type="library" name="develjar" level="project" />
    <orderEntry type="library" name="jar" level="project" />
    <orderEntry type="library" name="jena" level="project" />
  </component>
</module>

CDK - The Chemical Development Kit
 
Copyright 1997-2012 The CDK Development Team
License: LGPL v2, see doc/lgpl.license

1. Introduction

You are currently reading the README file for the Chemistry Development Project (CDK).
This project is hosted under http://cdk.sourceforge.net/
Please refer to these pages for updated information and the latest version of the CDK.

The CDK is an open-source library of algorithms for structural chemo- and bioinformatics, implemented in 
the programming language Java(tm). The library is published under terms of the the 
GNU Lesser General Public License v2. This has implications on what you can do with sources and
binaries of the CDK library. For details, please refer to the file LICENSE, which should have been
provided with this distribution.

PLEASE NOTE: This is a library of useful data structures and algorithms to manipulate them 
from the area of structural chemo- and bioinformatics. As such, it is intended for the use by
programmers, who wish to save some effort by reusing code. It is not intended for the enduser. 
If you consider yourself to be more like user, you might not find what you wanted. 
Please refer to other projects like the JChemPaint project (http://jchempaint.github.com/)
or the Jmol project (http://www.jmol.org/) for programs that actually take advantage of the 
CDK library.

2. Compiling

Compiling and jar-ing the software is done with Jakarta's 
Ant (http://jakarta.apache.org/ant/) 1.7.1 or better and Java 1.6.0 or better:

cdk/$ ls build.xml
build.xml
cdk/$ ant

"ant -p" gives a list of possible compilation targets. The default target is 'dist-all', which
creates a number of .jar files in the 'dist' directory corresponding to subsets of the CDK
functionality. For convenience, one large .jar file containing everything can be created using the
target 'dist-large' (using the command "ant dist-large"). This is also created in dist/jar and is
typically named something like 'cdk-1.4.11.jar'.

2.1 Creating the JavaDoc documentation for the API

The JavaDoc documentation for the API describes all of the CDK classes in detail. It functions as
the user manual for the CDK, although you should also look at the list of examples and tutorials
below. This documentation is created by 'ant' from the Java source code for the CDK as follows:

cdk/$ ls javadoc.xml
javadoc.xml
cdk/$ ant -buildfile javadoc.xml html

The documenation is created as a series of .html pages in doc/api. If you use firefox, you can read
the documentation using the following command:

cdk/$ firefox doc/api/index.html

3. Running tests

IMPORTANT: this requires the Git version of the sources, because the test files are not included in
the source code distribution.

After you compiled the code, you can do "ant test-all" to run the test suite of non-interactive, automated
tests. You might need to copy an appropriate junit.jar into your $ANT_HOME/lib
directory or somewhere else in your classpath.
Upon "ant dist-all test-dist-all test-all", you should see something like:

test:
Running org.openscience.cdk.test.CDKTests
Tests run: 1065, Failures: 7, Errors: 1, Time elapsed: 27,55 sec

As you can see, the vast majority of tests ran successfully, but that there
are failures and errors. The $CDK_HOME/reports/results.txt file contains
information about the outcome of the tests.

There are also run interactive tests, like the Controller2DTest. In order to try them, you can edit the "run"
target in the build.xml file to look like this:

	<target name="run" depends="dist">
		<java classname="org.openscience.cdk.test.ControllerTest" fork="yes">
			<arg value=""/>
			<classpath>
				<pathelement location="${dist}/jar/cdk.jar"/>
				<pathelement path="${java.class.path}"/>
				<pathelement location="."/>
				<fileset dir="jar">
				<include name="*.jar"/>
				</fileset>
			</classpath>
		</java>  
	</target>

Then, a "ant run" should give you a window where you can add bonds to a given structure.
Currently, there are more than 15000 test, of which a large part tests the data, datadebug and 
silent classes.

You can run the tests for an individual module with (for the core module):

cdk/$ ant -Dmodule=core compile-module jarTestdata test-module

4. Using CDK

CDK is a class library intended to be used by other programs. It will not run 
as a stand-alone program, although it contains some GUI- and command
line applications. In order to use the CDK in your program, you need to build
the distribution jars by running "ant dist-all". They will end up in
$CDK_HOME/dist/jar. Copy all cdk-*.jars as well as all jars from $CDK_HOME/jar
to the lib directory of the project for which you intend to have CDK support and
use them as you would use any other third party jar.

Alternatively, run "ant dist-large" to create a jar cdk-svn-YYYYMMDD.jar in
$CDK_HOME/dist/jar. This large jar contains all the CDK code and all third
party libraries that code depends on. 

5. Examples and tutorials

To get started using the CDK, you may be interested in the following websites which contain
examples and tutorials:

* http://pele.farmbio.uu.se/planetcdk/
* http://rguha.net/code/java/
* http://www.redbrick.dcu.ie/~noel/CDKJython.html

And for updates on CDK use cases:

* https://plus.google.com/103703750118158205464/posts
<project name="CDKEclipseBuild" default="fullBuild" basedir=".">

  <property name="classes.dir" value="build/classes" />
  <property name="classes.eclipse.dir" value="bin" />

  <target name="fullBuild" id="fullBuild" depends="preBuild"
          description="Default: full build" />

  <target name="preBuild" id="preBuild" depends=""
          description="Pre-build steps for Eclipse">
    <ant antfile="build.xml" target="javacc"/>
    <ant antfile="build.xml" target="runDoclet"/>
  </target>

</project>
source.. = src/main/
output.. = bin/
bin.includes = plugin.xml,\
               META-INF/,\
               .,\
               jar/,\
               develjar/com-sun-tools-doclets-Taglet.jar,\
               develjar/com-sun-javadoc.jar,\
               META-INF/MANIFEST.MF,\
               jar/jumbo-with-fix-by-jonalv.jar

# configuration file
#
version=1.5.1.git
# configuration file
#
<<<<<<< HEAD
version=1.4.10.git
=======
version=1.5.0.git
>>>>>>> 591623fd2a92bf5e2fbb094a0fe0a1f3309b3392
<project name="CDK" default="dist-all" basedir=".">

        <property file="build.props"/>

        <!-- compile options -->
        <property name="build.sysclasspath" value="ignore" />
        <property name="build.compiler" value="modern" />
        <property name="compile.target.version" value="1.5"/>
        <property name="debug" value="on" />
        <property name="deprecation" value="on" />
        <property name="optimization" value="off" />
        <property name="threadCount" value="4" />
        <property name="parallel" value="false"/>

        <!-- patches to apply -->

       <!-- directories -->
        <property name="build" value="build" />
        <property name="build.src" value="${build}/src" />
        <property name="sourcedist" value="sourcedist" />
        <property name="dist" value="dist" />
        <property name="doc" value="doc" />
        <property name="src" value="src" />
        <property name="lib" value="jar" />
        <property name="devellib" value="develjar" />
        <property name="src.tests" value="${src}/test/org/openscience/cdk/test" />
        <property name="reports.tests" value="reports" />
        <property name="appjars.dir" value="${dist}/appjars" />
        <property name="metainf" value="${src}/META-INF" />
 
        <!-- class to run for testing-->
        <property name="testclass" value="CDKTests" />
        <property name="arg1" value="" />
        <property name="arg2" value="" />
        <property name="arg3" value="" />
        <property name="arg4" value="" />

        <!-- jvm arguments -->
        <property name="jvmarg.cdk.debugging" value="true"
                  description="print debug logging statements"/>
        <property name="jvmarg.cdk.stdout" value="true"/>

        <!-- jar file names for libraries used for compiling -->
        <property name="javaccjar" value="javacc.jar" />
        <property name="antcontribjar" value="ant-contrib-1.0b3.jar" />
        <property name="vecmathjar" value="vecmath1.2-1.14.jar" />
        <property name="log4jjar" value="log4j.jar" />
        <property name="jgraphtjar" value="jgrapht-0.6.0.jar" />
        <property name="junitjar" value="junit-4.10.jar" />

        <property environment="env" />

    <!-- Include the ant-contrib goodies -->
    <taskdef resource="net/sf/antcontrib/antlib.xml">
        <classpath>
            <pathelement location="${devellib}/${antcontribjar}"/>
        </classpath>
    </taskdef>

<!--
    <shellscript shell="bash" outputproperty="svn.output">
     svn info
    </shellscript>
    <propertyregex property="svn.rev" input="${svn.output}" regexp="Revision: ([0-9]*)" select="\1" />
-->

    <target id="info" name="info" depends="check">
            <!-- Gives information about the building process. -->
            <echo message="Platform:" />
            <echo message="             OS: ${os.name}" />
            <echo message="   Architecture: ${os.arch}" />
            <echo message="        Version: ${os.version}" />
            <echo message=" Mac OS/X found: ${isMacOsX}" />
            <echo message="" />
            <echo message="Java/Ant Environment:" />
            <echo message="   Java version: ${java.version}" />
            <echo message="    Java vendor: ${java.vendor}" />
            <echo message="       Java dir: ${java.home}" />
            <echo message="   Java ext dir: ${java.ext.dirs}" />
            <echo message="    Ant version: ${ant.version}" />
            <echo message="    ${ANT_HOME}: ${ant.home}" />
            <echo message="       hasAnt17: ${hasAnt17}" />
            <echo message="" />
            <echo message="CDK Environment:" />
            <echo message="    CDK version: ${version}" />
            <echo message="      build.xml: $Id$" />
            <echo message="    Junit found: ${junit.present}" />
            <echo message=" --- required libraries ---" />
            <echo message="  Vecmath found: ${vecmath.present}" />
            <echo message="    Log4j found: ${log4j.present}" />
            <echo message="  JGraphT found: ${jgrapht.present}" />
            <echo message=" --- distributed (but optional) libraries ---" />
            <echo message="   CMLDOM found: ${cmllibs.present}" />
            <echo message=" --- optional libraries ---" />
            <echo message="" />
            <echo message="Compiling:" />
            <echo message="            for: ${build.compiler}" />
            <echo message="         target: ${compile.target.version}" />
            <echo message="          debug: ${debug}" />
            <echo message="    deprecation: ${deprecation}" />
            <echo message="   optimization: ${optimization}" />
            <echo message="       parallel: ${parallel}" />
            <echo message="        threads: ${threadCount}" />
            <echo message="" />
            <echo message="Available Targets" />
            <echo message="          clean: Remove class files and any temporary files" />
            <echo message="       dist-all: Compile all modules" />
            <echo message="       test-all: Performs a full JUnit test for all modules" />
            <echo message="     dist-large: Create the comprehensive jar, with all modules" />
            <echo message="  test-dist-all: Compile all test modules" />
            <echo message="test-dist-large: Create a single jar file with all test modules" />
            <echo message="    jarTestdata: Create the jar file with all test data. Used in testing" />
            <echo message="" />
        </target>

    <!-- See what platform were on -->
    
        <target id="checkPlatforms" name="checkPlatforms">
            <condition property="isMacOsX">
                <and>
                    <os family="mac"/>
                    <os family="unix"/>
                </and>
            </condition>
        </target>

        <target id="check" name="check" depends="checkPlatforms">
            <!-- Check wether Doclets are compiled and output is generated -->
            <uptodate property="dotjavafiles.uptodate"
                      targetfile="${build}/core.javafiles">
              <srcfiles dir="${src}" includes="**/*.java" />
            </uptodate>
            <condition property="dotjjfiles.uptodate">
              <and>
                <uptodate property="NomParserJavafiles.uptodate"
                          targetfile="${src}/main/org/openscience/cdk/iupac/parser/NomParser.java">
                  <srcfiles dir="${src}/main/" includes="org/openscience/cdk/iupac/parser/NomParser.jj" />
                </uptodate>
                <uptodate property="SMARTSParserJJTJavafiles.uptodate"
                		  targetfile="${src}/main/org/openscience/cdk/smiles/smarts/parser/SMARTSParser.java">
                  <srcfiles dir="${src}/main/" includes="org/openscience/cdk/smiles/smarts/parser/SMARTSParser.jj" />
                </uptodate>
              </and>
            </condition>

            <!-- Checks which parts of CDK can be build. -->

            <!-- test for optional jars -->
            <available property="vecmath.present"
                       file="${lib}/${vecmathjar}"/>
            <available property="log4j.present"
                       file="${lib}/${log4jjar}"/>
            <available property="jgrapht.present"
                       file="${lib}/${jgraphtjar}"/>

            <!-- test for optional jars -->
            <condition property="cmllibs.present">
              <or>
                <available file="${lib}/jumbo-with-fix-by-jonalv.jar"/>
              </or>
            </condition>

            <condition property="junit.present">
              <or>
                <available file="${ant.home}/lib/junit.jar"/>
                <available file="${devellib}/${junitjar}"/>
              </or>
            </condition>

            <!-- test Ant version -->
            <condition property="hasAnt17">
              <or>
              <contains string="${ant.version}" substring="1.7.1"/>
              <contains string="${ant.version}" substring="1.8"/>
              </or>
            </condition>


            <!-- test Java version -->
            <condition property="isJava13">
                <contains string="${java.version}" substring="1.3"/>
            </condition>
            <condition property="isJava14">
                <contains string="${java.version}" substring="1.4"/>
            </condition>
            <condition property="isJava15">
                <contains string="${java.version}" substring="1.5"/>
            </condition>
            <condition property="isJava16">
                <contains string="${java.version}" substring="1.6."/>
            </condition>
            <condition property="isJava17">
                <contains string="${java.version}" substring="1.7."/>
            </condition>
            <condition property="isJava14+">
                <or>
                    <contains string="${java.version}" substring="1.4"/>
                    <contains string="${java.version}" substring="1.5"/>
                    <contains string="${java.version}" substring="1.6"/>
                    <contains string="${java.version}" substring="1.7"/> 
                </or>
            </condition>
            <condition property="isJava15+">
                <or>
                    <contains string="${java.version}" substring="1.5"/>
                    <contains string="${java.version}" substring="1.6"/>
                    <contains string="${java.version}" substring="1.7"/>
                </or>
            </condition>
            <condition property="isNotJava15+">
                <not>
                  <or>
                    <contains string="${java.version}" substring="1.5"/>
                    <contains string="${java.version}" substring="1.6"/>
                    <contains string="${java.version}" substring="1.7"/>
                  </or>
            	</not>
            </condition>
            <fail if="isNotJava15+" message="This CDK release requires Java5 or better."/>
            <fail unless="hasAnt17" message="This CDK release requires Ant 1.7.1 or better."/>
        </target>


        <target id="init" name="init" depends="check, setupBuildDir"/>
        <target id="customize" name="customize" depends="javacc"/>

        <target id="setupBuildDir" name="setupBuildDir">
                <tstamp />
                <mkdir dir="${build}" />
                <mkdir dir="${sourcedist}" />
                <mkdir dir="${dist}" />
                <mkdir dir="${reports.tests}" />
        </target>

        <target id="clean" name="clean" description="Removes autogenerated files.">
                <delete>
                    <fileset dir="." includes="**/*~" />
                    <fileset dir="." includes="*.tar.gz" />
                    <fileset dir="." includes="*.zip" />
                    <fileset dir="." includes="*.rda" />
                    <fileset dir="${src}" includes="*.entitylist" />
                    <!-- remove java files generated with JavaCC -->
                    <fileset dir="${src}/main/org/openscience/cdk/smiles/smarts" includes="*.java">
                        <exclude name="SMARTSQueryTool.java" />
                    </fileset>
                    <fileset dir="${src}/main/org/openscience/cdk/smiles/smarts/parser" 
                             includes="SMARTSParser*.java,SMARTSParser.jj,JJT*,ParseException.java,SimpleCharStream.java,Token*.java" />
                    <fileset dir="${src}/main/org/openscience/cdk/iupac/parser" includes="*.java">
                        <!-- the next are from CVS -->
                        <exclude name="AttachedGroup.java" />
                        <exclude name="MoleculeBuilder.java" />
                    </fileset>
                    <fileset dir="${src}/main/">
                        <include name="net/sf/cdk/tools/*.class" />
                    </fileset>
                </delete>

                <delete dir="${build}" />
                <delete dir="${sourcedist}" />
                <delete dir="${dist}" />
                <delete dir="${reports.tests}" />
        </target>

        <target name="runDoclet" id="runDoclet" depends="check, customize">
            <echo>Not skipping doclet run...</echo>
            <mkdir dir="${build}" />
        	<javac includes="net/sf/cdk/tools/MakeJavafilesFiles.java"
        	    srcdir="${src}/main/" destdir="${build}" optimize="${optimization}"
        	    debug="${debug}" deprecation="${deprecation}" source="${compile.target.version}" target="${compile.target.version}"/>
        	<java classpath="${build}" classname="net.sf.cdk.tools.MakeJavafilesFiles">
                  <arg value="${src}/META-INF"/>
                  <arg value="${src}/main"/>
                  <arg value="${build}"/>
        	</java>
        	<java classpath="${build}" classname="net.sf.cdk.tools.MakeJavafilesFiles">
                  <arg value="${src}/META-INF"/>
                  <arg value="${src}/test"/>
                  <arg value="${build}"/>
        	</java>
        </target>

        <target id="compile-needed-test" name="compile-needed-test">
            <if>
                <matches string="${module}" pattern="^test"/>
                <then>
                    <property name="source" value="src/test"/>
                </then>
                <else>
                    <property name="source" value="src/main"/>
                </else>
            </if>
            <uptodate property="module-uptodate" targetfile="${dist}/jar/cdk-${module}.jar">
                <srcfiles dir="${source}">
                    <includesfile name="${build}/${module}.javafiles"/>
                </srcfiles>
            </uptodate>
        </target>

        <target id="compile-init" name="compile-init"
                depends="init, check, runDoclet"/>

        <target id="qa-module" name="qa-module"
                depends="check, dist.init">
          <echo message="Running QA for CDK's ${module} module" />

          <antcall target="test-module">
              <param name="module" value="${module}"/>
          </antcall>

          <ant antfile="javadoc.xml" target="compileDocTests"/>
          <ant antfile="javadoc.xml" target="ojdcheck-module">
              <property name="module" value="${module}"/>
          </ant>
          <ant antfile="pmd.xml" target="test-module">
              <property name="pmd.test" value="custom"/>
              <property name="module" value="${module}"/>
              <property name="lib" value="develjar" />
          </ant>
          <ant antfile="pmd-unused.xml" target="test-module">
              <property name="pmd.test" value="custom"/>
              <property name="module" value="${module}"/>
              <property name="lib" value="develjar" />
          </ant>
          <ant antfile="pmd-migrating.xml" target="test-module">
              <property name="pmd.test" value="migrating"/>
              <property name="module" value="${module}"/>
              <property name="lib" value="develjar" />
          </ant>
        </target>

        <target id="compile-module" name="compile-module"
                depends="check, dist.init, compile-needed-test"
                unless="module-uptodate">

            <if>
                <matches string="${module}" pattern="^test"/>
                <then>
                    <property name="source" value="src/test"/>
                </then>
                <else>
                    <property name="source" value="src/main"/>
                </else>
            </if>

            <echo message="Compiling classes for CDK's ${module} module from ${source}..." />

            <!-- check for availability for meta info files -->
            <available file="${metainf}/${module}.datafiles" property="module.datafiles.present"/>
            <available file="${metainf}/${module}.extrafiles" property="module.extrafiles.present"/>
            <available file="${metainf}/${module}.buildfiles" property="module.buildfiles.present"/>
            <available file="${metainf}/${module}.cdkdepends" property="module.cdkdepends.present"/>
            <available file="${metainf}/${module}.libdepends" property="module.libdepends.present"/>
            <available file="${metainf}/${module}.devellibdepends" property="module.devellibdepends.present"/>
            <available file="${metainf}/${module}.autogenerated" property="module.autogenerated.present"/>

            <!-- be somewhat informative -->
            <echo message="Datafiles defined: ${module.datafiles.present}"/>
            <echo message="Extra files defined: ${module.extrafiles.present}"/>
            <echo message="CDK dependencies defined: ${module.cdkdepends.present}"/>
            <echo message="Library dependencies defined: ${module.libdepends.present}"/>
            <echo message="Developer Library dependencies defined: ${module.devellibdepends.present}"/>
            <echo message="Autogenerated files specified: ${module.autogenerated.present}"/>

            <!-- normally javac compiles not just the given files, but also missing
                 classes that are in the same src/ directory. By making a copy first,
                 we explicitely make it impossible to compile files that are not
                 marked for a specific module -->
            <mkdir dir="${build.src}/${module}"/>
            <mkdir dir="${build}/${module}"/>
            <copy todir="${build.src}/${module}">
                <fileset dir="${source}">
                    <excludesfile name="${build}/java1.4+.javafiles" if="isJava13"/>
                    <!-- excludesfile name="${build}/java1.4.javafiles" unless="isJava14"/ -->
                    <!-- excludesfile name="${build}/java1.5.javafiles" unless="isJava15"/ -->
                    <excludesfile name="${build}/java1.5+.javafiles" if="isNotJava15"/>
                    <excludesfile name="${build}/ant1.6.javafiles" unless="hasAnt17"/>

                    <includesfile name="${build}/${module}.javafiles"/>
                    <includesfile name="${metainf}/${module}.autogenerated" if="module.autogenerated.present"/>
                </fileset>
            </copy>
            <copy todir="${build}" file="build.props" />

            <!-- ok, now that we have a copy, compile this copy -->
            <javac srcdir="${build.src}/${module}" destdir="${build}/${module}" optimize="${optimization}"
                    debug="${debug}" deprecation="${deprecation}" source="${compile.target.version}" target="${compile.target.version}">
                <classpath>
                    <fileset dir="${lib}" >
                        <exclude name="**/*" unless="module.libdepends.present" />
                        <includesfile name="${metainf}/${module}.libdepends" if="module.libdepends.present" />
                    </fileset>
                    <fileset dir="${devellib}">
                        <exclude name="**/*" unless="module.devellibdepends.present" />
                        <includesfile name="${metainf}/${module}.devellibdepends" if="module.devellibdepends.present" />
                    </fileset>
                    <fileset dir="${dist}/jar">
                        <exclude name="**/*" unless="module.cdkdepends.present" />
                        <includesfile name="${metainf}/${module}.cdkdepends" if="module.cdkdepends.present" />
                    </fileset>
                </classpath>

                <excludesfile name="${build}/java1.4+.javafiles" if="isJava13"/>
                <!-- excludesfile name="${build}/java1.4.javafiles" unless="isJava14"/ -->
                <!-- excludesfile name="${build}/java1.5.javafiles" unless="isJava15"/ -->
                <excludesfile name="${build}/java1.5+.javafiles" if="isNotJava15"/>
                <excludesfile name="${build}/ant1.6.javafiles" unless="hasAnt17"/>

                <includesfile name="${build}/${module}.javafiles"/>
                <includesfile name="${metainf}/${module}.autogenerated" if="module.autogenerated.present"/>
            </javac>

        	<!-- create a autogenerated.classes file, if applicable, so that these files can be included in the jar -->
            <if>
                <istrue value="${module.autogenerated.present}"/>
                <then>
                    <copy file="${metainf}/${module}.autogenerated" tofile="${build}/${module}.autogenerated.classes"
                          failonerror="false"/>
                    <replace dir="${build}" token=".java" value="*.class">
                        <include name="*.autogenerated.classes"/>
                    </replace>
                </then>
            </if>


            <!-- and then jar things up into the module jar -->
            <jar jarfile="${dist}/jar/cdk-${module}.jar">
               <fileset dir="${build}/${module}">
                    <includesfile name="${build}/${module}.classes" />
                    <includesfile name="${build}/${module}.autogenerated.classes" if="module.autogenerated.present"/>
                    <excludesfile name="${build}/java1.4+.classes" if="isJava13"/>
                    <!-- excludesfile name="${build}/java1.4.classes" unless="isJava14"/ -->
                    <!-- excludesfile name="${build}/java1.5.javafiles" unless="isJava15"/ -->
                    <excludesfile name="${build}/java1.5+.javafiles" if="isNotJava15"/>
                    <excludesfile name="${build}/ant1.6.classes" unless="hasAnt17"/>
               </fileset>
               <fileset dir="${build}">
                    <include name="${module}.javafiles" />
               </fileset>
               <fileset dir="${source}">
                    <exclude name="**/*" unless="module.datafiles.present"/>
                    <includesfile name="${metainf}/${module}.datafiles" if="module.datafiles.present" />
               </fileset>
               <fileset dir="${src}">
                    <exclude name="**/*" unless="module.extrafiles.present"/>
                    <includesfile name="${metainf}/${module}.extrafiles" if="module.extrafiles.present" />
               </fileset>
                <fileset dir="${build}">
                     <exclude name="**/*" unless="module.buildfiles.present"/>
                     <includesfile name="${metainf}/${module}.buildfiles" if="module.buildfiles.present" />
                </fileset>
            </jar>

        	<jar jarfile="${dist}/jar/cdk-${module}-sources.jar">
				<fileset dir="${build.src}/${module}">
					<include name="**/*.java" />
				</fileset>
			</jar>
        	
            <!-- clean up afterwards -->
            <!-- delete dir="${build.src}/${module}"/>
            <delete dir="${build}/${module}"/ -->
       </target>

        <!-- Convert the JavaCC .jj file to the correct .java files for the IUPAC parser -->
        <target id="javacc" name="javacc" depends="init, check" if="hasAnt17" unless="dotjjfiles.uptodate">
          <echo message="Compiling Ant 1.6 depending classes." />
          <!-- the IUPAC name parser -->
          <delete>
              <fileset id="javacc-generated"
                dir="${src}/main/org/openscience/cdk/iupac/parser/"
                includes="NomParser*.java,ParseException.java,SimpleCharStream.java,Token.java,TokenMgrError.java"/>
          </delete>
          <javacc target="${src}/main/org/openscience/cdk/iupac/parser/NomParser.jj"
            outputdirectory="${src}/main/org/openscience/cdk/iupac/parser/"
            javacchome="${lib}"/>         
          <delete>
              <fileset id="javacc-generated"
                dir="${src}/main/org/openscience/cdk/smiles/smarts/parser/"
                includes="SMARTSParser*.java,SMARTSParser.jj,JJT*,ParseException.java,SimpleCharStream.java,Token*.java"/>
          </delete>
          <jjtree target="${src}/main/org/openscience/cdk/smiles/smarts/parser/SMARTSParser.jjt"
                  javacchome="${lib}"
                  outputdirectory="${src}/main/org/openscience/cdk/smiles/smarts/parser/"/>
	 <javacc target="${src}/main/org/openscience/cdk/smiles/smarts/parser/SMARTSParser.jj"
                  javacchome="${lib}"
                  outputdirectory="${src}/main/org/openscience/cdk/smiles/smarts/parser/"/>

	 <!-- OK, we now need to do some replacements such as 
	      adding cdk.module tags and changing access modes
	  -->
         <replace dir="${src}/main/org/openscience/cdk/smiles/smarts/parser" 
	          excludes="AST*.java,SMARTSParser.jjt,SMARTSParser.jj,*Node.java"
                  token="package org.openscience.cdk.smiles.smarts.parser;" summary="true" >
                  <replacevalue>package org.openscience.cdk.smiles.smarts.parser;

/** 
*
* @cdk.module smarts 
*/</replacevalue>
         </replace>
        </target>

        <target id="dist.init" name="dist.init">
            <mkdir dir="${dist}/jar" />
        </target>

    <target id="dist-java3d" name="dist-java3d" depends="nocompile-java3d, compile-java3d"/>
    <target id="nocompile-java3d" name="nocompile-java3d" unless="${java3d.present}">
      <echo message="Java3d is not found. Removed depending functionality. Java3d can be downloaded from http://java.sun.com/."/>
    </target>
    <target id="compile-java3d" name="compile-java3d" if="${java3d.present}">
    	<antcall target="compile-module"><param name="module" value="java3d"/></antcall>
    </target>

        <target id="dist-optional" name="dist-optional" depends="dist-all"
        	description="Compile CDK modules that require optional libraries">
        	<antcall target="dist-java3d"/>
        </target>

    <target id="dist-all" name="dist-all" description="dist-all">
        <antcall target="compile-init"/>
        <foreach target="compile-module" param="module"
            parallel="${parallel}" maxthreads="${threadCount}"
            list="interfaces,annotation"/>
        <foreach target="compile-module" param="module"
            parallel="${parallel}" maxthreads="${threadCount}"
            list="core,ioformats"/>
        <foreach target="compile-module" param="module"
            parallel="${parallel}" maxthreads="${threadCount}"
            list="silent,data,dict,diff,qm,standard,log4j"/>
        <foreach target="compile-module" param="module" trim="yes"
            parallel="${parallel}" maxthreads="${threadCount}"
            list="datadebug,isomorphism,atomtype,render,valencycheck,
                  formula,cip"/>
        <foreach target="compile-module" param="module"
            parallel="${parallel}" maxthreads="${threadCount}"
            list="io,structgen"/>
        <foreach target="compile-module" param="module"
            parallel="${parallel}" maxthreads="${threadCount}"
            list="renderbasic"/>
        <foreach target="compile-module" param="module"
            parallel="${parallel}" maxthreads="${threadCount}"
            list="renderextra"/>
        <foreach target="compile-module" param="module"
            parallel="${parallel}" maxthreads="${threadCount}"
            list="pdb,smiles,sdg,inchi,libiocml"/>
        <foreach target="compile-module" param="module"
            parallel="${parallel}" maxthreads="${threadCount}"
            list="control,extra,fragment,reaction,pdbcml,libiomd"/>
        <foreach target="compile-module" param="module"
            parallel="${parallel}" maxthreads="${threadCount}"
            list="charges,smarts,signature"/>
        <foreach target="compile-module" param="module"
            parallel="${parallel}" maxthreads="${threadCount}"
            list="qm,qsar,ionpot,fingerprint,pcore,smsd,tautomer"/>
        <foreach target="compile-module" param="module"
            parallel="${parallel}" maxthreads="${threadCount}"
            list="renderawt"/>
        <foreach target="compile-module" param="module"
            parallel="${parallel}" maxthreads="${threadCount}"
            list="qsaratomic,qsarbond,qsarprotein,qsarcml,qsarmolecular"/>
        <foreach target="compile-module" param="module"
            parallel="${parallel}" maxthreads="${threadCount}"
            list="forcefield,qsarionpot,iordf"/>
        <foreach target="compile-module" param="module"
            parallel="${parallel}" maxthreads="${threadCount}"
            list="builder3d,builder3dtools"/>
        <foreach target="compile-module" param="module"
            parallel="${parallel}" maxthreads="${threadCount}"
            list="group"/>
    </target>

    <target id="test-dist-all" name="test-dist-all" description="test-dist-all">
        <antcall target="compile-init"/>
        <foreach target="compile-module" param="module"
            parallel="${parallel}" maxthreads="${threadCount}"
            list="test"/>
        <foreach target="compile-module" param="module" trim="true"
            parallel="${parallel}" maxthreads="${threadCount}"
            list="test-interfaces,test-libiocml,test-qsar,test-io,test-core,
        	      test-valencycheck,test-smarts,test-standard,test-reaction,
                  test-pcore,test-sdg,test-forcefield,test-fingerprint,
                  test-ionpot,test-qm,test-isomorphism,test-libiomd,test-dict,
                  test-diff,test-charges,test-inchi,test-formula,
                  test-render,test-ioformats,test-log4j,test-cip"/>
        <foreach target="compile-module" param="module" trim="true"
            parallel="${parallel}" maxthreads="${threadCount}"
            list="test-data,test-qsaratomic,test-qsarbond,
                  test-pdb,test-smiles,test-extra,test-fragment,test-atomtype,
                  test-structgen,test-iordf,test-silent"/>
        <foreach target="compile-module" param="module" trim="true"
            parallel="${parallel}" maxthreads="${threadCount}"
            list="test-qsarmolecular,test-builder3d,test-datadebug"/>
        <foreach target="compile-module" param="module"
            parallel="${parallel}" maxthreads="${threadCount}"
            list="test-qsarprotein,test-qsarionpot,test-smsd,test-tautomer"/>
        <foreach target="compile-module" param="module"
            parallel="${parallel}" maxthreads="${threadCount}"
            list="test-signature"/>
        <foreach target="compile-module" param="module"
            parallel="${parallel}" maxthreads="${threadCount}"
            list="test-renderbasic"/>
        <foreach target="compile-module" param="module"
            parallel="${parallel}" maxthreads="${threadCount}"
            list="test-renderawt"/>
        <foreach target="compile-module" param="module"
            parallel="${parallel}" maxthreads="${threadCount}"
            list="test-renderextra"/>
        <foreach target="compile-module" param="module"
            parallel="${parallel}" maxthreads="${threadCount}"
            list="test-group"/>
    </target>

	<target id="jarTestdata" name="jarTestdata" description="Creates jar files with test data.">
		<mkdir dir="${dist}/jar"/>
        <jar jarfile="${dist}/jar/cdk-testdata.jar">
            <fileset dir="${src}/test">
                <include name="data/**/*" />
            </fileset>
        </jar>
	</target>
	
	<target id="dist-large" name="dist-large" depends="dist-all"
            description="Builds one big jar file for the CDK, including third-party libraries.">

            <!-- first unjar the CDK and other jars we need -->
            <mkdir dir="${appjars.dir}"/>
            <unjar dest="${appjars.dir}">
                <fileset dir="${lib}">
                    <includesfile name="${metainf}/builder3d.libdepends"/>
                    <includesfile name="${metainf}/builder3dtools.libdepends"/>
                    <includesfile name="${metainf}/charges.libdepends"/>
                    <includesfile name="${metainf}/log4j.libdepends"/>
                    <includesfile name="${metainf}/control.libdepends"/>
                    <includesfile name="${metainf}/datadebug.libdepends"/>
                    <includesfile name="${metainf}/data.libdepends"/>
                    <includesfile name="${metainf}/silent.libdepends"/>
                    <includesfile name="${metainf}/extra.libdepends"/>
                    <includesfile name="${metainf}/cip.libdepends"/>
                    <includesfile name="${metainf}/io.libdepends"/>
                    <includesfile name="${metainf}/libiocml.libdepends"/>
                    <includesfile name="${metainf}/pdbcml.libdepends"/>
                    <includesfile name="${metainf}/pdb.libdepends"/>
                    <includesfile name="${metainf}/qsar.libdepends"/>
                    <includesfile name="${metainf}/qsaratomic.libdepends"/>
                    <includesfile name="${metainf}/qsarbond.libdepends"/>
                    <includesfile name="${metainf}/qsarmolecular.libdepends"/>
                    <includesfile name="${metainf}/qsarprotein.libdepends"/>
                    <includesfile name="${metainf}/qsarcml.libdepends"/>
                    <includesfile name="${metainf}/reaction.libdepends"/>
                    <includesfile name="${metainf}/render.libdepends"/>
                    <includesfile name="${metainf}/renderbasic.libdepends"/>
                    <includesfile name="${metainf}/renderextra.libdepends"/>
                    <includesfile name="${metainf}/renderawt.libdepends"/>
                    <includesfile name="${metainf}/standard.libdepends"/>
                    <includesfile name="${metainf}/valencycheck.libdepends"/>
                    <includesfile name="${metainf}/sdg.libdepends"/>
                    <includesfile name="${metainf}/forcefield.libdepends"/>
                    <includesfile name="${metainf}/inchi.libdepends"/>
                    <includesfile name="${metainf}/smarts.libdepends"/>
                    <includesfile name="${metainf}/smsd.libdepends"/>
                    <includesfile name="${metainf}/pcore.libdepends"/>
                    <includesfile name="${metainf}/formula.libdepends"/>
                    <includesfile name="${metainf}/isomorphism.libdepends"/>
                    <includesfile name="${metainf}/qm.libdepends"/>
                    <includesfile name="${metainf}/iordf.libdepends"/>
                    <includesfile name="${metainf}/signature.libdepends"/>
                </fileset>
                <fileset dir="${dist}/jar">
                    <include name="cdk-annotation.jar"/>
                    <include name="cdk-ioformats.jar"/>
                    <include name="cdk-atomtype.jar"/>
                    <include name="cdk-builder3d.jar"/>
                    <include name="cdk-builder3dtools.jar"/>
                    <include name="cdk-charges.jar"/>
                    <include name="cdk-core.jar"/>
                    <include name="cdk-cip.jar"/>
                    <include name="cdk-log4j.jar"/>
                    <include name="cdk-dict.jar"/>
                    <include name="cdk-diff.jar"/>
                    <include name="cdk-control.jar"/>
                    <include name="cdk-datadebug.jar"/>
                    <include name="cdk-data.jar"/>
                    <include name="cdk-silent.jar"/>
                    <include name="cdk-extra.jar"/>
                    <include name="cdk-fragment.jar"/>
                    <include name="cdk-interfaces.jar"/>
                    <include name="cdk-io.jar"/>
                    <include name="cdk-libiocml.jar"/>
                    <include name="cdk-libiomd.jar"/>
                    <include name="cdk-pdbcml.jar"/>
                    <include name="cdk-pdb.jar"/>
                    <include name="cdk-qsar.jar"/>
                    <include name="cdk-qsaratomic.jar"/>
                    <include name="cdk-qsarbond.jar"/>
                    <include name="cdk-qsarmolecular.jar"/>
                    <include name="cdk-qsarionpot.jar"/>
                    <include name="cdk-qsarprotein.jar"/>
                    <include name="cdk-qsarcml.jar"/>
                    <include name="cdk-reaction.jar"/>
                    <include name="cdk-render.jar"/>
                    <include name="cdk-renderbasic.jar"/>
                    <include name="cdk-renderextra.jar"/>
                    <include name="cdk-renderawt.jar"/>
                    <include name="cdk-standard.jar"/>
                    <include name="cdk-structgen.jar"/>
                    <include name="cdk-valencycheck.jar"/>
                    <include name="cdk-forcefield.jar"/>
                    <include name="cdk-smiles.jar"/>
                    <include name="cdk-smarts.jar"/>
                    <include name="cdk-fingerprint.jar"/>
                    <include name="cdk-sdg.jar"/>
                    <include name="cdk-inchi.jar"/>
                    <include name="cdk-pcore.jar"/>
                    <include name="cdk-formula.jar"/>
                    <include name="cdk-isomorphism.jar"/>
                    <include name="cdk-ionpot.jar"/>
                    <include name="cdk-smsd.jar"/>
                    <include name="cdk-iordf.jar"/>
                    <include name="cdk-signature.jar"/>
                    <include name="cdk-group.jar"/>
                    <include name="cdk-qm.jar"/>
                    <include name="cdk-tautomer.jar"/>
                </fileset>
            </unjar>

            <!-- then zip up things -->
            <jar jarfile="${dist}/jar/cdk-${version}.jar">
                <manifest>
                    <section name="org.openscience.cdk">
                        <attribute name="Specification-Title" value="The Chemistry Development Kit"/>
                        <attribute name="Specification-Version" value="1.4"/>
                        <attribute name="Specification-Vendor" value="The CDK Project"/>
                        <attribute name="Implementation-Title" value="org.openscience.cdk"/>
                        <attribute name="Implementation-Version" value="${version}"/>
                        <attribute name="Implementation-Vendor" value="The CDK Project"/>
                        <attribute name="X-Compile-Target-JDK" value="${compile.target.version}"/>
                    </section>
                </manifest>
                <fileset dir="${appjars.dir}">
                    <include name="**/*" />
                </fileset>
            </jar>
        </target>

        <target id="dist-pure" name="dist-pure" depends="dist-all"
            description="Builds one big jar file for the CDK, excluding third party libraries.">

            <!-- first unjar the CDK and other jars we need -->
            <mkdir dir="${appjars.dir}"/>
            <unjar dest="${appjars.dir}">
                <fileset dir="${dist}/jar">
                    <include name="cdk-annotation.jar"/>
                    <include name="cdk-builder3d.jar"/>
                    <include name="cdk-builder3dtools.jar"/>
                    <include name="cdk-charges.jar"/>
                    <include name="cdk-log4j.jar"/>
                    <include name="cdk-core.jar"/>
                    <include name="cdk-cip.jar"/>
                    <include name="cdk-control.jar"/>
                    <include name="cdk-datadebug.jar"/>
                    <include name="cdk-data.jar"/>
                    <include name="cdk-silent.jar"/>
                    <include name="cdk-diff.jar"/>
                    <include name="cdk-extra.jar"/>
                    <include name="cdk-fragment.jar"/>
                    <include name="cdk-interfaces.jar"/>
                    <include name="cdk-io.jar"/>
                    <include name="cdk-ioformats.jar"/>
                    <include name="cdk-libiocml.jar"/>
                    <include name="cdk-libiomd.jar"/>
                    <include name="cdk-pdbcml.jar"/>
                    <include name="cdk-pdb.jar"/>
                    <include name="cdk-qsar.jar"/>
                    <include name="cdk-qsaratomic.jar"/>
                    <include name="cdk-qsarbond.jar"/>
                    <include name="cdk-qsarmolecular.jar"/>
                    <include name="cdk-qsarionpot.jar"/>
                    <include name="cdk-qsarprotein.jar"/>
                    <include name="cdk-qsarcml.jar"/>
                    <include name="cdk-reaction.jar"/>
                    <include name="cdk-render.jar"/>
                    <include name="cdk-renderbasic.jar"/>
                    <include name="cdk-renderextra.jar"/>
                    <include name="cdk-renderawt.jar"/>
                    <include name="cdk-standard.jar"/>
                    <include name="cdk-structgen.jar"/>
                    <include name="cdk-valencycheck.jar"/>
                    <include name="cdk-forcefield.jar"/>
                    <include name="cdk-smarts.jar"/>
                    <include name="cdk-fingerprint.jar"/>
                    <include name="cdk-smiles.jar"/>
                    <include name="cdk-sdg.jar"/>
                    <include name="cdk-inchi.jar"/>
                    <include name="cdk-pcore.jar"/>
                    <include name="cdk-formula.jar"/>
		    <include name="cdk-atomtype.jar"/>
                    <include name="cdk-signature.jar"/>
                    <include name="cdk-tautomer.jar"/>
                    <include name="cdk-group.jar"/>
                </fileset>
            </unjar>

            <!-- then zip up things -->
            <jar jarfile="${dist}/jar/cdk-pure-${version}.jar">
                <manifest>
                    <section name="org.openscience.cdk">
                        <attribute name="Specification-Title" value="The Chemistry Development Kit"/>
                        <attribute name="Specification-Version" value="1.0"/>
                        <attribute name="Specification-Vendor" value="The CDK Project"/>
                        <attribute name="Implementation-Title" value="org.openscience.cdk"/>
                        <attribute name="Implementation-Version" value="${version}"/>
                        <attribute name="Implementation-Vendor" value="The CDK Project"/>
                        <attribute name="X-Compile-Target-JDK" value="${compile.target.version}"/>
                    </section>
                </manifest>
                <fileset dir="${appjars.dir}">
                    <include name="**/*" />
                </fileset>
            </jar>
        </target>

        <target id="dist-test-large" name="dist-test-large" depends="test-dist-all, jarTestdata"
            description="Builds on big jar file for the CDK test classes.">

            <!-- first unjar the CDK and other jars we need -->
            <mkdir dir="${appjars.dir}"/>
            <unjar dest="${appjars.dir}">
                <fileset dir="${lib}">
                    <includesfile name="${metainf}/test.libdepends"/>
                    <includesfile name="${metainf}/test-core.libdepends"/>
                    <includesfile name="${metainf}/test-data.libdepends"/>
                    <includesfile name="${metainf}/test-datadebug.libdepends"/>
                    <includesfile name="${metainf}/test-silent.libdepends"/>
                    <includesfile name="${metainf}/test-diff.libdepends"/>
                    <includesfile name="${metainf}/test-extra.libdepends"/>
                    <includesfile name="${metainf}/test-fragment.libdepends"/>
                    <includesfile name="${metainf}/test-builder3d.libdepends"/>
                    <includesfile name="${metainf}/test-forcefield.libdepends"/>
                    <includesfile name="${metainf}/test-inchi.libdepends"/>
                    <includesfile name="${metainf}/test-io.libdepends"/>
                    <includesfile name="${metainf}/test-pdb.libdepends"/>
                    <includesfile name="${metainf}/test-qsaratomic.libdepends"/>
                    <includesfile name="${metainf}/test-qsarbond.libdepends"/>
                    <includesfile name="${metainf}/test-qsarmolecular.libdepends"/>
                    <includesfile name="${metainf}/test-qsarionpot.libdepends"/>
                    <includesfile name="${metainf}/test-qsarprotein.libdepends"/>
                    <includesfile name="${metainf}/test-qsar.libdepends"/>
                    <includesfile name="${metainf}/test-reaction.libdepends"/>
                    <includesfile name="${metainf}/test-smarts.libdepends"/>
                    <includesfile name="${metainf}/test-smiles.libdepends"/>
                    <includesfile name="${metainf}/test-standard.libdepends"/>
                    <includesfile name="${metainf}/test-structgen.libdepends"/>
                    <includesfile name="${metainf}/test-valencycheck.libdepends"/>
                    <includesfile name="${metainf}/test-charges.libdepends"/>
                    <includesfile name="${metainf}/test-libiomd.libdepends"/>
                    <includesfile name="${metainf}/test-pcore.libdepends"/>
                    <includesfile name="${metainf}/test-formula.libdepends"/>
                    <includesfile name="${metainf}/test-render.libdepends"/>
                    <includesfile name="${metainf}/test-log4j.libdepends"/>
                    <includesfile name="${metainf}/test-signature.libdepends"/>
                    <includesfile name="${metainf}/test-cip.libdepends"/>
                </fileset>
                <fileset dir="${dist}/jar">
                    <include name="cdk-test.jar"/>
                    <include name="cdk-testdata.jar"/>
                    <include name="cdk-test-annotation.jar"/>
                    <include name="cdk-test-ioformats.jar"/>
                    <include name="cdk-test-core.jar"/>
                    <include name="cdk-test-data.jar"/>
                    <include name="cdk-test-datadebug.jar"/>
                    <include name="cdk-test-silent.jar"/>
                    <include name="cdk-test-diff.jar"/>
                    <include name="cdk-test-extra.jar"/>
                    <include name="cdk-test-fragment.jar"/>
                    <include name="cdk-test-builder3d.jar"/>
                    <include name="cdk-test-forcefield.jar"/>
                    <include name="cdk-test-inchi.jar"/>
                    <include name="cdk-test-io.jar"/>
                    <include name="cdk-test-pdb.jar"/>
                    <include name="cdk-test-qsaratomic.jar"/>
                    <include name="cdk-test-qsarbond.jar"/>
                    <include name="cdk-test-qsarmolecular.jar"/>
                    <include name="cdk-test-qsarionpot.jar"/>
                    <include name="cdk-test-qsarprotein.jar"/>
                    <include name="cdk-test-qsar.jar"/>
                    <include name="cdk-test-reaction.jar"/>
                    <include name="cdk-test-smarts.jar"/>
                    <include name="cdk-test-smiles.jar"/>
                    <include name="cdk-test-standard.jar"/>
                    <include name="cdk-test-structgen.jar"/>
                    <include name="cdk-test-valencycheck.jar"/>
                    <include name="cdk-test-charges.jar"/>
                    <include name="cdk-test-libiomd.jar"/>
                    <include name="cdk-test-pcore.jar"/>
                    <include name="cdk-test-formula.jar"/>
                    <include name="cdk-test-render.jar"/>
                    <include name="cdk-test-log4j.jar"/>
                    <include name="cdk-test-signature.jar"/>
		    <include name="cdk-test-cip.jar"/>
                    <include name="cdk-test-tautomer.jar"/>
                    <include name="cdk-test-group.jar"/>
                </fileset>
            </unjar>

            <!-- then zip up things -->
            <jar jarfile="${dist}/jar/cdk-test-${version}.jar">
                <manifest>
                    <attribute name="Main-Class" value="org.openscience.cdk.CDKTests"/>
                    <section name="org.openscience.cdk">
                        <attribute name="Specification-Title" value="The Chemistry Development Kit"/>
                        <attribute name="Specification-Version" value="1.4"/>
                        <attribute name="Specification-Vendor" value="The CDK Project"/>
                        <attribute name="Implementation-Title" value="org.openscience.cdk"/>
                        <attribute name="Implementation-Version" value="${version}"/>
                        <attribute name="Implementation-Vendor" value="The CDK Project"/>
                        <attribute name="X-Compile-Target-JDK" value="${compile.target.version}"/>
                    </section>
                </manifest>
                <fileset dir="${appjars.dir}">
                    <include name="**/*" />
                </fileset>
            </jar>
        </target>

        <target id="sourcedist" name="sourcedist"
                description="Builds the source packages.">
                <property name="package" value="cdk-src+libs-${version}"/>
                <property name="sourcedist.dir" value="${sourcedist}/${package}"/>
                <delete dir="${sourcedist.dir}"/>
                <copy todir="${sourcedist.dir}/${src}/main/">
                        <fileset dir="${src}/main/" includes="**/*.java" />
                        <fileset dir="${src}/main/" includes="**/*.jj" />
                        <fileset dir="${src}/main/" includes="**/*.jjt" />
                        <fileset dir="${src}/main/" includes="org/openscience/cdk/io/cml/data/**" />
                </copy>
                <copy todir="${sourcedist.dir}">
                        <fileset dir="." includes="build.props" />
                        <fileset dir="." includes="build.xml" />
                        <fileset dir="." includes="javadoc.xml" />
                        <fileset dir="." includes="README" />
                        <fileset dir="." includes="changelog*" />
                </copy>
            <copy todir="${sourcedist.dir}/jar">
                    <fileset dir="jar">
                        <exclude name="*.so"/>
                        <exclude name="*.dll"/>
                        <exclude name="jumbo-5.4.2-b2.jar"/>
                    </fileset>
            </copy>
            <copy todir="${sourcedist.dir}/doc/refs">
                    <fileset dir="doc/refs">
                        <include name="*.*"/>
                    </fileset>
            </copy>
            <copy todir="${sourcedist.dir}/develjar">
                    <fileset dir="develjar">
                        <exclude name="pmd-1.8.jar"/>
                        <exclude name="dbdoclet*.*"/>
                    </fileset>
            </copy>
            <copy todir="${sourcedist.dir}/src/META-INF">
                    <fileset dir="src/META-INF" />
            </copy>
                <copy todir="${sourcedist.dir}/${src}/main/">
                    <fileset dir="${src}/main/" includesfile="${src}/META-INF/atomtype.datafiles" />
                    <fileset dir="${src}/main/" includesfile="${src}/META-INF/builder3d.datafiles" />
                    <fileset dir="${src}/main/" includesfile="${src}/META-INF/core.datafiles" />
                    <fileset dir="${src}/main/" includesfile="${src}/META-INF/dict.datafiles" />
                    <fileset dir="${src}/main/" includesfile="${src}/META-INF/extra.datafiles" />
                    <fileset dir="${src}/main/" includesfile="${src}/META-INF/fingerprint.datafiles" />
                    <fileset dir="${src}/main/" includesfile="${src}/META-INF/forcefield.datafiles" />
                    <fileset dir="${src}/main/" includesfile="${src}/META-INF/io.datafiles" />
                    <fileset dir="${src}/main/" includesfile="${src}/META-INF/log4j.datafiles" />
                    <fileset dir="${src}/main/" includesfile="${src}/META-INF/pdb.datafiles" />
                    <fileset dir="${src}/main/" includesfile="${src}/META-INF/qsaratomic.datafiles" />
                    <fileset dir="${src}/main/" includesfile="${src}/META-INF/qsar.datafiles" />
                    <fileset dir="${src}/main/" includesfile="${src}/META-INF/qsarmolecular.datafiles" />
                    <fileset dir="${src}/main/" includesfile="${src}/META-INF/sdg.datafiles" />
                </copy>
                <mkdir dir="${sourcedist.dir}/doc/" />
                <copy todir="${sourcedist.dir}/doc/">
                    <fileset dir="doc/" includes="lgpl.license" />
                </copy>
                <mkdir dir="${sourcedist.dir}/doc/javadoc" />
                <!-- the below deteles are a workaround, because the above should not have copied
                     in the src/data and src/org/openscience/cdk/test dirs -->
                <delete dir="${sourcedist.dir}/src/test/data"/>

                <!-- now package things up -->
                <tar tarfile="${package}.tar" basedir="${sourcedist}/" includes="${package}/**" />
                <gzip zipfile="${package}.tar.gz" src="${package}.tar" />
                <delete file="${package}.tar" />
                <zip zipfile="${package}.zip" basedir="${sourcedist}/" includes="${package}/**" />
        </target>

        <target id="puredist" name="puredist" depends="init, runDoclet"
                description="Builds the source packages without third-party libaries.">
                <property name="package" value="cdk-${version}"/>
                <property name="sourcedist.dir" value="${sourcedist}/${package}"/>
                <delete dir="${sourcedist.dir}"/>
                <copy todir="${sourcedist.dir}/${src}/main">
                        <fileset dir="${src}/main/" includes="**/*.java" />
                        <fileset dir="${src}/main/" includes="**/*.jj" />
                        <fileset dir="${src}/main/" includes="**/*.jjt" />
                        <fileset dir="${src}/main/" includes="org/openscience/cdk/io/cml/data/**" />
                </copy>
                <copy todir="${sourcedist.dir}/doc/refs">
                        <fileset dir="doc/refs">
                            <include name="*.*"/>
                        </fileset>
                </copy>
                <copy todir="${sourcedist.dir}">
                        <fileset dir="." includes="build.props" />
                        <fileset dir="." includes="build.xml" />
                        <fileset dir="." includes="javadoc.xml" />
                        <fileset dir="." includes="README" />
                        <fileset dir="." includes="changelog*" />
                </copy>
                <copy todir="${sourcedist.dir}/src/META-INF">
                    <fileset dir="src/META-INF" />
               </copy>
                <copy todir="${sourcedist.dir}/${src}/main/">
                    <fileset dir="${src}/main/" includesfile="${src}/META-INF/atomtype.datafiles" />
                    <fileset dir="${src}/main/" includesfile="${src}/META-INF/builder3d.datafiles" />
                    <fileset dir="${src}/main/" includesfile="${src}/META-INF/core.datafiles" />
                    <fileset dir="${src}/main/" includesfile="${src}/META-INF/dict.datafiles" />
                    <fileset dir="${src}/main/" includesfile="${src}/META-INF/extra.datafiles" />
                    <fileset dir="${src}/main/" includesfile="${src}/META-INF/fingerprint.datafiles" />
                    <fileset dir="${src}/main/" includesfile="${src}/META-INF/forcefield.datafiles" />
                    <fileset dir="${src}/main/" includesfile="${src}/META-INF/io.datafiles" />
                    <fileset dir="${src}/main/" includesfile="${src}/META-INF/log4j.datafiles" />
                    <fileset dir="${src}/main/" includesfile="${src}/META-INF/pdb.datafiles" />
                    <fileset dir="${src}/main/" includesfile="${src}/META-INF/qsaratomic.datafiles" />
                    <fileset dir="${src}/main/" includesfile="${src}/META-INF/qsar.datafiles" />
                    <fileset dir="${src}/main/" includesfile="${src}/META-INF/qsarmolecular.datafiles" />
                    <fileset dir="${src}/main/" includesfile="${src}/META-INF/sdg.datafiles" />
                </copy>
                <mkdir dir="${sourcedist.dir}/doc/" />
                <copy todir="${sourcedist.dir}/doc/">
                    <fileset dir="doc/" includes="lgpl.license" />
                </copy>
                <mkdir dir="${sourcedist.dir}/doc/javadoc" />
                <!-- the below deteles are a workaround, because the above should not have copied
                     in the src/data and src/org/openscience/cdk/test dirs -->
                <delete dir="${sourcedist.dir}/src/data"/>
                <delete dir="${sourcedist.dir}/src/test"/>

                <!-- now package things up -->
                <tar tarfile="${package}.tar" basedir="${sourcedist}/" includes="${package}/**" />
                <gzip zipfile="${package}.tar.gz" src="${package}.tar" />
                <delete file="${package}.tar" />
        </target>

        <target id="noJunit" name="noJunit" depends="check" unless="junit.present">
            <fail message="JUnit is not installed in Ant. Please run ant with the option '-lib develjar/junit-4.10.jar'."/>
        </target>
        
		<target id="test-module" name="test-module" depends="noJunit"
	                description="Performs a full JUnit test for the CDK." 
	                if="junit.present">

            <echo message="Testing classes for CDK's ${module} module." />

            <!-- check for availability for meta info files -->
            <available file="${metainf}/test-${module}.cdkdepends" property="module.cdkdepends.present"/>
            <available file="${metainf}/test-${module}.libdepends" property="module.libdepends.present"/>
			<available file="${metainf}/test-${module}.devellibdepends" property="module.devellibdepends.present"/>        
			
            <!-- be somewhat informative -->
            <echo message="CDK dependencies defined: ${module.cdkdepends.present}"/>
            <echo message="Library dependencies defined: ${module.libdepends.present}"/>
			<echo message="Developer Library dependencies defined: ${module.devellibdepends.present}"/>

			<mkdir dir="${reports.tests}"/>
            <junit printsummary="yes" haltonfailure="no" fork="yes" maxmemory="256m">
                <classpath>
                     <fileset dir="${lib}" >
                         <exclude name="**/*" unless="module.libdepends.present" />
                         <includesfile name="${metainf}/test-${module}.libdepends" if="module.libdepends.present" />
                     </fileset>
                     <fileset dir="${devellib}">
                         <exclude name="**/*" unless="module.devellibdepends.present" />
                         <includesfile name="${metainf}/test-${module}.devellibdepends" if="module.devellibdepends.present" />
                     </fileset>
                     <fileset dir="${dist}/jar">
                         <exclude name="**/*" unless="module.cdkdepends.present" />
                         <includesfile name="${metainf}/test-${module}.cdkdepends" if="module.cdkdepends.present" />
                         <include name="cdk-test-${module}.jar" />
                     </fileset>
                 </classpath>
              	 <test name="org.openscience.cdk.modulesuites.M${module}Tests"
            	     haltonfailure="no"
            	     todir="${reports.tests}"
            	     outfile="result-${module}">
            	     <formatter type="brief" />
            	 </test>
			</junit>
        </target>
			
        <target id="test-all" name="test-all" depends="noJunit, dist-all, test-dist-all, jarTestdata"
                description="Performs a full JUnit test for the CDK." 
                if="junit.present">
            <foreach target="test-module" param="module" trim="true"
                list="core,data,datadebug,dict,diff,atomtype,standard,
                      io,builder3d,forcefield,valencycheck,charges,reaction,
                      smarts,fingerprint,smiles,qsar,qsaratomic,qsarbond,
                      qsarmolecular,qsarionpot,qsarprotein,pdb,pcore,inchi,
                      structgen,libiomd,libiocml,formula,render,extra,fragment,sdg,
                      ioformats,log4j,smsd,signature,iordf,cip,tautomer,
                      isomorphism,renderbasic,renderawt,renderextra,silent,group"/>
        </target>

        <target id="limitations" name="limitations" depends="noJunit, dist-all"
                description="Performs a JUnit tests that indicate limitations of certain CDK algorithms/classes.">
                <junit printsummary="yes" haltonfailure="yes" fork="yes">
                    <classpath>
                        <fileset dir="${dist}/jar">
                                <include name="cdk-*.jar" />
                        </fileset>
                        <fileset dir="${lib}">
                                <include name="*.jar" />
                        </fileset>
                        <fileset dir="${devellib}">
                                <include name="*.jar" />
                        </fileset>
                    </classpath>
                        <test name="org.openscience.cdk.limitations.AlgorithmLimitations"
                        haltonfailure="no"
                        todir="${reports.tests}"
                        outfile="limitations">
                                <formatter type="brief" />
                        </test>
                </junit>
        </target>

        <target id="run-test" name="run-test" depends="dist-all,test-dist-all" 
                description="Runs one specific JUnit test suite (org.openscience.cdk.&lt;class>) as a standalone application with 
-Dtestclass=&lt;class>.">
                <echo message="Running test class: testclass=${testclass}"/>
                <java classname="org.openscience.cdk.${testclass}" fork="yes" maxmemory="512m">
                    <jvmarg value="-Dcdk.debugging=${jvmarg.cdk.debugging}"/>
                    <jvmarg value="-Dcdk.debug.stdout=${jvmarg.cdk.stdout}"/>
                    <classpath>
                        <fileset dir="${dist}/jar/">
                                <include name="*.jar" />
                        </fileset>
                        <fileset dir="${lib}">
                                <include name="*.jar" />
                        </fileset>
                        <fileset dir="${devellib}">
                                <include name="*.jar" />
                        </fileset>
                    </classpath>
                </java>
        </target>

        <target id="junit-test" name="junit-test" depends="dist-all,jarTestdata,test-dist-all,noJunit"
                description="Runs one specific JUnit test suite (org.openscience.cdk.&lt;class>) with -Dtestclass=&lt;class>.">
                <echo message="JUnit tests class: testclass=${testclass} [JVM Arguments: cdk.debugging=${cdk.debugging}, ${jvmarg.cdk.stdout}]"/>
                <junit printsummary="yes" haltonfailure="no" fork="yes" maxmemory="512m">
                    <jvmarg value="-Dcdk.debugging=${jvmarg.cdk.debugging}"/>
                    <jvmarg value="-Dcdk.debug.stdout=${jvmarg.cdk.stdout}"/>
                    <classpath>
                        <fileset dir="${dist}/jar/">
                                <include name="*.jar" />
                        </fileset>
                        <pathelement path="${java.class.path}" />
                        <pathelement location="." />
                        <fileset dir="${lib}">
                                <include name="*.jar" />
                        </fileset>
                        <fileset dir="${devellib}">
                                <include name="*.jar" />
                        </fileset>
                    </classpath>
                    <test name="org.openscience.cdk.${testclass}"
                        haltonfailure="no"
                        todir="${reports.tests}"
                        outfile="result.${testclass}">
                        <formatter type="brief" />
                    </test>
                </junit>
        </target>

        <target id="run" name="run" depends="dist-all" 
                description="Runs an application (org.openscience.cdk.&lt;class>) with -Drunclass=&lt;class>.">
                <java classname="org.openscience.cdk.${runclass}" fork="yes" >
                    <jvmarg value="-Dcdk.debugging=${jvmarg.cdk.debugging}"/>
                    <jvmarg value="-Dcdk.debug.stdout=${jvmarg.cdk.stdout}"/>
                    <arg value="${arg1}" />
                    <arg value="${arg2}" />
                    <arg value="${arg3}" />
                    <arg value="${arg4}" />
                    <classpath>
                        <fileset dir="${dist}/jar">
                                <include name="*.jar" />
                        </fileset>
                        <fileset dir="${lib}">
                                <include name="*.jar" />
                        </fileset>
                    </classpath>
                </java>
        </target>

</project>
2012-06-19 09:13:23,147 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@38dda25b
2012-06-19 09:13:23,149 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3a64c34eorg.openscience.cdk.tools.LoggingToolTestDebugTrue@3a64c34e
2012-06-19 09:13:23,149 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2d5253d51
2012-06-19 09:13:23,150 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@77fddc311.0
2012-06-19 09:13:23,150 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3b835282true
2012-06-19 09:13:23,151 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2a9df354org.openscience.cdk.tools.LoggingToolTestDebugTrue@2a9df354org.openscience.cdk.tools.LoggingToolTestDebugTrue@2a9df354org.openscience.cdk.tools.LoggingToolTestDebugTrue@2a9df354org.openscience.cdk.tools.LoggingToolTestDebugTrue@2a9df354
2012-06-19 09:13:23,151 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@67d225a7org.openscience.cdk.tools.LoggingToolTestDebugTrue@67d225a7org.openscience.cdk.tools.LoggingToolTestDebugTrue@67d225a7org.openscience.cdk.tools.LoggingToolTestDebugTrue@67d225a7
2012-06-19 09:13:23,152 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@15a62c31org.openscience.cdk.tools.LoggingToolTestDebugTrue@15a62c31org.openscience.cdk.tools.LoggingToolTestDebugTrue@15a62c31
2012-06-19 09:13:23,153 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - Exception: null
2012-06-19 09:13:23,154 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.lang.Exception
2012-06-19 09:13:23,154 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at org.openscience.cdk.tools.AbstractLoggingToolTest.testDebug_ExceptionWithNullMessage(AbstractLoggingToolTest.java:75)
2012-06-19 09:13:23,154 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
2012-06-19 09:13:23,154 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
2012-06-19 09:13:23,154 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
2012-06-19 09:13:23,155 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@39e87719
2012-06-19 09:13:23,156 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4ce32802org.openscience.cdk.tools.LoggingToolTestDebugTrue@4ce32802
2012-06-19 09:13:23,156 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@5557c2bd1
2012-06-19 09:13:23,157 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@74b232101.0
2012-06-19 09:13:23,157 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@5ef4f44atrue
2012-06-19 09:13:23,158 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@23d256faorg.openscience.cdk.tools.LoggingToolTestDebugTrue@23d256faorg.openscience.cdk.tools.LoggingToolTestDebugTrue@23d256faorg.openscience.cdk.tools.LoggingToolTestDebugTrue@23d256faorg.openscience.cdk.tools.LoggingToolTestDebugTrue@23d256fa
2012-06-19 09:13:23,158 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@464c4975org.openscience.cdk.tools.LoggingToolTestDebugTrue@464c4975org.openscience.cdk.tools.LoggingToolTestDebugTrue@464c4975org.openscience.cdk.tools.LoggingToolTestDebugTrue@464c4975
2012-06-19 09:13:23,159 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3a6ac461org.openscience.cdk.tools.LoggingToolTestDebugTrue@3a6ac461org.openscience.cdk.tools.LoggingToolTestDebugTrue@3a6ac461
2012-06-19 09:13:23,159 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3782da3d
2012-06-19 09:13:23,160 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6fc5f743org.openscience.cdk.tools.LoggingToolTestDebugTrue@6fc5f743
2012-06-19 09:13:23,160 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2dec89091
2012-06-19 09:13:23,161 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@418c56d1.0
2012-06-19 09:13:23,161 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@76497934true
2012-06-19 09:13:23,161 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@51b48197org.openscience.cdk.tools.LoggingToolTestDebugTrue@51b48197org.openscience.cdk.tools.LoggingToolTestDebugTrue@51b48197org.openscience.cdk.tools.LoggingToolTestDebugTrue@51b48197org.openscience.cdk.tools.LoggingToolTestDebugTrue@51b48197
2012-06-19 09:13:23,162 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@21a80a69org.openscience.cdk.tools.LoggingToolTestDebugTrue@21a80a69org.openscience.cdk.tools.LoggingToolTestDebugTrue@21a80a69org.openscience.cdk.tools.LoggingToolTestDebugTrue@21a80a69
2012-06-19 09:13:23,162 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@1f4384c2org.openscience.cdk.tools.LoggingToolTestDebugTrue@1f4384c2org.openscience.cdk.tools.LoggingToolTestDebugTrue@1f4384c2
2012-06-19 09:13:23,163 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@9c0ec97
2012-06-19 09:13:23,163 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@58ecb281org.openscience.cdk.tools.LoggingToolTestDebugTrue@58ecb281
2012-06-19 09:13:23,164 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@1bbb60c31
2012-06-19 09:13:23,164 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2acdb06e1.0
2012-06-19 09:13:23,165 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@25fa1bb6true
2012-06-19 09:13:23,165 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@47315d34org.openscience.cdk.tools.LoggingToolTestDebugTrue@47315d34org.openscience.cdk.tools.LoggingToolTestDebugTrue@47315d34org.openscience.cdk.tools.LoggingToolTestDebugTrue@47315d34org.openscience.cdk.tools.LoggingToolTestDebugTrue@47315d34
2012-06-19 09:13:23,166 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@79de256forg.openscience.cdk.tools.LoggingToolTestDebugTrue@79de256forg.openscience.cdk.tools.LoggingToolTestDebugTrue@79de256forg.openscience.cdk.tools.LoggingToolTestDebugTrue@79de256f
2012-06-19 09:13:23,166 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4ce2cb55org.openscience.cdk.tools.LoggingToolTestDebugTrue@4ce2cb55org.openscience.cdk.tools.LoggingToolTestDebugTrue@4ce2cb55
2012-06-19 09:13:23,167 [main] FATAL org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3d9360e2
2012-06-19 09:13:23,167 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.class.path: /Users/johnmay/workspace/cdk/jar/log4j.jar:/Users/johnmay/workspace/cdk/jar/vecmath1.2-1.14.jar:/Users/johnmay/workspace/cdk/develjar/junit-4.10.jar:/Users/johnmay/workspace/cdk/dist/jar/cdk-annotation.jar:/Users/johnmay/workspace/cdk/dist/jar/cdk-core.jar:/Users/johnmay/workspace/cdk/dist/jar/cdk-interfaces.jar:/Users/johnmay/workspace/cdk/dist/jar/cdk-log4j.jar:/Users/johnmay/workspace/cdk/dist/jar/cdk-test-core.jar:/Users/johnmay/workspace/cdk/dist/jar/cdk-test-log4j.jar:/Users/johnmay/workspace/cdk/dist/jar/cdk-test.jar:/Applications/IntelliJ IDEA 11.app/lib/ant/lib/ant-launcher.jar:/Applications/IntelliJ IDEA 11.app/lib/ant/lib/ant.jar:/Applications/IntelliJ IDEA 11.app/lib/ant/lib/ant-junit.jar
2012-06-19 09:13:23,168 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.name        : Mac OS X
2012-06-19 09:13:23,168 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.version     : 10.6.8
2012-06-19 09:13:23,168 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.arch        : x86_64
2012-06-19 09:13:23,168 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.version   : 1.6.0_33
2012-06-19 09:13:23,168 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.vendor    : Apple Inc.
2012-07-16 08:49:12,901 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@5557c2bd
2012-07-16 08:49:12,940 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@464c4975org.openscience.cdk.tools.LoggingToolTestDebugTrue@464c4975
2012-07-16 08:49:12,941 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3a6ac4611
2012-07-16 08:49:12,942 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3782da3d1.0
2012-07-16 08:49:12,943 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6fc5f743true
2012-07-16 08:49:12,944 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2dec8909org.openscience.cdk.tools.LoggingToolTestDebugTrue@2dec8909org.openscience.cdk.tools.LoggingToolTestDebugTrue@2dec8909org.openscience.cdk.tools.LoggingToolTestDebugTrue@2dec8909org.openscience.cdk.tools.LoggingToolTestDebugTrue@2dec8909
2012-07-16 08:49:12,945 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@418c56dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@418c56dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@418c56dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@418c56d
2012-07-16 08:49:12,945 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@76497934org.openscience.cdk.tools.LoggingToolTestDebugTrue@76497934org.openscience.cdk.tools.LoggingToolTestDebugTrue@76497934
2012-07-16 08:49:12,971 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - Exception: null
2012-07-16 08:49:12,973 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.lang.Exception
2012-07-16 08:49:12,973 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at org.openscience.cdk.tools.AbstractLoggingToolTest.testDebug_ExceptionWithNullMessage(AbstractLoggingToolTest.java:75)
2012-07-16 08:49:12,973 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
2012-07-16 08:49:12,973 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
2012-07-16 08:49:12,973 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
2012-07-16 08:49:12,975 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@9c0ec97
2012-07-16 08:49:12,976 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@58ecb281org.openscience.cdk.tools.LoggingToolTestDebugTrue@58ecb281
2012-07-16 08:49:12,976 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@1bbb60c31
2012-07-16 08:49:12,977 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2acdb06e1.0
2012-07-16 08:49:12,977 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@25fa1bb6true
2012-07-16 08:49:12,978 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@47315d34org.openscience.cdk.tools.LoggingToolTestDebugTrue@47315d34org.openscience.cdk.tools.LoggingToolTestDebugTrue@47315d34org.openscience.cdk.tools.LoggingToolTestDebugTrue@47315d34org.openscience.cdk.tools.LoggingToolTestDebugTrue@47315d34
2012-07-16 08:49:12,978 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@79de256forg.openscience.cdk.tools.LoggingToolTestDebugTrue@79de256forg.openscience.cdk.tools.LoggingToolTestDebugTrue@79de256forg.openscience.cdk.tools.LoggingToolTestDebugTrue@79de256f
2012-07-16 08:49:12,996 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@676bd8eaorg.openscience.cdk.tools.LoggingToolTestDebugTrue@676bd8eaorg.openscience.cdk.tools.LoggingToolTestDebugTrue@676bd8ea
2012-07-16 08:49:12,997 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@596e1fb1
2012-07-16 08:49:12,998 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4ce2cb55org.openscience.cdk.tools.LoggingToolTestDebugTrue@4ce2cb55
2012-07-16 08:49:12,999 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3d9360e21
2012-07-16 08:49:13,005 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@16bdb5031.0
2012-07-16 08:49:13,006 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@b6e39ftrue
2012-07-16 08:49:13,007 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6719dc16org.openscience.cdk.tools.LoggingToolTestDebugTrue@6719dc16org.openscience.cdk.tools.LoggingToolTestDebugTrue@6719dc16org.openscience.cdk.tools.LoggingToolTestDebugTrue@6719dc16org.openscience.cdk.tools.LoggingToolTestDebugTrue@6719dc16
2012-07-16 08:49:13,008 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@52c05d3borg.openscience.cdk.tools.LoggingToolTestDebugTrue@52c05d3borg.openscience.cdk.tools.LoggingToolTestDebugTrue@52c05d3borg.openscience.cdk.tools.LoggingToolTestDebugTrue@52c05d3b
2012-07-16 08:49:13,008 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@5328f6eeorg.openscience.cdk.tools.LoggingToolTestDebugTrue@5328f6eeorg.openscience.cdk.tools.LoggingToolTestDebugTrue@5328f6ee
2012-07-16 08:49:13,009 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@266bade9
2012-07-16 08:49:13,010 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6766afb3org.openscience.cdk.tools.LoggingToolTestDebugTrue@6766afb3
2012-07-16 08:49:13,010 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@69945ce1
2012-07-16 08:49:13,011 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@38b5dac41.0
2012-07-16 08:49:13,012 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2b2d96f2true
2012-07-16 08:49:13,012 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3e110003org.openscience.cdk.tools.LoggingToolTestDebugTrue@3e110003org.openscience.cdk.tools.LoggingToolTestDebugTrue@3e110003org.openscience.cdk.tools.LoggingToolTestDebugTrue@3e110003org.openscience.cdk.tools.LoggingToolTestDebugTrue@3e110003
2012-07-16 08:49:13,013 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4e17e4caorg.openscience.cdk.tools.LoggingToolTestDebugTrue@4e17e4caorg.openscience.cdk.tools.LoggingToolTestDebugTrue@4e17e4caorg.openscience.cdk.tools.LoggingToolTestDebugTrue@4e17e4ca
2012-07-16 08:49:13,014 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4760a26forg.openscience.cdk.tools.LoggingToolTestDebugTrue@4760a26forg.openscience.cdk.tools.LoggingToolTestDebugTrue@4760a26f
2012-07-16 08:49:13,014 [main] FATAL org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@19484a05
2012-07-16 08:49:13,052 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.class.path: /Users/johnmay/workspace/johnmay-cdk/jar/log4j.jar:/Users/johnmay/workspace/johnmay-cdk/jar/vecmath1.2-1.14.jar:/Users/johnmay/workspace/johnmay-cdk/develjar/junit-4.10.jar:/Users/johnmay/workspace/johnmay-cdk/dist/jar/cdk-annotation.jar:/Users/johnmay/workspace/johnmay-cdk/dist/jar/cdk-core.jar:/Users/johnmay/workspace/johnmay-cdk/dist/jar/cdk-interfaces.jar:/Users/johnmay/workspace/johnmay-cdk/dist/jar/cdk-log4j.jar:/Users/johnmay/workspace/johnmay-cdk/dist/jar/cdk-test-core.jar:/Users/johnmay/workspace/johnmay-cdk/dist/jar/cdk-test-log4j.jar:/Users/johnmay/workspace/johnmay-cdk/dist/jar/cdk-test.jar:/usr/share/java/ant-1.8.2/lib/ant-launcher.jar:/usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-junit.jar:/usr/share/ant/lib/ant-junit4.jar
2012-07-16 08:49:13,053 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.name        : Mac OS X
2012-07-16 08:49:13,053 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.version     : 10.6.8
2012-07-16 08:49:13,053 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.arch        : x86_64
2012-07-16 08:49:13,053 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.version   : 1.6.0_27
2012-07-16 08:49:13,053 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.vendor    : Apple Inc.
2012-07-16 09:10:30,616 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@74b23210
2012-07-16 09:10:30,649 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3a6ac461org.openscience.cdk.tools.LoggingToolTestDebugTrue@3a6ac461
2012-07-16 09:10:30,650 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3782da3d1
2012-07-16 09:10:30,650 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6fc5f7431.0
2012-07-16 09:10:30,651 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2dec8909true
2012-07-16 09:10:30,651 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@418c56dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@418c56dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@418c56dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@418c56dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@418c56d
2012-07-16 09:10:30,652 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@76497934org.openscience.cdk.tools.LoggingToolTestDebugTrue@76497934org.openscience.cdk.tools.LoggingToolTestDebugTrue@76497934org.openscience.cdk.tools.LoggingToolTestDebugTrue@76497934
2012-07-16 09:10:30,652 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@51b48197org.openscience.cdk.tools.LoggingToolTestDebugTrue@51b48197org.openscience.cdk.tools.LoggingToolTestDebugTrue@51b48197
2012-07-16 09:10:30,652 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - Exception: null
2012-07-16 09:10:30,654 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.lang.Exception
2012-07-16 09:10:30,654 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at org.openscience.cdk.tools.AbstractLoggingToolTest.testDebug_ExceptionWithNullMessage(AbstractLoggingToolTest.java:75)
2012-07-16 09:10:30,654 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
2012-07-16 09:10:30,654 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
2012-07-16 09:10:30,654 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
2012-07-16 09:10:30,655 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@58ecb281
2012-07-16 09:10:30,655 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@1bbb60c3org.openscience.cdk.tools.LoggingToolTestDebugTrue@1bbb60c3
2012-07-16 09:10:30,655 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2acdb06e1
2012-07-16 09:10:30,656 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@25fa1bb61.0
2012-07-16 09:10:30,656 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@47315d34true
2012-07-16 09:10:30,657 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@79de256forg.openscience.cdk.tools.LoggingToolTestDebugTrue@79de256forg.openscience.cdk.tools.LoggingToolTestDebugTrue@79de256forg.openscience.cdk.tools.LoggingToolTestDebugTrue@79de256forg.openscience.cdk.tools.LoggingToolTestDebugTrue@79de256f
2012-07-16 09:10:30,657 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@676bd8eaorg.openscience.cdk.tools.LoggingToolTestDebugTrue@676bd8eaorg.openscience.cdk.tools.LoggingToolTestDebugTrue@676bd8eaorg.openscience.cdk.tools.LoggingToolTestDebugTrue@676bd8ea
2012-07-16 09:10:30,657 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@596e1fb1org.openscience.cdk.tools.LoggingToolTestDebugTrue@596e1fb1org.openscience.cdk.tools.LoggingToolTestDebugTrue@596e1fb1
2012-07-16 09:10:30,658 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4ce2cb55
2012-07-16 09:10:30,659 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3d9360e2org.openscience.cdk.tools.LoggingToolTestDebugTrue@3d9360e2
2012-07-16 09:10:30,659 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@16bdb5031
2012-07-16 09:10:30,660 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@b6e39f1.0
2012-07-16 09:10:30,660 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6719dc16true
2012-07-16 09:10:30,660 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@52c05d3borg.openscience.cdk.tools.LoggingToolTestDebugTrue@52c05d3borg.openscience.cdk.tools.LoggingToolTestDebugTrue@52c05d3borg.openscience.cdk.tools.LoggingToolTestDebugTrue@52c05d3borg.openscience.cdk.tools.LoggingToolTestDebugTrue@52c05d3b
2012-07-16 09:10:30,661 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@5328f6eeorg.openscience.cdk.tools.LoggingToolTestDebugTrue@5328f6eeorg.openscience.cdk.tools.LoggingToolTestDebugTrue@5328f6eeorg.openscience.cdk.tools.LoggingToolTestDebugTrue@5328f6ee
2012-07-16 09:10:30,661 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@266bade9org.openscience.cdk.tools.LoggingToolTestDebugTrue@266bade9org.openscience.cdk.tools.LoggingToolTestDebugTrue@266bade9
2012-07-16 09:10:30,662 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6766afb3
2012-07-16 09:10:30,662 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@69945ceorg.openscience.cdk.tools.LoggingToolTestDebugTrue@69945ce
2012-07-16 09:10:30,663 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@38b5dac41
2012-07-16 09:10:30,663 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2b2d96f21.0
2012-07-16 09:10:30,663 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3e110003true
2012-07-16 09:10:30,664 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4e17e4caorg.openscience.cdk.tools.LoggingToolTestDebugTrue@4e17e4caorg.openscience.cdk.tools.LoggingToolTestDebugTrue@4e17e4caorg.openscience.cdk.tools.LoggingToolTestDebugTrue@4e17e4caorg.openscience.cdk.tools.LoggingToolTestDebugTrue@4e17e4ca
2012-07-16 09:10:30,664 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2adb1d4org.openscience.cdk.tools.LoggingToolTestDebugTrue@2adb1d4org.openscience.cdk.tools.LoggingToolTestDebugTrue@2adb1d4org.openscience.cdk.tools.LoggingToolTestDebugTrue@2adb1d4
2012-07-16 09:10:30,665 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@19484a05org.openscience.cdk.tools.LoggingToolTestDebugTrue@19484a05org.openscience.cdk.tools.LoggingToolTestDebugTrue@19484a05
2012-07-16 09:10:30,665 [main] FATAL org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@58f39b3a
2012-07-16 09:10:30,666 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.class.path: /Users/johnmay/workspace/johnmay-cdk/jar/log4j.jar:/Users/johnmay/workspace/johnmay-cdk/jar/vecmath1.2-1.14.jar:/Users/johnmay/workspace/johnmay-cdk/develjar/junit-4.10.jar:/Users/johnmay/workspace/johnmay-cdk/dist/jar/cdk-annotation.jar:/Users/johnmay/workspace/johnmay-cdk/dist/jar/cdk-core.jar:/Users/johnmay/workspace/johnmay-cdk/dist/jar/cdk-interfaces.jar:/Users/johnmay/workspace/johnmay-cdk/dist/jar/cdk-log4j.jar:/Users/johnmay/workspace/johnmay-cdk/dist/jar/cdk-test-core.jar:/Users/johnmay/workspace/johnmay-cdk/dist/jar/cdk-test-log4j.jar:/Users/johnmay/workspace/johnmay-cdk/dist/jar/cdk-test.jar:/usr/share/java/ant-1.8.2/lib/ant-launcher.jar:/usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-junit.jar:/usr/share/ant/lib/ant-junit4.jar
2012-07-16 09:10:30,667 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.name        : Mac OS X
2012-07-16 09:10:30,667 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.version     : 10.6.8
2012-07-16 09:10:30,667 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.arch        : x86_64
2012-07-16 09:10:30,667 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.version   : 1.6.0_27
2012-07-16 09:10:30,667 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.vendor    : Apple Inc.
2012-07-20 12:30:07,294 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4ce32802
2012-07-20 12:30:07,330 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@23d256faorg.openscience.cdk.tools.LoggingToolTestDebugTrue@23d256fa
2012-07-20 12:30:07,330 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@464c49751
2012-07-20 12:30:07,331 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3a6ac4611.0
2012-07-20 12:30:07,331 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3782da3dtrue
2012-07-20 12:30:07,332 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6fc5f743org.openscience.cdk.tools.LoggingToolTestDebugTrue@6fc5f743org.openscience.cdk.tools.LoggingToolTestDebugTrue@6fc5f743org.openscience.cdk.tools.LoggingToolTestDebugTrue@6fc5f743org.openscience.cdk.tools.LoggingToolTestDebugTrue@6fc5f743
2012-07-20 12:30:07,332 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2dec8909org.openscience.cdk.tools.LoggingToolTestDebugTrue@2dec8909org.openscience.cdk.tools.LoggingToolTestDebugTrue@2dec8909org.openscience.cdk.tools.LoggingToolTestDebugTrue@2dec8909
2012-07-20 12:30:07,333 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@418c56dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@418c56dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@418c56d
2012-07-20 12:30:07,333 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - Exception: null
2012-07-20 12:30:07,335 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.lang.Exception
2012-07-20 12:30:07,335 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at org.openscience.cdk.tools.AbstractLoggingToolTest.testDebug_ExceptionWithNullMessage(AbstractLoggingToolTest.java:75)
2012-07-20 12:30:07,335 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
2012-07-20 12:30:07,335 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
2012-07-20 12:30:07,335 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
2012-07-20 12:30:07,337 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@1f4384c2
2012-07-20 12:30:07,338 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@9c0ec97org.openscience.cdk.tools.LoggingToolTestDebugTrue@9c0ec97
2012-07-20 12:30:07,338 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@58ecb2811
2012-07-20 12:30:07,339 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@1bbb60c31.0
2012-07-20 12:30:07,339 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2acdb06etrue
2012-07-20 12:30:07,340 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@25fa1bb6org.openscience.cdk.tools.LoggingToolTestDebugTrue@25fa1bb6org.openscience.cdk.tools.LoggingToolTestDebugTrue@25fa1bb6org.openscience.cdk.tools.LoggingToolTestDebugTrue@25fa1bb6org.openscience.cdk.tools.LoggingToolTestDebugTrue@25fa1bb6
2012-07-20 12:30:07,341 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@47315d34org.openscience.cdk.tools.LoggingToolTestDebugTrue@47315d34org.openscience.cdk.tools.LoggingToolTestDebugTrue@47315d34org.openscience.cdk.tools.LoggingToolTestDebugTrue@47315d34
2012-07-20 12:30:07,341 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@79de256forg.openscience.cdk.tools.LoggingToolTestDebugTrue@79de256forg.openscience.cdk.tools.LoggingToolTestDebugTrue@79de256f
2012-07-20 12:30:07,342 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@676bd8ea
2012-07-20 12:30:07,342 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@596e1fb1org.openscience.cdk.tools.LoggingToolTestDebugTrue@596e1fb1
2012-07-20 12:30:07,343 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4ce2cb551
2012-07-20 12:30:07,343 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3d9360e21.0
2012-07-20 12:30:07,344 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@16bdb503true
2012-07-20 12:30:07,345 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@b6e39forg.openscience.cdk.tools.LoggingToolTestDebugTrue@b6e39forg.openscience.cdk.tools.LoggingToolTestDebugTrue@b6e39forg.openscience.cdk.tools.LoggingToolTestDebugTrue@b6e39forg.openscience.cdk.tools.LoggingToolTestDebugTrue@b6e39f
2012-07-20 12:30:07,346 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6719dc16org.openscience.cdk.tools.LoggingToolTestDebugTrue@6719dc16org.openscience.cdk.tools.LoggingToolTestDebugTrue@6719dc16org.openscience.cdk.tools.LoggingToolTestDebugTrue@6719dc16
2012-07-20 12:30:07,346 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@52c05d3borg.openscience.cdk.tools.LoggingToolTestDebugTrue@52c05d3borg.openscience.cdk.tools.LoggingToolTestDebugTrue@52c05d3b
2012-07-20 12:30:07,347 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@5328f6ee
2012-07-20 12:30:07,347 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@266bade9org.openscience.cdk.tools.LoggingToolTestDebugTrue@266bade9
2012-07-20 12:30:07,348 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6766afb31
2012-07-20 12:30:07,348 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@69945ce1.0
2012-07-20 12:30:07,349 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@38b5dac4true
2012-07-20 12:30:07,350 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2b2d96f2org.openscience.cdk.tools.LoggingToolTestDebugTrue@2b2d96f2org.openscience.cdk.tools.LoggingToolTestDebugTrue@2b2d96f2org.openscience.cdk.tools.LoggingToolTestDebugTrue@2b2d96f2org.openscience.cdk.tools.LoggingToolTestDebugTrue@2b2d96f2
2012-07-20 12:30:07,350 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3e110003org.openscience.cdk.tools.LoggingToolTestDebugTrue@3e110003org.openscience.cdk.tools.LoggingToolTestDebugTrue@3e110003org.openscience.cdk.tools.LoggingToolTestDebugTrue@3e110003
2012-07-20 12:30:07,351 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4e17e4caorg.openscience.cdk.tools.LoggingToolTestDebugTrue@4e17e4caorg.openscience.cdk.tools.LoggingToolTestDebugTrue@4e17e4ca
2012-07-20 12:30:07,351 [main] FATAL org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2adb1d4
2012-07-20 12:30:07,353 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.class.path: /Users/johnmay/workspace/github/johnmay/cdk/jar/log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/jar/vecmath1.2-1.14.jar:/Users/johnmay/workspace/github/johnmay/cdk/develjar/junit-4.10.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-annotation.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-core.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-interfaces.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test-core.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test-log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test.jar:/usr/share/java/ant-1.8.2/lib/ant-launcher.jar:/usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-junit.jar:/usr/share/ant/lib/ant-junit4.jar
2012-07-20 12:30:07,354 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.name        : Mac OS X
2012-07-20 12:30:07,355 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.version     : 10.6.8
2012-07-20 12:30:07,355 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.arch        : x86_64
2012-07-20 12:30:07,355 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.version   : 1.6.0_27
2012-07-20 12:30:07,355 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.vendor    : Apple Inc.
2012-07-20 16:52:14,256 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@74b23210
2012-07-20 16:52:14,274 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3a6ac461org.openscience.cdk.tools.LoggingToolTestDebugTrue@3a6ac461
2012-07-20 16:52:14,274 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3782da3d1
2012-07-20 16:52:14,275 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6fc5f7431.0
2012-07-20 16:52:14,276 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2dec8909true
2012-07-20 16:52:14,276 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@418c56dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@418c56dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@418c56dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@418c56dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@418c56d
2012-07-20 16:52:14,277 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@76497934org.openscience.cdk.tools.LoggingToolTestDebugTrue@76497934org.openscience.cdk.tools.LoggingToolTestDebugTrue@76497934org.openscience.cdk.tools.LoggingToolTestDebugTrue@76497934
2012-07-20 16:52:14,278 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@51b48197org.openscience.cdk.tools.LoggingToolTestDebugTrue@51b48197org.openscience.cdk.tools.LoggingToolTestDebugTrue@51b48197
2012-07-20 16:52:14,278 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - Exception: null
2012-07-20 16:52:14,280 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.lang.Exception
2012-07-20 16:52:14,280 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at org.openscience.cdk.tools.AbstractLoggingToolTest.testDebug_ExceptionWithNullMessage(AbstractLoggingToolTest.java:75)
2012-07-20 16:52:14,280 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
2012-07-20 16:52:14,280 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
2012-07-20 16:52:14,280 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
2012-07-20 16:52:14,281 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@58ecb281
2012-07-20 16:52:14,282 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@1bbb60c3org.openscience.cdk.tools.LoggingToolTestDebugTrue@1bbb60c3
2012-07-20 16:52:14,283 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2acdb06e1
2012-07-20 16:52:14,283 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@25fa1bb61.0
2012-07-20 16:52:14,284 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@47315d34true
2012-07-20 16:52:14,284 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@79de256forg.openscience.cdk.tools.LoggingToolTestDebugTrue@79de256forg.openscience.cdk.tools.LoggingToolTestDebugTrue@79de256forg.openscience.cdk.tools.LoggingToolTestDebugTrue@79de256forg.openscience.cdk.tools.LoggingToolTestDebugTrue@79de256f
2012-07-20 16:52:14,285 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@676bd8eaorg.openscience.cdk.tools.LoggingToolTestDebugTrue@676bd8eaorg.openscience.cdk.tools.LoggingToolTestDebugTrue@676bd8eaorg.openscience.cdk.tools.LoggingToolTestDebugTrue@676bd8ea
2012-07-20 16:52:14,285 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@596e1fb1org.openscience.cdk.tools.LoggingToolTestDebugTrue@596e1fb1org.openscience.cdk.tools.LoggingToolTestDebugTrue@596e1fb1
2012-07-20 16:52:14,286 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4ce2cb55
2012-07-20 16:52:14,286 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3d9360e2org.openscience.cdk.tools.LoggingToolTestDebugTrue@3d9360e2
2012-07-20 16:52:14,286 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@16bdb5031
2012-07-20 16:52:14,287 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@b6e39f1.0
2012-07-20 16:52:14,287 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6719dc16true
2012-07-20 16:52:14,288 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@52c05d3borg.openscience.cdk.tools.LoggingToolTestDebugTrue@52c05d3borg.openscience.cdk.tools.LoggingToolTestDebugTrue@52c05d3borg.openscience.cdk.tools.LoggingToolTestDebugTrue@52c05d3borg.openscience.cdk.tools.LoggingToolTestDebugTrue@52c05d3b
2012-07-20 16:52:14,288 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@5328f6eeorg.openscience.cdk.tools.LoggingToolTestDebugTrue@5328f6eeorg.openscience.cdk.tools.LoggingToolTestDebugTrue@5328f6eeorg.openscience.cdk.tools.LoggingToolTestDebugTrue@5328f6ee
2012-07-20 16:52:14,289 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@266bade9org.openscience.cdk.tools.LoggingToolTestDebugTrue@266bade9org.openscience.cdk.tools.LoggingToolTestDebugTrue@266bade9
2012-07-20 16:52:14,289 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6766afb3
2012-07-20 16:52:14,289 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@69945ceorg.openscience.cdk.tools.LoggingToolTestDebugTrue@69945ce
2012-07-20 16:52:14,290 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@38b5dac41
2012-07-20 16:52:14,290 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2b2d96f21.0
2012-07-20 16:52:14,290 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3e110003true
2012-07-20 16:52:14,291 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4e17e4caorg.openscience.cdk.tools.LoggingToolTestDebugTrue@4e17e4caorg.openscience.cdk.tools.LoggingToolTestDebugTrue@4e17e4caorg.openscience.cdk.tools.LoggingToolTestDebugTrue@4e17e4caorg.openscience.cdk.tools.LoggingToolTestDebugTrue@4e17e4ca
2012-07-20 16:52:14,291 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2adb1d4org.openscience.cdk.tools.LoggingToolTestDebugTrue@2adb1d4org.openscience.cdk.tools.LoggingToolTestDebugTrue@2adb1d4org.openscience.cdk.tools.LoggingToolTestDebugTrue@2adb1d4
2012-07-20 16:52:14,292 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@19484a05org.openscience.cdk.tools.LoggingToolTestDebugTrue@19484a05org.openscience.cdk.tools.LoggingToolTestDebugTrue@19484a05
2012-07-20 16:52:14,292 [main] FATAL org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@58f39b3a
2012-07-20 16:52:14,293 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.class.path: /Users/johnmay/workspace/github/johnmay/cdk/jar/log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/jar/vecmath1.2-1.14.jar:/Users/johnmay/workspace/github/johnmay/cdk/develjar/junit-4.10.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-annotation.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-core.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-interfaces.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test-core.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test-log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test.jar:/usr/share/java/ant-1.8.2/lib/ant-launcher.jar:/usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-junit.jar:/usr/share/ant/lib/ant-junit4.jar
2012-07-20 16:52:14,293 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.name        : Mac OS X
2012-07-20 16:52:14,294 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.version     : 10.6.8
2012-07-20 16:52:14,294 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.arch        : x86_64
2012-07-20 16:52:14,294 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.version   : 1.6.0_27
2012-07-20 16:52:14,294 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.vendor    : Apple Inc.
2012-07-20 17:03:54,655 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@5557c2bd
2012-07-20 17:03:54,656 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@464c4975org.openscience.cdk.tools.LoggingToolTestDebugTrue@464c4975
2012-07-20 17:03:54,656 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3a6ac4611
2012-07-20 17:03:54,657 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3782da3d1.0
2012-07-20 17:03:54,657 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6fc5f743true
2012-07-20 17:03:54,658 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2dec8909org.openscience.cdk.tools.LoggingToolTestDebugTrue@2dec8909org.openscience.cdk.tools.LoggingToolTestDebugTrue@2dec8909org.openscience.cdk.tools.LoggingToolTestDebugTrue@2dec8909org.openscience.cdk.tools.LoggingToolTestDebugTrue@2dec8909
2012-07-20 17:03:54,658 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@418c56dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@418c56dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@418c56dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@418c56d
2012-07-20 17:03:54,658 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@76497934org.openscience.cdk.tools.LoggingToolTestDebugTrue@76497934org.openscience.cdk.tools.LoggingToolTestDebugTrue@76497934
2012-07-20 17:03:54,659 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - Exception: null
2012-07-20 17:03:54,660 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.lang.Exception
2012-07-20 17:03:54,660 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at org.openscience.cdk.tools.AbstractLoggingToolTest.testDebug_ExceptionWithNullMessage(AbstractLoggingToolTest.java:75)
2012-07-20 17:03:54,660 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
2012-07-20 17:03:54,660 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
2012-07-20 17:03:54,660 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
2012-07-20 17:03:54,661 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@9c0ec97
2012-07-20 17:03:54,661 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@58ecb281org.openscience.cdk.tools.LoggingToolTestDebugTrue@58ecb281
2012-07-20 17:03:54,662 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@1bbb60c31
2012-07-20 17:03:54,662 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2acdb06e1.0
2012-07-20 17:03:54,662 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@25fa1bb6true
2012-07-20 17:03:54,663 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@47315d34org.openscience.cdk.tools.LoggingToolTestDebugTrue@47315d34org.openscience.cdk.tools.LoggingToolTestDebugTrue@47315d34org.openscience.cdk.tools.LoggingToolTestDebugTrue@47315d34org.openscience.cdk.tools.LoggingToolTestDebugTrue@47315d34
2012-07-20 17:03:54,663 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@79de256forg.openscience.cdk.tools.LoggingToolTestDebugTrue@79de256forg.openscience.cdk.tools.LoggingToolTestDebugTrue@79de256forg.openscience.cdk.tools.LoggingToolTestDebugTrue@79de256f
2012-07-20 17:03:54,663 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@676bd8eaorg.openscience.cdk.tools.LoggingToolTestDebugTrue@676bd8eaorg.openscience.cdk.tools.LoggingToolTestDebugTrue@676bd8ea
2012-07-20 17:03:54,664 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@596e1fb1
2012-07-20 17:03:54,664 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4ce2cb55org.openscience.cdk.tools.LoggingToolTestDebugTrue@4ce2cb55
2012-07-20 17:03:54,665 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3d9360e21
2012-07-20 17:03:54,665 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@16bdb5031.0
2012-07-20 17:03:54,665 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@b6e39ftrue
2012-07-20 17:03:54,666 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6719dc16org.openscience.cdk.tools.LoggingToolTestDebugTrue@6719dc16org.openscience.cdk.tools.LoggingToolTestDebugTrue@6719dc16org.openscience.cdk.tools.LoggingToolTestDebugTrue@6719dc16org.openscience.cdk.tools.LoggingToolTestDebugTrue@6719dc16
2012-07-20 17:03:54,666 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@52c05d3borg.openscience.cdk.tools.LoggingToolTestDebugTrue@52c05d3borg.openscience.cdk.tools.LoggingToolTestDebugTrue@52c05d3borg.openscience.cdk.tools.LoggingToolTestDebugTrue@52c05d3b
2012-07-20 17:03:54,667 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@5328f6eeorg.openscience.cdk.tools.LoggingToolTestDebugTrue@5328f6eeorg.openscience.cdk.tools.LoggingToolTestDebugTrue@5328f6ee
2012-07-20 17:03:54,667 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@266bade9
2012-07-20 17:03:54,667 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6766afb3org.openscience.cdk.tools.LoggingToolTestDebugTrue@6766afb3
2012-07-20 17:03:54,668 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@69945ce1
2012-07-20 17:03:54,668 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@38b5dac41.0
2012-07-20 17:03:54,668 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2b2d96f2true
2012-07-20 17:03:54,669 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3e110003org.openscience.cdk.tools.LoggingToolTestDebugTrue@3e110003org.openscience.cdk.tools.LoggingToolTestDebugTrue@3e110003org.openscience.cdk.tools.LoggingToolTestDebugTrue@3e110003org.openscience.cdk.tools.LoggingToolTestDebugTrue@3e110003
2012-07-20 17:03:54,669 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4e17e4caorg.openscience.cdk.tools.LoggingToolTestDebugTrue@4e17e4caorg.openscience.cdk.tools.LoggingToolTestDebugTrue@4e17e4caorg.openscience.cdk.tools.LoggingToolTestDebugTrue@4e17e4ca
2012-07-20 17:03:54,670 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4760a26forg.openscience.cdk.tools.LoggingToolTestDebugTrue@4760a26forg.openscience.cdk.tools.LoggingToolTestDebugTrue@4760a26f
2012-07-20 17:03:54,670 [main] FATAL org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@19484a05
2012-07-20 17:03:54,671 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.class.path: /Users/johnmay/workspace/github/johnmay/cdk/jar/log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/jar/vecmath1.2-1.14.jar:/Users/johnmay/workspace/github/johnmay/cdk/develjar/junit-4.10.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-annotation.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-core.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-interfaces.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test-core.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test-log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test.jar:/usr/share/java/ant-1.8.2/lib/ant-launcher.jar:/usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-junit.jar:/usr/share/ant/lib/ant-junit4.jar
2012-07-20 17:03:54,671 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.name        : Mac OS X
2012-07-20 17:03:54,671 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.version     : 10.6.8
2012-07-20 17:03:54,671 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.arch        : x86_64
2012-07-20 17:03:54,671 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.version   : 1.6.0_27
2012-07-20 17:03:54,671 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.vendor    : Apple Inc.
2012-07-20 17:17:20,669 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@5557c2bd
2012-07-20 17:17:20,691 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@464c4975org.openscience.cdk.tools.LoggingToolTestDebugTrue@464c4975
2012-07-20 17:17:20,691 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3a6ac4611
2012-07-20 17:17:20,692 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3782da3d1.0
2012-07-20 17:17:20,692 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6fc5f743true
2012-07-20 17:17:20,693 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2dec8909org.openscience.cdk.tools.LoggingToolTestDebugTrue@2dec8909org.openscience.cdk.tools.LoggingToolTestDebugTrue@2dec8909org.openscience.cdk.tools.LoggingToolTestDebugTrue@2dec8909org.openscience.cdk.tools.LoggingToolTestDebugTrue@2dec8909
2012-07-20 17:17:20,694 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@418c56dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@418c56dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@418c56dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@418c56d
2012-07-20 17:17:20,694 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@76497934org.openscience.cdk.tools.LoggingToolTestDebugTrue@76497934org.openscience.cdk.tools.LoggingToolTestDebugTrue@76497934
2012-07-20 17:17:20,695 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - Exception: null
2012-07-20 17:17:20,696 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.lang.Exception
2012-07-20 17:17:20,696 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at org.openscience.cdk.tools.AbstractLoggingToolTest.testDebug_ExceptionWithNullMessage(AbstractLoggingToolTest.java:75)
2012-07-20 17:17:20,696 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
2012-07-20 17:17:20,696 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
2012-07-20 17:17:20,696 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
2012-07-20 17:17:20,697 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@9c0ec97
2012-07-20 17:17:20,698 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@58ecb281org.openscience.cdk.tools.LoggingToolTestDebugTrue@58ecb281
2012-07-20 17:17:20,698 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@1bbb60c31
2012-07-20 17:17:20,699 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2acdb06e1.0
2012-07-20 17:17:20,699 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@25fa1bb6true
2012-07-20 17:17:20,700 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@47315d34org.openscience.cdk.tools.LoggingToolTestDebugTrue@47315d34org.openscience.cdk.tools.LoggingToolTestDebugTrue@47315d34org.openscience.cdk.tools.LoggingToolTestDebugTrue@47315d34org.openscience.cdk.tools.LoggingToolTestDebugTrue@47315d34
2012-07-20 17:17:20,700 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@79de256forg.openscience.cdk.tools.LoggingToolTestDebugTrue@79de256forg.openscience.cdk.tools.LoggingToolTestDebugTrue@79de256forg.openscience.cdk.tools.LoggingToolTestDebugTrue@79de256f
2012-07-20 17:17:20,700 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@676bd8eaorg.openscience.cdk.tools.LoggingToolTestDebugTrue@676bd8eaorg.openscience.cdk.tools.LoggingToolTestDebugTrue@676bd8ea
2012-07-20 17:17:20,701 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@596e1fb1
2012-07-20 17:17:20,701 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4ce2cb55org.openscience.cdk.tools.LoggingToolTestDebugTrue@4ce2cb55
2012-07-20 17:17:20,702 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3d9360e21
2012-07-20 17:17:20,702 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@16bdb5031.0
2012-07-20 17:17:20,702 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@b6e39ftrue
2012-07-20 17:17:20,703 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6719dc16org.openscience.cdk.tools.LoggingToolTestDebugTrue@6719dc16org.openscience.cdk.tools.LoggingToolTestDebugTrue@6719dc16org.openscience.cdk.tools.LoggingToolTestDebugTrue@6719dc16org.openscience.cdk.tools.LoggingToolTestDebugTrue@6719dc16
2012-07-20 17:17:20,703 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@52c05d3borg.openscience.cdk.tools.LoggingToolTestDebugTrue@52c05d3borg.openscience.cdk.tools.LoggingToolTestDebugTrue@52c05d3borg.openscience.cdk.tools.LoggingToolTestDebugTrue@52c05d3b
2012-07-20 17:17:20,703 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@5328f6eeorg.openscience.cdk.tools.LoggingToolTestDebugTrue@5328f6eeorg.openscience.cdk.tools.LoggingToolTestDebugTrue@5328f6ee
2012-07-20 17:17:20,704 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@266bade9
2012-07-20 17:17:20,704 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6766afb3org.openscience.cdk.tools.LoggingToolTestDebugTrue@6766afb3
2012-07-20 17:17:20,705 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@69945ce1
2012-07-20 17:17:20,705 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@38b5dac41.0
2012-07-20 17:17:20,705 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2b2d96f2true
2012-07-20 17:17:20,706 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3e110003org.openscience.cdk.tools.LoggingToolTestDebugTrue@3e110003org.openscience.cdk.tools.LoggingToolTestDebugTrue@3e110003org.openscience.cdk.tools.LoggingToolTestDebugTrue@3e110003org.openscience.cdk.tools.LoggingToolTestDebugTrue@3e110003
2012-07-20 17:17:20,706 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4e17e4caorg.openscience.cdk.tools.LoggingToolTestDebugTrue@4e17e4caorg.openscience.cdk.tools.LoggingToolTestDebugTrue@4e17e4caorg.openscience.cdk.tools.LoggingToolTestDebugTrue@4e17e4ca
2012-07-20 17:17:20,707 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4760a26forg.openscience.cdk.tools.LoggingToolTestDebugTrue@4760a26forg.openscience.cdk.tools.LoggingToolTestDebugTrue@4760a26f
2012-07-20 17:17:20,707 [main] FATAL org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@19484a05
2012-07-20 17:17:20,708 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.class.path: /Users/johnmay/workspace/github/johnmay/cdk/jar/log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/jar/vecmath1.2-1.14.jar:/Users/johnmay/workspace/github/johnmay/cdk/develjar/junit-4.10.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-annotation.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-core.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-interfaces.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test-core.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test-log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test.jar:/usr/share/java/ant-1.8.2/lib/ant-launcher.jar:/usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-junit.jar:/usr/share/ant/lib/ant-junit4.jar
2012-07-20 17:17:20,709 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.name        : Mac OS X
2012-07-20 17:17:20,709 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.version     : 10.6.8
2012-07-20 17:17:20,709 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.arch        : x86_64
2012-07-20 17:17:20,709 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.version   : 1.6.0_27
2012-07-20 17:17:20,709 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.vendor    : Apple Inc.
2012-07-21 12:43:00,396 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@74b23210
2012-07-21 12:43:00,413 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3a6ac461org.openscience.cdk.tools.LoggingToolTestDebugTrue@3a6ac461
2012-07-21 12:43:00,414 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3782da3d1
2012-07-21 12:43:00,414 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6fc5f7431.0
2012-07-21 12:43:00,414 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2dec8909true
2012-07-21 12:43:00,415 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@418c56dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@418c56dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@418c56dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@418c56dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@418c56d
2012-07-21 12:43:00,415 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@76497934org.openscience.cdk.tools.LoggingToolTestDebugTrue@76497934org.openscience.cdk.tools.LoggingToolTestDebugTrue@76497934org.openscience.cdk.tools.LoggingToolTestDebugTrue@76497934
2012-07-21 12:43:00,416 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@51b48197org.openscience.cdk.tools.LoggingToolTestDebugTrue@51b48197org.openscience.cdk.tools.LoggingToolTestDebugTrue@51b48197
2012-07-21 12:43:00,416 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - Exception: null
2012-07-21 12:43:00,417 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.lang.Exception
2012-07-21 12:43:00,417 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at org.openscience.cdk.tools.AbstractLoggingToolTest.testDebug_ExceptionWithNullMessage(AbstractLoggingToolTest.java:75)
2012-07-21 12:43:00,417 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
2012-07-21 12:43:00,417 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
2012-07-21 12:43:00,417 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
2012-07-21 12:43:00,418 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@58ecb281
2012-07-21 12:43:00,419 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@1bbb60c3org.openscience.cdk.tools.LoggingToolTestDebugTrue@1bbb60c3
2012-07-21 12:43:00,419 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2acdb06e1
2012-07-21 12:43:00,419 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@25fa1bb61.0
2012-07-21 12:43:00,420 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@47315d34true
2012-07-21 12:43:00,420 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@79de256forg.openscience.cdk.tools.LoggingToolTestDebugTrue@79de256forg.openscience.cdk.tools.LoggingToolTestDebugTrue@79de256forg.openscience.cdk.tools.LoggingToolTestDebugTrue@79de256forg.openscience.cdk.tools.LoggingToolTestDebugTrue@79de256f
2012-07-21 12:43:00,421 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@676bd8eaorg.openscience.cdk.tools.LoggingToolTestDebugTrue@676bd8eaorg.openscience.cdk.tools.LoggingToolTestDebugTrue@676bd8eaorg.openscience.cdk.tools.LoggingToolTestDebugTrue@676bd8ea
2012-07-21 12:43:00,421 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@596e1fb1org.openscience.cdk.tools.LoggingToolTestDebugTrue@596e1fb1org.openscience.cdk.tools.LoggingToolTestDebugTrue@596e1fb1
2012-07-21 12:43:00,421 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4ce2cb55
2012-07-21 12:43:00,422 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3d9360e2org.openscience.cdk.tools.LoggingToolTestDebugTrue@3d9360e2
2012-07-21 12:43:00,422 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@16bdb5031
2012-07-21 12:43:00,423 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@b6e39f1.0
2012-07-21 12:43:00,423 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6719dc16true
2012-07-21 12:43:00,423 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@52c05d3borg.openscience.cdk.tools.LoggingToolTestDebugTrue@52c05d3borg.openscience.cdk.tools.LoggingToolTestDebugTrue@52c05d3borg.openscience.cdk.tools.LoggingToolTestDebugTrue@52c05d3borg.openscience.cdk.tools.LoggingToolTestDebugTrue@52c05d3b
2012-07-21 12:43:00,424 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@5328f6eeorg.openscience.cdk.tools.LoggingToolTestDebugTrue@5328f6eeorg.openscience.cdk.tools.LoggingToolTestDebugTrue@5328f6eeorg.openscience.cdk.tools.LoggingToolTestDebugTrue@5328f6ee
2012-07-21 12:43:00,424 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@266bade9org.openscience.cdk.tools.LoggingToolTestDebugTrue@266bade9org.openscience.cdk.tools.LoggingToolTestDebugTrue@266bade9
2012-07-21 12:43:00,424 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6766afb3
2012-07-21 12:43:00,425 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@69945ceorg.openscience.cdk.tools.LoggingToolTestDebugTrue@69945ce
2012-07-21 12:43:00,425 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@38b5dac41
2012-07-21 12:43:00,426 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2b2d96f21.0
2012-07-21 12:43:00,426 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3e110003true
2012-07-21 12:43:00,426 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4e17e4caorg.openscience.cdk.tools.LoggingToolTestDebugTrue@4e17e4caorg.openscience.cdk.tools.LoggingToolTestDebugTrue@4e17e4caorg.openscience.cdk.tools.LoggingToolTestDebugTrue@4e17e4caorg.openscience.cdk.tools.LoggingToolTestDebugTrue@4e17e4ca
2012-07-21 12:43:00,427 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2adb1d4org.openscience.cdk.tools.LoggingToolTestDebugTrue@2adb1d4org.openscience.cdk.tools.LoggingToolTestDebugTrue@2adb1d4org.openscience.cdk.tools.LoggingToolTestDebugTrue@2adb1d4
2012-07-21 12:43:00,427 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@19484a05org.openscience.cdk.tools.LoggingToolTestDebugTrue@19484a05org.openscience.cdk.tools.LoggingToolTestDebugTrue@19484a05
2012-07-21 12:43:00,428 [main] FATAL org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@58f39b3a
2012-07-21 12:43:00,429 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.class.path: /Users/johnmay/workspace/github/johnmay/cdk/jar/log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/jar/vecmath1.2-1.14.jar:/Users/johnmay/workspace/github/johnmay/cdk/develjar/junit-4.10.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-annotation.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-core.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-interfaces.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test-core.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test-log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test.jar:/usr/share/java/ant-1.8.2/lib/ant-launcher.jar:/usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-junit.jar:/usr/share/ant/lib/ant-junit4.jar
2012-07-21 12:43:00,429 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.name        : Mac OS X
2012-07-21 12:43:00,429 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.version     : 10.6.8
2012-07-21 12:43:00,429 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.arch        : x86_64
2012-07-21 12:43:00,430 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.version   : 1.6.0_27
2012-07-21 12:43:00,430 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.vendor    : Apple Inc.
2012-07-21 13:28:44,778 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@464c4975
2012-07-21 13:28:44,797 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2dec8909org.openscience.cdk.tools.LoggingToolTestDebugTrue@2dec8909
2012-07-21 13:28:44,798 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@418c56d1
2012-07-21 13:28:44,798 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@764979341.0
2012-07-21 13:28:44,798 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@51b48197true
2012-07-21 13:28:44,799 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@21a80a69org.openscience.cdk.tools.LoggingToolTestDebugTrue@21a80a69org.openscience.cdk.tools.LoggingToolTestDebugTrue@21a80a69org.openscience.cdk.tools.LoggingToolTestDebugTrue@21a80a69org.openscience.cdk.tools.LoggingToolTestDebugTrue@21a80a69
2012-07-21 13:28:44,799 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@1f4384c2org.openscience.cdk.tools.LoggingToolTestDebugTrue@1f4384c2org.openscience.cdk.tools.LoggingToolTestDebugTrue@1f4384c2org.openscience.cdk.tools.LoggingToolTestDebugTrue@1f4384c2
2012-07-21 13:28:44,800 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@9c0ec97org.openscience.cdk.tools.LoggingToolTestDebugTrue@9c0ec97org.openscience.cdk.tools.LoggingToolTestDebugTrue@9c0ec97
2012-07-21 13:28:44,800 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - Exception: null
2012-07-21 13:28:44,801 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.lang.Exception
2012-07-21 13:28:44,801 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at org.openscience.cdk.tools.AbstractLoggingToolTest.testDebug_ExceptionWithNullMessage(AbstractLoggingToolTest.java:75)
2012-07-21 13:28:44,801 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
2012-07-21 13:28:44,801 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
2012-07-21 13:28:44,801 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
2012-07-21 13:28:44,803 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@25fa1bb6
2012-07-21 13:28:44,803 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@47315d34org.openscience.cdk.tools.LoggingToolTestDebugTrue@47315d34
2012-07-21 13:28:44,803 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@79de256f1
2012-07-21 13:28:44,804 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@676bd8ea1.0
2012-07-21 13:28:44,804 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@596e1fb1true
2012-07-21 13:28:44,804 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4ce2cb55org.openscience.cdk.tools.LoggingToolTestDebugTrue@4ce2cb55org.openscience.cdk.tools.LoggingToolTestDebugTrue@4ce2cb55org.openscience.cdk.tools.LoggingToolTestDebugTrue@4ce2cb55org.openscience.cdk.tools.LoggingToolTestDebugTrue@4ce2cb55
2012-07-21 13:28:44,805 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3d9360e2org.openscience.cdk.tools.LoggingToolTestDebugTrue@3d9360e2org.openscience.cdk.tools.LoggingToolTestDebugTrue@3d9360e2org.openscience.cdk.tools.LoggingToolTestDebugTrue@3d9360e2
2012-07-21 13:28:44,806 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@16bdb503org.openscience.cdk.tools.LoggingToolTestDebugTrue@16bdb503org.openscience.cdk.tools.LoggingToolTestDebugTrue@16bdb503
2012-07-21 13:28:44,806 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@b6e39f
2012-07-21 13:28:44,806 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6719dc16org.openscience.cdk.tools.LoggingToolTestDebugTrue@6719dc16
2012-07-21 13:28:44,807 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@52c05d3b1
2012-07-21 13:28:44,807 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@5328f6ee1.0
2012-07-21 13:28:44,807 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@266bade9true
2012-07-21 13:28:44,808 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6766afb3org.openscience.cdk.tools.LoggingToolTestDebugTrue@6766afb3org.openscience.cdk.tools.LoggingToolTestDebugTrue@6766afb3org.openscience.cdk.tools.LoggingToolTestDebugTrue@6766afb3org.openscience.cdk.tools.LoggingToolTestDebugTrue@6766afb3
2012-07-21 13:28:44,808 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@69945ceorg.openscience.cdk.tools.LoggingToolTestDebugTrue@69945ceorg.openscience.cdk.tools.LoggingToolTestDebugTrue@69945ceorg.openscience.cdk.tools.LoggingToolTestDebugTrue@69945ce
2012-07-21 13:28:44,808 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@38b5dac4org.openscience.cdk.tools.LoggingToolTestDebugTrue@38b5dac4org.openscience.cdk.tools.LoggingToolTestDebugTrue@38b5dac4
2012-07-21 13:28:44,809 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2b2d96f2
2012-07-21 13:28:44,809 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3e110003org.openscience.cdk.tools.LoggingToolTestDebugTrue@3e110003
2012-07-21 13:28:44,810 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4e17e4ca1
2012-07-21 13:28:44,810 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2adb1d41.0
2012-07-21 13:28:44,810 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@5975d6abtrue
2012-07-21 13:28:44,811 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4760a26forg.openscience.cdk.tools.LoggingToolTestDebugTrue@4760a26forg.openscience.cdk.tools.LoggingToolTestDebugTrue@4760a26forg.openscience.cdk.tools.LoggingToolTestDebugTrue@4760a26forg.openscience.cdk.tools.LoggingToolTestDebugTrue@4760a26f
2012-07-21 13:28:44,811 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@19484a05org.openscience.cdk.tools.LoggingToolTestDebugTrue@19484a05org.openscience.cdk.tools.LoggingToolTestDebugTrue@19484a05org.openscience.cdk.tools.LoggingToolTestDebugTrue@19484a05
2012-07-21 13:28:44,812 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@61542a75org.openscience.cdk.tools.LoggingToolTestDebugTrue@61542a75org.openscience.cdk.tools.LoggingToolTestDebugTrue@61542a75
2012-07-21 13:28:44,812 [main] FATAL org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@5caf993e
2012-07-21 13:28:44,813 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.class.path: /Users/johnmay/workspace/github/johnmay/cdk/jar/log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/jar/vecmath1.2-1.14.jar:/Users/johnmay/workspace/github/johnmay/cdk/develjar/junit-4.5.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-annotation.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-core.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-interfaces.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test-core.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test-log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test.jar:/usr/share/java/ant-1.8.2/lib/ant-launcher.jar:/usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-junit.jar:/usr/share/ant/lib/ant-junit4.jar
2012-07-21 13:28:44,814 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.name        : Mac OS X
2012-07-21 13:28:44,814 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.version     : 10.6.8
2012-07-21 13:28:44,814 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.arch        : x86_64
2012-07-21 13:28:44,814 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.version   : 1.6.0_27
2012-07-21 13:28:44,814 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.vendor    : Apple Inc.
2012-07-21 16:22:20,210 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@464c4975
2012-07-21 16:22:20,226 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2dec8909org.openscience.cdk.tools.LoggingToolTestDebugTrue@2dec8909
2012-07-21 16:22:20,227 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@418c56d1
2012-07-21 16:22:20,228 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@764979341.0
2012-07-21 16:22:20,228 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@51b48197true
2012-07-21 16:22:20,229 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@21a80a69org.openscience.cdk.tools.LoggingToolTestDebugTrue@21a80a69org.openscience.cdk.tools.LoggingToolTestDebugTrue@21a80a69org.openscience.cdk.tools.LoggingToolTestDebugTrue@21a80a69org.openscience.cdk.tools.LoggingToolTestDebugTrue@21a80a69
2012-07-21 16:22:20,229 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@1f4384c2org.openscience.cdk.tools.LoggingToolTestDebugTrue@1f4384c2org.openscience.cdk.tools.LoggingToolTestDebugTrue@1f4384c2org.openscience.cdk.tools.LoggingToolTestDebugTrue@1f4384c2
2012-07-21 16:22:20,230 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@9c0ec97org.openscience.cdk.tools.LoggingToolTestDebugTrue@9c0ec97org.openscience.cdk.tools.LoggingToolTestDebugTrue@9c0ec97
2012-07-21 16:22:20,230 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - Exception: null
2012-07-21 16:22:20,232 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.lang.Exception
2012-07-21 16:22:20,232 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at org.openscience.cdk.tools.AbstractLoggingToolTest.testDebug_ExceptionWithNullMessage(AbstractLoggingToolTest.java:75)
2012-07-21 16:22:20,232 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
2012-07-21 16:22:20,232 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
2012-07-21 16:22:20,232 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
2012-07-21 16:22:20,233 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@25fa1bb6
2012-07-21 16:22:20,234 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@47315d34org.openscience.cdk.tools.LoggingToolTestDebugTrue@47315d34
2012-07-21 16:22:20,250 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@79de256f1
2012-07-21 16:22:20,251 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@676bd8ea1.0
2012-07-21 16:22:20,251 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@596e1fb1true
2012-07-21 16:22:20,251 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4ce2cb55org.openscience.cdk.tools.LoggingToolTestDebugTrue@4ce2cb55org.openscience.cdk.tools.LoggingToolTestDebugTrue@4ce2cb55org.openscience.cdk.tools.LoggingToolTestDebugTrue@4ce2cb55org.openscience.cdk.tools.LoggingToolTestDebugTrue@4ce2cb55
2012-07-21 16:22:20,252 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3d9360e2org.openscience.cdk.tools.LoggingToolTestDebugTrue@3d9360e2org.openscience.cdk.tools.LoggingToolTestDebugTrue@3d9360e2org.openscience.cdk.tools.LoggingToolTestDebugTrue@3d9360e2
2012-07-21 16:22:20,252 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@16bdb503org.openscience.cdk.tools.LoggingToolTestDebugTrue@16bdb503org.openscience.cdk.tools.LoggingToolTestDebugTrue@16bdb503
2012-07-21 16:22:20,253 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@b6e39f
2012-07-21 16:22:20,253 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6719dc16org.openscience.cdk.tools.LoggingToolTestDebugTrue@6719dc16
2012-07-21 16:22:20,254 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@52c05d3b1
2012-07-21 16:22:20,254 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@5328f6ee1.0
2012-07-21 16:22:20,255 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@266bade9true
2012-07-21 16:22:20,255 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6766afb3org.openscience.cdk.tools.LoggingToolTestDebugTrue@6766afb3org.openscience.cdk.tools.LoggingToolTestDebugTrue@6766afb3org.openscience.cdk.tools.LoggingToolTestDebugTrue@6766afb3org.openscience.cdk.tools.LoggingToolTestDebugTrue@6766afb3
2012-07-21 16:22:20,255 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@69945ceorg.openscience.cdk.tools.LoggingToolTestDebugTrue@69945ceorg.openscience.cdk.tools.LoggingToolTestDebugTrue@69945ceorg.openscience.cdk.tools.LoggingToolTestDebugTrue@69945ce
2012-07-21 16:22:20,256 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@38b5dac4org.openscience.cdk.tools.LoggingToolTestDebugTrue@38b5dac4org.openscience.cdk.tools.LoggingToolTestDebugTrue@38b5dac4
2012-07-21 16:22:20,256 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2b2d96f2
2012-07-21 16:22:20,257 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3e110003org.openscience.cdk.tools.LoggingToolTestDebugTrue@3e110003
2012-07-21 16:22:20,257 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4e17e4ca1
2012-07-21 16:22:20,258 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2adb1d41.0
2012-07-21 16:22:20,258 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@5975d6abtrue
2012-07-21 16:22:20,258 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4760a26forg.openscience.cdk.tools.LoggingToolTestDebugTrue@4760a26forg.openscience.cdk.tools.LoggingToolTestDebugTrue@4760a26forg.openscience.cdk.tools.LoggingToolTestDebugTrue@4760a26forg.openscience.cdk.tools.LoggingToolTestDebugTrue@4760a26f
2012-07-21 16:22:20,259 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@19484a05org.openscience.cdk.tools.LoggingToolTestDebugTrue@19484a05org.openscience.cdk.tools.LoggingToolTestDebugTrue@19484a05org.openscience.cdk.tools.LoggingToolTestDebugTrue@19484a05
2012-07-21 16:22:20,259 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@58f39b3aorg.openscience.cdk.tools.LoggingToolTestDebugTrue@58f39b3aorg.openscience.cdk.tools.LoggingToolTestDebugTrue@58f39b3a
2012-07-21 16:22:20,261 [main] FATAL org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@5caf993e
2012-07-21 16:22:20,262 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.class.path: /Users/johnmay/workspace/github/johnmay/cdk/jar/log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/jar/vecmath1.2-1.14.jar:/Users/johnmay/workspace/github/johnmay/cdk/develjar/junit-4.5.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-annotation.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-core.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-interfaces.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test-core.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test-log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test.jar:/usr/share/java/ant-1.8.2/lib/ant-launcher.jar:/usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-junit.jar:/usr/share/ant/lib/ant-junit4.jar
2012-07-21 16:22:20,262 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.name        : Mac OS X
2012-07-21 16:22:20,262 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.version     : 10.6.8
2012-07-21 16:22:20,262 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.arch        : x86_64
2012-07-21 16:22:20,263 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.version   : 1.6.0_27
2012-07-21 16:22:20,263 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.vendor    : Apple Inc.
2012-07-29 20:00:19,870 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6b7547a3
2012-07-29 20:00:20,038 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@75ee0563true
2012-07-29 20:00:20,047 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@5da3e311org.openscience.cdk.tools.LoggingToolTestDebugTrue@5da3e311org.openscience.cdk.tools.LoggingToolTestDebugTrue@5da3e311org.openscience.cdk.tools.LoggingToolTestDebugTrue@5da3e311org.openscience.cdk.tools.LoggingToolTestDebugTrue@5da3e311
2012-07-29 20:00:20,089 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3290a11eorg.openscience.cdk.tools.LoggingToolTestDebugTrue@3290a11eorg.openscience.cdk.tools.LoggingToolTestDebugTrue@3290a11eorg.openscience.cdk.tools.LoggingToolTestDebugTrue@3290a11e
2012-07-29 20:00:20,101 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3541d281org.openscience.cdk.tools.LoggingToolTestDebugTrue@3541d281org.openscience.cdk.tools.LoggingToolTestDebugTrue@3541d281
2012-07-29 20:00:20,102 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@74632e77org.openscience.cdk.tools.LoggingToolTestDebugTrue@74632e77
2012-07-29 20:00:20,103 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@1b7fc2531
2012-07-29 20:00:20,117 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@60aee53f1.0
2012-07-29 20:00:20,118 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - Exception: null
2012-07-29 20:00:20,120 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.lang.Exception
2012-07-29 20:00:20,120 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at org.openscience.cdk.tools.AbstractLoggingToolTest.testDebug_ExceptionWithNullMessage(AbstractLoggingToolTest.java:75)
2012-07-29 20:00:20,120 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
2012-07-29 20:00:20,121 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
2012-07-29 20:00:20,121 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
2012-07-29 20:00:20,122 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@765a7159
2012-07-29 20:00:20,123 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2bc7c6c3org.openscience.cdk.tools.LoggingToolTestDebugTrue@2bc7c6c3
2012-07-29 20:00:20,123 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@48ca42a91
2012-07-29 20:00:20,123 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@56de8a941.0
2012-07-29 20:00:20,124 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2c5c271atrue
2012-07-29 20:00:20,124 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@560b32b6org.openscience.cdk.tools.LoggingToolTestDebugTrue@560b32b6org.openscience.cdk.tools.LoggingToolTestDebugTrue@560b32b6org.openscience.cdk.tools.LoggingToolTestDebugTrue@560b32b6org.openscience.cdk.tools.LoggingToolTestDebugTrue@560b32b6
2012-07-29 20:00:20,125 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@792e76dborg.openscience.cdk.tools.LoggingToolTestDebugTrue@792e76dborg.openscience.cdk.tools.LoggingToolTestDebugTrue@792e76dborg.openscience.cdk.tools.LoggingToolTestDebugTrue@792e76db
2012-07-29 20:00:20,125 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@597d6204org.openscience.cdk.tools.LoggingToolTestDebugTrue@597d6204org.openscience.cdk.tools.LoggingToolTestDebugTrue@597d6204
2012-07-29 20:00:20,126 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@36ae2282
2012-07-29 20:00:20,126 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@625ba0d9org.openscience.cdk.tools.LoggingToolTestDebugTrue@625ba0d9
2012-07-29 20:00:20,127 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6d9d39011
2012-07-29 20:00:20,127 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6d09a8df1.0
2012-07-29 20:00:20,128 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@152e0066true
2012-07-29 20:00:20,128 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@7f1c3366org.openscience.cdk.tools.LoggingToolTestDebugTrue@7f1c3366org.openscience.cdk.tools.LoggingToolTestDebugTrue@7f1c3366org.openscience.cdk.tools.LoggingToolTestDebugTrue@7f1c3366org.openscience.cdk.tools.LoggingToolTestDebugTrue@7f1c3366
2012-07-29 20:00:20,128 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@1472aebcorg.openscience.cdk.tools.LoggingToolTestDebugTrue@1472aebcorg.openscience.cdk.tools.LoggingToolTestDebugTrue@1472aebcorg.openscience.cdk.tools.LoggingToolTestDebugTrue@1472aebc
2012-07-29 20:00:20,129 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@752dc320org.openscience.cdk.tools.LoggingToolTestDebugTrue@752dc320org.openscience.cdk.tools.LoggingToolTestDebugTrue@752dc320
2012-07-29 20:00:20,129 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@f65a5fa
2012-07-29 20:00:20,129 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@5a73c7fborg.openscience.cdk.tools.LoggingToolTestDebugTrue@5a73c7fb
2012-07-29 20:00:20,130 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@674e5e211
2012-07-29 20:00:20,130 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4a05fd831.0
2012-07-29 20:00:20,130 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4f46c96ctrue
2012-07-29 20:00:20,131 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3051fa1dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@3051fa1dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@3051fa1dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@3051fa1dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@3051fa1d
2012-07-29 20:00:20,131 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@55fb9eb3org.openscience.cdk.tools.LoggingToolTestDebugTrue@55fb9eb3org.openscience.cdk.tools.LoggingToolTestDebugTrue@55fb9eb3org.openscience.cdk.tools.LoggingToolTestDebugTrue@55fb9eb3
2012-07-29 20:00:20,131 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@7a7025deorg.openscience.cdk.tools.LoggingToolTestDebugTrue@7a7025deorg.openscience.cdk.tools.LoggingToolTestDebugTrue@7a7025de
2012-07-29 20:00:20,132 [main] FATAL org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@58c6509e
2012-07-29 20:00:20,132 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.class.path: /Users/johnmay/workspace/github/johnmay/cdk/jar/log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/jar/vecmath1.2-1.14.jar:/Users/johnmay/workspace/github/johnmay/cdk/develjar/junit-4.5.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-annotation.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-core.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-interfaces.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test-core.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test-log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test.jar:/usr/share/java/ant-1.8.2/lib/ant-launcher.jar:/usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-junit.jar:/usr/share/ant/lib/ant-junit4.jar
2012-07-29 20:00:20,133 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.name        : Mac OS X
2012-07-29 20:00:20,133 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.version     : 10.8
2012-07-29 20:00:20,133 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.arch        : x86_64
2012-07-29 20:00:20,133 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.version   : 1.7.0_05
2012-07-29 20:00:20,133 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.vendor    : Oracle Corporation
2012-07-29 21:51:54,402 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@366815e4
2012-07-29 21:51:54,430 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6bfa2e2e1
2012-07-29 21:51:54,433 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@75ee0563org.openscience.cdk.tools.LoggingToolTestDebugTrue@75ee0563
2012-07-29 21:51:54,434 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@5da3e3111.0
2012-07-29 21:51:54,435 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@31706444true
2012-07-29 21:51:54,436 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@49c6c5b7org.openscience.cdk.tools.LoggingToolTestDebugTrue@49c6c5b7org.openscience.cdk.tools.LoggingToolTestDebugTrue@49c6c5b7org.openscience.cdk.tools.LoggingToolTestDebugTrue@49c6c5b7org.openscience.cdk.tools.LoggingToolTestDebugTrue@49c6c5b7
2012-07-29 21:51:54,437 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@18de9738org.openscience.cdk.tools.LoggingToolTestDebugTrue@18de9738org.openscience.cdk.tools.LoggingToolTestDebugTrue@18de9738org.openscience.cdk.tools.LoggingToolTestDebugTrue@18de9738
2012-07-29 21:51:54,437 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3d99ea49org.openscience.cdk.tools.LoggingToolTestDebugTrue@3d99ea49org.openscience.cdk.tools.LoggingToolTestDebugTrue@3d99ea49
2012-07-29 21:51:54,438 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - Exception: null
2012-07-29 21:51:54,440 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.lang.Exception
2012-07-29 21:51:54,440 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at org.openscience.cdk.tools.AbstractLoggingToolTest.testDebug_ExceptionWithNullMessage(AbstractLoggingToolTest.java:75)
2012-07-29 21:51:54,440 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
2012-07-29 21:51:54,441 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
2012-07-29 21:51:54,441 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
2012-07-29 21:51:54,443 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@7fcd296b
2012-07-29 21:51:54,443 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@765a7159org.openscience.cdk.tools.LoggingToolTestDebugTrue@765a7159
2012-07-29 21:51:54,444 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2bc7c6c31
2012-07-29 21:51:54,445 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@48ca42a91.0
2012-07-29 21:51:54,445 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@56de8a94true
2012-07-29 21:51:54,446 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2c5c271aorg.openscience.cdk.tools.LoggingToolTestDebugTrue@2c5c271aorg.openscience.cdk.tools.LoggingToolTestDebugTrue@2c5c271aorg.openscience.cdk.tools.LoggingToolTestDebugTrue@2c5c271aorg.openscience.cdk.tools.LoggingToolTestDebugTrue@2c5c271a
2012-07-29 21:51:54,446 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@560b32b6org.openscience.cdk.tools.LoggingToolTestDebugTrue@560b32b6org.openscience.cdk.tools.LoggingToolTestDebugTrue@560b32b6
2012-07-29 21:51:54,447 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@792e76dborg.openscience.cdk.tools.LoggingToolTestDebugTrue@792e76dborg.openscience.cdk.tools.LoggingToolTestDebugTrue@792e76dborg.openscience.cdk.tools.LoggingToolTestDebugTrue@792e76db
2012-07-29 21:51:54,447 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@597d6204
2012-07-29 21:51:54,448 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@36ae2282org.openscience.cdk.tools.LoggingToolTestDebugTrue@36ae2282
2012-07-29 21:51:54,449 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@625ba0d91
2012-07-29 21:51:54,449 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6d9d39011.0
2012-07-29 21:51:54,450 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6d09a8dftrue
2012-07-29 21:51:54,450 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@152e0066org.openscience.cdk.tools.LoggingToolTestDebugTrue@152e0066org.openscience.cdk.tools.LoggingToolTestDebugTrue@152e0066org.openscience.cdk.tools.LoggingToolTestDebugTrue@152e0066org.openscience.cdk.tools.LoggingToolTestDebugTrue@152e0066
2012-07-29 21:51:54,451 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@7f1c3366org.openscience.cdk.tools.LoggingToolTestDebugTrue@7f1c3366org.openscience.cdk.tools.LoggingToolTestDebugTrue@7f1c3366org.openscience.cdk.tools.LoggingToolTestDebugTrue@7f1c3366
2012-07-29 21:51:54,451 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@1472aebcorg.openscience.cdk.tools.LoggingToolTestDebugTrue@1472aebcorg.openscience.cdk.tools.LoggingToolTestDebugTrue@1472aebc
2012-07-29 21:51:54,452 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@752dc320
2012-07-29 21:51:54,452 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@f65a5faorg.openscience.cdk.tools.LoggingToolTestDebugTrue@f65a5fa
2012-07-29 21:51:54,453 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@5a73c7fb1
2012-07-29 21:51:54,454 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@674e5e211.0
2012-07-29 21:51:54,454 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4a05fd83true
2012-07-29 21:51:54,455 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4f46c96corg.openscience.cdk.tools.LoggingToolTestDebugTrue@4f46c96corg.openscience.cdk.tools.LoggingToolTestDebugTrue@4f46c96corg.openscience.cdk.tools.LoggingToolTestDebugTrue@4f46c96corg.openscience.cdk.tools.LoggingToolTestDebugTrue@4f46c96c
2012-07-29 21:51:54,455 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3051fa1dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@3051fa1dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@3051fa1dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@3051fa1d
2012-07-29 21:51:54,456 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@55fb9eb3org.openscience.cdk.tools.LoggingToolTestDebugTrue@55fb9eb3org.openscience.cdk.tools.LoggingToolTestDebugTrue@55fb9eb3
2012-07-29 21:51:54,457 [main] FATAL org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@7a7025de
2012-07-29 21:51:54,458 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.class.path: /Users/johnmay/workspace/github/johnmay/cdk/jar/log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/jar/vecmath1.2-1.14.jar:/Users/johnmay/workspace/github/johnmay/cdk/develjar/junit-4.5.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-annotation.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-core.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-interfaces.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test-core.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test-log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test.jar:/usr/share/java/ant-1.8.2/lib/ant-launcher.jar:/usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-junit.jar:/usr/share/ant/lib/ant-junit4.jar
2012-07-29 21:51:54,458 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.name        : Mac OS X
2012-07-29 21:51:54,458 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.version     : 10.8
2012-07-29 21:51:54,458 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.arch        : x86_64
2012-07-29 21:51:54,458 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.version   : 1.7.0_05
2012-07-29 21:51:54,458 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.vendor    : Oracle Corporation
2012-08-02 13:38:31,170 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@746f2a75
2012-08-02 13:38:31,337 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@7f1bfcfc1
2012-08-02 13:38:31,343 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@67e45961
2012-08-02 13:38:31,449 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4c0a7e2eorg.openscience.cdk.tools.LoggingToolTestDebugTrue@4c0a7e2e
2012-08-02 13:38:31,458 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@44e225021.0
2012-08-02 13:38:31,467 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@9234336
2012-08-02 13:38:31,485 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6a1192e9true
2012-08-02 13:38:31,499 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@27c43566org.openscience.cdk.tools.LoggingToolTestDebugTrue@27c43566org.openscience.cdk.tools.LoggingToolTestDebugTrue@27c43566org.openscience.cdk.tools.LoggingToolTestDebugTrue@27c43566org.openscience.cdk.tools.LoggingToolTestDebugTrue@27c43566
2012-08-02 13:38:31,516 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@428dcfeforg.openscience.cdk.tools.LoggingToolTestDebugTrue@428dcfeforg.openscience.cdk.tools.LoggingToolTestDebugTrue@428dcfeforg.openscience.cdk.tools.LoggingToolTestDebugTrue@428dcfef
2012-08-02 13:38:31,590 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@280cb229org.openscience.cdk.tools.LoggingToolTestDebugTrue@280cb229org.openscience.cdk.tools.LoggingToolTestDebugTrue@280cb229
2012-08-02 13:38:31,591 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - Exception: null
2012-08-02 13:38:31,593 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.lang.Exception
2012-08-02 13:38:31,593 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at org.openscience.cdk.tools.AbstractLoggingToolTest.testDebug_ExceptionWithNullMessage(AbstractLoggingToolTest.java:75)
2012-08-02 13:38:31,594 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
2012-08-02 13:38:31,594 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
2012-08-02 13:38:31,594 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
2012-08-02 13:38:31,594 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6b02b23dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@6b02b23d
2012-08-02 13:38:31,595 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@7e03f9ad1.0
2012-08-02 13:38:31,596 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@36fd0d7dtrue
2012-08-02 13:38:31,596 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@1f80a5bforg.openscience.cdk.tools.LoggingToolTestDebugTrue@1f80a5bforg.openscience.cdk.tools.LoggingToolTestDebugTrue@1f80a5bforg.openscience.cdk.tools.LoggingToolTestDebugTrue@1f80a5bforg.openscience.cdk.tools.LoggingToolTestDebugTrue@1f80a5bf
2012-08-02 13:38:31,597 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3701aec1org.openscience.cdk.tools.LoggingToolTestDebugTrue@3701aec1org.openscience.cdk.tools.LoggingToolTestDebugTrue@3701aec1org.openscience.cdk.tools.LoggingToolTestDebugTrue@3701aec1
2012-08-02 13:38:31,597 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4f781d1dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@4f781d1dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@4f781d1d
2012-08-02 13:38:31,598 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@56bf83ad
2012-08-02 13:38:31,598 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@375dff59org.openscience.cdk.tools.LoggingToolTestDebugTrue@375dff59
2012-08-02 13:38:31,612 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@7c2748741
2012-08-02 13:38:31,613 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@7705f7591.0
2012-08-02 13:38:31,614 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@28b2311btrue
2012-08-02 13:38:31,614 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4ab5f87corg.openscience.cdk.tools.LoggingToolTestDebugTrue@4ab5f87corg.openscience.cdk.tools.LoggingToolTestDebugTrue@4ab5f87corg.openscience.cdk.tools.LoggingToolTestDebugTrue@4ab5f87corg.openscience.cdk.tools.LoggingToolTestDebugTrue@4ab5f87c
2012-08-02 13:38:31,615 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@70ccbb35org.openscience.cdk.tools.LoggingToolTestDebugTrue@70ccbb35org.openscience.cdk.tools.LoggingToolTestDebugTrue@70ccbb35org.openscience.cdk.tools.LoggingToolTestDebugTrue@70ccbb35
2012-08-02 13:38:31,615 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@1116ce6eorg.openscience.cdk.tools.LoggingToolTestDebugTrue@1116ce6eorg.openscience.cdk.tools.LoggingToolTestDebugTrue@1116ce6e
2012-08-02 13:38:31,616 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@704aa085
2012-08-02 13:38:31,616 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3370b55borg.openscience.cdk.tools.LoggingToolTestDebugTrue@3370b55b
2012-08-02 13:38:31,616 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2c9283bf1
2012-08-02 13:38:31,617 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@470787751.0
2012-08-02 13:38:31,617 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3f4e36c1true
2012-08-02 13:38:31,618 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@27ecd95forg.openscience.cdk.tools.LoggingToolTestDebugTrue@27ecd95forg.openscience.cdk.tools.LoggingToolTestDebugTrue@27ecd95forg.openscience.cdk.tools.LoggingToolTestDebugTrue@27ecd95forg.openscience.cdk.tools.LoggingToolTestDebugTrue@27ecd95f
2012-08-02 13:38:31,618 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2eb30073org.openscience.cdk.tools.LoggingToolTestDebugTrue@2eb30073org.openscience.cdk.tools.LoggingToolTestDebugTrue@2eb30073org.openscience.cdk.tools.LoggingToolTestDebugTrue@2eb30073
2012-08-02 13:38:31,619 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@69e295f8org.openscience.cdk.tools.LoggingToolTestDebugTrue@69e295f8org.openscience.cdk.tools.LoggingToolTestDebugTrue@69e295f8
2012-08-02 13:38:31,619 [main] FATAL org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@1ae40317
2012-08-02 13:38:31,620 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.class.path: /Users/johnmay/workspace/github/johnmay/cdk/jar/log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/jar/vecmath1.2-1.14.jar:/Users/johnmay/workspace/github/johnmay/cdk/develjar/junit-4.10.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-annotation.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-core.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-interfaces.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test-core.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test-log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test.jar:/usr/share/java/ant-1.8.2/lib/ant-launcher.jar:/usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-junit.jar:/usr/share/ant/lib/ant-junit4.jar
2012-08-02 13:38:31,620 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.name        : Mac OS X
2012-08-02 13:38:31,621 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.version     : 10.8
2012-08-02 13:38:31,621 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.arch        : x86_64
2012-08-02 13:38:31,621 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.version   : 1.7.0_05
2012-08-02 13:38:31,621 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.vendor    : Oracle Corporation
2012-08-02 13:55:13,162 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4b11a903
2012-08-02 13:55:13,191 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@53d5aeb1
2012-08-02 13:55:13,192 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@7f1bfcfcorg.openscience.cdk.tools.LoggingToolTestDebugTrue@7f1bfcfc
2012-08-02 13:55:13,193 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@67e45961.0
2012-08-02 13:55:13,194 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@5ed5064btrue
2012-08-02 13:55:13,194 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@73905690org.openscience.cdk.tools.LoggingToolTestDebugTrue@73905690org.openscience.cdk.tools.LoggingToolTestDebugTrue@73905690org.openscience.cdk.tools.LoggingToolTestDebugTrue@73905690org.openscience.cdk.tools.LoggingToolTestDebugTrue@73905690
2012-08-02 13:55:13,195 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@9234336org.openscience.cdk.tools.LoggingToolTestDebugTrue@9234336org.openscience.cdk.tools.LoggingToolTestDebugTrue@9234336org.openscience.cdk.tools.LoggingToolTestDebugTrue@9234336
2012-08-02 13:55:13,195 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6a1192e9org.openscience.cdk.tools.LoggingToolTestDebugTrue@6a1192e9org.openscience.cdk.tools.LoggingToolTestDebugTrue@6a1192e9
2012-08-02 13:55:13,195 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - Exception: null
2012-08-02 13:55:13,197 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.lang.Exception
2012-08-02 13:55:13,197 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at org.openscience.cdk.tools.AbstractLoggingToolTest.testDebug_ExceptionWithNullMessage(AbstractLoggingToolTest.java:75)
2012-08-02 13:55:13,197 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
2012-08-02 13:55:13,197 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
2012-08-02 13:55:13,197 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
2012-08-02 13:55:13,198 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@14c82493
2012-08-02 13:55:13,199 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@5fd9398dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@5fd9398d
2012-08-02 13:55:13,199 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2e5189241
2012-08-02 13:55:13,199 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6b02b23d1.0
2012-08-02 13:55:13,200 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@7e03f9adtrue
2012-08-02 13:55:13,200 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@36fd0d7dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@36fd0d7dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@36fd0d7dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@36fd0d7dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@36fd0d7d
2012-08-02 13:55:13,201 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@1f80a5bforg.openscience.cdk.tools.LoggingToolTestDebugTrue@1f80a5bforg.openscience.cdk.tools.LoggingToolTestDebugTrue@1f80a5bforg.openscience.cdk.tools.LoggingToolTestDebugTrue@1f80a5bf
2012-08-02 13:55:13,201 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3701aec1org.openscience.cdk.tools.LoggingToolTestDebugTrue@3701aec1org.openscience.cdk.tools.LoggingToolTestDebugTrue@3701aec1
2012-08-02 13:55:13,201 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4f781d1d
2012-08-02 13:55:13,202 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@56bf83adorg.openscience.cdk.tools.LoggingToolTestDebugTrue@56bf83ad
2012-08-02 13:55:13,202 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@375dff591
2012-08-02 13:55:13,203 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@7c2748741.0
2012-08-02 13:55:13,203 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@7705f759true
2012-08-02 13:55:13,203 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@28b2311borg.openscience.cdk.tools.LoggingToolTestDebugTrue@28b2311borg.openscience.cdk.tools.LoggingToolTestDebugTrue@28b2311borg.openscience.cdk.tools.LoggingToolTestDebugTrue@28b2311borg.openscience.cdk.tools.LoggingToolTestDebugTrue@28b2311b
2012-08-02 13:55:13,204 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4ab5f87corg.openscience.cdk.tools.LoggingToolTestDebugTrue@4ab5f87corg.openscience.cdk.tools.LoggingToolTestDebugTrue@4ab5f87corg.openscience.cdk.tools.LoggingToolTestDebugTrue@4ab5f87c
2012-08-02 13:55:13,204 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@70ccbb35org.openscience.cdk.tools.LoggingToolTestDebugTrue@70ccbb35org.openscience.cdk.tools.LoggingToolTestDebugTrue@70ccbb35
2012-08-02 13:55:13,205 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@1116ce6e
2012-08-02 13:55:13,205 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@704aa085org.openscience.cdk.tools.LoggingToolTestDebugTrue@704aa085
2012-08-02 13:55:13,206 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3370b55b1
2012-08-02 13:55:13,206 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2c9283bf1.0
2012-08-02 13:55:13,206 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@47078775true
2012-08-02 13:55:13,207 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3f4e36c1org.openscience.cdk.tools.LoggingToolTestDebugTrue@3f4e36c1org.openscience.cdk.tools.LoggingToolTestDebugTrue@3f4e36c1org.openscience.cdk.tools.LoggingToolTestDebugTrue@3f4e36c1org.openscience.cdk.tools.LoggingToolTestDebugTrue@3f4e36c1
2012-08-02 13:55:13,207 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@27ecd95forg.openscience.cdk.tools.LoggingToolTestDebugTrue@27ecd95forg.openscience.cdk.tools.LoggingToolTestDebugTrue@27ecd95forg.openscience.cdk.tools.LoggingToolTestDebugTrue@27ecd95f
2012-08-02 13:55:13,207 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2eb30073org.openscience.cdk.tools.LoggingToolTestDebugTrue@2eb30073org.openscience.cdk.tools.LoggingToolTestDebugTrue@2eb30073
2012-08-02 13:55:13,208 [main] FATAL org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@69e295f8
2012-08-02 13:55:13,209 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.class.path: /Users/johnmay/workspace/github/johnmay/cdk/jar/log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/jar/vecmath1.2-1.14.jar:/Users/johnmay/workspace/github/johnmay/cdk/develjar/junit-4.10.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-annotation.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-core.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-interfaces.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test-core.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test-log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test.jar:/usr/share/java/ant-1.8.2/lib/ant-launcher.jar:/usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-junit.jar:/usr/share/ant/lib/ant-junit4.jar
2012-08-02 13:55:13,209 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.name        : Mac OS X
2012-08-02 13:55:13,209 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.version     : 10.8
2012-08-02 13:55:13,209 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.arch        : x86_64
2012-08-02 13:55:13,209 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.version   : 1.7.0_05
2012-08-02 13:55:13,209 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.vendor    : Oracle Corporation
2012-10-22 17:22:04,245 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@26250f55
2012-10-22 17:22:04,377 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@a3a7a74org.openscience.cdk.tools.LoggingToolTestDebugTrue@a3a7a74
2012-10-22 17:22:04,414 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@53d5aeb1
2012-10-22 17:22:04,452 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@7f1bfcfc
2012-10-22 17:22:04,507 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@67e45961.0
2012-10-22 17:22:04,508 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@5ed5064b1
2012-10-22 17:22:04,509 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@73905690true
2012-10-22 17:22:04,509 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@9234336
2012-10-22 17:22:04,510 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6a1192e9org.openscience.cdk.tools.LoggingToolTestDebugTrue@6a1192e9org.openscience.cdk.tools.LoggingToolTestDebugTrue@6a1192e9org.openscience.cdk.tools.LoggingToolTestDebugTrue@6a1192e9org.openscience.cdk.tools.LoggingToolTestDebugTrue@6a1192e9
2012-10-22 17:22:04,511 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6c4e760borg.openscience.cdk.tools.LoggingToolTestDebugTrue@6c4e760borg.openscience.cdk.tools.LoggingToolTestDebugTrue@6c4e760borg.openscience.cdk.tools.LoggingToolTestDebugTrue@6c4e760b
2012-10-22 17:22:04,511 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@132803baorg.openscience.cdk.tools.LoggingToolTestDebugTrue@132803baorg.openscience.cdk.tools.LoggingToolTestDebugTrue@132803ba
2012-10-22 17:22:04,512 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - Exception: null
2012-10-22 17:22:04,513 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.lang.Exception
2012-10-22 17:22:04,513 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at org.openscience.cdk.tools.AbstractLoggingToolTest.testDebug_ExceptionWithNullMessage(AbstractLoggingToolTest.java:75)
2012-10-22 17:22:04,528 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
2012-10-22 17:22:04,528 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
2012-10-22 17:22:04,528 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
2012-10-22 17:22:04,529 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2e518924org.openscience.cdk.tools.LoggingToolTestDebugTrue@2e518924
2012-10-22 17:22:04,529 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6b02b23d1.0
2012-10-22 17:22:04,530 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@7e03f9adtrue
2012-10-22 17:22:04,530 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@36fd0d7dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@36fd0d7dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@36fd0d7dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@36fd0d7dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@36fd0d7d
2012-10-22 17:22:04,539 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@1f80a5bforg.openscience.cdk.tools.LoggingToolTestDebugTrue@1f80a5bforg.openscience.cdk.tools.LoggingToolTestDebugTrue@1f80a5bforg.openscience.cdk.tools.LoggingToolTestDebugTrue@1f80a5bf
2012-10-22 17:22:04,541 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3701aec1org.openscience.cdk.tools.LoggingToolTestDebugTrue@3701aec1org.openscience.cdk.tools.LoggingToolTestDebugTrue@3701aec1
2012-10-22 17:22:04,541 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4f781d1dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@4f781d1d
2012-10-22 17:22:04,541 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@56bf83ad1
2012-10-22 17:22:04,542 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@375dff591.0
2012-10-22 17:22:04,542 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@7c274874true
2012-10-22 17:22:04,542 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@7705f759org.openscience.cdk.tools.LoggingToolTestDebugTrue@7705f759org.openscience.cdk.tools.LoggingToolTestDebugTrue@7705f759org.openscience.cdk.tools.LoggingToolTestDebugTrue@7705f759org.openscience.cdk.tools.LoggingToolTestDebugTrue@7705f759
2012-10-22 17:22:04,543 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@28b2311borg.openscience.cdk.tools.LoggingToolTestDebugTrue@28b2311borg.openscience.cdk.tools.LoggingToolTestDebugTrue@28b2311borg.openscience.cdk.tools.LoggingToolTestDebugTrue@28b2311b
2012-10-22 17:22:04,543 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4ab5f87corg.openscience.cdk.tools.LoggingToolTestDebugTrue@4ab5f87corg.openscience.cdk.tools.LoggingToolTestDebugTrue@4ab5f87c
2012-10-22 17:22:04,544 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@70ccbb35
2012-10-22 17:22:04,544 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@1116ce6eorg.openscience.cdk.tools.LoggingToolTestDebugTrue@1116ce6e
2012-10-22 17:22:04,544 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@704aa0851
2012-10-22 17:22:04,545 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3370b55b1.0
2012-10-22 17:22:04,545 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2c9283bftrue
2012-10-22 17:22:04,545 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@47078775org.openscience.cdk.tools.LoggingToolTestDebugTrue@47078775org.openscience.cdk.tools.LoggingToolTestDebugTrue@47078775org.openscience.cdk.tools.LoggingToolTestDebugTrue@47078775org.openscience.cdk.tools.LoggingToolTestDebugTrue@47078775
2012-10-22 17:22:04,546 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3f4e36c1org.openscience.cdk.tools.LoggingToolTestDebugTrue@3f4e36c1org.openscience.cdk.tools.LoggingToolTestDebugTrue@3f4e36c1org.openscience.cdk.tools.LoggingToolTestDebugTrue@3f4e36c1
2012-10-22 17:22:04,546 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@27ecd95forg.openscience.cdk.tools.LoggingToolTestDebugTrue@27ecd95forg.openscience.cdk.tools.LoggingToolTestDebugTrue@27ecd95f
2012-10-22 17:22:04,547 [main] FATAL org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2eb30073
2012-10-22 17:22:04,548 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.class.path: /Users/johnmay/workspace/github/johnmay/cdk/jar/log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/jar/vecmath1.2-1.14.jar:/Users/johnmay/workspace/github/johnmay/cdk/develjar/junit-4.10.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-annotation.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-core.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-interfaces.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test-core.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test-log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test.jar:/usr/share/java/ant-1.8.2/lib/ant-launcher.jar:/usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-junit.jar:/usr/share/ant/lib/ant-junit4.jar
2012-10-22 17:22:04,548 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.name        : Mac OS X
2012-10-22 17:22:04,548 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.version     : 10.8.2
2012-10-22 17:22:04,548 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.arch        : x86_64
2012-10-22 17:22:04,548 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.version   : 1.7.0_05
2012-10-22 17:22:04,548 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.vendor    : Oracle Corporation
2012-10-22 17:37:47,606 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@746f2a75
2012-10-22 17:37:47,661 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@7f1bfcfc
2012-10-22 17:37:47,662 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@67e45961
2012-10-22 17:37:47,663 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4c0a7e2e
2012-10-22 17:37:47,663 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@44e225021
2012-10-22 17:37:47,664 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@5aebc9a2org.openscience.cdk.tools.LoggingToolTestDebugTrue@5aebc9a2
2012-10-22 17:37:47,665 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2e02d9501.0
2012-10-22 17:37:47,683 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@27c43566true
2012-10-22 17:37:47,683 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@428dcfeforg.openscience.cdk.tools.LoggingToolTestDebugTrue@428dcfeforg.openscience.cdk.tools.LoggingToolTestDebugTrue@428dcfeforg.openscience.cdk.tools.LoggingToolTestDebugTrue@428dcfeforg.openscience.cdk.tools.LoggingToolTestDebugTrue@428dcfef
2012-10-22 17:37:47,684 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@280cb229org.openscience.cdk.tools.LoggingToolTestDebugTrue@280cb229org.openscience.cdk.tools.LoggingToolTestDebugTrue@280cb229org.openscience.cdk.tools.LoggingToolTestDebugTrue@280cb229
2012-10-22 17:37:47,684 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@5984b649org.openscience.cdk.tools.LoggingToolTestDebugTrue@5984b649org.openscience.cdk.tools.LoggingToolTestDebugTrue@5984b649
2012-10-22 17:37:47,685 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - Exception: null
2012-10-22 17:37:47,686 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.lang.Exception
2012-10-22 17:37:47,686 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at org.openscience.cdk.tools.AbstractLoggingToolTest.testDebug_ExceptionWithNullMessage(AbstractLoggingToolTest.java:75)
2012-10-22 17:37:47,687 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
2012-10-22 17:37:47,687 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
2012-10-22 17:37:47,687 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
2012-10-22 17:37:47,687 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@7e03f9adorg.openscience.cdk.tools.LoggingToolTestDebugTrue@7e03f9ad
2012-10-22 17:37:47,688 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@36fd0d7d1.0
2012-10-22 17:37:47,688 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@1f80a5bftrue
2012-10-22 17:37:47,689 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3701aec1org.openscience.cdk.tools.LoggingToolTestDebugTrue@3701aec1org.openscience.cdk.tools.LoggingToolTestDebugTrue@3701aec1org.openscience.cdk.tools.LoggingToolTestDebugTrue@3701aec1org.openscience.cdk.tools.LoggingToolTestDebugTrue@3701aec1
2012-10-22 17:37:47,689 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4f781d1dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@4f781d1dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@4f781d1dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@4f781d1d
2012-10-22 17:37:47,690 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@56bf83adorg.openscience.cdk.tools.LoggingToolTestDebugTrue@56bf83adorg.openscience.cdk.tools.LoggingToolTestDebugTrue@56bf83ad
2012-10-22 17:37:47,690 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@375dff59org.openscience.cdk.tools.LoggingToolTestDebugTrue@375dff59
2012-10-22 17:37:47,691 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@7c2748741
2012-10-22 17:37:47,691 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@7705f7591.0
2012-10-22 17:37:47,692 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@28b2311btrue
2012-10-22 17:37:47,692 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4ab5f87corg.openscience.cdk.tools.LoggingToolTestDebugTrue@4ab5f87corg.openscience.cdk.tools.LoggingToolTestDebugTrue@4ab5f87corg.openscience.cdk.tools.LoggingToolTestDebugTrue@4ab5f87corg.openscience.cdk.tools.LoggingToolTestDebugTrue@4ab5f87c
2012-10-22 17:37:47,692 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@70ccbb35org.openscience.cdk.tools.LoggingToolTestDebugTrue@70ccbb35org.openscience.cdk.tools.LoggingToolTestDebugTrue@70ccbb35org.openscience.cdk.tools.LoggingToolTestDebugTrue@70ccbb35
2012-10-22 17:37:47,693 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@1116ce6eorg.openscience.cdk.tools.LoggingToolTestDebugTrue@1116ce6eorg.openscience.cdk.tools.LoggingToolTestDebugTrue@1116ce6e
2012-10-22 17:37:47,693 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@704aa085
2012-10-22 17:37:47,694 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3370b55borg.openscience.cdk.tools.LoggingToolTestDebugTrue@3370b55b
2012-10-22 17:37:47,695 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2c9283bf1
2012-10-22 17:37:47,695 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@470787751.0
2012-10-22 17:37:47,696 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3f4e36c1true
2012-10-22 17:37:47,696 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@27ecd95forg.openscience.cdk.tools.LoggingToolTestDebugTrue@27ecd95forg.openscience.cdk.tools.LoggingToolTestDebugTrue@27ecd95forg.openscience.cdk.tools.LoggingToolTestDebugTrue@27ecd95forg.openscience.cdk.tools.LoggingToolTestDebugTrue@27ecd95f
2012-10-22 17:37:47,697 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2eb30073org.openscience.cdk.tools.LoggingToolTestDebugTrue@2eb30073org.openscience.cdk.tools.LoggingToolTestDebugTrue@2eb30073org.openscience.cdk.tools.LoggingToolTestDebugTrue@2eb30073
2012-10-22 17:37:47,697 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@69e295f8org.openscience.cdk.tools.LoggingToolTestDebugTrue@69e295f8org.openscience.cdk.tools.LoggingToolTestDebugTrue@69e295f8
2012-10-22 17:37:47,698 [main] FATAL org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@1ae40317
2012-10-22 17:37:47,699 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.class.path: /Users/johnmay/workspace/github/johnmay/cdk/jar/log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/jar/vecmath1.2-1.14.jar:/Users/johnmay/workspace/github/johnmay/cdk/develjar/junit-4.10.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-annotation.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-core.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-interfaces.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test-core.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test-log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test.jar:/usr/share/java/ant-1.8.2/lib/ant-launcher.jar:/usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-junit.jar:/usr/share/ant/lib/ant-junit4.jar
2012-10-22 17:37:47,699 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.name        : Mac OS X
2012-10-22 17:37:47,699 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.version     : 10.8.2
2012-10-22 17:37:47,699 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.arch        : x86_64
2012-10-22 17:37:47,700 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.version   : 1.7.0_05
2012-10-22 17:37:47,700 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.vendor    : Oracle Corporation
2012-10-22 18:03:53,316 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2e4ca30b
2012-10-22 18:03:53,347 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@67e45961
2012-10-22 18:03:53,348 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4c0a7e2e
2012-10-22 18:03:53,348 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@44e22502org.openscience.cdk.tools.LoggingToolTestDebugTrue@44e22502
2012-10-22 18:03:53,349 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@5aebc9a21
2012-10-22 18:03:53,350 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2e02d9501.0
2012-10-22 18:03:53,351 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@27c43566
2012-10-22 18:03:53,351 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@428dcfeftrue
2012-10-22 18:03:53,352 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6c4e760borg.openscience.cdk.tools.LoggingToolTestDebugTrue@6c4e760borg.openscience.cdk.tools.LoggingToolTestDebugTrue@6c4e760borg.openscience.cdk.tools.LoggingToolTestDebugTrue@6c4e760borg.openscience.cdk.tools.LoggingToolTestDebugTrue@6c4e760b
2012-10-22 18:03:53,353 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@5984b649org.openscience.cdk.tools.LoggingToolTestDebugTrue@5984b649org.openscience.cdk.tools.LoggingToolTestDebugTrue@5984b649org.openscience.cdk.tools.LoggingToolTestDebugTrue@5984b649
2012-10-22 18:03:53,353 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@17dba089org.openscience.cdk.tools.LoggingToolTestDebugTrue@17dba089org.openscience.cdk.tools.LoggingToolTestDebugTrue@17dba089
2012-10-22 18:03:53,354 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - Exception: null
2012-10-22 18:03:53,356 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.lang.Exception
2012-10-22 18:03:53,356 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at org.openscience.cdk.tools.AbstractLoggingToolTest.testDebug_ExceptionWithNullMessage(AbstractLoggingToolTest.java:75)
2012-10-22 18:03:53,356 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
2012-10-22 18:03:53,356 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
2012-10-22 18:03:53,356 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
2012-10-22 18:03:53,357 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@36fd0d7dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@36fd0d7d
2012-10-22 18:03:53,357 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@1f80a5bf1.0
2012-10-22 18:03:53,358 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3701aec1true
2012-10-22 18:03:53,358 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4f781d1dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@4f781d1dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@4f781d1dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@4f781d1dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@4f781d1d
2012-10-22 18:03:53,359 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@56bf83adorg.openscience.cdk.tools.LoggingToolTestDebugTrue@56bf83adorg.openscience.cdk.tools.LoggingToolTestDebugTrue@56bf83adorg.openscience.cdk.tools.LoggingToolTestDebugTrue@56bf83ad
2012-10-22 18:03:53,359 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@375dff59org.openscience.cdk.tools.LoggingToolTestDebugTrue@375dff59org.openscience.cdk.tools.LoggingToolTestDebugTrue@375dff59
2012-10-22 18:03:53,359 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@7c274874org.openscience.cdk.tools.LoggingToolTestDebugTrue@7c274874
2012-10-22 18:03:53,360 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@7705f7591
2012-10-22 18:03:53,361 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@28b2311b1.0
2012-10-22 18:03:53,361 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4ab5f87ctrue
2012-10-22 18:03:53,362 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@70ccbb35org.openscience.cdk.tools.LoggingToolTestDebugTrue@70ccbb35org.openscience.cdk.tools.LoggingToolTestDebugTrue@70ccbb35org.openscience.cdk.tools.LoggingToolTestDebugTrue@70ccbb35org.openscience.cdk.tools.LoggingToolTestDebugTrue@70ccbb35
2012-10-22 18:03:53,362 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@1116ce6eorg.openscience.cdk.tools.LoggingToolTestDebugTrue@1116ce6eorg.openscience.cdk.tools.LoggingToolTestDebugTrue@1116ce6eorg.openscience.cdk.tools.LoggingToolTestDebugTrue@1116ce6e
2012-10-22 18:03:53,363 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@704aa085org.openscience.cdk.tools.LoggingToolTestDebugTrue@704aa085org.openscience.cdk.tools.LoggingToolTestDebugTrue@704aa085
2012-10-22 18:03:53,363 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3370b55b
2012-10-22 18:03:53,364 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2c9283bforg.openscience.cdk.tools.LoggingToolTestDebugTrue@2c9283bf
2012-10-22 18:03:53,364 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@470787751
2012-10-22 18:03:53,365 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3f4e36c11.0
2012-10-22 18:03:53,365 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@27ecd95ftrue
2012-10-22 18:03:53,366 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2eb30073org.openscience.cdk.tools.LoggingToolTestDebugTrue@2eb30073org.openscience.cdk.tools.LoggingToolTestDebugTrue@2eb30073org.openscience.cdk.tools.LoggingToolTestDebugTrue@2eb30073org.openscience.cdk.tools.LoggingToolTestDebugTrue@2eb30073
2012-10-22 18:03:53,366 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@69e295f8org.openscience.cdk.tools.LoggingToolTestDebugTrue@69e295f8org.openscience.cdk.tools.LoggingToolTestDebugTrue@69e295f8org.openscience.cdk.tools.LoggingToolTestDebugTrue@69e295f8
2012-10-22 18:03:53,367 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@1ae40317org.openscience.cdk.tools.LoggingToolTestDebugTrue@1ae40317org.openscience.cdk.tools.LoggingToolTestDebugTrue@1ae40317
2012-10-22 18:03:53,368 [main] FATAL org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6f86e8cb
2012-10-22 18:03:53,368 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.class.path: /Users/johnmay/workspace/github/johnmay/cdk/jar/log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/jar/vecmath1.2-1.14.jar:/Users/johnmay/workspace/github/johnmay/cdk/develjar/junit-4.10.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-annotation.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-core.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-interfaces.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test-core.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test-log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test.jar:/usr/share/java/ant-1.8.2/lib/ant-launcher.jar:/usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-junit.jar:/usr/share/ant/lib/ant-junit4.jar
2012-10-22 18:03:53,369 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.name        : Mac OS X
2012-10-22 18:03:53,369 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.version     : 10.8.2
2012-10-22 18:03:53,369 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.arch        : x86_64
2012-10-22 18:03:53,369 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.version   : 1.7.0_05
2012-10-22 18:03:53,369 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.vendor    : Oracle Corporation
2012-10-28 21:41:33,515 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2e4ca30b
2012-10-28 21:41:33,787 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@67e45961
2012-10-28 21:41:33,852 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4c0a7e2eorg.openscience.cdk.tools.LoggingToolTestDebugTrue@4c0a7e2e
2012-10-28 21:41:33,860 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@44e225021.0
2012-10-28 21:41:33,861 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@9234336true
2012-10-28 21:41:33,866 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6a1192e9org.openscience.cdk.tools.LoggingToolTestDebugTrue@6a1192e9org.openscience.cdk.tools.LoggingToolTestDebugTrue@6a1192e9org.openscience.cdk.tools.LoggingToolTestDebugTrue@6a1192e9org.openscience.cdk.tools.LoggingToolTestDebugTrue@6a1192e9
2012-10-28 21:41:33,866 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@27c43566org.openscience.cdk.tools.LoggingToolTestDebugTrue@27c43566org.openscience.cdk.tools.LoggingToolTestDebugTrue@27c43566org.openscience.cdk.tools.LoggingToolTestDebugTrue@27c43566
2012-10-28 21:41:33,876 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@428dcfeforg.openscience.cdk.tools.LoggingToolTestDebugTrue@428dcfeforg.openscience.cdk.tools.LoggingToolTestDebugTrue@428dcfef
2012-10-28 21:41:33,877 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - Exception: null
2012-10-28 21:41:33,879 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.lang.Exception
2012-10-28 21:41:33,887 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at org.openscience.cdk.tools.AbstractLoggingToolTest.testDebug_ExceptionWithNullMessage(AbstractLoggingToolTest.java:75)
2012-10-28 21:41:33,888 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
2012-10-28 21:41:33,888 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
2012-10-28 21:41:33,888 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
2012-10-28 21:41:33,889 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2e518924
2012-10-28 21:41:33,889 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6b02b23dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@6b02b23d
2012-10-28 21:41:33,890 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@7e03f9ad1
2012-10-28 21:41:33,890 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@36fd0d7d1.0
2012-10-28 21:41:33,891 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@1f80a5bftrue
2012-10-28 21:41:33,891 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3701aec1org.openscience.cdk.tools.LoggingToolTestDebugTrue@3701aec1org.openscience.cdk.tools.LoggingToolTestDebugTrue@3701aec1org.openscience.cdk.tools.LoggingToolTestDebugTrue@3701aec1org.openscience.cdk.tools.LoggingToolTestDebugTrue@3701aec1
2012-10-28 21:41:33,891 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4f781d1dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@4f781d1dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@4f781d1dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@4f781d1d
2012-10-28 21:41:33,892 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@56bf83adorg.openscience.cdk.tools.LoggingToolTestDebugTrue@56bf83adorg.openscience.cdk.tools.LoggingToolTestDebugTrue@56bf83ad
2012-10-28 21:41:33,892 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@375dff59
2012-10-28 21:41:33,892 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@7c274874org.openscience.cdk.tools.LoggingToolTestDebugTrue@7c274874
2012-10-28 21:41:33,893 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@7705f7591
2012-10-28 21:41:33,893 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@28b2311b1.0
2012-10-28 21:41:33,893 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4ab5f87ctrue
2012-10-28 21:41:33,894 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@70ccbb35org.openscience.cdk.tools.LoggingToolTestDebugTrue@70ccbb35org.openscience.cdk.tools.LoggingToolTestDebugTrue@70ccbb35org.openscience.cdk.tools.LoggingToolTestDebugTrue@70ccbb35org.openscience.cdk.tools.LoggingToolTestDebugTrue@70ccbb35
2012-10-28 21:41:33,894 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@1116ce6eorg.openscience.cdk.tools.LoggingToolTestDebugTrue@1116ce6eorg.openscience.cdk.tools.LoggingToolTestDebugTrue@1116ce6eorg.openscience.cdk.tools.LoggingToolTestDebugTrue@1116ce6e
2012-10-28 21:41:33,895 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@704aa085org.openscience.cdk.tools.LoggingToolTestDebugTrue@704aa085org.openscience.cdk.tools.LoggingToolTestDebugTrue@704aa085
2012-10-28 21:41:33,895 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3370b55b
2012-10-28 21:41:33,895 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2c9283bforg.openscience.cdk.tools.LoggingToolTestDebugTrue@2c9283bf
2012-10-28 21:41:33,896 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@470787751
2012-10-28 21:41:33,896 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3f4e36c11.0
2012-10-28 21:41:33,897 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@27ecd95ftrue
2012-10-28 21:41:33,897 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2eb30073org.openscience.cdk.tools.LoggingToolTestDebugTrue@2eb30073org.openscience.cdk.tools.LoggingToolTestDebugTrue@2eb30073org.openscience.cdk.tools.LoggingToolTestDebugTrue@2eb30073org.openscience.cdk.tools.LoggingToolTestDebugTrue@2eb30073
2012-10-28 21:41:33,898 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@69e295f8org.openscience.cdk.tools.LoggingToolTestDebugTrue@69e295f8org.openscience.cdk.tools.LoggingToolTestDebugTrue@69e295f8org.openscience.cdk.tools.LoggingToolTestDebugTrue@69e295f8
2012-10-28 21:41:33,898 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@1ae40317org.openscience.cdk.tools.LoggingToolTestDebugTrue@1ae40317org.openscience.cdk.tools.LoggingToolTestDebugTrue@1ae40317
2012-10-28 21:41:33,899 [main] FATAL org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6f86e8cb
2012-10-28 21:41:33,900 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.class.path: /Users/johnmay/workspace/github/johnmay/cdk/jar/log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/jar/vecmath1.2-1.14.jar:/Users/johnmay/workspace/github/johnmay/cdk/develjar/junit-4.10.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-annotation.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-core.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-interfaces.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test-core.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test-log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test.jar:/Users/johnmay/Library/Frameworks/junit-4.10.jar:/usr/share/java/ant-1.8.2/lib/ant-launcher.jar:/usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-junit.jar:/usr/share/ant/lib/ant-junit4.jar
2012-10-28 21:41:33,900 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.name        : Mac OS X
2012-10-28 21:41:33,900 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.version     : 10.8.2
2012-10-28 21:41:33,900 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.arch        : x86_64
2012-10-28 21:41:33,900 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.version   : 1.7.0_05
2012-10-28 21:41:33,900 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.vendor    : Oracle Corporation
2012-10-28 22:01:27,982 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@745f0d2e
2012-10-28 22:01:28,007 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@44e225021
2012-10-28 22:01:28,008 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@5aebc9a2
2012-10-28 22:01:28,009 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2e02d950org.openscience.cdk.tools.LoggingToolTestDebugTrue@2e02d950
2012-10-28 22:01:28,010 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3d092ac91.0
2012-10-28 22:01:28,029 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@428dcfeftrue
2012-10-28 22:01:28,030 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6c4e760borg.openscience.cdk.tools.LoggingToolTestDebugTrue@6c4e760borg.openscience.cdk.tools.LoggingToolTestDebugTrue@6c4e760borg.openscience.cdk.tools.LoggingToolTestDebugTrue@6c4e760borg.openscience.cdk.tools.LoggingToolTestDebugTrue@6c4e760b
2012-10-28 22:01:28,030 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@132803baorg.openscience.cdk.tools.LoggingToolTestDebugTrue@132803baorg.openscience.cdk.tools.LoggingToolTestDebugTrue@132803baorg.openscience.cdk.tools.LoggingToolTestDebugTrue@132803ba
2012-10-28 22:01:28,031 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@280cb229org.openscience.cdk.tools.LoggingToolTestDebugTrue@280cb229org.openscience.cdk.tools.LoggingToolTestDebugTrue@280cb229
2012-10-28 22:01:28,032 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - Exception: null
2012-10-28 22:01:28,033 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.lang.Exception
2012-10-28 22:01:28,033 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at org.openscience.cdk.tools.AbstractLoggingToolTest.testDebug_ExceptionWithNullMessage(AbstractLoggingToolTest.java:75)
2012-10-28 22:01:28,033 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
2012-10-28 22:01:28,033 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
2012-10-28 22:01:28,033 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
2012-10-28 22:01:28,034 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@36fd0d7dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@36fd0d7d
2012-10-28 22:01:28,034 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@1f80a5bf1
2012-10-28 22:01:28,034 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3701aec11.0
2012-10-28 22:01:28,035 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4f781d1dtrue
2012-10-28 22:01:28,035 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@56bf83adorg.openscience.cdk.tools.LoggingToolTestDebugTrue@56bf83adorg.openscience.cdk.tools.LoggingToolTestDebugTrue@56bf83adorg.openscience.cdk.tools.LoggingToolTestDebugTrue@56bf83adorg.openscience.cdk.tools.LoggingToolTestDebugTrue@56bf83ad
2012-10-28 22:01:28,035 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@375dff59org.openscience.cdk.tools.LoggingToolTestDebugTrue@375dff59org.openscience.cdk.tools.LoggingToolTestDebugTrue@375dff59org.openscience.cdk.tools.LoggingToolTestDebugTrue@375dff59
2012-10-28 22:01:28,036 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@7c274874org.openscience.cdk.tools.LoggingToolTestDebugTrue@7c274874org.openscience.cdk.tools.LoggingToolTestDebugTrue@7c274874
2012-10-28 22:01:28,036 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@7705f759
2012-10-28 22:01:28,037 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@28b2311borg.openscience.cdk.tools.LoggingToolTestDebugTrue@28b2311b
2012-10-28 22:01:28,037 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4ab5f87c1
2012-10-28 22:01:28,038 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@70ccbb351.0
2012-10-28 22:01:28,038 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@1116ce6etrue
2012-10-28 22:01:28,038 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@704aa085org.openscience.cdk.tools.LoggingToolTestDebugTrue@704aa085org.openscience.cdk.tools.LoggingToolTestDebugTrue@704aa085org.openscience.cdk.tools.LoggingToolTestDebugTrue@704aa085org.openscience.cdk.tools.LoggingToolTestDebugTrue@704aa085
2012-10-28 22:01:28,039 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3370b55borg.openscience.cdk.tools.LoggingToolTestDebugTrue@3370b55borg.openscience.cdk.tools.LoggingToolTestDebugTrue@3370b55borg.openscience.cdk.tools.LoggingToolTestDebugTrue@3370b55b
2012-10-28 22:01:28,039 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2c9283bforg.openscience.cdk.tools.LoggingToolTestDebugTrue@2c9283bforg.openscience.cdk.tools.LoggingToolTestDebugTrue@2c9283bf
2012-10-28 22:01:28,040 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@47078775
2012-10-28 22:01:28,040 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3f4e36c1org.openscience.cdk.tools.LoggingToolTestDebugTrue@3f4e36c1
2012-10-28 22:01:28,040 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@27ecd95f1
2012-10-28 22:01:28,041 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2eb300731.0
2012-10-28 22:01:28,041 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@69e295f8true
2012-10-28 22:01:28,041 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@1ae40317org.openscience.cdk.tools.LoggingToolTestDebugTrue@1ae40317org.openscience.cdk.tools.LoggingToolTestDebugTrue@1ae40317org.openscience.cdk.tools.LoggingToolTestDebugTrue@1ae40317org.openscience.cdk.tools.LoggingToolTestDebugTrue@1ae40317
2012-10-28 22:01:28,042 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6f86e8cborg.openscience.cdk.tools.LoggingToolTestDebugTrue@6f86e8cborg.openscience.cdk.tools.LoggingToolTestDebugTrue@6f86e8cborg.openscience.cdk.tools.LoggingToolTestDebugTrue@6f86e8cb
2012-10-28 22:01:28,042 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@21da0a1org.openscience.cdk.tools.LoggingToolTestDebugTrue@21da0a1org.openscience.cdk.tools.LoggingToolTestDebugTrue@21da0a1
2012-10-28 22:01:28,043 [main] FATAL org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@671cab1c
2012-10-28 22:01:28,043 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.class.path: /Users/johnmay/workspace/github/johnmay/cdk/jar/log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/jar/vecmath1.2-1.14.jar:/Users/johnmay/workspace/github/johnmay/cdk/develjar/junit-4.10.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-annotation.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-core.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-interfaces.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test-core.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test-log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test.jar:/Users/johnmay/Library/Frameworks/junit-4.10.jar:/usr/share/java/ant-1.8.2/lib/ant-launcher.jar:/usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-junit.jar:/usr/share/ant/lib/ant-junit4.jar
2012-10-28 22:01:28,044 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.name        : Mac OS X
2012-10-28 22:01:28,044 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.version     : 10.8.2
2012-10-28 22:01:28,044 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.arch        : x86_64
2012-10-28 22:01:28,044 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.version   : 1.7.0_05
2012-10-28 22:01:28,044 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.vendor    : Oracle Corporation
2012-10-28 22:14:33,244 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@745f0d2e
2012-10-28 22:14:33,281 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@44e22502
2012-10-28 22:14:33,285 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@5aebc9a21
2012-10-28 22:14:33,296 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2e02d950org.openscience.cdk.tools.LoggingToolTestDebugTrue@2e02d950
2012-10-28 22:14:33,297 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3d092ac91.0
2012-10-28 22:14:33,297 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@428dcfeftrue
2012-10-28 22:14:33,302 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6c4e760borg.openscience.cdk.tools.LoggingToolTestDebugTrue@6c4e760borg.openscience.cdk.tools.LoggingToolTestDebugTrue@6c4e760borg.openscience.cdk.tools.LoggingToolTestDebugTrue@6c4e760borg.openscience.cdk.tools.LoggingToolTestDebugTrue@6c4e760b
2012-10-28 22:14:33,311 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@132803baorg.openscience.cdk.tools.LoggingToolTestDebugTrue@132803baorg.openscience.cdk.tools.LoggingToolTestDebugTrue@132803baorg.openscience.cdk.tools.LoggingToolTestDebugTrue@132803ba
2012-10-28 22:14:33,311 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@280cb229org.openscience.cdk.tools.LoggingToolTestDebugTrue@280cb229org.openscience.cdk.tools.LoggingToolTestDebugTrue@280cb229
2012-10-28 22:14:33,312 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - Exception: null
2012-10-28 22:14:33,314 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.lang.Exception
2012-10-28 22:14:33,314 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at org.openscience.cdk.tools.AbstractLoggingToolTest.testDebug_ExceptionWithNullMessage(AbstractLoggingToolTest.java:75)
2012-10-28 22:14:33,314 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
2012-10-28 22:14:33,314 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
2012-10-28 22:14:33,314 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
2012-10-28 22:14:33,323 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@36fd0d7dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@36fd0d7d
2012-10-28 22:14:33,323 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@1f80a5bf1
2012-10-28 22:14:33,324 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3701aec11.0
2012-10-28 22:14:33,324 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4f781d1dtrue
2012-10-28 22:14:33,325 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@56bf83adorg.openscience.cdk.tools.LoggingToolTestDebugTrue@56bf83adorg.openscience.cdk.tools.LoggingToolTestDebugTrue@56bf83adorg.openscience.cdk.tools.LoggingToolTestDebugTrue@56bf83adorg.openscience.cdk.tools.LoggingToolTestDebugTrue@56bf83ad
2012-10-28 22:14:33,325 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@375dff59org.openscience.cdk.tools.LoggingToolTestDebugTrue@375dff59org.openscience.cdk.tools.LoggingToolTestDebugTrue@375dff59org.openscience.cdk.tools.LoggingToolTestDebugTrue@375dff59
2012-10-28 22:14:33,326 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@7c274874org.openscience.cdk.tools.LoggingToolTestDebugTrue@7c274874org.openscience.cdk.tools.LoggingToolTestDebugTrue@7c274874
2012-10-28 22:14:33,326 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@7705f759
2012-10-28 22:14:33,327 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@28b2311borg.openscience.cdk.tools.LoggingToolTestDebugTrue@28b2311b
2012-10-28 22:14:33,327 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4ab5f87c1
2012-10-28 22:14:33,327 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@70ccbb351.0
2012-10-28 22:14:33,328 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@1116ce6etrue
2012-10-28 22:14:33,328 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@704aa085org.openscience.cdk.tools.LoggingToolTestDebugTrue@704aa085org.openscience.cdk.tools.LoggingToolTestDebugTrue@704aa085org.openscience.cdk.tools.LoggingToolTestDebugTrue@704aa085org.openscience.cdk.tools.LoggingToolTestDebugTrue@704aa085
2012-10-28 22:14:33,350 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3370b55borg.openscience.cdk.tools.LoggingToolTestDebugTrue@3370b55borg.openscience.cdk.tools.LoggingToolTestDebugTrue@3370b55borg.openscience.cdk.tools.LoggingToolTestDebugTrue@3370b55b
2012-10-28 22:14:33,389 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2c9283bforg.openscience.cdk.tools.LoggingToolTestDebugTrue@2c9283bforg.openscience.cdk.tools.LoggingToolTestDebugTrue@2c9283bf
2012-10-28 22:14:33,394 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@47078775
2012-10-28 22:14:33,399 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3f4e36c1org.openscience.cdk.tools.LoggingToolTestDebugTrue@3f4e36c1
2012-10-28 22:14:33,414 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@27ecd95f1
2012-10-28 22:14:33,416 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2eb300731.0
2012-10-28 22:14:33,430 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@69e295f8true
2012-10-28 22:14:33,439 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@1ae40317org.openscience.cdk.tools.LoggingToolTestDebugTrue@1ae40317org.openscience.cdk.tools.LoggingToolTestDebugTrue@1ae40317org.openscience.cdk.tools.LoggingToolTestDebugTrue@1ae40317org.openscience.cdk.tools.LoggingToolTestDebugTrue@1ae40317
2012-10-28 22:14:33,439 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6f86e8cborg.openscience.cdk.tools.LoggingToolTestDebugTrue@6f86e8cborg.openscience.cdk.tools.LoggingToolTestDebugTrue@6f86e8cborg.openscience.cdk.tools.LoggingToolTestDebugTrue@6f86e8cb
2012-10-28 22:14:33,446 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@21da0a1org.openscience.cdk.tools.LoggingToolTestDebugTrue@21da0a1org.openscience.cdk.tools.LoggingToolTestDebugTrue@21da0a1
2012-10-28 22:14:33,447 [main] FATAL org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@671cab1c
2012-10-28 22:14:33,454 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.class.path: /Users/johnmay/workspace/github/johnmay/cdk/jar/log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/jar/vecmath1.2-1.14.jar:/Users/johnmay/workspace/github/johnmay/cdk/develjar/junit-4.10.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-annotation.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-core.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-interfaces.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test-core.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test-log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test.jar:/Users/johnmay/Library/Frameworks/junit-4.10.jar:/usr/share/java/ant-1.8.2/lib/ant-launcher.jar:/usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-junit.jar:/usr/share/ant/lib/ant-junit4.jar
2012-10-28 22:14:33,465 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.name        : Mac OS X
2012-10-28 22:14:33,465 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.version     : 10.8.2
2012-10-28 22:14:33,465 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.arch        : x86_64
2012-10-28 22:14:33,465 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.version   : 1.7.0_05
2012-10-28 22:14:33,465 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.vendor    : Oracle Corporation
2012-10-29 22:26:06,660 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2e4ca30b
2012-10-29 22:26:07,088 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@67e45961
2012-10-29 22:26:07,117 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4c0a7e2eorg.openscience.cdk.tools.LoggingToolTestDebugTrue@4c0a7e2e
2012-10-29 22:26:07,124 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@44e225021.0
2012-10-29 22:26:07,124 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@9234336true
2012-10-29 22:26:07,131 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6a1192e9org.openscience.cdk.tools.LoggingToolTestDebugTrue@6a1192e9org.openscience.cdk.tools.LoggingToolTestDebugTrue@6a1192e9org.openscience.cdk.tools.LoggingToolTestDebugTrue@6a1192e9org.openscience.cdk.tools.LoggingToolTestDebugTrue@6a1192e9
2012-10-29 22:26:07,299 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@428dcfeforg.openscience.cdk.tools.LoggingToolTestDebugTrue@428dcfeforg.openscience.cdk.tools.LoggingToolTestDebugTrue@428dcfeforg.openscience.cdk.tools.LoggingToolTestDebugTrue@428dcfef
2012-10-29 22:26:07,326 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6c4e760borg.openscience.cdk.tools.LoggingToolTestDebugTrue@6c4e760borg.openscience.cdk.tools.LoggingToolTestDebugTrue@6c4e760b
2012-10-29 22:26:07,326 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - Exception: null
2012-10-29 22:26:07,329 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.lang.Exception
2012-10-29 22:26:07,329 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at org.openscience.cdk.tools.AbstractLoggingToolTest.testDebug_ExceptionWithNullMessage(AbstractLoggingToolTest.java:75)
2012-10-29 22:26:07,329 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
2012-10-29 22:26:07,329 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
2012-10-29 22:26:07,329 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
2012-10-29 22:26:07,331 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6b02b23d
2012-10-29 22:26:07,332 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@7e03f9adorg.openscience.cdk.tools.LoggingToolTestDebugTrue@7e03f9ad
2012-10-29 22:26:07,332 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@36fd0d7d1
2012-10-29 22:26:07,333 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@1f80a5bf1.0
2012-10-29 22:26:07,333 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3701aec1true
2012-10-29 22:26:07,334 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4f781d1dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@4f781d1dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@4f781d1dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@4f781d1dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@4f781d1d
2012-10-29 22:26:07,335 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@56bf83adorg.openscience.cdk.tools.LoggingToolTestDebugTrue@56bf83adorg.openscience.cdk.tools.LoggingToolTestDebugTrue@56bf83adorg.openscience.cdk.tools.LoggingToolTestDebugTrue@56bf83ad
2012-10-29 22:26:07,335 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@375dff59org.openscience.cdk.tools.LoggingToolTestDebugTrue@375dff59org.openscience.cdk.tools.LoggingToolTestDebugTrue@375dff59
2012-10-29 22:26:07,336 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@7c274874
2012-10-29 22:26:07,336 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@7705f759org.openscience.cdk.tools.LoggingToolTestDebugTrue@7705f759
2012-10-29 22:26:07,336 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@28b2311b1
2012-10-29 22:26:07,337 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4ab5f87c1.0
2012-10-29 22:26:07,337 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@70ccbb35true
2012-10-29 22:26:07,337 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@1116ce6eorg.openscience.cdk.tools.LoggingToolTestDebugTrue@1116ce6eorg.openscience.cdk.tools.LoggingToolTestDebugTrue@1116ce6eorg.openscience.cdk.tools.LoggingToolTestDebugTrue@1116ce6eorg.openscience.cdk.tools.LoggingToolTestDebugTrue@1116ce6e
2012-10-29 22:26:07,338 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@704aa085org.openscience.cdk.tools.LoggingToolTestDebugTrue@704aa085org.openscience.cdk.tools.LoggingToolTestDebugTrue@704aa085org.openscience.cdk.tools.LoggingToolTestDebugTrue@704aa085
2012-10-29 22:26:07,339 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3370b55borg.openscience.cdk.tools.LoggingToolTestDebugTrue@3370b55borg.openscience.cdk.tools.LoggingToolTestDebugTrue@3370b55b
2012-10-29 22:26:07,339 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2c9283bf
2012-10-29 22:26:07,362 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@47078775org.openscience.cdk.tools.LoggingToolTestDebugTrue@47078775
2012-10-29 22:26:07,363 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3f4e36c11
2012-10-29 22:26:07,364 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@27ecd95f1.0
2012-10-29 22:26:07,364 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2eb30073true
2012-10-29 22:26:07,365 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@69e295f8org.openscience.cdk.tools.LoggingToolTestDebugTrue@69e295f8org.openscience.cdk.tools.LoggingToolTestDebugTrue@69e295f8org.openscience.cdk.tools.LoggingToolTestDebugTrue@69e295f8org.openscience.cdk.tools.LoggingToolTestDebugTrue@69e295f8
2012-10-29 22:26:07,365 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@1ae40317org.openscience.cdk.tools.LoggingToolTestDebugTrue@1ae40317org.openscience.cdk.tools.LoggingToolTestDebugTrue@1ae40317org.openscience.cdk.tools.LoggingToolTestDebugTrue@1ae40317
2012-10-29 22:26:07,366 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6f86e8cborg.openscience.cdk.tools.LoggingToolTestDebugTrue@6f86e8cborg.openscience.cdk.tools.LoggingToolTestDebugTrue@6f86e8cb
2012-10-29 22:26:07,367 [main] FATAL org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@21da0a1
2012-10-29 22:26:07,368 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.class.path: /Users/johnmay/workspace/github/johnmay/cdk/jar/log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/jar/vecmath1.2-1.14.jar:/Users/johnmay/workspace/github/johnmay/cdk/develjar/junit-4.10.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-annotation.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-core.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-interfaces.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test-core.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test-log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test.jar:/usr/share/java/ant-1.8.2/lib/ant-launcher.jar:/usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-junit.jar:/usr/share/ant/lib/ant-junit4.jar
2012-10-29 22:26:07,369 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.name        : Mac OS X
2012-10-29 22:26:07,369 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.version     : 10.8.2
2012-10-29 22:26:07,369 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.arch        : x86_64
2012-10-29 22:26:07,369 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.version   : 1.7.0_05
2012-10-29 22:26:07,369 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.vendor    : Oracle Corporation
2012-10-31 14:00:24,165 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@60b25572
2012-10-31 14:00:24,230 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@5da3e3111
2012-10-31 14:00:24,232 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3290a11eorg.openscience.cdk.tools.LoggingToolTestDebugTrue@3290a11e
2012-10-31 14:00:24,233 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3541d2811.0
2012-10-31 14:00:24,272 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@18de9738true
2012-10-31 14:00:24,272 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3d99ea49org.openscience.cdk.tools.LoggingToolTestDebugTrue@3d99ea49org.openscience.cdk.tools.LoggingToolTestDebugTrue@3d99ea49org.openscience.cdk.tools.LoggingToolTestDebugTrue@3d99ea49org.openscience.cdk.tools.LoggingToolTestDebugTrue@3d99ea49
2012-10-31 14:00:24,272 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@43e47e37org.openscience.cdk.tools.LoggingToolTestDebugTrue@43e47e37org.openscience.cdk.tools.LoggingToolTestDebugTrue@43e47e37org.openscience.cdk.tools.LoggingToolTestDebugTrue@43e47e37
2012-10-31 14:00:24,273 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4e1a6fb3org.openscience.cdk.tools.LoggingToolTestDebugTrue@4e1a6fb3org.openscience.cdk.tools.LoggingToolTestDebugTrue@4e1a6fb3
2012-10-31 14:00:24,273 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - Exception: null
2012-10-31 14:00:24,275 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.lang.Exception
2012-10-31 14:00:24,275 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at org.openscience.cdk.tools.AbstractLoggingToolTest.testDebug_ExceptionWithNullMessage(AbstractLoggingToolTest.java:75)
2012-10-31 14:00:24,275 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
2012-10-31 14:00:24,275 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
2012-10-31 14:00:24,275 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
2012-10-31 14:00:24,276 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2bc7c6c3
2012-10-31 14:00:24,276 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@48ca42a9org.openscience.cdk.tools.LoggingToolTestDebugTrue@48ca42a9
2012-10-31 14:00:24,276 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@56de8a941
2012-10-31 14:00:24,277 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2c5c271a1.0
2012-10-31 14:00:24,277 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@560b32b6true
2012-10-31 14:00:24,277 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@792e76dborg.openscience.cdk.tools.LoggingToolTestDebugTrue@792e76dborg.openscience.cdk.tools.LoggingToolTestDebugTrue@792e76dborg.openscience.cdk.tools.LoggingToolTestDebugTrue@792e76dborg.openscience.cdk.tools.LoggingToolTestDebugTrue@792e76db
2012-10-31 14:00:24,278 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@597d6204org.openscience.cdk.tools.LoggingToolTestDebugTrue@597d6204org.openscience.cdk.tools.LoggingToolTestDebugTrue@597d6204org.openscience.cdk.tools.LoggingToolTestDebugTrue@597d6204
2012-10-31 14:00:24,278 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@36ae2282org.openscience.cdk.tools.LoggingToolTestDebugTrue@36ae2282org.openscience.cdk.tools.LoggingToolTestDebugTrue@36ae2282
2012-10-31 14:00:24,278 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@625ba0d9
2012-10-31 14:00:24,279 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6d9d3901org.openscience.cdk.tools.LoggingToolTestDebugTrue@6d9d3901
2012-10-31 14:00:24,279 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6d09a8df1
2012-10-31 14:00:24,279 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@152e00661.0
2012-10-31 14:00:24,280 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@7f1c3366true
2012-10-31 14:00:24,280 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@1472aebcorg.openscience.cdk.tools.LoggingToolTestDebugTrue@1472aebcorg.openscience.cdk.tools.LoggingToolTestDebugTrue@1472aebcorg.openscience.cdk.tools.LoggingToolTestDebugTrue@1472aebcorg.openscience.cdk.tools.LoggingToolTestDebugTrue@1472aebc
2012-10-31 14:00:24,280 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@752dc320org.openscience.cdk.tools.LoggingToolTestDebugTrue@752dc320org.openscience.cdk.tools.LoggingToolTestDebugTrue@752dc320org.openscience.cdk.tools.LoggingToolTestDebugTrue@752dc320
2012-10-31 14:00:24,281 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@f65a5faorg.openscience.cdk.tools.LoggingToolTestDebugTrue@f65a5faorg.openscience.cdk.tools.LoggingToolTestDebugTrue@f65a5fa
2012-10-31 14:00:24,281 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@5a73c7fb
2012-10-31 14:00:24,281 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@674e5e21org.openscience.cdk.tools.LoggingToolTestDebugTrue@674e5e21
2012-10-31 14:00:24,282 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4a05fd831
2012-10-31 14:00:24,282 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4f46c96c1.0
2012-10-31 14:00:24,282 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3051fa1dtrue
2012-10-31 14:00:24,283 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@55fb9eb3org.openscience.cdk.tools.LoggingToolTestDebugTrue@55fb9eb3org.openscience.cdk.tools.LoggingToolTestDebugTrue@55fb9eb3org.openscience.cdk.tools.LoggingToolTestDebugTrue@55fb9eb3org.openscience.cdk.tools.LoggingToolTestDebugTrue@55fb9eb3
2012-10-31 14:00:24,283 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@7a7025deorg.openscience.cdk.tools.LoggingToolTestDebugTrue@7a7025deorg.openscience.cdk.tools.LoggingToolTestDebugTrue@7a7025deorg.openscience.cdk.tools.LoggingToolTestDebugTrue@7a7025de
2012-10-31 14:00:24,284 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@58c6509eorg.openscience.cdk.tools.LoggingToolTestDebugTrue@58c6509eorg.openscience.cdk.tools.LoggingToolTestDebugTrue@58c6509e
2012-10-31 14:00:24,284 [main] FATAL org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@43d6e29a
2012-10-31 14:00:24,285 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.class.path: /Users/johnmay/workspace/github/johnmay/cdk/jar/log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/jar/vecmath1.2-1.14.jar:/Users/johnmay/workspace/github/johnmay/cdk/develjar/junit-4.5.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-annotation.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-core.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-interfaces.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test-core.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test-log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test.jar:/usr/share/java/ant-1.8.2/lib/ant-launcher.jar:/usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-junit.jar:/usr/share/ant/lib/ant-junit4.jar
2012-10-31 14:00:24,285 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.name        : Mac OS X
2012-10-31 14:00:24,285 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.version     : 10.8.2
2012-10-31 14:00:24,285 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.arch        : x86_64
2012-10-31 14:00:24,285 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.version   : 1.7.0_05
2012-10-31 14:00:24,285 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.vendor    : Oracle Corporation
2012-11-02 08:52:26,685 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@746f2a75
2012-11-02 08:52:26,715 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@7f1bfcfc1
2012-11-02 08:52:26,741 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@67e4596
2012-11-02 08:52:26,755 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4c0a7e2eorg.openscience.cdk.tools.LoggingToolTestDebugTrue@4c0a7e2e
2012-11-02 08:52:26,756 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@44e225021.0
2012-11-02 08:52:26,757 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@9234336true
2012-11-02 08:52:26,758 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6a1192e9org.openscience.cdk.tools.LoggingToolTestDebugTrue@6a1192e9org.openscience.cdk.tools.LoggingToolTestDebugTrue@6a1192e9org.openscience.cdk.tools.LoggingToolTestDebugTrue@6a1192e9org.openscience.cdk.tools.LoggingToolTestDebugTrue@6a1192e9
2012-11-02 08:52:26,758 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@27c43566org.openscience.cdk.tools.LoggingToolTestDebugTrue@27c43566org.openscience.cdk.tools.LoggingToolTestDebugTrue@27c43566org.openscience.cdk.tools.LoggingToolTestDebugTrue@27c43566
2012-11-02 08:52:26,759 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@428dcfeforg.openscience.cdk.tools.LoggingToolTestDebugTrue@428dcfeforg.openscience.cdk.tools.LoggingToolTestDebugTrue@428dcfef
2012-11-02 08:52:26,760 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - Exception: null
2012-11-02 08:52:26,762 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.lang.Exception
2012-11-02 08:52:26,762 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at org.openscience.cdk.tools.AbstractLoggingToolTest.testDebug_ExceptionWithNullMessage(AbstractLoggingToolTest.java:75)
2012-11-02 08:52:26,762 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
2012-11-02 08:52:26,762 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
2012-11-02 08:52:26,762 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
2012-11-02 08:52:26,763 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2e518924org.openscience.cdk.tools.LoggingToolTestDebugTrue@2e518924
2012-11-02 08:52:26,763 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6b02b23d1
2012-11-02 08:52:26,764 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@7e03f9ad1.0
2012-11-02 08:52:26,764 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@36fd0d7dtrue
2012-11-02 08:52:26,765 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@1f80a5bforg.openscience.cdk.tools.LoggingToolTestDebugTrue@1f80a5bforg.openscience.cdk.tools.LoggingToolTestDebugTrue@1f80a5bforg.openscience.cdk.tools.LoggingToolTestDebugTrue@1f80a5bforg.openscience.cdk.tools.LoggingToolTestDebugTrue@1f80a5bf
2012-11-02 08:52:26,766 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3701aec1org.openscience.cdk.tools.LoggingToolTestDebugTrue@3701aec1org.openscience.cdk.tools.LoggingToolTestDebugTrue@3701aec1org.openscience.cdk.tools.LoggingToolTestDebugTrue@3701aec1
2012-11-02 08:52:26,766 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4f781d1dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@4f781d1dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@4f781d1d
2012-11-02 08:52:26,766 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@56bf83ad
2012-11-02 08:52:26,767 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@375dff59org.openscience.cdk.tools.LoggingToolTestDebugTrue@375dff59
2012-11-02 08:52:26,767 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@7c2748741
2012-11-02 08:52:26,768 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@7705f7591.0
2012-11-02 08:52:26,768 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@28b2311btrue
2012-11-02 08:52:26,768 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4ab5f87corg.openscience.cdk.tools.LoggingToolTestDebugTrue@4ab5f87corg.openscience.cdk.tools.LoggingToolTestDebugTrue@4ab5f87corg.openscience.cdk.tools.LoggingToolTestDebugTrue@4ab5f87corg.openscience.cdk.tools.LoggingToolTestDebugTrue@4ab5f87c
2012-11-02 08:52:26,769 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@70ccbb35org.openscience.cdk.tools.LoggingToolTestDebugTrue@70ccbb35org.openscience.cdk.tools.LoggingToolTestDebugTrue@70ccbb35org.openscience.cdk.tools.LoggingToolTestDebugTrue@70ccbb35
2012-11-02 08:52:26,769 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@1116ce6eorg.openscience.cdk.tools.LoggingToolTestDebugTrue@1116ce6eorg.openscience.cdk.tools.LoggingToolTestDebugTrue@1116ce6e
2012-11-02 08:52:26,770 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@704aa085
2012-11-02 08:52:26,771 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3370b55borg.openscience.cdk.tools.LoggingToolTestDebugTrue@3370b55b
2012-11-02 08:52:26,771 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2c9283bf1
2012-11-02 08:52:26,771 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@470787751.0
2012-11-02 08:52:26,772 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3f4e36c1true
2012-11-02 08:52:26,772 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@27ecd95forg.openscience.cdk.tools.LoggingToolTestDebugTrue@27ecd95forg.openscience.cdk.tools.LoggingToolTestDebugTrue@27ecd95forg.openscience.cdk.tools.LoggingToolTestDebugTrue@27ecd95forg.openscience.cdk.tools.LoggingToolTestDebugTrue@27ecd95f
2012-11-02 08:52:26,773 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2eb30073org.openscience.cdk.tools.LoggingToolTestDebugTrue@2eb30073org.openscience.cdk.tools.LoggingToolTestDebugTrue@2eb30073org.openscience.cdk.tools.LoggingToolTestDebugTrue@2eb30073
2012-11-02 08:52:26,773 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@69e295f8org.openscience.cdk.tools.LoggingToolTestDebugTrue@69e295f8org.openscience.cdk.tools.LoggingToolTestDebugTrue@69e295f8
2012-11-02 08:52:26,774 [main] FATAL org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@1ae40317
2012-11-02 08:52:26,775 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.class.path: /Users/johnmay/workspace/github/johnmay/cdk/jar/log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/jar/vecmath1.2-1.14.jar:/Users/johnmay/workspace/github/johnmay/cdk/develjar/junit-4.10.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-annotation.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-core.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-interfaces.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test-core.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test-log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test.jar:/usr/share/java/ant-1.8.2/lib/ant-launcher.jar:/usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-junit.jar:/usr/share/ant/lib/ant-junit4.jar
2012-11-02 08:52:26,775 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.name        : Mac OS X
2012-11-02 08:52:26,775 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.version     : 10.8.2
2012-11-02 08:52:26,776 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.arch        : x86_64
2012-11-02 08:52:26,776 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.version   : 1.7.0_05
2012-11-02 08:52:26,776 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.vendor    : Oracle Corporation
2012-11-04 12:19:48,427 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@366815e4
2012-11-04 12:19:48,788 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6bfa2e2e1
2012-11-04 12:19:48,857 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@5da3e311
2012-11-04 12:19:48,882 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3290a11eorg.openscience.cdk.tools.LoggingToolTestDebugTrue@3290a11e
2012-11-04 12:19:48,884 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3541d2811.0
2012-11-04 12:19:48,884 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@18de9738true
2012-11-04 12:19:48,884 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3d99ea49org.openscience.cdk.tools.LoggingToolTestDebugTrue@3d99ea49org.openscience.cdk.tools.LoggingToolTestDebugTrue@3d99ea49org.openscience.cdk.tools.LoggingToolTestDebugTrue@3d99ea49org.openscience.cdk.tools.LoggingToolTestDebugTrue@3d99ea49
2012-11-04 12:19:48,885 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@43e47e37org.openscience.cdk.tools.LoggingToolTestDebugTrue@43e47e37org.openscience.cdk.tools.LoggingToolTestDebugTrue@43e47e37org.openscience.cdk.tools.LoggingToolTestDebugTrue@43e47e37
2012-11-04 12:19:48,885 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4e1a6fb3org.openscience.cdk.tools.LoggingToolTestDebugTrue@4e1a6fb3org.openscience.cdk.tools.LoggingToolTestDebugTrue@4e1a6fb3
2012-11-04 12:19:48,886 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - Exception: null
2012-11-04 12:19:48,889 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.lang.Exception
2012-11-04 12:19:48,889 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at org.openscience.cdk.tools.AbstractLoggingToolTest.testDebug_ExceptionWithNullMessage(AbstractLoggingToolTest.java:75)
2012-11-04 12:19:48,889 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
2012-11-04 12:19:48,889 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
2012-11-04 12:19:48,889 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
2012-11-04 12:19:48,890 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2bc7c6c3org.openscience.cdk.tools.LoggingToolTestDebugTrue@2bc7c6c3
2012-11-04 12:19:48,890 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@48ca42a91
2012-11-04 12:19:48,891 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@56de8a941.0
2012-11-04 12:19:48,891 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2c5c271atrue
2012-11-04 12:19:48,892 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@560b32b6org.openscience.cdk.tools.LoggingToolTestDebugTrue@560b32b6org.openscience.cdk.tools.LoggingToolTestDebugTrue@560b32b6org.openscience.cdk.tools.LoggingToolTestDebugTrue@560b32b6org.openscience.cdk.tools.LoggingToolTestDebugTrue@560b32b6
2012-11-04 12:19:48,892 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@792e76dborg.openscience.cdk.tools.LoggingToolTestDebugTrue@792e76dborg.openscience.cdk.tools.LoggingToolTestDebugTrue@792e76dborg.openscience.cdk.tools.LoggingToolTestDebugTrue@792e76db
2012-11-04 12:19:48,893 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@597d6204org.openscience.cdk.tools.LoggingToolTestDebugTrue@597d6204org.openscience.cdk.tools.LoggingToolTestDebugTrue@597d6204
2012-11-04 12:19:48,893 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@36ae2282
2012-11-04 12:19:48,893 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@625ba0d9org.openscience.cdk.tools.LoggingToolTestDebugTrue@625ba0d9
2012-11-04 12:19:48,894 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6d9d39011
2012-11-04 12:19:48,894 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6d09a8df1.0
2012-11-04 12:19:48,895 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@152e0066true
2012-11-04 12:19:48,895 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@7f1c3366org.openscience.cdk.tools.LoggingToolTestDebugTrue@7f1c3366org.openscience.cdk.tools.LoggingToolTestDebugTrue@7f1c3366org.openscience.cdk.tools.LoggingToolTestDebugTrue@7f1c3366org.openscience.cdk.tools.LoggingToolTestDebugTrue@7f1c3366
2012-11-04 12:19:48,896 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@1472aebcorg.openscience.cdk.tools.LoggingToolTestDebugTrue@1472aebcorg.openscience.cdk.tools.LoggingToolTestDebugTrue@1472aebcorg.openscience.cdk.tools.LoggingToolTestDebugTrue@1472aebc
2012-11-04 12:19:48,896 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@752dc320org.openscience.cdk.tools.LoggingToolTestDebugTrue@752dc320org.openscience.cdk.tools.LoggingToolTestDebugTrue@752dc320
2012-11-04 12:19:48,896 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@f65a5fa
2012-11-04 12:19:48,897 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@5a73c7fborg.openscience.cdk.tools.LoggingToolTestDebugTrue@5a73c7fb
2012-11-04 12:19:48,897 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@674e5e211
2012-11-04 12:19:48,897 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4a05fd831.0
2012-11-04 12:19:48,897 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4f46c96ctrue
2012-11-04 12:19:48,898 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3051fa1dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@3051fa1dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@3051fa1dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@3051fa1dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@3051fa1d
2012-11-04 12:19:48,898 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@55fb9eb3org.openscience.cdk.tools.LoggingToolTestDebugTrue@55fb9eb3org.openscience.cdk.tools.LoggingToolTestDebugTrue@55fb9eb3org.openscience.cdk.tools.LoggingToolTestDebugTrue@55fb9eb3
2012-11-04 12:19:48,899 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@7a7025deorg.openscience.cdk.tools.LoggingToolTestDebugTrue@7a7025deorg.openscience.cdk.tools.LoggingToolTestDebugTrue@7a7025de
2012-11-04 12:19:48,899 [main] FATAL org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@58c6509e
2012-11-04 12:19:48,900 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.class.path: /Users/johnmay/workspace/github/johnmay/cdk/jar/log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/jar/vecmath1.2-1.14.jar:/Users/johnmay/workspace/github/johnmay/cdk/develjar/junit-4.5.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-annotation.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-core.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-interfaces.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test-core.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test-log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test.jar:/usr/share/java/ant-1.8.2/lib/ant-launcher.jar:/usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-junit.jar:/usr/share/ant/lib/ant-junit4.jar
2012-11-04 12:19:48,900 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.name        : Mac OS X
2012-11-04 12:19:48,900 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.version     : 10.8.2
2012-11-04 12:19:48,900 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.arch        : x86_64
2012-11-04 12:19:48,901 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.version   : 1.7.0_05
2012-11-04 12:19:48,901 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.vendor    : Oracle Corporation
2012-11-04 13:43:43,573 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@94265ae
2012-11-04 13:43:43,934 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3541d2811
2012-11-04 13:43:44,028 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@1b7fc253org.openscience.cdk.tools.LoggingToolTestDebugTrue@1b7fc253
2012-11-04 13:43:44,030 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@60aee53f1.0
2012-11-04 13:43:44,030 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4e1a6fb3true
2012-11-04 13:43:44,031 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@299b78d4org.openscience.cdk.tools.LoggingToolTestDebugTrue@299b78d4org.openscience.cdk.tools.LoggingToolTestDebugTrue@299b78d4org.openscience.cdk.tools.LoggingToolTestDebugTrue@299b78d4org.openscience.cdk.tools.LoggingToolTestDebugTrue@299b78d4
2012-11-04 13:43:44,031 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@1e19bba3org.openscience.cdk.tools.LoggingToolTestDebugTrue@1e19bba3org.openscience.cdk.tools.LoggingToolTestDebugTrue@1e19bba3org.openscience.cdk.tools.LoggingToolTestDebugTrue@1e19bba3
2012-11-04 13:43:44,032 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2b6dd9c5org.openscience.cdk.tools.LoggingToolTestDebugTrue@2b6dd9c5org.openscience.cdk.tools.LoggingToolTestDebugTrue@2b6dd9c5
2012-11-04 13:43:44,032 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - Exception: null
2012-11-04 13:43:44,034 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.lang.Exception
2012-11-04 13:43:44,034 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at org.openscience.cdk.tools.AbstractLoggingToolTest.testDebug_ExceptionWithNullMessage(AbstractLoggingToolTest.java:75)
2012-11-04 13:43:44,034 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
2012-11-04 13:43:44,035 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
2012-11-04 13:43:44,035 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
2012-11-04 13:43:44,036 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2c5c271a
2012-11-04 13:43:44,037 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@560b32b6org.openscience.cdk.tools.LoggingToolTestDebugTrue@560b32b6
2012-11-04 13:43:44,038 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@792e76db1
2012-11-04 13:43:44,070 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@597d62041.0
2012-11-04 13:43:44,070 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@36ae2282true
2012-11-04 13:43:44,071 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@625ba0d9org.openscience.cdk.tools.LoggingToolTestDebugTrue@625ba0d9org.openscience.cdk.tools.LoggingToolTestDebugTrue@625ba0d9org.openscience.cdk.tools.LoggingToolTestDebugTrue@625ba0d9org.openscience.cdk.tools.LoggingToolTestDebugTrue@625ba0d9
2012-11-04 13:43:44,083 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6d9d3901org.openscience.cdk.tools.LoggingToolTestDebugTrue@6d9d3901org.openscience.cdk.tools.LoggingToolTestDebugTrue@6d9d3901org.openscience.cdk.tools.LoggingToolTestDebugTrue@6d9d3901
2012-11-04 13:43:44,084 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6d09a8dforg.openscience.cdk.tools.LoggingToolTestDebugTrue@6d09a8dforg.openscience.cdk.tools.LoggingToolTestDebugTrue@6d09a8df
2012-11-04 13:43:44,084 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@152e0066
2012-11-04 13:43:44,096 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@7f1c3366org.openscience.cdk.tools.LoggingToolTestDebugTrue@7f1c3366
2012-11-04 13:43:44,096 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@1472aebc1
2012-11-04 13:43:44,097 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@752dc3201.0
2012-11-04 13:43:44,097 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@f65a5fatrue
2012-11-04 13:43:44,109 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@5a73c7fborg.openscience.cdk.tools.LoggingToolTestDebugTrue@5a73c7fborg.openscience.cdk.tools.LoggingToolTestDebugTrue@5a73c7fborg.openscience.cdk.tools.LoggingToolTestDebugTrue@5a73c7fborg.openscience.cdk.tools.LoggingToolTestDebugTrue@5a73c7fb
2012-11-04 13:43:44,109 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@674e5e21org.openscience.cdk.tools.LoggingToolTestDebugTrue@674e5e21org.openscience.cdk.tools.LoggingToolTestDebugTrue@674e5e21org.openscience.cdk.tools.LoggingToolTestDebugTrue@674e5e21
2012-11-04 13:43:44,117 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4a05fd83org.openscience.cdk.tools.LoggingToolTestDebugTrue@4a05fd83org.openscience.cdk.tools.LoggingToolTestDebugTrue@4a05fd83
2012-11-04 13:43:44,118 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4f46c96c
2012-11-04 13:43:44,127 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3051fa1dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@3051fa1d
2012-11-04 13:43:44,128 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@55fb9eb31
2012-11-04 13:43:44,134 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@7a7025de1.0
2012-11-04 13:43:44,134 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@58c6509etrue
2012-11-04 13:43:44,134 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@43d6e29aorg.openscience.cdk.tools.LoggingToolTestDebugTrue@43d6e29aorg.openscience.cdk.tools.LoggingToolTestDebugTrue@43d6e29aorg.openscience.cdk.tools.LoggingToolTestDebugTrue@43d6e29aorg.openscience.cdk.tools.LoggingToolTestDebugTrue@43d6e29a
2012-11-04 13:43:44,135 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@50b70f41org.openscience.cdk.tools.LoggingToolTestDebugTrue@50b70f41org.openscience.cdk.tools.LoggingToolTestDebugTrue@50b70f41org.openscience.cdk.tools.LoggingToolTestDebugTrue@50b70f41
2012-11-04 13:43:44,145 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@224a9dcdorg.openscience.cdk.tools.LoggingToolTestDebugTrue@224a9dcdorg.openscience.cdk.tools.LoggingToolTestDebugTrue@224a9dcd
2012-11-04 13:43:44,146 [main] FATAL org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@50be0f51
2012-11-04 13:43:44,146 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.class.path: /Users/johnmay/workspace/github/johnmay/cdk/jar/log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/jar/vecmath1.2-1.14.jar:/Users/johnmay/workspace/github/johnmay/cdk/develjar/junit-4.5.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-annotation.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-core.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-interfaces.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test-core.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test-log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test.jar:/usr/share/java/ant-1.8.2/lib/ant-launcher.jar:/usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-junit.jar:/usr/share/ant/lib/ant-junit4.jar
2012-11-04 13:43:44,147 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.name        : Mac OS X
2012-11-04 13:43:44,147 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.version     : 10.8.2
2012-11-04 13:43:44,147 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.arch        : x86_64
2012-11-04 13:43:44,147 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.version   : 1.7.0_05
2012-11-04 13:43:44,147 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.vendor    : Oracle Corporation
2012-11-04 18:58:52,358 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@94265ae
2012-11-04 18:58:52,446 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3541d2811
2012-11-04 18:58:52,468 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@74632e77org.openscience.cdk.tools.LoggingToolTestDebugTrue@74632e77
2012-11-04 18:58:52,470 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@1b7fc2531.0
2012-11-04 18:58:52,471 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@43e47e37true
2012-11-04 18:58:52,472 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4e1a6fb3org.openscience.cdk.tools.LoggingToolTestDebugTrue@4e1a6fb3org.openscience.cdk.tools.LoggingToolTestDebugTrue@4e1a6fb3org.openscience.cdk.tools.LoggingToolTestDebugTrue@4e1a6fb3org.openscience.cdk.tools.LoggingToolTestDebugTrue@4e1a6fb3
2012-11-04 18:58:52,472 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@299b78d4org.openscience.cdk.tools.LoggingToolTestDebugTrue@299b78d4org.openscience.cdk.tools.LoggingToolTestDebugTrue@299b78d4org.openscience.cdk.tools.LoggingToolTestDebugTrue@299b78d4
2012-11-04 18:58:52,473 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@1e19bba3org.openscience.cdk.tools.LoggingToolTestDebugTrue@1e19bba3org.openscience.cdk.tools.LoggingToolTestDebugTrue@1e19bba3
2012-11-04 18:58:52,473 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - Exception: null
2012-11-04 18:58:52,476 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.lang.Exception
2012-11-04 18:58:52,476 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at org.openscience.cdk.tools.AbstractLoggingToolTest.testDebug_ExceptionWithNullMessage(AbstractLoggingToolTest.java:75)
2012-11-04 18:58:52,476 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
2012-11-04 18:58:52,476 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
2012-11-04 18:58:52,476 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
2012-11-04 18:58:52,484 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@56de8a94
2012-11-04 18:58:52,485 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2c5c271aorg.openscience.cdk.tools.LoggingToolTestDebugTrue@2c5c271a
2012-11-04 18:58:52,485 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@560b32b61
2012-11-04 18:58:52,486 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@792e76db1.0
2012-11-04 18:58:52,486 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@597d6204true
2012-11-04 18:58:52,486 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@36ae2282org.openscience.cdk.tools.LoggingToolTestDebugTrue@36ae2282org.openscience.cdk.tools.LoggingToolTestDebugTrue@36ae2282org.openscience.cdk.tools.LoggingToolTestDebugTrue@36ae2282org.openscience.cdk.tools.LoggingToolTestDebugTrue@36ae2282
2012-11-04 18:58:52,487 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@625ba0d9org.openscience.cdk.tools.LoggingToolTestDebugTrue@625ba0d9org.openscience.cdk.tools.LoggingToolTestDebugTrue@625ba0d9org.openscience.cdk.tools.LoggingToolTestDebugTrue@625ba0d9
2012-11-04 18:58:52,487 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6d9d3901org.openscience.cdk.tools.LoggingToolTestDebugTrue@6d9d3901org.openscience.cdk.tools.LoggingToolTestDebugTrue@6d9d3901
2012-11-04 18:58:52,487 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6d09a8df
2012-11-04 18:58:52,488 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@152e0066org.openscience.cdk.tools.LoggingToolTestDebugTrue@152e0066
2012-11-04 18:58:52,488 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@7f1c33661
2012-11-04 18:58:52,488 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@1472aebc1.0
2012-11-04 18:58:52,489 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@752dc320true
2012-11-04 18:58:52,489 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@f65a5faorg.openscience.cdk.tools.LoggingToolTestDebugTrue@f65a5faorg.openscience.cdk.tools.LoggingToolTestDebugTrue@f65a5faorg.openscience.cdk.tools.LoggingToolTestDebugTrue@f65a5faorg.openscience.cdk.tools.LoggingToolTestDebugTrue@f65a5fa
2012-11-04 18:58:52,489 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@5a73c7fborg.openscience.cdk.tools.LoggingToolTestDebugTrue@5a73c7fborg.openscience.cdk.tools.LoggingToolTestDebugTrue@5a73c7fborg.openscience.cdk.tools.LoggingToolTestDebugTrue@5a73c7fb
2012-11-04 18:58:52,490 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@674e5e21org.openscience.cdk.tools.LoggingToolTestDebugTrue@674e5e21org.openscience.cdk.tools.LoggingToolTestDebugTrue@674e5e21
2012-11-04 18:58:52,490 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4a05fd83
2012-11-04 18:58:52,490 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4f46c96corg.openscience.cdk.tools.LoggingToolTestDebugTrue@4f46c96c
2012-11-04 18:58:52,491 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3051fa1d1
2012-11-04 18:58:52,491 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@55fb9eb31.0
2012-11-04 18:58:52,492 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@7a7025detrue
2012-11-04 18:58:52,492 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@58c6509eorg.openscience.cdk.tools.LoggingToolTestDebugTrue@58c6509eorg.openscience.cdk.tools.LoggingToolTestDebugTrue@58c6509eorg.openscience.cdk.tools.LoggingToolTestDebugTrue@58c6509eorg.openscience.cdk.tools.LoggingToolTestDebugTrue@58c6509e
2012-11-04 18:58:52,492 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@43d6e29aorg.openscience.cdk.tools.LoggingToolTestDebugTrue@43d6e29aorg.openscience.cdk.tools.LoggingToolTestDebugTrue@43d6e29aorg.openscience.cdk.tools.LoggingToolTestDebugTrue@43d6e29a
2012-11-04 18:58:52,493 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@50b70f41org.openscience.cdk.tools.LoggingToolTestDebugTrue@50b70f41org.openscience.cdk.tools.LoggingToolTestDebugTrue@50b70f41
2012-11-04 18:58:52,493 [main] FATAL org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@224a9dcd
2012-11-04 18:58:52,494 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.class.path: /Users/johnmay/workspace/github/johnmay/cdk/jar/log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/jar/vecmath1.2-1.14.jar:/Users/johnmay/workspace/github/johnmay/cdk/develjar/junit-4.5.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-annotation.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-core.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-interfaces.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test-core.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test-log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test.jar:/usr/share/java/ant-1.8.2/lib/ant-launcher.jar:/usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-junit.jar:/usr/share/ant/lib/ant-junit4.jar
2012-11-04 18:58:52,494 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.name        : Mac OS X
2012-11-04 18:58:52,494 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.version     : 10.8.2
2012-11-04 18:58:52,494 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.arch        : x86_64
2012-11-04 18:58:52,494 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.version   : 1.7.0_05
2012-11-04 18:58:52,494 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.vendor    : Oracle Corporation
2012-11-09 11:47:08,966 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4b11a903
2012-11-09 11:47:09,266 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@44e225021
2012-11-09 11:47:09,341 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@5aebc9a2
2012-11-09 11:47:09,377 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2e02d950org.openscience.cdk.tools.LoggingToolTestDebugTrue@2e02d950
2012-11-09 11:47:09,402 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3d092ac91.0
2012-11-09 11:47:09,415 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@428dcfeftrue
2012-11-09 11:47:09,424 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6c4e760borg.openscience.cdk.tools.LoggingToolTestDebugTrue@6c4e760borg.openscience.cdk.tools.LoggingToolTestDebugTrue@6c4e760borg.openscience.cdk.tools.LoggingToolTestDebugTrue@6c4e760borg.openscience.cdk.tools.LoggingToolTestDebugTrue@6c4e760b
2012-11-09 11:47:09,436 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@132803baorg.openscience.cdk.tools.LoggingToolTestDebugTrue@132803baorg.openscience.cdk.tools.LoggingToolTestDebugTrue@132803baorg.openscience.cdk.tools.LoggingToolTestDebugTrue@132803ba
2012-11-09 11:47:09,437 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@280cb229org.openscience.cdk.tools.LoggingToolTestDebugTrue@280cb229org.openscience.cdk.tools.LoggingToolTestDebugTrue@280cb229
2012-11-09 11:47:09,476 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - Exception: null
2012-11-09 11:47:09,479 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.lang.Exception
2012-11-09 11:47:09,479 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at org.openscience.cdk.tools.AbstractLoggingToolTest.testDebug_ExceptionWithNullMessage(AbstractLoggingToolTest.java:75)
2012-11-09 11:47:09,479 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
2012-11-09 11:47:09,479 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
2012-11-09 11:47:09,479 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - 	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
2012-11-09 11:47:09,480 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@36fd0d7dorg.openscience.cdk.tools.LoggingToolTestDebugTrue@36fd0d7d
2012-11-09 11:47:09,480 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@1f80a5bf1
2012-11-09 11:47:09,481 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3701aec11.0
2012-11-09 11:47:09,481 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4f781d1dtrue
2012-11-09 11:47:09,482 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@56bf83adorg.openscience.cdk.tools.LoggingToolTestDebugTrue@56bf83adorg.openscience.cdk.tools.LoggingToolTestDebugTrue@56bf83adorg.openscience.cdk.tools.LoggingToolTestDebugTrue@56bf83adorg.openscience.cdk.tools.LoggingToolTestDebugTrue@56bf83ad
2012-11-09 11:47:09,483 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@375dff59org.openscience.cdk.tools.LoggingToolTestDebugTrue@375dff59org.openscience.cdk.tools.LoggingToolTestDebugTrue@375dff59org.openscience.cdk.tools.LoggingToolTestDebugTrue@375dff59
2012-11-09 11:47:09,483 [main] ERROR org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@7c274874org.openscience.cdk.tools.LoggingToolTestDebugTrue@7c274874org.openscience.cdk.tools.LoggingToolTestDebugTrue@7c274874
2012-11-09 11:47:09,484 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@7705f759
2012-11-09 11:47:09,484 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@28b2311borg.openscience.cdk.tools.LoggingToolTestDebugTrue@28b2311b
2012-11-09 11:47:09,485 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@4ab5f87c1
2012-11-09 11:47:09,485 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@70ccbb351.0
2012-11-09 11:47:09,486 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@1116ce6etrue
2012-11-09 11:47:09,487 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@704aa085org.openscience.cdk.tools.LoggingToolTestDebugTrue@704aa085org.openscience.cdk.tools.LoggingToolTestDebugTrue@704aa085org.openscience.cdk.tools.LoggingToolTestDebugTrue@704aa085org.openscience.cdk.tools.LoggingToolTestDebugTrue@704aa085
2012-11-09 11:47:09,487 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3370b55borg.openscience.cdk.tools.LoggingToolTestDebugTrue@3370b55borg.openscience.cdk.tools.LoggingToolTestDebugTrue@3370b55borg.openscience.cdk.tools.LoggingToolTestDebugTrue@3370b55b
2012-11-09 11:47:09,488 [main] WARN  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2c9283bforg.openscience.cdk.tools.LoggingToolTestDebugTrue@2c9283bforg.openscience.cdk.tools.LoggingToolTestDebugTrue@2c9283bf
2012-11-09 11:47:09,488 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@47078775
2012-11-09 11:47:09,489 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@3f4e36c1org.openscience.cdk.tools.LoggingToolTestDebugTrue@3f4e36c1
2012-11-09 11:47:09,489 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@27ecd95f1
2012-11-09 11:47:09,490 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@2eb300731.0
2012-11-09 11:47:09,490 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@69e295f8true
2012-11-09 11:47:09,491 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@1ae40317org.openscience.cdk.tools.LoggingToolTestDebugTrue@1ae40317org.openscience.cdk.tools.LoggingToolTestDebugTrue@1ae40317org.openscience.cdk.tools.LoggingToolTestDebugTrue@1ae40317org.openscience.cdk.tools.LoggingToolTestDebugTrue@1ae40317
2012-11-09 11:47:09,491 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@6f86e8cborg.openscience.cdk.tools.LoggingToolTestDebugTrue@6f86e8cborg.openscience.cdk.tools.LoggingToolTestDebugTrue@6f86e8cborg.openscience.cdk.tools.LoggingToolTestDebugTrue@6f86e8cb
2012-11-09 11:47:09,492 [main] INFO  org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@21da0a1org.openscience.cdk.tools.LoggingToolTestDebugTrue@21da0a1org.openscience.cdk.tools.LoggingToolTestDebugTrue@21da0a1
2012-11-09 11:47:09,492 [main] FATAL org.openscience.cdk.tools.LoggingToolTestDebugTrue - org.openscience.cdk.tools.LoggingToolTestDebugTrue@671cab1c
2012-11-09 11:47:09,493 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.class.path: /Users/johnmay/workspace/github/johnmay/cdk/jar/log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/jar/vecmath1.2-1.14.jar:/Users/johnmay/workspace/github/johnmay/cdk/develjar/junit-4.10.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-annotation.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-core.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-interfaces.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test-core.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test-log4j.jar:/Users/johnmay/workspace/github/johnmay/cdk/dist/jar/cdk-test.jar:/usr/share/java/ant-1.8.2/lib/ant-launcher.jar:/usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-junit.jar:/usr/share/ant/lib/ant-junit4.jar
2012-11-09 11:47:09,494 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.name        : Mac OS X
2012-11-09 11:47:09,494 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.version     : 10.8.2
2012-11-09 11:47:09,494 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - os.arch        : x86_64
2012-11-09 11:47:09,494 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.version   : 1.7.0_05
2012-11-09 11:47:09,494 [main] DEBUG org.openscience.cdk.tools.LoggingToolTestDebugTrue - java.vendor    : Oracle Corporation
CHANGELOG
---------
This changelog is automatically generated from the:

  git log --pretty=format:"* %s (%aN <%ae>)" --no-merges <LAST-TAG>..HEAD >> changelog.txt

1.3.0
-----------
* Removed old changelog files (Egon Willighagen <egonw@users.sourceforge.net>)
* Capability to read and write reaction properties information. Added theirs corresponding tests (Miguel Rojas Cherto <miguelrojasch@yahoo.es>)
* Fixed serialization of IAtom's with null formal charge to not cause NullPointerExceptions (Egon Willighagen <egonw@users.sourceforge.net>)
* Added unit test for serialization of null formal charges into the MDL molfile format (which currently fails) (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed a typo from the previous merge (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Updated Javadocs for SMARTS query tool to indicate unsupported features (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Cleaned up source file to remove spurious line endings (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Bumped version number (Egon Willighagen <egonw@users.sourceforge.net>)
* The formal charge of the IAtomcontainer is transfered to IMolecularFormula (Miguel Rojas Cherto <miguelrojasch@yahoo.es>)
* Fixed bug 2787332 The old bond array in the gasteiger charge calculation was set to the wrong size (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Updated to fix bug 2788357 SMARTSQueryTool now catches TokenMgrError in the constructor and throws a CDKException. Also added unit test to check for this (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Added new taglet to process cdk.githash tag and link Javadocs to sources in Git repo (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Updated cdk.svnrev tags to cdk.githash tags (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Bug_2787332. Added test for the Triclosan molecule (InChI=1S/C12H7Cl3O2/c13-7-1-3-11(9(15)5-7)17-12-4-2-8(14)6-10(12)16/h1-6,1 6H) the IPMolecularLearningDescriptor caluclation fails with java.lang.ArrayIndexOutOfBoundsException: 24. (Miguel Rojas Cherto <miguelrojasch@yahoo.es>)
* Removed obsolete renderer code: either use cdk-1.0.x or jchempaint-primary (Egon Willighagen <egonw@users.sourceforge.net>)
* Added test for bug 2786624 in the parser test suite (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Added links to PMD pages (Egon Willighagen <egonw@users.sourceforge.net>)
* Added link to JUnit stats (Egon Willighagen <egonw@users.sourceforge.net>)
* Added list of classes in the module, with links to Nightly@Pele (Egon Willighagen <egonw@users.sourceforge.net>)
* Added set up for creating module HTML pages (Egon Willighagen <egonw@users.sourceforge.net>)
* Added set up for creating module HTML pages (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed links. Suboptimal, as the path is still hardcoded to a single Nightly instance, but we do not have the XML framework yet to summarize things over all Nightlies (running different JDKs, OSs, etc) (Egon Willighagen <egonw@users.sourceforge.net>)
* Updated version number (Egon Willighagen <egonw@users.sourceforge.net>)
* Added test to ensure IAtomContainers are not sneaked in via IMoleculeSet.add(IAtomContainerSet) (Egon Willighagen <egonw@users.sourceforge.net>)
* Overwritten addAtomContainer(IAtomContainer, double) too, to throw an IllegalArgumentException when a non-IMolecule is passed (Egon Willighagen <egonw@users.sourceforge.net>)
* Now throws an IllegalArgumentException when it is tried to store an IAtomContainer which is not an IMolecule (Egon Willighagen <egonw@users.sourceforge.net>)
* Added unit test for #2784182 (Egon Willighagen <egonw@users.sourceforge.net>)
* new test with reserpine (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* Added taglets for threading safety (Egon Willighagen <egonw@users.sourceforge.net>)
* With one atom or less, we define it to be connected, as there is no partitioning needed (fixes #2784209, NullPointerException on IAtomContainer with no atoms) (Egon Willighagen <egonw@users.sourceforge.net>)
* Added unit test for bug #2784209 which currently fails (Egon Willighagen <egonw@users.sourceforge.net>)
* More removal of explicit org.openscience.cdk package names: throws clauses (Egon Willighagen <egonw@users.sourceforge.net>)
* More removal of explicit org.openscience.cdk package names (Egon Willighagen <egonw@users.sourceforge.net>)
* More removal of explicit org.openscience.cdk package names: for new org.openscience.cdk.Foo() calls (Egon Willighagen <egonw@users.sourceforge.net>)
* Removed explicit org.openscience.cdk.interfaces packages names (fixes #2783549) (Egon Willighagen <egonw@users.sourceforge.net>)
* Removed explicit package names, in favor of imports, for org.openscience.cdk in the datadebug module (fixes #2783549) (Egon Willighagen <egonw@users.sourceforge.net>)
* Removed explicit package names, in favor of imports, for org.openscience.cdk in the data module (fixes #2783549) (Egon Willighagen <egonw@users.sourceforge.net>)
* breakout of recursion option on AllRingsFinder (mark_rynbeek <markr@ebi.ac.uk>)
* Extraction from the string elemental formula the charge. (Miguel Rojas Cherto <miguelrojasch@yahoo.es>)
* Extraction from the string elemental formula the charge. (Miguel Rojas Cherto <miguelrojasch@yahoo.es>)
* Controller of the mass when it is out of the range (Miguel Rojas Cherto <miguelrojasch@yahoo.es>)
* Updated source and test to address review issues. Updated typos in Javadocs and added link to AllRingFinder. Move instatiation of SMARTS matcher to constructor. The element count array is now of length 120. Updated JUnit test to remove superflous prints and updated copyright (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Moved the pubchem fingerprinter to the fingerprinter module, since it needs SMARTS which is not a dependency of the standard module (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Added more test cases comparing our FP's with those provided by Pubchem (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Updated Javadocs, cleaned up some tests (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Added test for benzene (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Updated SMARTS patterns to use H count specifications rather than explicit H matches (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Initial version of Pubchem fingerprints based on the public domain NCGC code. Includes unit tests (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Updated to intelligently add H's to a PLANAR3 N, fixes bug 2781199 (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Added test case for bug 2781199 (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* calls to CDKException constructor made within a catch block now include the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* calls to CDKException constructor made within a catch block now include the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* calls to CDKException constructor made within a catch block now include the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* calls to CDKException constructor made within a catch block now include the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* calls to CDKException constructor made within a catch block now include the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* calls to CDKException constructor made within a catch block now include the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* calls to CDKException constructor made within a catch block now include the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* calls to CDKException constructor made within a catch block now include the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* calls to CDKException constructor made within a catch block now include the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* calls to CDKException constructor made within a catch block now includes the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* calls to CDKException constructor made within a catch block now includes the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* calls to CDKException constructor made within a catch block now includes the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* calls to CDKException constructor made within a catch block now includes the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* calls to CDKException constructor made within a catch block now includes the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* Updated unit tests to employ equals tests. Fixed Javadocs. Address comments wrt the original patch (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* removed needless white space (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Refactored to provide a query container specifically for pharmacophore queries. (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Updated the toString tests (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Added test methods for the new toString methods. Also added test method annotations (Rajarshi Guha <rajarshi.guha@gmail.com>)
* provided toString methods for the pcore query classes (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Added a unit test to ensure SD fields are read for all molecules (Egon Willighagen <egonw@users.sourceforge.net>)
* Added unit test for bug 1579235, which checks for aromaticity in indolizine (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Updated code to use 1.5 idioms and remove use of Iterator (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Added links to PMD pages (Egon Willighagen <egonw@users.sourceforge.net>)
* Added link to JUnit stats (Egon Willighagen <egonw@users.sourceforge.net>)
* Added list of classes in the module, with links to Nightly@Pele (Egon Willighagen <egonw@users.sourceforge.net>)
* Added set up for creating module HTML pages (Egon Willighagen <egonw@users.sourceforge.net>)
* Added set up for creating module HTML pages (Egon Willighagen <egonw@users.sourceforge.net>)
* Updated build system to take into account non public classes as well. Also updated ChiIndexUtils to be package private (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* split up test (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* new files (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* more tests for cml reading (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* Added unit test for #1848591: incorrect Murcko framework (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed cast, remove redundant full package name (Egon Willighagen <egonw@users.sourceforge.net>)
* Added unit test for #2692107 (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed typo: missing 's' (Egon Willighagen <egonw@users.sourceforge.net>)
* Added unit test for #1848591: incorrect Murcko framework (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed cast, remove redundant full package name (Egon Willighagen <egonw@users.sourceforge.net>)
* Added unit test for #2692107 (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed typo: missing 's' (Egon Willighagen <egonw@users.sourceforge.net>)
* Use the proper folder name, including the CDK version (Egon Willighagen <egonw@users.sourceforge.net>)
* 1.2.1 release being prepared (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed bug 2714283, which properly throws an exception when rings are not closed properly. If a ring is not closed with the appropriate ring number, InvalidSmilesException is thrown. Matches Daylight behavior (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Fixed bug 2729120 and added unit test (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Updated comment to fix bug 2768643. (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Partial fix for bug 2719237. Made getBondOrderSum static, added unit test for it (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Typo: proteinl -> protein (Egon Willighagen <egonw@users.sourceforge.net>)
* Made class public, to unbreak adding it to the build/*.javafiles (Egon Willighagen <egonw@users.sourceforge.net>)
* Partially fixed SMARTS matching for R0. Updated target molecule initialization to explicitly (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Fixed dubious equality test. A private method was checking Double objects via reference. (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Added test method annotation. Completes coverage for data module (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Refactored ChiIndexUtils to make it package private. Cleans up public API, since it is only used by chi descriptor code. Updated all dependent classes. Moved test code (which needs to be filled in!) as well (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Code cleanup of ChiIndexUtils. Converted to 1.5 idioms (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Clean up of PathTools and added test method annotation, so that core is completely covered (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Fixed the previous commit to edit the cdk.keyword line, not the cdk.module line (Egon Willighagen <egonw@users.sourceforge.net>)
* More consistent keywords used (Egon Willighagen <egonw@users.sourceforge.net>)
* Added a test to ensure that Integer objects are compared by value rather than reference (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Added a test case to check that atom container diffs are correct when using deserialized objects (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Fixed IntegerDifference so that it actually checks the integer value rather than references of the Integer object. Fixes the problem whereby an object serialized to disk and then deserialized does not match the original object (i.e., non empty diff string) (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Applied patch #2675819 (Stefan Kuhn): Patch to add a removeReaction to reactionSet (Egon Willighagen <egonw@users.sourceforge.net>)
* Added generics (Egon Willighagen <egonw@users.sourceforge.net>)
* Added generics, one last time... Leander should work by now... (Egon Willighagen <egonw@users.sourceforge.net>)
* Use interface instead of implementation (Egon Willighagen <egonw@users.sourceforge.net>)
* Some other code cleanup (Egon Willighagen <egonw@users.sourceforge.net>)
* Added generics, here too (Egon Willighagen <egonw@users.sourceforge.net>)
* Added generics, here too (Egon Willighagen <egonw@users.sourceforge.net>)
* Use interface instead of implementation (Egon Willighagen <egonw@users.sourceforge.net>)
* Added generics (Egon Willighagen <egonw@users.sourceforge.net>)
* Added generics (Egon Willighagen <egonw@users.sourceforge.net>)
* Added generics (Egon Willighagen <egonw@users.sourceforge.net>)
* Added generics (Egon Willighagen <egonw@users.sourceforge.net>)
* Added generics (Egon Willighagen <egonw@users.sourceforge.net>)
* Removed an unused import (Egon Willighagen <egonw@users.sourceforge.net>)
* Use IAtomContainer instead of IMolecule, as the actual matching is using IAtomContainers already (fixes #2686249) (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed a ClassCastException (fixes #2685134) (Egon Willighagen <egonw@users.sourceforge.net>)
* Added source attrib to fix building the Ubuntu .deb (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed Help build system: use doclet jars in develjar/; updated for new src folder src/main; removed very outdated use of rt.jar (Egon Willighagen <egonw@users.sourceforge.net>)
* Removed libdepends include for test-ioformats, which does not actually have libdepends (Egon Willighagen <egonw@users.sourceforge.net>)
* Updated so that if a target atom has no symbol (such as pseudo atoms) the match returns false (rather than an NPE) (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Fixed proper handling of #n SMARTS querys (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Added test case for bug 2686473 (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Added note on Ant 1.7.1 required (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed a NPE source: 'null == 2' causes an exception, so first test for nullness (Egon Willighagen <egon.willighagen@gmail.com>)
* Added a missing dep (Egon Willighagen <egon.willighagen@gmail.com>)
* Correction of the solution (egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* added method to calculate the Total Mass Number given a IMolecularFormula (egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* Added copyright info (egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* Added missing dep (egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* Rearranged the order of operations and provided a useful message. Added bug annotation (egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* Updated test to check that a aromatic molecle coming from two diferent sources (kekule and aromatic SMILES) gets represented internally as the same thing. Currently does not (egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* removed "throws CDKException" from method StructureResonanceGenerator.setReactions(List<IReactionProcess> newReactionsList). And depending methods as StabilizationCharges.calculatePositive. It was producing some incoherences: org.openscience.cdk.charges.StabilizationCharges row 83: Unreachable catch block for CDKException. This exception is never thrown from the try statement body. (egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* Fixed a bunch of Javadoc errors (egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* Added method to IAtomTypeMatcher to perceive types for all atoms in the container; allowing some removal of redundant calculations, and the addition of calculation of molecular properties, like aromaticity, as used in the Sybyl atom type matcher (egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* Updated tests: findType(IAC, IAtom) cannot detect aromaticity; but findType(IAtomContainer) does, but not tested yet (egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* added a convenience constructor to smilesgenerator, improved a test to test the aromaticity behaviour (egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* Fixed copyright notice for 2009 (Egon Willighagen <egon.willighagen@gmail.com>)
* Fixed duplicate storage of layout templates, which only belong in the sdg module, not extra module too (Egon Willighagen <egon.willighagen@gmail.com>)
* used interfaces where possible and updated to 1.5 idioms (Rajarshi Guha <rguha@localhost.localdomain>)
* Updated to use interfaces where possible and cleaned up code to use 1.5 idioms (Rajarshi Guha <rguha@localhost.localdomain>)
* Added unit test for a ONS Solubility solute, which fails to be parsed when RDF. But does not fail here. (egonw <egon.willighagen@gmail.com>)
* Export the jniinchi lib (Egon Willighagen <egon.willighagen@gmail.com>)
* Fixed a few test class instantiation problems (Egon Willighagen <egon.willighagen@gmail.com>)
* Fixed constructor: wrong file format; add getClassLoader() (Egon Willighagen <egon.willighagen@gmail.com>)
* Fixed for NewCDKTestCase -> CDKTestCase renaming (Egon Willighagen <egon.willighagen@gmail.com>)
* Added all existent reaction tests in MreactionTest (miguelrojasch <miguelrojasch@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* Added dictionary which reads from a reaction-process.owl the mechanism for specific type reaction. (miguelrojasch <miguelrojasch@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* Invalid smiles string (miguelrojasch <miguelrojasch@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* Set new methods to read new schemes of the reactions dictionary (miguelrojasch <miguelrojasch@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* Added testMethod value for Junit4 (miguelrojasch <miguelrojasch@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* For each data class, also test inherited methods for super classes implementing inherited superinterfaces (Egon Willighagen <egon.willighagen@gmail.com>)

1.3.1
-----------
* Bumped version for 1.3.1 release (Egon Willighagen <egonw@users.sourceforge.net>)
* Added some extra lines, hopefully fixing the conflicts all the time (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed param name (Egon Willighagen <egonw@users.sourceforge.net>)
* Updated the makefp3d target to work with the current build system (Egon Willighagen <egonw@users.sourceforge.net>)
* Set up a branch for the 1.2.4 release (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixes bug 2898399. Updates to the SMARTS parser to handle proper matching for explicit hydrogens (including H, 1H, 2H and 3H). SMARTSQueryVisitor updated to take into account different isotopes of H.  Also updated unit tests to take into account proper H matching. Added a unit test to further check H matching. (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Added tests to match hydrogens (mark_rynbeek <markr@ebi.ac.uk>)
* Fixed junior issue 1816529: Missing Java5 generics for atomContainers() Iterator (Uli Köhler <ulikoehler@online.de>)
* Reworked the tests for bug 2898032. Updated Javadocs for smiles generator (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Added unit test to confirm and check for bug 2898032 (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Fixed junior issue 1802586: Misuse of assertTrue for tested strings (Uli Köhler <ulikoehler@online.de>)
* Made the AtomContainerPermutors IAtomContainer implementation independent (Egon Willighagen <egonw@users.sourceforge.net>)
* Updated UIT to handle single atom queries and added a unit test for bug 2888845. Also updated Javadocs to specifically note behavior of single atom queries (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Fixed the dist-large target: removed to no longer existing .libdepends after the log4j module patch (Egon Willighagen <egonw@users.sourceforge.net>)
* Implemented instantiating custom loggers; example in the unit test class (Egon Willighagen <egonw@users.sourceforge.net>)
* Added the use of the SystemOutLoggingTool as back up (Egon Willighagen <egonw@users.sourceforge.net>)
* Added a ILoggerTool implementation for STDOUT (Egon Willighagen <egonw@users.sourceforge.net>)
* Dig up and updated the copyright history (Egon Willighagen <egonw@users.sourceforge.net>)
* Factored out initialization of the tool, to allow reusing the code for other logger class names (Egon Willighagen <egonw@users.sourceforge.net>)
* Moved the log4j.jar depending LoggingTool into a separate module (Egon Willighagen <egonw@users.sourceforge.net>)
* Introduces the ILoggingTool interface and a factory so that CDK code no longer needs to depend on LoggingTool which depends on Apache's Log4j library. (Egon Willighagen <egonw@users.sourceforge.net>)
* Added generation of java source jars (Peter Odéus <peter.odeus@gmail.com>)
* Fixed matchers to allow XML without new lines (closes #2832835) (Egon Willighagen <egonw@users.sourceforge.net>)
* Added unit tests for detection of PubChem XML files. (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed matchers to allow XML without new lines (closes #2832835) (Egon Willighagen <egonw@users.sourceforge.net>)
* Added unit tests for detection of PubChem XML files. (Egon Willighagen <egonw@users.sourceforge.net>)
* Added reading of E/Z stereochemistry from double bonds in MDL V2000 molfiles. (Egon Willighagen <egon.willighagen@gmail.com>)
* A minor fix to clean up a PDMD warning (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Overwrite unit tests, because there are no change events passed around at all for the NoNotification interface implementations (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing unit tests for IChemModel event propagation for the ICrystal field (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed propagation of change events to IChemModel when modifications are made in child IChemObjects (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed unit tests: the IChemModel.setFoo(null) should actually give a change event on the listener of the IChemModel, and not after unregistering of the Foo object. (Egon Willighagen <egonw@users.sourceforge.net>)
* Synchronized with the Blue Obelisk version (Egon Willighagen <egonw@users.sourceforge.net>)
* Added unit test to the function of the new IO setting to force 2D coordinate output. (Egon Willighagen <egonw@users.sourceforge.net>)
* Added writer IO option to force writing of 2D coordinates if 3D coordinates are present too, which now are preferably outputted. (Egon Willighagen <egonw@users.sourceforge.net>)
* Added unit test to verify that if 2D and 3D coordinates are available, the 3D coordinates are outputted. (Egon Willighagen <egonw@users.sourceforge.net>)
* Changed IBond.get/setStereo() to use a IBond.Stereo enumeration instead of an int (fixes #2855850): (Egon Willighagen <egon.willighagen@gmail.com>)
* Fixed Taglets: only return HTML if the Tag is really given; the toString() method is given for all cases, not just when the tag is found (Egon Willighagen <egonw@users.sourceforge.net>)
* Added the Mannhold LogP descriptor (Egon Willighagen <egonw@users.sourceforge.net>)
* Added the Mannhold LogP descriptor to the ontology (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixeda bug which was causing various parts of the DescriptorEngine to fail - it was trying to instantiate a non-descriptor class which happens to reside in the descriptor package directory. This fix is a bit kludgy - ideally only descriptors should be in that directory (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Fixes ClassCastException when not IMolecule (Arvid Berg <goglepox@users.sourceforge.net>)
* Upgraded to PMD 2.4.5 with many bug fixes, giving more accurate error reports (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing dependency on cdk-diff, being used in one of the unit tests (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed methods names to match those in the test class (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed test method name to match the expected patters, fixing a coverage test fail (Egon Willighagen <egonw@users.sourceforge.net>)
* Removed duplicate code: MolecularFormulaTest now extends AbstractMolecularFormulaTest (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed test method annotation to point to the right method (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing @TestMethod annotation (Egon Willighagen <egonw@users.sourceforge.net>)
* Added modules that were missing from the PMD testing (Egon Willighagen <egonw@users.sourceforge.net>)
* Added modules that were missing from the doccheck testing (Egon Willighagen <egonw@users.sourceforge.net>)
* Added reference to IUPAC documentation about stereochemistry visualization. (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* Patch for bug 2843445. Aims to fix generation of NaN coordinates by SDG (mark_rynbeek <markr@ebi.ac.uk>)
* Added missing dependency introduced by the use of AbstractFingerprinterTest in test-standard. (Egon Willighagen <egonw@users.sourceforge.net>)
* Updated the unit test classes for all IFingerprinter implementations to use the new AbstractFingerprinter class; a few unit tests actually fail (Egon Willighagen <egonw@users.sourceforge.net>)
* Extracted an AbstractFingerprinterTest with unit tests that should really apply to all IFingerprinter implementations (Egon Willighagen <egonw@users.sourceforge.net>)
* Clean up of layout. (Jonathan Alversson <jonathan.alvarsson@gmail.com>)
* Fix the unit test to not give a 'input must support mark' exception on some platforms, by wrapping the InputStream in a BufferedInputStream. (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing dependencies (Egon Willighagen <egonw@users.sourceforge.net>)
* Added ioformats to modules to test (Egon Willighagen <egonw@users.sourceforge.net>)
* Use StringBuilder to aggregate the field data, which gives an huge performance boost for SD file where multiline field data is found. (Egon Willighagen <egonw@users.sourceforge.net>)
* Use StringBuilder to aggregate the field data, which gives an huge performance boost for SD file where very much field data, like the ChEBI_complete.sdf (Egon Willighagen <egonw@users.sourceforge.net>)
* Factored out steps in reading the SD file data block (Egon Willighagen <egonw@users.sourceforge.net>)
* Bumped version, to make it clear this is not the 1.2.3 release (Egon Willighagen <egonw@users.sourceforge.net>)
* Bumped version, to make it clear this is not the 1.3.0 release (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed registering on the cdk.threadnonsage tag (closes #2796362) (Egon Willighagen <egonw@users.sourceforge.net>)
* Removed obsolete pattern from old svnrev tag (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed JavaDoc to remove traces of the old svnrev Tag (Egon Willighagen <egonw@users.sourceforge.net>)
* Synchronized exception message with implementation (fixes #2844333) (Egon Willighagen <egonw@users.sourceforge.net>)
* Made class private again, per authors request (Egon Willighagen <egonw@users.sourceforge.net>)
* Any class will do, not just public, final and abstract (Egon Willighagen <egonw@users.sourceforge.net>)
* Two further compile fixes after the merge with CDK 1.2.x (Egon Willighagen <egonw@users.sourceforge.net>)
* Made the class public, to fix a compile problem introduced by the merge with CDK 1.2.x (Egon Willighagen <egonw@users.sourceforge.net>)
* Added ant task to calculate JavaNCSS code statistics (Egon Willighagen <egonw@users.sourceforge.net>)
* Added JavaNCSS 32.53 (LGPL 3.0) (Egon Willighagen <egonw@users.sourceforge.net>)
* The Pauling Electronegativity is copied in configure as well. I can't see why not copy everything we have. (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* Revert "added a test for bug 2831420": (Egon Willighagen <egonw@users.sourceforge.net>)
* Patch for bug 2843445. Aims to fix generation of NaN coordinates by SDG (mark_rynbeek <markr@ebi.ac.uk>)
* added a test for bug 2831420 (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* added a test for bug #2831420 (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* Made InChIGeneratorFactory a singleton. (jonalv <jonathan.alvarsson@gmail.com>)
* Layout. (jonalv <jonathan.alvarsson@gmail.com>)
* Added bug annotation (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* test case for bug #2846213 (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* Fixed perception of N.planar3 where N.sp2 was detected, by now taking into account the given hydrogen count. (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed perception of benzene with all single bond, but hydrogen count 1 and bonds flagged aromatic. In this case, the type is C.sp2 not C.sp3. (Egon Willighagen <egonw@users.sourceforge.net>)
* Added assertions to unit test for values being not null (Egon Willighagen <egonw@users.sourceforge.net>)
* Added two unit tests for the same problem: carbon atom types are not correctly perceived if bond order info is SINGLE only, and hydrogen count and aromaticity flag is set. (Egon Willighagen <egonw@users.sourceforge.net>)
* Moved class into a org.openscience.cdk package, which seems to work now. I'm puzzled why it did not before. Solved several unit test fails. (Egon Willighagen <egonw@users.sourceforge.net>)
* Unsealed the XOM jar to allow having the CustomSerializer (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed Javadocs error (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Fixed a wrong javadoc tag. Also removed svn tag in the SMARTS parser JJT file, replaced with git tag (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Added support for 'public enum's (Egon Willighagen <egonw@users.sourceforge.net>)
* corrected bug in bondtools.isStereo(IAtomContainer container, IAtom stereoAtom). A comparision of atom symbols in a nested loop was using the counter of the outer loop twice. Note it worked before, because there is a sort of fallback to Morgan numbers. fallback to morgan (fixes #2830287) (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* added a new test for bondtools (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* Fixed inconsistency between accepts() and write: also support writing of IAtomContainerSet and IAtomContainer as accepts() indicates (fixes #2827745) (Egon Willighagen <egonw@users.sourceforge.net>)
* General test for testing consistency between write() and accepts(), testing that all accepted IChemObject's can also be written (Egon Willighagen <egonw@users.sourceforge.net>)
* Added unit test for bug #2826961: inconsistent atom typing for two SMILES. Unit test does not show a fail, ruling out a CDK bug (Egon Willighagen <egonw@users.sourceforge.net>)
* Remove erroneous throws statement (Egon Willighagen <egonw@users.sourceforge.net>)
* Bug found calculating the exact mass given a molecular formula when it is negative charged. (Miguel Rojas Cherto <miguelrojasch@gmail.com>)
* Fixed reading of the cdk/dict/data/elements.owl database which is now in OWL (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed issue 2458210: use assertNotNull(foo) etc instead of assertTrue(foo != null). (Uli Köhler <ulikoehler@online.de>)
* Added minimum equivalents for BondManipulator.getMaximumBondOrder() methods (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixes asserts: after removal *no* change should be recorded (Egon Willighagen <egonw@users.sourceforge.net>)
* Added IO option to disable generator of XML declaration statements in the output CML. (Egon Willighagen <egonw@users.sourceforge.net>)
* Added generics, and consistified code by always returning a List<?> of the same '?'. (And some 80 chars fixes in the JavaDocs.) (Egon Willighagen <egonw@users.sourceforge.net>)
* Added unit tests to test that when a [Molecule|Reaction|Ring]Set has been removed from a ChemModel, the ChemModel should unregister as listener. (Egon Willighagen <egonw@users.sourceforge.net>)
* Added unit tests for event propagation from [Molecule|Reaction|Ring]Sets to ChemModel. (Egon Willighagen <egonw@users.sourceforge.net>)
* More testing of flags. (Egon Willighagen <egonw@users.sourceforge.net>)
* Fix for junior job id: [ 1837692 ] Test methods should throw only one Exception. (Paul Turner <paulturner@users.sourceforge.net>)
* Fixed missing imports and wrapped to 80 chars (Egon Willighagen <egonw@users.sourceforge.net>)
* Better excpetion handling in builder3d: (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)

1.3.2
-----------
* Use the new error reporting IO API
* Added a new IO API for reporting file format errors.
* A new test for canonicalLabeler. I first tried in an older checkout, where it failed, but it works in master. I think we can still put the test in, more tests are better.
* Unit test for bug #2944080
* Added the atom-atom mapping for all atom containing the reactant molecules
* Removed the bond mapping from the reaction. It will only contain atom-atom mapping functionality
* Initiating only one time the function LonePairElectronChecker
* Added getExampleReactants and getExpectedProducts method for all reaction.type test.
* The IMapping interface had a class comment which probably was a copy&paste artefact. Changed this.
* Fixed license info .meta file for JavaCC
* Removed bit which explain how to apply the LGPL to source (fixes #2926775)
* CDKHydrogenAdder should not attempt addImplicitHydrogen for pseudo atoms in an atom container
* Added unit test for adding hydrogens to IPseudoAtom, which current causes a NPE
* MDLV2000Reader throws exception for query bond types
* MDL reading and writing and stereo bond types
* Added a helper method GeometryTools.getRectangle2D() to get the space occupied by an IAtomContainer
* Reimplemented shiftContainer(IAtomContainer, Rectangle2D, Rectange2D, double) originally implemented as jchempaint-primary patch 9200bdc4d68dc8f70373a62eaec51357b680d5e6 by Stefan Kuhn: fixing the detection of overlap, and added missing unit tests
* Added IO option to allow saving aromatic SMILES
* Added missing unit testing for the SMILESWriter
* Moved Normalizer into a separate package, in reply to discussion around patch #2905749, making space for a uniform platform for structure normalization: cdk.normalize
* Attached are some more license files.
* The log4j.jar is version 1.2.15.
* More completed files attached.
* They were incomplete, as many other files still are.
* Fixed conflict in LICENSE file due to merge from cdk-1.2.x branch
* Added a QA target
* Use local PMD and JUnit reports if available
* Added option to run it on just one module
* Added info for dependencies
* Created a list, to be able to add license information
* Added missing copyright/license header
* Catch a SocketException when there is no internet
* Output where it is working on
* Removed empty lines
* Added initial license information, based on the information sent by Stefan
* [PATCH] SSSR Test
* Bucky ball test molecule
* Patch from Ulrich Bauer regarding ringsearch bauer@math.uni-goettingen.de
* Update code example in JavaDoc reflecting the current API (fixes #2914791)
* Minor fixes for the RasmolColors class.
* New classes for Rasmol color scheme
* Updated UIT matching for the single atom case so that it correctly handles queries that are plain atom containers
* Updated fingerprinter to fix bug 2819557. Updated JUnit tests to take into account new fingerprints. Also cleaned up the template extractor code and regenerated fingerprints for builder3d. Also updated the build file to properly include dependency jars for the makefp3d target
* Added a datafile entry for the standard module to store the VDW radii etc for the periodic table
* Fixed reading of SD file properties
* Added unit test for a MDL SD file with mutliple data fields
* Added unit test for data fields to allow to start with '>' (bug #2911300).
* Added testing that properties are read from test6.sdf
* Updated license info of third party libraries
* Fixed JavaDoc: added missing period at end of first sentence, removed useless @throws clause, added missing @cdk.bug tag
* Package fixing release: fixed building JavaDoc from source dist
* Added missing references file to the source dist (full and pure)
* Removed source folders of Doclets, which are not part of the release, and should not be compiled for JavaDoc generation anyway
* Removed java pkg removed by the periodic table patch from the Eclipse project classpath
* Made the unit test more informative
* Added test case for bug 2819557
* The AtomType(String) constructor is updated so that only formal charge is set to 0 as indicated in the Javadocs. All other fields are set ot UNSET. Javadocs were updated to make this explicit
* Updated canonical labeler to make use of the PeriodicTable class so that even if an input molecule was not configured we can still get a valid atomic number. This makes SMILES generation a little more robust (cf bug 2898032)
* Added OpenJavaDocCheck library (new BSD licensed) and written a custom JavaDoc checks.
* Additional constant
* added a constant for untyped atoms
* Updated to avoid use of deprecated StringBufferInputStream
* added a test for single-line inchi with several branches
* the inchi reader was written in such a way that it 1) needed a further line after the inchi=, which was not read, but needed to avoid npes 2) It could only process one branch on a level 3) it required the inchi line to start with INChI, newer versions require InChI= All this has been fixed
* Start angles should be different for different size rings
* Sorting of containers in a AtomContainerSet
* Added new test class to the module suite
* New comparators for AtomContainer
* Refactored periodic table element to be a standalone class, so independent of the data module. This is OK, since the class is really just a struct to hold PT data for a given element. As opposed to being a basis of an elemental representation. Also, this class is entirely private to this package, so it doesn't really matter what it is. Updated associated unit tests
* Some minor code clean up
* Updated to remove Symbols and all associated tests and usages. Replaced with PeriodicTable
* Moved PT related tests to their own package. Updated test suites
* Added method (and test) to get symbol from atomic number and also get element counts
* Updated module membership. Also made everything bu tmain PT class package private
* Moved PT related classes into their own package
* Added a test to MoleculeSetTest, which tests that the clone() does not change the MoleculeSEt
* Added some extra lines, hopefully fixing the conflicts all the time

1.3.3
---------
* Updated JavaDoc to explicitly state that g2 must be a substructure of g1 (Egon Willighagen <egonw@users.sourceforge.net>)
* More unit tests for the MCSS problem in bug report 2944080. (Egon Willighagen <egon.willighagen@gmail.com>)
* Simplified the code using the new 'T read(T)' API used in MDLV2000Reader as defined by the ISimpleChemObjectReader (Egon Willighagen <egonw@users.sourceforge.net>)
* Updated for the new generics 'T read(T)' API in ISimpleChemObjectReader. (Egon Willighagen <egonw@users.sourceforge.net>)
* Introduced generics allowing the return type to be identical to the passed argument. It does require implementing classes to be updated with the new API too. (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing dependency, fixing the unit test reading a file from data/ (Egon Willighagen <egonw@users.sourceforge.net>)
* added working implementations for PartialFilledStructureMerger and CrossoverMachine (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* added working implementations for PartialFilledStructureMerger and CrossoverMachine (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* tests for crossover machine and PartialFilledStructureMerger (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* tests for crossover machine and PartialFilledStructureMerger (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* added dependency (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* Fixed use of global isRef variable, to make it threading-safe (Egon Willighagen <egonw@users.sourceforge.net>)
* Added control 'isref' creating a CML with reaction and listmolecules (Miguel Rojas Cherto <miguelrojasch@gmail.com>)
* Removed unused import (Egon Willighagen <egonw@users.sourceforge.net>)
* Removed last bits of implementation details from the API: now uses List<> instead of ArrayList<> (Egon Willighagen <egonw@users.sourceforge.net>)
* Removed output to STDOUT (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed some spelling errors and added JavaDoc links (Egon Willighagen <egonw@users.sourceforge.net>)
* Synchronized behavior with the MDLV2000Reader (addressing bug #2942196) (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing @cdk.bug tag and used interfaces where possible (Egon Willighagen <egonw@users.sourceforge.net>)
* Added a test case for GeometryTools.has2DCoordinatesNew where a mol file has a single atom with 0,0,0 as coordinate. This is not considered a 2d coordinate right now, but in a way it is one. (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* added a method to make cyclopentane to MoleculeFactory (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* Added missing unit test for getClosestAtom(double, double, IAtomContainer, IAtom) (Egon Willighagen <egon.willighagen@gmail.com>)
* Improve performance: to find the closest atom, we do can simply use the squared distances. The smaller than relation is equivalent in normal and squared distance space. (Egon Willighagen <egon.willighagen@gmail.com>)
* Added a unit test to see of the calculated bond length average includes bonds in all IAtomContainer's (Egon Willighagen <egon.willighagen@gmail.com>)
* Added second test for getClosestAtom(), now with more than two atoms (Egon Willighagen <egon.willighagen@gmail.com>)
* Added E and Z as allowed configurations (Egon Willighagen <egon.willighagen@gmail.com>)
* Added UP_OR_DOWN_INVERTED, which is the equivalent of UP_OR_DOWN but with a different stereocenter (Egon Willighagen <egon.willighagen@gmail.com>)
* Extended JavaDoc, explaining how these IBond.Stereo types define the stereocenter, and indicating for each type explicitly which atom is the stereocenter (Egon Willighagen <egon.willighagen@gmail.com>)
* Added convenience method to find the closest atom to a given point. (shk3 <shk3@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* unified the layout at cleanup and loading of molecules (Stefan Kuhn <shk3@users.sf.net>)
* Reimplemented shiftReactionVertical(IReaction, Rectangle2D, Rectange2D, double) originally implemented as jchempaint-primary patch 1cab8c3c9350ada9b1d054712189720c865e502a by Stefan Kuhn: now reuses other methods (fixing the movement of the reaction agents), and added missing unit tests (Egon Willighagen <egon.willighagen@gmail.com>)
* Added a getBondLengthAverage(IReaction reaction) method, a rewritten version of 1cab8c3c9350ada9b1d054712189720c865e502a by Stefan Kuhn, and the matching unit test (Egon Willighagen <egon.willighagen@gmail.com>)
* Add a GeometryTools method to get atoms near another atom (Gilleain). Added unit test for the new method (Egon). (gilleain <gilleain@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* Moved IAtomColorer and ICDKChangeListener from the standard module to the interfaces module (egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* Updated to include the float and binary information found in PubChem (Brian Gilman <gilmanb@gmail.com>)
* Ant has a release 1.8 that should be accepted in build.xml (Mark Rynbeek <markr@localhost.localdomain>)
* Master is open for patches... (Egon Willighagen <egonw@users.sourceforge.net>)

1.3.4
--------
* RGroup queries (Mark Rynbeek <markr@localhost.localdomain>)
* Junit test data for RGroup queries (Mark Rynbeek <markr@localhost.localdomain>)
* R-group query changes for MDL reading/writing (Mark Rynbeek <markr@localhost.localdomain>)
* Fixed taking into account larger ring systems when one ring is in itself already aromatic (fixes #2976054) (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed cloning of properties with null values by always using HashMap (fixes #2975800) (Egon Willighagen <egonw@users.sourceforge.net>)
* Added four and six coordinate neutral platinum atom types. (Egon Willighagen <egonw@users.sourceforge.net>)
* Shortened the SMILES to only contain the aromatic atoms, allowing a foreach loop: replaced for-loop by a foreach-loop, solving also the not testing all atoms in the testAromaticty() test. (Egon Willighagen <egonw@users.sourceforge.net>)
* Added InChI, and link to existing pyrolle test, using a different SMILES (Egon Willighagen <egonw@users.sourceforge.net>)
* Added tests for two cases of aromatic rings (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* Updated the OpenJavaDocCheck library to 0.3 (Egon Willighagen <egonw@users.sourceforge.net>)
* Added @cdk.bug annotation, and restricted testing to the bug (Egon Willighagen <egonw@users.sourceforge.net>)
* Removed try/catch to retain the stacktrace of where the NPE occurs (Egon Willighagen <egonw@users.sourceforge.net>)
* Test checking for NPE when cloning with property with null as value (Arvid Berg <goglepox@users.sourceforge.net>)
* Improved JavaDoc: (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed line lengths (Egon Willighagen <egonw@users.sourceforge.net>)
* Added a test to MDLRXNReaderTest which checks of different numbering for the same mapping gives the same result. x (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* The shiftContainer method did not correctly calculate how much the container needs to to shifted. (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* Some performance tuning for SmilesGenerator. In detail: - createSMILESWithoutCheckForMultipleMolecules public, so it can be called directly without doing partitioning - aromaticity detection optional - avoids unecessary BondTools.isStereo calls if non-chiral smiles is wished (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* made logging in the AllRingsFinder optional, this helps with performance. (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* Loosened the perception of N.planar3 atom types: the Hueckel system consist of more than one ring, so looking just at the ring to which the atom belongs does not make sense (Egon Willighagen <egonw@users.sourceforge.net>)
* Added unit tests for atom type perception of more N.planar3 atom types (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing copyright statement and import (Egon Willighagen <egonw@users.sourceforge.net>)
* The MDLWriter ignored titles when writing a ChemModel (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* Simplified the ILoggingTool interface by using Object... (Egon Willighagen <egonw@users.sourceforge.net>)
* Added IO option to allow saving aromatic SMILES (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing unit testing for the SMILESWriter (Egon Willighagen <egonw@users.sourceforge.net>)

1.3.5
--------
* Fix for getBestAlignmentForLabelXY (Arvid Berg <goglepox@users.sourceforge.net>)
* Test for getBestAlignmentForLabelXY (Arvid Berg <goglepox@users.sourceforge.net>)
* Renamed the ligancy classes to use the term tetrahedral since they implicitly encode for tetrahedral chirality (Rajarshi Guha <rajarshi.guha@gmail.com>)
* fixed PMD errors on Use instanceof against interfaces not implementations and few more Signed-off-by: Syed Asad Rahman <s9asad@gmail.com> (Syed Asad Rahman <s9asad@gmail.com>)
* Renamed the ligancy classes to use the term tetrahedral since they implicitly encode for tetrahedral chirality (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Introducing PMD test for CDK specific issues: (Egon Willighagen <egonw@users.sourceforge.net>)
* Removed unstable forcefield code (Egon Willighagen <egonw@users.sourceforge.net>)
* Added copyright and license header (Rajarshi Guha <rajarshi.guha@gmail.com>)
* The createSMILES() methods now take IAtomContainer rather than IMolecule. Originally, IMolecule was the type since it was assumed that SMILES would only be generated for connected components - but the code already handles disconnected components. Since IAtomContainers are meant to support that, this change makes sense. Also a result is that we don't have to convert a IAtomContainer to IMolecule to generate SMILES (Rajarshi Guha <rajarshi.guha@gmail.com>)
* updated test cases Signed-off-by: Syed Asad Rahman <s9asad@gmail.com> (Syed Asad Rahman <s9asad@gmail.com>)
* add on patches (Syed Asad Rahman <s9asad@gmail.com>)
* fixed makeAtomsMapOfBondsMap with test (Syed Asad Rahman <s9asad@gmail.com>)
* Emergency fix: IAminoAcid instead of AminoAcid (Egon Willighagen <egonw@users.sourceforge.net>)
* A few more interfaces instead of implementations (Egon Willighagen <egonw@users.sourceforge.net>)
* Replaced use of implementations by interfaces (Egon Willighagen <egonw@users.sourceforge.net>)
* Use an interface instead of an implementation as type (Egon Willighagen <egonw@users.sourceforge.net>)
* Use interfaces instead of implementation (Egon Willighagen <egonw@users.sourceforge.net>)
* MDL reading and writing atom value line, including test cases (M L Rijnbeek <markr@ebi.ac.uk>)
* Added another test to check that a query larger than the target does not match (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Test cases for MCS updated (Syed Asad Rahman <s9asad@gmail.com>)
* updated MCS solution count in the VF lib, depricated turbo MCS and provided methods for timeout (Syed Asad Rahman <s9asad@gmail.com>)
* updated test for single atom (Syed Asad Rahman <s9asad@gmail.com>)
* Replaced outdated URL with entry in WikiPedia (fixes #3002741) (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed outdated JavaDoc I forgot to remove (fixes #3002409) (Egon Willighagen <egonw@users.sourceforge.net>)
* Included the qm module in the dist-all (fixes #3002622) (Egon Willighagen <egonw@users.sourceforge.net>)
* Cleaned up unthrown exceptions (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Removed use of SMARTS parser in the test code so that a new dependency is not required (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* removed unwated checks (Syed Asad Rahman <s9asad@gmail.com>)
* commented unused code (Syed Asad Rahman <s9asad@gmail.com>)
* test cases for the IQueryAtomContainer support in the SMSD with exceptions fixed (Syed Asad Rahman <s9asad@gmail.com>)
* test cases for the IQueryAtomContainer support in the SMSD (Syed Asad Rahman <s9asad@gmail.com>)
* IQuery* support for the SMSD, will help in SMART based searches (Syed Asad Rahman <s9asad@gmail.com>)
* Turbomode MCS search added (Syed Asad Rahman <s9asad@gmail.com>)
* Turbo mode MCS search added Signed-off-by: Syed Asad Rahman <s9asad@gmail.com> (Syed Asad Rahman <s9asad@gmail.com>)
* removed unwanted test case Signed-off-by: Syed Asad Rahman <s9asad@gmail.com> (Syed Asad Rahman <s9asad@gmail.com>)
* VF Sub search turbo mode (Syed Asad Rahman <s9asad@gmail.com>)
* Updated the SMSD code for turbo mode substructure search Refactored the SMSD class itself (Syed Asad Rahman <s9asad@gmail.com>)
* Added two test cases by Daniel from my blog: http://chem-bla-ics.blogspot.com/2010/05/cip-rules-2-parsing-and-from-smiles.html (Egon Willighagen <egonw@users.sourceforge.net>)
* Added two more unit tests, related to ring closing (Egon Willighagen <egonw@users.sourceforge.net>)
* SMILES @ and @@ chiralities are now fully read. (Egon Willighagen <egonw@users.sourceforge.net>)
* Added unit tests with various chiral SMILES situations. (Egon Willighagen <egonw@users.sourceforge.net>)
* Implemented stereo chemistry for atoms with four ligands (Egon Willighagen <egonw@users.sourceforge.net>)
* Patch to generalize the stereo chemistry handling. (Egon Willighagen <egonw@users.sourceforge.net>)
* Minor fix to build.xml to ensure that SMSD code gets included in the large jar file (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Added JavaDoc testing to the QA task; removed module-uptodate which checked if the module was already compiled causing the target to be skipped (Egon Willighagen <egonw@users.sourceforge.net>)
* I made sure the MDLV2000Reader considers 0,0,0 coordinates in files with a single atom as 2d and 3d coordinates. The MDLReader does not handle the 0,0,0 case explicitly, so I just added a test for 2d. It might be better to have uniforma handling, but I will file a bug report for that. (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* The RXNReaders/Writers now all handle Atom-Atom-Mappings. This was only done in the MDLRXNReader till now (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* Atom-Atom-Mapping is now read and written in MDL files. Note the reading until now was into ID field, which is not in line with description of ID field in ChemObject (Returns the identifier (ID) of this object). Also added tests for MDLWriter/Reader/2000Reader. (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* Flexibility for ring start angles. (mark_rynbeek <markr@ebi.ac.uk>)
* more mdl reader writer tests (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* Revert "Additional constant" (Stefan Kuhn <stefan.kuhn@ebi.ac.uk>)
* Added a test case for short line mol files. Patch by S.Kuhn, reworked by M.Rijnbeek. (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* MDL reading and writing UP_OR_DOWN (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* Removal of references to removed R-CDK bridge (Egon Willighagen <egonw@users.sourceforge.net>)
* Removed the R-based model package and associated jar files and test code (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Removal of references to removed R-CDK bridge (Egon Willighagen <egonw@users.sourceforge.net>)
* Removed the R-based model package and associated jar files and test code (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Removal of references to removed R-CDK bridge (Egon Willighagen <egonw@users.sourceforge.net>)
* Removed DocCheck from Eclipse' Build Path (Egon Willighagen <egonw@users.sourceforge.net>)
* Removed obsolete castings, or replaced by more general ones (Egon Willighagen <egonw@users.sourceforge.net>)
* added  @Test Signed-off-by: Syed Asad Rahman <s9asad@gmail.com> (Syed Asad Rahman <s9asad@gmail.com>)
* added CDKRMapHandlerTest (Syed Asad Rahman <s9asad@gmail.com>)
* added CDKRMapHandlerTest Signed-off-by: Syed Asad Rahman <s9asad@gmail.com> (Syed Asad Rahman <s9asad@gmail.com>)
* The big SMSD patch. (Syed Asad Rahman <asad@ebi.ac.uk>)
* Fixed a ClassCastException in a unit test; I messed up (mea culpa) (Egon Willighagen <egonw@users.sourceforge.net>)
* Copied code from the DefaultChemObjectBuilder to handle the IBond constructor that takes an IAtom[] which I had forgotten to port to DebugChemObjectBuilder and NoNotificationChemObjectBuilder (fixes a few regressions) (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed NullPointerExceptions for LonePair's and SingleElectron's constructed with the no-argument constructors (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing cloning of single electrons (Egon Willighagen <egonw@users.sourceforge.net>)
* Do not try to clone the atom if it does not exist (Egon Willighagen <egonw@users.sourceforge.net>)
* MDL reading and writing valency (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* Line separator fix for RGroup writer (Mark Rijnbeek <mark_rynbeek@users.sf.net>)
* de-Javadoc numerous comments (fixes #2980066) (Carl Masak <cmasak@gmail.com>)
* More extensive testing for removeHydrogens in atomcontainers with hetero atoms without Hs (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* Be a bit more forthcoming with debug messages: report also the parameter types of the method (Egon Willighagen <egonw@users.sourceforge.net>)
* This patch makes sure that the removeHydrogens method in AtomContainerManipulator sets hydrogenCoutn to 0 if no hydrogens were on a heavy atom. Till now, this was null, which was at least not good, in a way even wrong. (Stefan Kuhn <Stefan.Kuhn@ebi.ac.uk>)
* converted uses of indexOf to startsWith/contains (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Updated HIN reader to fix bug 2984581 (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Added unit test to see of arrays are properly cloned, and that array entries of the original are not overwritten (Egon Willighagen <egonw@users.sourceforge.net>)
* Unit test that the IAtom[] array is properly cloned, and overwriting entries in the clone does not overwrite entries on the original (Egon Willighagen <egonw@users.sourceforge.net>)
* Removed duplication of cloning. (Egon Willighagen <egonw@users.sourceforge.net>)
* Apparently the super.clone() does not clone the pointer to the IAtomContainer[], causing a clone() followed by changing containers in the clone to overwrite the original IAtomContainer[]. Fixed by creating a new array. (Egon Willighagen <egonw@users.sourceforge.net>)
* Moved test from the specific class to the abstract tests, as the behavior should be the same for NNMoleculeSet and DebugMoleculeSet too (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed a typo in the test method name (Egon Willighagen <egonw@users.sourceforge.net>)
* Got rid of some debug prints (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Fixed a regex bug which prevented the engine from properly loading descriptor class names (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Some code cleanup to make it more idiomatic Java (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* New IChemObjectBuilder interface: (Egon Willighagen <egonw@users.sourceforge.net>)
* Bumped version to indicate this is post 1.3.4 release (Egon Willighagen <egonw@users.sourceforge.net>)
* Two more tests for the issue: atom typing works fine; aromaticity detection fails: one ring is detected as aromatic (that with two nitrogesn), so that it does not consider the double ring, marking the other ring as non-aromatic (Egon Willighagen <egonw@users.sourceforge.net>)

1.3.6
--------
* Updated copyright to 2010 (Egon Willighagen <egonw@users.sourceforge.net>)
* Compare values not objects (fixes #3061263) (Egon Willighagen <egonw@users.sourceforge.net>)
* Unit test to reproduce failing atom type perception with one of the options to create a -1 Integer object (Egon Willighagen <egonw@users.sourceforge.net>)
* Smiles parser setting to preserve aromaticity as provided in the Smiles String itself. (Mark Rynbeek <markr@localhost.localdomain>)
* Added two further unit tests: one to see if the descriptor properly 'ignores' hydrogens; a second to reproduce the numbers in the original Wiener paper from 1947 (Egon Willighagen <egonw@users.sourceforge.net>)
* Renabled test which was (accidentally?) outcommented when switching to JUnit4 in commit 06a1a3dd (Egon Willighagen <egonw@users.sourceforge.net>)
* Added a reference to the original Wiener paper (Egon Willighagen <egonw@users.sourceforge.net>)
* No need to declare throws for other Exception's if the superclass is already declared thrown itself (also, no need to define java.lang explicitly) (Egon Willighagen <egonw@users.sourceforge.net>)
* Minor cleanup: corrected copyright statement; simplified JavaDoc by removing empty parameter table (Egon Willighagen <egonw@users.sourceforge.net>)
* Replaced inline citation by reference to the main bibliography (Egon Willighagen <egonw@users.sourceforge.net>)
* Implementation of a descriptor to measure molecular complexity in terms of sp3 to sp2 ratio of carbon atoms (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Updated javadocs and added extra unit test (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Implementation of a descriptor to measure molecular complexity in terms of sp3 to sp2 ratio of carbon atoms (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Removed output to STDOUT (Egon Willighagen <egonw@users.sourceforge.net>)
* Fix for branching bracket issue when generating SMILES for BrC1C(Br)C(Br)C(Br)C(Br)C1Br (Saravanaraj <raj@plantbio.uga.edu>)
* Unit test for bug #3040273. (Saravanaraj <raj@plantbio.uga.edu>)
* Fixed hybridization information: these are sp3 hybridized systems (Egon Willighagen <egonw@users.sourceforge.net>)
* More missing elements for SMILES parsing problems reported in bug #3048501 (Egon Willighagen <egonw@users.sourceforge.net>)
* Unit tests for SMILES parsing bugs reported in #3048501 (Egon Willighagen <egonw@users.sourceforge.net>)
* Upper case the first character to also properly recognize lower cased 'aromatic' two-character element symbols (fixes SMILES parsign of things like c1[se]ccccc1 (Egon Willighagen <egonw@users.sourceforge.net>)
* JavaDoc fixes: correct @cdk.cite use, and small typo (Egon Willighagen <egonw@users.sourceforge.net>)
* Updated the JavaDoc for an API changed a while ago: the getInChIToStructure() method now takes an IChemObjectBuilder as second argument (fixes #3035890) (Egon Willighagen <egonw@users.sourceforge.net>)
* Updated the JavaDoc for the atoms() Iterable API change (fixes #3034824) (Egon Willighagen <egonw@users.sourceforge.net>)
* Added the maven build file (closes #3042475) (Egon Willighagen <egonw@users.sourceforge.net>)
* a)removed blank/unused methods and fixed imports Signed-off-by: Syed Asad Rahman <s9asad@gmail.com> (Syed Asad Rahman <s9asad@gmail.com>)
* a)IMatch to Match and constructor call for state used TargetProperties for faster processing Signed-off-by: Syed Asad Rahman <s9asad@gmail.com> (Syed Asad Rahman <s9asad@gmail.com>)
* a)Assert cleaned and fixed b)Correct ASSERT imports used (Syed Asad Rahman <s9asad@gmail.com>)
* Removed unused code (Syed Asad Rahman <s9asad@gmail.com>)
* Updated checking of indices which now are -1 if unset, instead of null (Syed Asad Rahman <s9asad@gmail.com>)
* a) Default constructor supported as per changes in the CDK b) VFMCS index error should point to -1 not null Signed-off-by: Syed Asad Rahman <s9asad@gmail.com> (Syed Asad Rahman <s9asad@gmail.com>)
* a)Refactored matchers, atom matcher and bond matcher b)getTanimoto score fixed for single atoms (Syed Asad Rahman <s9asad@gmail.com>)
* Updates for the getImplicitHydrogenCount() renaming (Egon Willighagen <egonw@users.sourceforge.net>)
* The smsd module now depends on the signature module (Egon Willighagen <egonw@users.sourceforge.net>)
* Latest SMSD code 1.2.0: Major changes are: (Syed Asad Rahman <s9asad@gmail.com>)
* Use the factory to not depend on an implementation (Egon Willighagen <egonw@users.sourceforge.net>)
* Renamed get/setHydrogenCount() to get/setImplicitHydrogenCount(), per report #3020065 (Egon Willighagen <egonw@users.sourceforge.net>)
* Introduced a helper class with info about the CDK library: the version number, which is read from the build.props which is now included in the cdk-core.jar (Egon Willighagen <egonw@users.sourceforge.net>)
* Also take into account super classes (Egon Willighagen <egonw@users.sourceforge.net>)
* Renamed MDLWriter into MDLV2000Writer (implements #3029447) (Egon Willighagen <egonw@users.sourceforge.net>)
* Assert pattern has the expected value as first argument (Egon Willighagen <egonw@users.sourceforge.net>)
* Use the builder pattern to instantiate an IIsotope (Egon Willighagen <egonw@users.sourceforge.net>)
* MDLV2000 reader interprets D and T without M ISO line mandatory (Mark Rynbeek <markr@localhost.localdomain>)
* Use the PT class to see if something can be an element and removing the redundant element symbol info (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed annotation with TestMethod, not TestClass (fixes #3016632) (Egon Willighagen <egonw@users.sourceforge.net>)
* Skip inner classes for @cdk.module and @cdk.githash JavaDoc tests (fixes #3043084) (Egon Willighagen <egonw@users.sourceforge.net>)
* Throw a CDKException when a QUADRUPLE bond order is in the input, which is not supported by the MDL/Symyx molfile format (fixes #3029352) (Egon Willighagen <egonw@users.sourceforge.net>)
* Deal with a special situation: pyridine N-oxide in the non-charge-separated representation, with a N.sp2.3 nitrogen, with two double bonds. Previously, any ring-outward double bond would disqualify the ring as aromatic. This compound is now an exception. (Egon Willighagen <egonw@users.sourceforge.net>)
* Assert the compound is aromatic (fixes false negative) (Egon Willighagen <egonw@users.sourceforge.net>)
* Exporting the signatures jar (maclean <gilleain.torrance@gmail.com>)
* Removed the OpenJavaDocCheck Jazzy extension which was not supposed to go in; it's not ready for prime time (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing dependencies (fixes failing unit tests) (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing dependencies (fixes failing unit tests) (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing dependency (Egon Willighagen <egonw@users.sourceforge.net>)
* Release CDK 1.2.6.1 (Egon Willighagen <egonw@users.sourceforge.net>)
* Copy the 2D templates into the source distribution (Egon Willighagen <egonw@users.sourceforge.net>)
* Added finally blocks to MolHandler to close its input streams, with proper logging calls if it fails Fixes bug #3032568 (Jules Kerssemakers <j.kerssemakers@cmbi.ru.nl>)
* UIT timeout fix (Andreas Truszkowski <andreas1981@users.sourceforge.net>)
* Cleaned up exception handling in TemplateHandler.loadTemplates() to be more specific and less pessimistic. (Jules Kerssemakers <j.kerssemakers@cmbi.ru.nl>)
* QSAR descriptor values made serializeable (Andreas Truszkowski <andreas1981@users.sourceforge.net>)
* Fixed assertion to compare two Vector3d's (Egon Willighagen <egonw@users.sourceforge.net>)
* Added test to assert that two Vector3d's are identical (Egon Willighagen <egonw@users.sourceforge.net>)
* All methods now tested (maclean <gilleain.torrance@gmail.com>)
* Hooking up test machinery (maclean <gilleain.torrance@gmail.com>)
* Altered the getTetrahedralDescription to be get stereo and return ITetrahedralChirality.Stereo (maclean <gilleain.torrance@gmail.com>)
* Moved Stereotool to stereo package (maclean <gilleain.torrance@gmail.com>)
* Convenience method that returns chirality descriptor (R/S) given four atoms in priority order (maclean <gilleain.torrance@gmail.com>)
* Missing docs (maclean <gilleain.torrance@gmail.com>)
* Copyright statements (maclean <gilleain.torrance@gmail.com>)
* Just to be paranoid, test +/- tetrahedra above and below the XY plane (maclean <gilleain.torrance@gmail.com>)
* Tests for square planar shapes, trig bipyr, and oct (maclean <gilleain.torrance@gmail.com>)
* Cleanup and fixing (I think) of the trigonal bipyramidal method (maclean <gilleain.torrance@gmail.com>)
* Test for 3 colinear points (maclean <gilleain.torrance@gmail.com>)
* Better docs (maclean <gilleain.torrance@gmail.com>)
* Tests for tetrahedral sign, some basic defined vectors (maclean <gilleain.torrance@gmail.com>)
* Test class, and name change of distanceToPlane to show that it returns signed (+/-) distance (maclean <gilleain.torrance@gmail.com>)
* Initial go at the StereoTool - functions taken from Jmol's smiles package for 3D stereo checking (maclean <gilleain.torrance@gmail.com>)
* Updated OB note and robustified unit tests (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Added support for multi-molecule mol2 files. Updated source and added unit test and test file (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Updated cdk-1.2.x patches for master API (Egon Willighagen <egonw@users.sourceforge.net>)
* Release 1.2.6 (Egon Willighagen <egonw@users.sourceforge.net>)
* Updated the DebugBond unit test too now: new DebugBond() has zero atoms (Egon Willighagen <egonw@users.sourceforge.net>)
* Backport patch, to make the patches compile with cdk-1.2.x (Egon Willighagen <egonw@users.sourceforge.net>)
* Additional patch to reduce atom count on setAtom(null, int) and unit tests for the setAtom(IAtom, int) behavior. (Egon Willighagen <egonw@users.sourceforge.net>)
* Also fix the new NNBond() == 0 atoms for the nonotify module (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed Bond() constructor to create a bond with zero atoms. Also fixed setAtom(IAtom, int) to increase the atom count if a null entry is filled with a non-null IAtom. (Egon Willighagen <egonw@users.sourceforge.net>)
* Updated test to assume new Bond() creates a bond with zero atoms (Egon Willighagen <egonw@users.sourceforge.net>)
* Added two unit tests for aromatic N-oxides that are the basis for failures in SMARTS matching (Rajarshi Guha <rajarshi.guha@gmail.com>)
* added javadoc to IChemObjectReader explaining the split between ISimple and IIterating ChemObjectReaders (Jules Kerssemakers <j.kerssemakers@cmbi.ru.nl>)
* Exceptions when clone atomless ISingleElectron and ILonePair too (Egon Willighagen <egonw@users.sourceforge.net>)
* Unit test for ArrayIndexOutOfBoundsException occuring when trying to clone an IAtomContainer with an IBond with no IAtoms (Egon Willighagen <egonw@users.sourceforge.net>)
* Added unit tests for SMILES with failing atom typing, from email on the cdk-devel mailing list June 11 2010 (Egon Willighagen <egonw@users.sourceforge.net>)
* Added the N.oxide atom type, for structures like (CH3)N=O (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed reading of SD properties: keep the first line too (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing dependency (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed unit test: surely there is no atom with symbol 0... how long has this been failing?? (Egon Willighagen <egonw@users.sourceforge.net>)
* Updated fingerprinter javadoc (Rajarshi  Guha <rajarshi.guha@gmail.com>)
* Added a test class to aromaticity of three compounds: the last incorrectly fails (Egon Willighagen <egonw@users.sourceforge.net>)
* Also except N.amide as part of an aromatic ring (Egon Willighagen <egonw@users.sourceforge.net>)
* Added a test class to repeat atom type perception and test consistency (Egon Willighagen <egonw@users.sourceforge.net>)
* Unit test fix: the molecules *is* aromatic, as we should assume it is. Fixes a big goof up (Egon Willighagen <egonw@users.sourceforge.net>)
* Replace special chars where spaces are supposed to occur, fixing the fail of the unit tests every now and then (Egon Willighagen <egonw@users.sourceforge.net>)
* BooleanIOSetting to let MDLWriter output bond type 4 (aromatic) (Mark Rijnbeek <markr@ebi.ac.uk>)
* Reorderd imports (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Added test cases to check that the code runs when faced with covalently bonded metals. Currenly on failure is due to the presence of Pt, for which we do not have a valency in AtomValence (Rajarshi Guha <rajarshi.guha@gmail.com>)
* chemfilter improvised Signed-off-by: Syed Asad Rahman <s9asad@gmail.com> (Syed Asad Rahman <s9asad@gmail.com>)
* SMSD Test cases updated as per new code Signed-off-by: Syed Asad Rahman <s9asad@gmail.com> (Syed Asad Rahman <s9asad@gmail.com>)
* SMSD Test cases updated as per new code Signed-off-by: Syed Asad Rahman <s9asad@gmail.com> (Syed Asad Rahman <s9asad@gmail.com>)
* added ExtAtomContainerManipulator Signed-off-by: Syed Asad Rahman <s9asad@gmail.com> (Syed Asad Rahman <s9asad@gmail.com>)
* deleted ext Signed-off-by: Syed Asad Rahman <s9asad@gmail.com> (Syed Asad Rahman <s9asad@gmail.com>)
* updated SMSD code Signed-off-by: Syed Asad Rahman <s9asad@gmail.com> (Syed Asad Rahman <s9asad@gmail.com>)
* updated SMSD code Signed-off-by: Syed Asad Rahman <s9asad@gmail.com> (Syed Asad Rahman <s9asad@gmail.com>)
* Convenience constructors for AtomSignature that take IAtoms rather than atom indices (maclean <gilleain.torrance@gmail.com>)
* Added missing jar meta file for the Signatures library (Egon Willighagen <egonw@users.sourceforge.net>)
* Updated to reflect the upstream jar name (Egon Willighagen <egonw@users.sourceforge.net>)
* Abstract methods not part of API are now protected, to discourage thier use (maclean <gilleain.torrance@gmail.com>)
* Various fixes to tests (maclean <gilleain.torrance@gmail.com>)
* Added the missing assert: runCoverageTest() returns a boolean stating the success (Egon Willighagen <egonw@users.sourceforge.net>)
* cdk.cite references for two Faulon papers (maclean <gilleain.torrance@gmail.com>)
* More missing javadocs - notably the class documentation for AtomSignature and MoleculeSignature (maclean <gilleain.torrance@gmail.com>)
* Mising constructor javadoc, and inheritdoc annotation on AtomSignature (maclean <gilleain.torrance@gmail.com>)
* Final missing test (maclean <gilleain.torrance@gmail.com>)
* Atom signature test methods (maclean <gilleain.torrance@gmail.com>)
* Molecule signature tests (maclean <gilleain.torrance@gmail.com>)
* Signature quotient graph test method (maclean <gilleain.torrance@gmail.com>)
* Missing test for Orbit::iterator (maclean <gilleain.torrance@gmail.com>)
* Removed unused import (Egon Willighagen <egonw@users.sourceforge.net>)
* Molecule From Signature Builder tests (maclean <gilleain.torrance@gmail.com>)
* All orbit methods tested (maclean <gilleain.torrance@gmail.com>)
* Finally correct junit annotations, and sort test (maclean <gilleain.torrance@gmail.com>)
* BeforeClass method must be static; better clone test (maclean <gilleain.torrance@gmail.com>)
* Fixes some problems flagged by PMD (maclean <gilleain.torrance@gmail.com>)
* Use junit's BeforeClass instead of Before annotation (maclean <gilleain.torrance@gmail.com>)
* Added missing githash tags, to add links in the JavaDoc to the source code repository (Egon Willighagen <egonw@users.sourceforge.net>)
* Inherit JavaDoc where methods overwrite a super method (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed PMD warnings: more descriptive field names; use of Integer.valueOf() (Egon Willighagen <egonw@users.sourceforge.net>)
* Added test method annotation for the clone() method (Egon Willighagen <egonw@users.sourceforge.net>)
* Removed some unnecessary imports (maclean <gilleain.torrance@gmail.com>)
* Test orbit cloning (maclean <gilleain.torrance@gmail.com>)
* Improved canonical label method in graph signature (maclean <gilleain.torrance@gmail.com>)
* Integer invariants, and updated signatures jarfile (maclean <gilleain.torrance@gmail.com>)
* Added JavaDoc HTML generation for the signature module (Egon Willighagen <egonw@users.sourceforge.net>)
* Hooked in PMD testing for the signature module (Egon Willighagen <egonw@users.sourceforge.net>)
* Defined dependencies for the test module (Egon Willighagen <egonw@users.sourceforge.net>)
* Hooked the signature module into the CDK build system (Egon Willighagen <egonw@users.sourceforge.net>)
* Removed the dependency on the nonotify module (Egon Willighagen <egonw@users.sourceforge.net>)
* Created a CDK style module test suite (Egon Willighagen <egonw@users.sourceforge.net>)
* MoleculeFromSignatureBuilder tests (maclean <gilleain.torrance@gmail.com>)
* Extend from CDKTestCase and use the slow running test check (maclean <gilleain.torrance@gmail.com>)
* Fixed and cleaned up molecule signature tests (maclean <gilleain.torrance@gmail.com>)
* Initial commit of signature package (maclean <gilleain.torrance@gmail.com>)
* Added OpenJavaDocCheck 0.5 - the Jazzy spell checking extension (Egon Willighagen <egonw@users.sourceforge.net>)
* specify fail behavior (returns null) in javadoc (jonalv <jonathan.alvarsson@gmail.com>)
* Added PMD tests for detecting misuse of TestClass and TestMethod, e.g. TestClass on a method. (fixes #3014808) (Egon Willighagen <egonw@users.sourceforge.net>)
* Removed two lines added in master to the removed doccheck target (Egon Willighagen <egonw@users.sourceforge.net>)
* Improved javadoc generation using a link tag, so that references to java library classes are resolved properly (maclean <gilleain.torrance@gmail.com>)
* Update OpenJavaDocCheck to 0.5: fixing a few false positives (Egon Willighagen <egonw@users.sourceforge.net>)
* Removed use of the proprietary DocCheck utility (Egon Willighagen <egonw@users.sourceforge.net>)
* OpenJavaDocCheck errors are fixed for SMSD related modules Signed-off-by: Syed Asad Rahman <s9asad@gmail.com> (Syed Asad Rahman <s9asad@gmail.com>)
* solved cdk-Bugs-3006773 : small JavaDoc errors in the smsd module (Syed Asad Rahman <s9asad@gmail.com>)
* Fix for character spacing for "APO" line in RGFile output (Mark Rynbeek <markr@localhost.localdomain>)
* Branch open for commits for the future 1.3.6 (Egon Willighagen <egonw@users.sourceforge.net>)
* Use the new tests in more situations (Egon Willighagen <egonw@users.sourceforge.net>)

1.3.7
--------
* Replaced the broken links with new ones (fixes #3108471) (Egon Willighagen <egonw@users.sourceforge.net>)
* Upgraded to the final JNI-InChI 0.7: (Egon Willighagen <egonw@users.sourceforge.net>)
* Renamed test class to conform the expected naming pattern (Egon Willighagen <egonw@users.sourceforge.net>)
* Factored out a AbstractCDKObjectTest now used in AbstractAtomParity test, to add the missing unit test (Egon Willighagen <egonw@users.sourceforge.net>)
* Overwrite the default public constructor because this class is not supposed to be instantiated. (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing TestMethod annotation (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing unit test (Egon Willighagen <egonw@users.sourceforge.net>)
* Strongly typed the comparator, removing no longer valid tests (Egon Willighagen <egonw@users.sourceforge.net>)
* Removed an obsolete test (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed unit test: test the correct class (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing TestMethod annotation (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing dependency (Egon Willighagen <egonw@users.sourceforge.net>)
* Renamed methods according to naming coverage testing naming scheme (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing classificatins to some descriptors (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Use a builder more efficiently (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing sulphur atom type as found in thiosulphonate (fixes #3080848) (Egon Willighagen <egonw@users.sourceforge.net>)
* Added acidic and basic group count descriptors (implements #3056330) (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing atom type: positively charged P with three neighbors, of which one double bonded (Egon Willighagen <egonw@users.sourceforge.net>)
* Added a unit test for the C=[N+]=[N-] functional group (Egon Willighagen <egonw@users.sourceforge.net>)
* Updated string generation for molecular formulae that address bug 3071473 (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Added missing dependency (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing dependency (Egon Willighagen <egonw@users.sourceforge.net>)
* Added unit test for bug 2871303, which appears to be resolved now (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Added unit test for bug 2853035, which appears to be resolved now (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Added unit test for bug 3001616, which appears to be resolved now (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Overwrite tests from AbstractChemObject to ensure that no change events are thrown when properties are changed, which was fixed in June in patch 2fe119c3a874dabb9bfb66ea2adbaaa6b2e6ed5d (Egon Willighagen <egonw@users.sourceforge.net>)
* Removed merge artefact (Egon Willighagen <egonw@users.sourceforge.net>)
* test for streams returning false on ready() (vedina <jeliazkova.nina@gmail.com>)
* Revert "Updated isotope to have proper equals and hashCode methods" (Egon Willighagen <egonw@users.sourceforge.net>)
* Revert "Updated molecular formula to use the new equals method from Isotope. This methods checks for equality of two instances using symbol, mass num, exact mass and natural abundance" (Egon Willighagen <egonw@users.sourceforge.net>)
* Revert "Updated MF manipulator to properly evaluate total mass and generate formula string correctly, even when there are multiple isotopes of the same element. Added unit test. Simplified molecular formula to properly use the isotopes map as an actual map" (Egon Willighagen <egonw@users.sourceforge.net>)
* Updated Javadocs, since Egon is a nice guy :) (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Actually put in a test (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Implementation of the Fmf descriptor described by Yang et al, J Med Chem, 2010. The descriptor is described i in Yang et al, J Med Chem 2010, and is an approach to characterizing molecular complexity based on the Murcko framework (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Added missing dependency (Egon Willighagen <egonw@users.sourceforge.net>)
* Updated MF manipulator to properly evaluate total mass and generate formula string correctly, even when there are multiple isotopes of the same element. Added unit test. Simplified molecular formula to properly use the isotopes map as an actual map (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Updated molecular formula to use the new equals method from Isotope. This methods checks for equality of two instances using symbol, mass num, exact mass and natural abundance (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Updated isotope to have proper equals and hashCode methods (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Added unit test and test file for bug 2917084 (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Added coverage testing for constructors (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed the CDKSourceCodeWrite to create compilable source code (Egon Willighagen <egonw@users.sourceforge.net>)
* Added use of Groovy to test if the output compiles (Egon Willighagen <egonw@users.sourceforge.net>)
* Updated Murcko code so that we save the appropriatley cloned framework. Also updated unit tests (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Added missing entry for compiling the iordf module (Egon Willighagen <egonw@users.sourceforge.net>)
* Updated for API changes in the IChemObjectBuilder (Egon Willighagen <egonw@users.sourceforge.net>)
* Updated for API change for get/setImplicitHydrogens() (Egon Willighagen <egonw@users.sourceforge.net>)
* Copied the inchi module into the sinchi module, providing Standard InChI support with JNI-InChI 0.7. (Egon Willighagen <egonw@users.sourceforge.net>)
* Added iordf to the ojdcheck target (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing dependencies for the test module for iordf (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing JavaDoc for the iordf module (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing JavaDoc (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed a PMD warning: too short variable name (Egon Willighagen <egonw@users.sourceforge.net>)
* Reduced complexity by introducing two maps (Egon Willighagen <egonw@users.sourceforge.net>)
* Prefixed the hybridization constants with HYBRID_ (Egon Willighagen <egonw@users.sourceforge.net>)
* Made final static full upper case, as requested by PMD (Egon Willighagen <egonw@users.sourceforge.net>)
* Removed output to STDOUT (Egon Willighagen <egonw@users.sourceforge.net>)
* Added iordf to dist-large (Egon Willighagen <egonw@users.sourceforge.net>)
* Added (de)serialization of the IPseudoAtom fields to RDF (Egon Willighagen <egonw@users.sourceforge.net>)
* Added (de)serialization of the IElectronContainer fields to RDF (Egon Willighagen <egonw@users.sourceforge.net>)
* Added (de)serialization of the IIsotope fields to RDF (Egon Willighagen <egonw@users.sourceforge.net>)
* Added a few missing dependencies (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed module allocation (Egon Willighagen <egonw@users.sourceforge.net>)
* Added roundtripping for IAtomType.formalCharge (Egon Willighagen <egonw@users.sourceforge.net>)
* Hooked in testing for iordf (Egon Willighagen <egonw@users.sourceforge.net>)
* Reuse of earlier extracted helper methods (Egon Willighagen <egonw@users.sourceforge.net>)
* Added roundtripping of IAtom.atomtypeName and .maxBondOrder (Egon Willighagen <egonw@users.sourceforge.net>)
* Test all bond types (Egon Willighagen <egonw@users.sourceforge.net>)
* Added roundtrip of IElement.atomicNumber and IAtomType.hybridization (Egon Willighagen <egonw@users.sourceforge.net>)
* Added roundtrip of IChemObject.identifier (Egon Willighagen <egonw@users.sourceforge.net>)
* Added read and write of IBond and .order (Egon Willighagen <egonw@users.sourceforge.net>)
* Added class JavaDoc (Egon Willighagen <egonw@users.sourceforge.net>)
* Added method to create identifiers based on the hashCode (Egon Willighagen <egonw@users.sourceforge.net>)
* Added read/write of IAtom.symbol in RDF (Egon Willighagen <egonw@users.sourceforge.net>)
* Added a Java API version of the CDK ontology (not synched to the OWL) (Egon Willighagen <egonw@users.sourceforge.net>)
* Added reader and writer for the CDKOWL/N3 format (Egon Willighagen <egonw@users.sourceforge.net>)
* Added framework to convert the CDK data model into a JEna Model (Egon Willighagen <egonw@users.sourceforge.net>)
* Defined a new format, serializing the CDK data model into the Web Ontology Language (OWL) in the Notation3 (N3) format. (Egon Willighagen <egonw@users.sourceforge.net>)
* Bumped version to indicate it is the development version (Egon Willighagen <egonw@users.sourceforge.net>)
* Throw a change event when an existing property is removed (fixes #2993561). (Egon Willighagen <egonw@users.sourceforge.net>)
* Do no pass stereo information when none (null) was read (Egon Willighagen <egonw@users.sourceforge.net>)
* Three fixes: extended the JavaDoc, reset the isInterrupted boolean when an interruption occured, and marked how interruption should be used (which means sequential calls, not parallel) (Egon Willighagen <egonw@users.sourceforge.net>)
* Added testing of the isOK() method (Egon Willighagen <egonw@users.sourceforge.net>)
* Because the DeduceBondSystemTool does not consider rings with more than 7 atoms, we can speed up ring finding by setting the (new) maxRingSize parameter (Egon Willighagen <egonw@users.sourceforge.net>)
* Added a constructor to set a custom ring finder instance (e.g. with a time out set) (Egon Willighagen <egonw@users.sourceforge.net>)
* Added build/*.javafiles to the .classpath so that the coverage unit tests succeed in Eclipse (Egon Willighagen <egonw@users.sourceforge.net>)
* modified to avoid InputStreamReader.ready() method (vedina <jeliazkova.nina@gmail.com>)
* Added unit tests for bug 3088164 (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Updated to ensure that we properly handle tag separator lines that may not be completely empty (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Fixed bug in reading a SDF property whose value is a single space (Rajarshi Guha <rajarshi.guha@gmail.com>)
* removed debug code and add another check in the unit test (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Added another unit test (Rajarshi Guha <rajarshi.guha@gmail.com>)
* New package for fragmentation algorithms - currently exhaustive and Murcko. Added unit tests and updated code to use the new Murcko fragmenters. Removed old murcko fragmenter which was unmaintainable. Additional unit tests have been added and Javadocs have been improved (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Added new test method for aromatic bonds (Egon Willighagen <egonw@users.sourceforge.net>)
* Build molecules with aromatic bonds if labelled with 'p' (maclean <gilleain.torrance@gmail.com>)
* Aromatic bond (output) support for signatures (maclean <gilleain.torrance@gmail.com>)
* - MDLReader.java AtomAtomMapping property set as String instead of Integer (unknown <Gott@.(none)>)
* Added a 'reader' for MoSS output files, which reads the given substructures as IMolecule's, as we do not have a proper data model for query structures yet (Egon Willighagen <egonw@users.sourceforge.net>)
* Added a format definition for the output of the MoSS software (Egon Willighagen <egonw@users.sourceforge.net>)
* Check for a null major isotope, which happens with R-groups (maclean <gilleain.torrance@gmail.com>)
* Small typo fix to point to the correct test class (Egon Willighagen <egonw@users.sourceforge.net>)
* Four unit tests that test if the fingerprint calculation is affected by atom or bond permutation (Egon Willighagen <egonw@users.sourceforge.net>)
* Updated version and confirmed inception year (Egon Willighagen <egonw@users.sourceforge.net>)
* Updated getVersion method to not print to stdout (Rajarshi  Guha <rajarshi.guha@gmail.com>)

1.3.8
--------
* Updated the changelog (Egon Willighagen <egonw@users.sourceforge.net>)
* Updated the README (Egon Willighagen <egonw@users.sourceforge.net>)
* Bumped version for release 1.3.8 (Egon Willighagen <egonw@users.sourceforge.net>)
* Added description of IO settings to the writers JavaDoc (fixes #3029445) (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing unit tests (Egon Willighagen <egonw@users.sourceforge.net>)
* Changed method names to versions expected by the coverage testing system (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing test annotation (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing dependency (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed returning the monomer names when no strands are defined (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed counting the number of monomers when no strands are defined (Egon Willighagen <egonw@users.sourceforge.net>)
* Restored the previous behavior of a zero default charge, fixing very many unit tests (Egon Willighagen <egonw@users.sourceforge.net>)
* Moved packaging of the PeriodicTable data to the new model too (Egon Willighagen <egonw@users.sourceforge.net>)
* Updated Atom(String) constructor to call the Atom(Element) constructor, so that even if we instantiate an atom just by symbol we still get an atomic number. Needed to update the Element constructor to accept Integer (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Moved the test classes from the standard to the core TestSuite too (Egon Willighagen <egonw@users.sourceforge.net>)
* Updated module assignments (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Added unit tests for H-bond donor/acceptor for bug #3133610 (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed typo in JavaDoc (Egon Willighagen <egonw@users.sourceforge.net>)
* Fixed isotope class to get the proper isotope if mass number is available, rather than using the major isotope by default (Rajarshi Guha <rajarshi.guha@gmail.com>)
* Added some documentation for possibly non-obvious methods (Rajarshi Guha <rajarshi.guha@gmail.com>)
* AminoAcidCountDescriptor constructor made thread safe (Andreas Truszkowski <andreas1981@users.sourceforge.net>)
* System.out.println() removed in ProtonTotalPartialChargeDescriptor.java (Andreas Truszkowski <andreas1981@users.sourceforge.net>)
* Added missing copyright/license and cdk.module statements (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing JavaDoc and unit tests for VisitedAtoms (Egon Willighagen <egonw@users.sourceforge.net>)
* Added a simple code example for how to use the CIPTool (Egon Willighagen <egonw@users.sourceforge.net>)
* Made a few classes private to the package (Egon Willighagen <egonw@users.sourceforge.net>)
* Added comment in JavaDoc about the sorted nature of the method input (Egon Willighagen <egonw@users.sourceforge.net>)
* Added unit test for aromatic molecular signatures (Egon Willighagen <egonw@users.sourceforge.net>)
* Added testing of bromochlorofluoroiodomethane (Egon Willighagen <egonw@users.sourceforge.net>)
* Only consider recursion if all ligand atoms are identical and equal in number (fixes R detection in PubChem CID 42475007) (Egon Willighagen <egonw@users.sourceforge.net>)
* Keep track of which atoms have already been visited, to properly terminate when we give up (Egon Willighagen <egonw@users.sourceforge.net>)
* Added unit tests to uncover a non-termination issue in the CIP algorithm reported by Ola (Egon Willighagen <egonw@users.sourceforge.net>)
* Added unit test to make sure no chirality is detected for the FC(Me)(Me)R carbon (Egon Willighagen <egonw@users.sourceforge.net>)
* Test case for another termination problem: the previous 'fix' broke the proper ordering of ligands when there is more than one, IAOI one ligand count was only 1 (thanx to Gilleain for spotting this) (Egon Willighagen <egonw@users.sourceforge.net>)
* Test case provided by Gilleain around termination, using the SMILES as input (Egon Willighagen <egonw@users.sourceforge.net>)
* Set up a CIP module. (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing @TestMethod annotation for LoggingTool (Egon Willighagen <egonw@users.sourceforge.net>)
* Added missing @TestMethod annotation (Egon Willighagen <egonw@users.sourceforge.net>)
* Converted all readers to the new read() API (Egon Willighagen <egonw@users.sourceforge.net>)
* Branch open for 1.3.8 patches (Egon Willighagen <egonw@users.sourceforge.net>)
* Compile fixes caused by rebasing artefacts as some modules still change bits in order modules (Egon Willighagen <egon.willighagen@gmail.com>)
* Refactored reaction boxes into a IGeneratorParameter (Egon Willighagen <egon.willighagen@gmail.com>)
* Refactored foreground color into a IGeneratorParameter (Egon Willighagen <egon.willighagen@gmail.com>)
* Refactored showIm/ExplicitHydrogens as IGeneratorParameter (Egon Willighagen <egon.willighagen@gmail.com>)
* Using IRenderer<T> interface instead of implementation (maclean <gilleain.torrance@gmail.com>)
* More types in renderers, and associations between renderers (maclean <gilleain.torrance@gmail.com>)
* Point to the interfaces rather than the implementation (Egon Willighagen <egon.willighagen@gmail.com>)
* Refactored into IRenderer<T extends IChemObject> with modules implementations for IAtomContainer (the existing AtomContainerRenderer), IMoleculeSet, IReaction, IReactionSet, and IChemModel (all for from the existing, overloaded Renderer) (render). (Egon Willighagen <egon.willighagen@gmail.com>)
* Yeah, the last fix. The 'render' module is now PMD, JUnit4, and JavaDoc clean (Egon Willighagen <egon.willighagen@gmail.com>)
* More JavaDoc and PMD fixes: removed an unused parameter, throws non-generic exception, fixed JavaDoc errors and added missing JavaDoc (render). (Egon Willighagen <egon.willighagen@gmail.com>)
* Fixed some PMD warnings: longer variable names (render). (Egon Willighagen <egon.willighagen@gmail.com>)
* Fixed a NPE: if the atom does not have a atomic number defined, return the default color (Egon Willighagen <egon.willighagen@gmail.com>)
* Added missing unit tests and matching annotation for the render module (Egon Willighagen <egon.willighagen@gmail.com>)
* Added a few missing test methods for the RendererModel (Egon Willighagen <egon.willighagen@gmail.com>)
* Added missing TestClass/-Method annotations and test methods for the default colors (Egon Willighagen <egon.willighagen@gmail.com>)
* JavaDoc updates: added missing bits (render). (Egon Willighagen <egon.willighagen@gmail.com>)
* Added missing dependency of test-render on annotation (Egon Willighagen <egon.willighagen@gmail.com>)
* Report the unregistered parameter class name (Egon Willighagen <egon.willighagen@gmail.com>)
* Fixed getting the default value of a parameter: do not reuse getParameter() but use some local logic to instantiate a new instance if needed (Egon Willighagen <egon.willighagen@gmail.com>)
* Added the RendererModel.get(paramType) convenience method (Egon Willighagen <egon.willighagen@gmail.com>)
* Renamed get/setRenderingParameter methods to shorter names (render). (Egon Willighagen <egon.willighagen@gmail.com>)
* Throw an exception when a parameter value is requested, but not set yet by registering the appropriate generator (Egon Willighagen <egon.willighagen@gmail.com>)
* Added getDefaultRenderingParameter convience method, using generics powers (Egon Willighagen <egon.willighagen@gmail.com>)
* Added setRenderingParameter convenience method, using generics powers (Arvid Berg <goglepox@users.sourceforge.net>)
* Removed obsolete RenderingPatameters class (Egon Willighagen <egon.willighagen@gmail.com>)
* Changed wedge width to rendering parameter (maclean <gilleain.torrance@gmail.com>)
* Removed IAtomContainerGenerator and IReactionGenerator in favor if using generics: IGenerator<T extends IChemObject> (render). (Egon Willighagen <egon.willighagen@gmail.com>)
* Moved ExternalHighlightColor into RendererModel for now, to solve a compile dependency (Egon Willighagen <egon.willighagen@gmail.com>)
* Converted hoverOverColor to the new rendering parameter API (Egon Willighagen <egon.willighagen@gmail.com>)
* Converted externalHighlightColor to the new rendering parameter API (Egon Willighagen <egon.willighagen@gmail.com>)
* Converted mappingColor and mappingLineWidth to the new rendering parameter API (Egon Willighagen <egon.willighagen@gmail.com>)
* Converted boundsColor to the new rendering parameter API (Egon Willighagen <egon.willighagen@gmail.com>)
* Converted zoomFactor, scale, bondLength, and arrowHeadWidth to the new rendering parameter API (Egon Willighagen <egon.willighagen@gmail.com>)
* Fixed returning of the actual paramater value, instead of a new instance all the time: getClass().getClass() != getClass() (Egon Willighagen <egon.willighagen@gmail.com>)
* Unit test for returning the parameter value, instead of a new instance all the time (Egon Willighagen <egon.willighagen@gmail.com>)
* Removed to unused imports (Egon Willighagen <egon.willighagen@gmail.com>)
* Split up the old IGenerator interface into IGenerator and IAtomContainerGenerator, the first now only containing the method for getting the parameters (Egon Willighagen <egon.willighagen@gmail.com>)
* Factored out a ColorHash IRenderingParamater (Egon Willighagen <egon.willighagen@gmail.com>)
* Converted BondDistance into an IGeneratorParameter (Egon Willighagen <egon.willighagen@gmail.com>)
* Converted FontName and FontStyle into IGeneratorParameters (Egon Willighagen <egon.willighagen@gmail.com>)
* Converted useAntiAliasing into a IGeneratorParameter (Egon Willighagen <egon.willighagen@gmail.com>)
* Converted ringProportion to IGeneratorParameter variants (Egon Willighagen <egon.willighagen@gmail.com>)
* Converted showAromaticity and cdkStyleAromaticity to IGeneratorParameter variants (Egon Willighagen <egon.willighagen@gmail.com>)
* Converted bondWidth and defaultBondColor into IGeneratorParameter's (Egon Willighagen <egon.willighagen@gmail.com>)
* Removed last four rendering parameters from BasicAtomGenerator: isCompact, compactShape, isKekule, and showEndCarbons (Egon Willighagen <egon.willighagen@gmail.com>)
* Moved the atom radius into the new rendering parameter API (renderbasic module) (Egon Willighagen <egon.willighagen@gmail.com>)
* Moved rendering parameters for atom draw colors to the new IGeneratorParameter API (Egon Willighagen <egon.willighagen@gmail.com>)
* Removed the background color from the RenderingModel and placed it in a new BasicSceneGenerator (Egon Willighagen <egon.willighagen@gmail.com>)
* Added a method to list all rendering parameters know to the current renderer (Egon Willighagen <egon.willighagen@gmail.com>)
* Added missing @cdk.githash tags (Egon Willighagen <egon.willighagen@gmail.com>)
* The default atom color is white, not black, according to the implementation (Egon Willighagen <egon.willighagen@gmail.com>)
* Fixed a null pointer exception: return the default color, if the atom has no charge (Egon Willighagen <egon.willighagen@gmail.com>)
* Updated test: apparently, the values for Color.PINK can change between JVM releases? (Egon Willighagen <egon.willighagen@gmail.com>)
* Made method public static, as expected by the JUnit framework (Egon Willighagen <egon.willighagen@gmail.com>)
* Converted margin into the RenderingParameter variant (Egon Willighagen <egon.willighagen@gmail.com>)
* Changed generic definition (Arvid Berg <goglepox@users.sourceforge.net>)
* Moved the atom radius into the new rendering parameter API (render module) (Egon Willighagen <egon.willighagen@gmail.com>)
* Moved rendering parameters for atom draw colors to the new IGeneratorParameter API (Egon Willighagen <egon.willighagen@gmail.com>)
* Set up a API to retrieve a IRenderingParameter from the RenderModel (Egon Willighagen <egon.willighagen@gmail.com>)
* Return the default if the value has not been overwritten with setValue() (Scooter Morris <scooter@cgl.ucsf.edu>)
* Changed getParameters() to use IGeneratorParameter<?> (Arvid Berg <goglepox@users.sourceforge.net>)
* Applied Arvids suggestions: use generics instead of Object; also now provides an abstract default class which IGeneratorParameter implementation can inherit for the basic get/set functionality (Egon Willighagen <egon.willighagen@gmail.com>)
* Added an IGeneratorParameter interface, to tie parameters to the modules to which they apply. Parameters *can* be reused, by following the rendering module dependencies. (Egon Willighagen <egon.willighagen@gmail.com>)
* Added missing JavaDoc to render interfaces (Egon Willighagen <egon.willighagen@gmail.com>)
* Added missing JavaDoc for getColor() methods (Egon Willighagen <egon.willighagen@gmail.com>)
* Added IRenderer methods needed for the Controllers. (Egon Willighagen <egon.willighagen@gmail.com>)
* Introducing IRenderer, to solve some dependencies (Egon Willighagen <egon.willighagen@gmail.com>)
* Setting up the new render infrastructure. (Egon Willighagen <egon.willighagen@gmail.com>)#!/usr/bin/groovy

/* Copyright (C) 2009  Egon Willighagen <egonw@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 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.
 */
import java.util.regex.Matcher
import java.util.regex.Pattern

def nightly = "http://pele.farmbio.uu.se/nightly-1.2.x/"

ant = new AntBuilder()

ant.delete(dir:"doc/modules")
ant.mkdir(dir:"doc/modules")

def basedir = new File("src/META-INF")
files = new ArrayList();
if (args[0] != null) {
  files.add(new File(basedir, args[0] + ".cdkdepends"));
} else {
  files = basedir.listFiles().grep(~/.*cdkdepends$/)
  files.add(new File(basedir,"annotation.cdkdepends"))
  files.add(new File(basedir,"interfaces.cdkdepends"))
}
files.each { file ->
  println "Processing $file";
  m = (file =~ ~/\/([-|\w]*)\.cdkdepends/)
  module = m[0][1]

  def writer = new StringWriter()  
  def builder = new groovy.xml.MarkupBuilder(writer) 
  builder.html(){ 
    head(){ 
      title("CDK Module: " + module){} 
    } 
    body(){
      h1("CDK Module: " + module)
      if (!module.contains("test")) {
        h2("QA Reports")
        p(){
          localReport = new File("reports/result-"+module + ".txt")
          if (localReport.exists()) {
            // use local
            localReport.eachLine {
              if (it =~ ~/Tests\srun/) {
                stats = it
              }
            }
            span("JUnit: " + stats)
          } else {
            // use remote
            junitURL = nightly+"test/result-"+module
            stats = "";
            try {
              junitURL.toURL().eachLine {
                if (it =~ ~/Tests\srun/) {
                  stats = it
                }
              }
              a(href:junitURL,"JUnit")
              span(": " + stats)
            } catch (FileNotFoundException exc) {
            } catch (SocketException exc) {}
          }
        }
      }
      p(){
        a(href:nightly+"javadoc/$module/", "DocCheck Results")
      }
      p(){
        span("PDM: ")
        localReport = new File("reports/pmd/"+module + ".xml")
        if (localReport.exists()) {
          def pmd = null
          try {
            pmd = new XmlParser().parseText(localReport.text)
            span("Violations=" + pmd.file.violation.size())
          } catch (Exception exception) {}
        } else {
          a(href:nightly+"pmd/"+module+".html", "all")
        }
        localReport = new File("reports/pmd-unused/"+module + ".xml")
        if (localReport.exists()) {
          def pmd = null
          try {
            pmd = new XmlParser().parseText(localReport.text)
            span("Violations=" + pmd.file.violation.size())
          } catch (Exception exception) {}
        } else {
          a(href:nightly+"pmd-unused/"+module+".html", "unused")
        }
        localReport = new File("reports/pmd-migrating/"+module + ".xml")
        if (localReport.exists()) {
          def pmd = null
          try {
            pmd = new XmlParser().parseText(localReport.text)
            span("Violations=" + pmd.file.violation.size())
          } catch (Exception exception) {}
        } else {
          a(href:nightly+"pmd-migrating/"+module+".html", "migration")
        }
      }
      h2("Depends")
      p(){
        if (file.exists()) {
          b("CDK")
          file.text.eachLine{
            dependency = (it =~ ~/cdk-([-|\w]*)\.jar/)[0][1]
            a(href:dependency+".html", dependency)
          }
        }
      }
      libdepends = new File(basedir, module + ".libdepends")
      p(){
        if (libdepends.exists()) {
          b("Libraries")
          ul() {
            libdepends.text.eachLine{ libdep ->
              if (libdep.length() > 0) {
                p() {
                  span(libdep + ": ")
                  configFile = new File("jar/" + libdep + ".meta")
                  if (configFile.exists()) {
                    config = readProperties(configFile);
                    ul() {
                      config.keySet().each { section ->
                        libProps = config.get(section);
                        p() {
                          span(libProps.get("Library"))
                          if (libProps.containsKey("Version")) {
                            span(" " + libProps.get("Version"))
                          }
                          br()
                          if (libProps.containsKey("Copyright")) {
                            span(libProps.get("Copyright"))
                            br()
                          }
                          span(libProps.get("License"))
                        }
                      }
                    }
                  }
                }
              }
            }
          }
        }
      }
      h2("Classes")
      classes = new File("build/" + module + ".javafiles").text
      classes.eachLine {
        classURL = it.replaceAll(/.java/,"")
        clazz = classURL.replaceAll(/\//,".")
        a(href:nightly+"api/"+classURL+".html", clazz)
        br()
      }
    }
  } 
  new File("doc/modules/" + module + ".html").write(writer.toString())
}

public Map readProperties(File file) {
  Map props = new HashMap();
  Map sectionProps = null;
  file.text.eachLine { line ->
    line.trim();
    if (line.startsWith("#")) {
      // skip line
    } else if (line.startsWith("[") && line.endsWith("]")) {
      section = line.substring(line.indexOf("[")+1, line.indexOf("]"));
      sectionProps = new HashMap();
      props.put(section, sectionProps);
    } else if (line.contains("=")) {
      def keyValue = line.split("=")
      if (sectionProps == null) {
        print "ERROR: property without required section header";
        System.exit(-1);
      }
      sectionProps.put(keyValue[0], keyValue[1]);
    }
  }
  return props;
}
<project name="CDK" default="dist-all" basedir=".">

        <property file="build.props"/>

        <!-- directories -->
        <property name="build" value="build" />
        <property name="build.src" value="${build}/src" />
        <property name="sourcedist" value="sourcedist" />
        <property name="dist" value="dist" />
        <property name="doc" value="doc" />
        <property name="src" value="src" />
        <property name="lib" value="jar" />
        <property name="devellib" value="develjar" />
        <property name="src.tests" value="${src}/test/org/openscience/cdk/test" />
        <property name="reports.tests" value="reports" />
        <property name="appjars.dir" value="${dist}/appjars" />
        <property name="metainf" value="${src}/META-INF" />
 
        <!-- jar file names for libraries used for compiling -->
        <property name="javaccjar" value="javacc.jar" />
        <property name="antcontribjar" value="ant-contrib-1.0b3.jar" />
        <property name="vecmathjar" value="vecmath1.2-1.14.jar" />
        <property name="log4jjar" value="log4j.jar" />
        <property name="jgraphtjar" value="jgrapht-0.6.0.jar" />
        <property name="junitjar" value="junit-4.10.jar" />
        <property name="xercesjar" value="xercesImpl-2.9.0.jar" />

        <property environment="env" />

    <!-- Include the JavaNCSS goodies -->
    <taskdef name="javancss" classname="javancss.JavancssAntTask">
        <classpath>
            <pathelement location="${devellib}/${javaccjar}"/>
            <pathelement location="${devellib}/javancss.jar"/>
            <pathelement location="${devellib}/ccl.jar"/>
            <pathelement location="${devellib}/jhbasic.jar"/>
        </classpath>
    </taskdef>
    <!-- Include the ant-contrib goodies -->
    <taskdef resource="net/sf/antcontrib/antlib.xml">
        <classpath>
            <pathelement location="${devellib}/${antcontribjar}"/>
        </classpath>
    </taskdef>

    <target id="info" name="info" depends="check">
            <!-- Gives information about the building process. -->
            <echo message="Platform:" />
            <echo message="             OS: ${os.name}" />
            <echo message="   Architecture: ${os.arch}" />
            <echo message="        Version: ${os.version}" />
            <echo message=" Mac OS/X found: ${isMacOsX}" />
            <echo message="" />
            <echo message="Java/Ant Environment:" />
            <echo message="   Java version: ${java.version}" />
            <echo message="    Java vendor: ${java.vendor}" />
            <echo message="       Java dir: ${java.home}" />
            <echo message="   Java ext dir: ${java.ext.dirs}" />
            <echo message="    Ant version: ${ant.version}" />
            <echo message="    ${ANT_HOME}: ${ant.home}" />
            <echo message="       hasAnt17: ${hasAnt17}" />
            <echo message="" />
            <echo message="CDK Environment:" />
            <echo message="    CDK version: ${version}" />
            <echo message="      build.xml: $Id$" />
            <echo message="    Junit found: ${junit.present}" />
            <echo message=" --- required libraries ---" />
            <echo message="  Vecmath found: ${vecmath.present}" />
            <echo message="    Log4j found: ${log4j.present}" />
            <echo message="  JGraphT found: ${jgrapht.present}" />
            <echo message=" --- distributed (but optional) libraries ---" />
            <echo message="   CMLDOM found: ${cmllibs.present}" />
        </target>

    <!-- See what platform were on -->
    
        <target id="checkPlatforms" name="checkPlatforms">
            <condition property="isMacOsX">
                <and>
                    <os family="mac"/>
                    <os family="unix"/>
                </and>
            </condition>
        </target>

    <target name="checkCopyright" id="checkCopyright" depends="check, customize">
        <echo>Checking copyright info...</echo>
        <mkdir dir="${build}" />
        <javac includes="net/sf/cdk/tools/copyright/CheckCopyrightStatements.java"
            srcdir="${src}/main/" destdir="${build}" optimize="${optimization}"
            debug="${debug}" deprecation="${deprecation}"/>
        <java classpath="${build}" classname="net.sf.cdk.tools.copyright.CheckCopyrightStatements">
              <arg value="${src}/META-INF"/>
              <arg value="${src}/main"/>
              <arg value="${build}"/>
        </java>
    </target>

    <target name="javancss" id="javancss" depends="runDoclet">
        <mkdir dir="${build}" />
        <echo>Calculating source statistics...</echo>
	<javancss srcdir="${src}/main" includes="**/*.java"
            generateReport="true"
            outputfile="${build}/cdk_metrics.xml"
            format="plain"
	    classMetrics="false"
	    functionMetrics="false"
	/>
	<javancss srcdir="${src}/test" includes="**/*.java"
            generateReport="true"
            outputfile="${build}/cdktest_metrics.xml"
            format="plain"
	    classMetrics="false"
	    functionMetrics="false"
	/>
    </target>

    <!-- Regenerate template fingerprints in case the fingerprint code has been updated
	 so that fingerprint bits are different from a previous version -->
    <target name="makefp3d" id="makefp3d">
      <antcall target="compile-module"><param name="module" value="builder3dtools"/></antcall>
      <gunzip src="${src}/main/org/openscience/cdk/modeling/builder3d/data/ringTemplateStructures.sdf.gz"
	      dest="${src}/main/org/openscience/cdk/modeling/builder3d/data/" />
      <java classname="org.openscience.cdk.modeling.builder3d.TemplateExtractor">
	<classpath>
	  <pathelement location="jar/${jgraphtjar}"/>
          <pathelement location="jar/${xercesjar}"/>
          <pathelement location="jar/${vecmathjar}"/>
          <pathelement path="${dist}/jar/cdk-builder3dtools.jar" />
          <pathelement path="${dist}/jar/cdk-interfaces.jar" />
          <pathelement path="${dist}/jar/cdk-nonotify.jar" />
          <pathelement path="${dist}/jar/cdk-standard.jar" />
          <pathelement path="${dist}/jar/cdk-core.jar" />
          <pathelement path="${dist}/jar/cdk-io.jar" />
          <pathelement path="${dist}/jar/cdk-ioformats.jar" />
          <pathelement path="${dist}/jar/cdk-data.jar" />
          <pathelement path="${dist}/jar/cdk-isomorphism.jar" />
          <pathelement path="${dist}/jar/cdk-fingerprint.jar" />
	</classpath>
	<arg value="${src}/main/org/openscience/cdk/modeling/builder3d/data/ringTemplateStructures.sdf" />
	<arg value="${src}/main/org/openscience/cdk/modeling/builder3d/data/ringTemplateFingerprints.txt" />
	<arg value="True" />
	<arg value="True" />
      </java>
      <gzip src="${src}/main/org/openscience/cdk/modeling/builder3d/data/ringTemplateFingerprints.txt"
	    destfile="${src}/main/org/openscience/cdk/modeling/builder3d/data/ringTemplateFingerprints.txt.gz" />
      <delete file="${src}/main/org/openscience/cdk/modeling/builder3d/data/ringTemplateStructures.sdf"/>
      <delete file="${src}/main/org/openscience/cdk/modeling/builder3d/data/ringTemplateFingerprints.txt"/>
    </target>

</project>
<project name="CDK Documentation" default="doc" basedir=".">

    <property name="build.dir" value="build" />
    <property name="doc.dir" value="doc" />
    <property name="docbook-xsl" value="docbook-xsl-1.61.2" />
    <property name="docbook.dir" value="${build.dir}/${docbook-xsl}" />

    <target id="init" name="init">
        <tstamp />
        <mkdir dir="${build.dir}" />
        <uptodate property="userGuide.uptodate" targetfile="${build.dir}/${doc.dir}/UserGuide/index.html">
            <srcfiles dir="${doc.dir}/user-guide" includes="*.xml" />
        </uptodate>
        <uptodate property="docbook-xsl.uptodate"
	        targetfile="${build.dir}/${docbook-xsl}"
	        srcfile="${doc.dir}/${docbook-xsl}.tar.gz" />
    </target>

    <target name="initdoc" depends="check.docbook" />
  
    <target name="check.docbook" depends="init" unless="docbook-xsl.uptodate" >
        <delete dir="${build.dir}/${docbook-xsl}" />
        <mkdir dir="${build.dir}/${docbook-xsl}" />
        <untar src="${doc.dir}/${docbook-xsl}.tar.gz" dest="${build.dir}"
            compression="gzip" />
    </target>

    <target name="userGuide" id="userGuide" depends="initdoc" unless="userGuide.uptodate" >
        <echo message="Generating UserGuide" />
        <mkdir dir="${build.dir}/${doc.dir}/UserGuide" />
        <xslt basedir="${doc.dir}/user-guide"
              includes="guide.xml" 
              destdir="${build.dir}/${doc.dir}/UserGuide" 
              style="${docbook.dir}/html/chunk.xsl"/>
    </target>

    <target id="doc" name="doc" depends="userGuide"/>
    
    <target id="clean" name="clean" description="Removes files and dirs that can be restored by other tasks">
        <delete dir="${build.dir}/${doc.dir}" />
        <delete dir="${build.dir}/${docbook-xsl}" />
    </target>

</project>



<project name="CDK" default="html" basedir=".">

    <property file="build.props"/>

    <!-- $Id$ -->

    <property name="vecmath.src" value="gcj/vecmath" />
    <property name="vecmath.javadoc.dir" value="doc/vecmath/api" />

    <property name="src" value="src" />
    <property name="javadoc.dir" value="doc/cdk-javadoc-${version}" />
    <property name="doxygen.dir" value="doc/doxygen" />

    <property name="pathtojava3d" value="" />

    <!-- directories -->
    <property name="build" value="build" />
    <property name="lib" value="jar" />
    <property name="devellib" value="develjar" />
    <property name="dist" value="dist" />
    <property name="metainf" value="${src}/META-INF" />

	<!-- Used in the html task to properly link to java library classes -->
	<property name="javaURL" value="http://java.sun.com/j2se/1.5.0/docs/api/"/>
	
    <path id="project.class.path">
        <pathelement location="." />
        <fileset dir="jar">
            <include name="*.jar" />
        </fileset>
        <fileset dir="${pathtojava3d}">
            <include name="*.jar" />
        </fileset>
    </path>

    <taskdef name="doxygen" classname="org.doxygen.tools.DoxygenTask"
            classpath="develjar/ant_doxygen.jar" />

    <target name="doxygen" id="doxygen">
        <mkdir dir="${doxygen.dir}" />
        <doxygen>
            <property name="INPUT" value="src/" />
            <property name="PROJECT_NAME" value="The Chemistry Development Kit" />
            <property name="OUTPUT_DIRECTORY" value="${doxygen.dir}" />
            <property name="OPTIMIZE_OUTPUT_JAVA" value="YES" />
            <property name="UML_LOOK" value="YES" />
            <property name="ALIASES" value='"cdk.module=Is part of the CDK module:"' />
        </doxygen>
    </target>

</project>



<project name="CDK" default="html" basedir=".">

    <property file="build.props"/>

    <!-- $Id$ -->

    <property name="vecmath.src" value="gcj/vecmath" />
    <property name="vecmath.javadoc.dir" value="doc/vecmath/api" />

    <property name="src" value="src" />
    <property name="javadoc.dir" value="doc/cdk-javadoc-${version}" />

    <property name="pathtojava3d" value="" />

    <!-- directories -->
    <property name="build" value="build" />
    <property name="lib" value="jar" />
    <property name="devellib" value="develjar" />
    <property name="dist" value="dist" />
    <property name="metainf" value="${src}/META-INF" />

	<!-- Used in the html task to properly link to java library classes -->
	<property name="javaURL" value="http://java.sun.com/j2se/1.5.0/docs/api/"/>
	
    <path id="project.class.path">
        <pathelement location="." />
        <fileset dir="jar">
            <include name="*.jar" />
        </fileset>
        <fileset dir="${pathtojava3d}">
            <include name="*.jar" />
        </fileset>
    </path>

    <target name="html" depends="compileTaglets">
        <mkdir dir="${javadoc.dir}" />

        <!-- Call javacc target in build.xml to re-generate the source code -->
        <ant antfile="build.xml" target="javacc"/>
   <tstamp>
                <format property="TODAY_SVN" pattern="yyyyMMdd" locale="en" />
            </tstamp>
        <javadoc destdir="${javadoc.dir}"
                 author="true" version="true" use="true"
                 public="true"
                 encoding="UTF-8"
                 windowtitle="CDK ${version} API - created on ${TODAY_SVN}">
            <classpath>
                <pathelement location="." />
                <fileset dir="${lib}">
                    <include name="*.jar" />
                </fileset>
                <pathelement location="." />
                <fileset dir="${lib}/jena">
                    <include name="*.jar" />
                </fileset>
                <fileset dir="${devellib}">
                    <include name="*.jar" />
                </fileset>
                 <dirset dir="src/main">
                     <include name="net/**/*"/>
                 </dirset>
            </classpath>
            <tag name="cdk.set" scope="all" description="Belongs to the set:" />
            <tag name="cdk.keyword" scope="all" description="Keywords:" />
            <tag name="cdk.created" scope="all" description="Created on:" />
            <tag name="cdk.require" scope="all" description="Requires:" />
            <tag name="cdk.depends" scope="all" description="Required library to be able to run this class:" />
            <tag name="cdk.builddepends" scope="all" description="Required library to be able to compile this class:" />
            <tag name="cdk.todo" scope="all" description="To do:" />
            <tag name="cdk.license" scope="all" description="License:" />
            <taglet name="net.sf.cdk.tools.doclets.CDKCiteTaglet" path="jar/xom-1.1.jar:src/main" />
            <taglet name="net.sf.cdk.tools.doclets.CDKModuleTaglet" path="jar/xom-1.1.jar:src/main" />
            <taglet name="net.sf.cdk.tools.doclets.CDKBugTaglet" path="jar/xom-1.1.jar:src/main" />
            <taglet name="net.sf.cdk.tools.doclets.CDKDictRefTaglet" path="jar/xom-1.1.jar:src/main" />
            <taglet name="net.sf.cdk.tools.doclets.CDKInChITaglet" path="jar/xom-1.1.jar:src/main" />
            <taglet name="net.sf.cdk.tools.doclets.CDKThreadSafeTaglet" path="jar/xom-1.1.jar:src/main" />
            <taglet name="net.sf.cdk.tools.doclets.CDKThreadNonSafeTaglet" path="jar/xom-1.1.jar:src/main" />
            <taglet name="net.sf.cdk.tools.doclets.CDKGitTaglet" path="jar/xom-1.1.jar:src/main" />
            <taglet name="net.sf.cdk.tools.doclets.CDKIOOptionsTaglet" path="jar/xom-1.1.jar:src/main">
              <path>
                <pathelement location="." />
                <fileset dir="dist/jar">
                  <include name="*.jar" />
                </fileset>
                <fileset dir="${lib}">
                  <include name="*.jar" />
                </fileset>
                <fileset dir="${lib}/jena">
                  <include name="*.jar" />
                </fileset>
              </path>
            </taglet>
            <packageset dir="${src}/main" defaultexcludes="yes">
                <include name="org/openscience/cdk/**" />
            </packageset>
        	<link href="${javaURL}"/>
        </javadoc>
    </target>

    <target name="vecmath.html">
        <mkdir dir="${vecmath.javadoc.dir}" />

        <javadoc destdir="${vecmath.javadoc.dir}"
                 author="true" version="true" use="true"
                 public="true"
                 windowtitle="VecMath API">
            <classpath refid="project.class.path" />
            <packageset dir="${vecmath.src}" defaultexcludes="yes">
                <include name="javax/vecmath/**" />
            </packageset>
        </javadoc>
    </target>

  <target name="jjdoc" description="Create JJDoc documentation from the .jj file">   
    <mkdir dir="doc/iupac-parser"/>
    <jjdoc target="${src}/main/org/openscience/cdk/iupac/parser/NomParser.jj"
      outputfile="doc/iupac-parser/ParserBNF.html"
      javacchome="jar"/>
  </target>

  <target name="ojdcheck" depends="compileDocTests">
      <antcall target="ojdcheck-module"><param name="module" value="interfaces"/></antcall>
      <antcall target="ojdcheck-module"><param name="module" value="core"/></antcall>
      <antcall target="ojdcheck-module"><param name="module" value="cip"/></antcall>
      <antcall target="ojdcheck-module"><param name="module" value="data"/></antcall>
      <antcall target="ojdcheck-module"><param name="module" value="datadebug"/></antcall>
      <antcall target="ojdcheck-module"><param name="module" value="standard"/></antcall>
      <antcall target="ojdcheck-module"><param name="module" value="atomtype"/></antcall>
      <antcall target="ojdcheck-module"><param name="module" value="dict"/></antcall>
      <antcall target="ojdcheck-module"><param name="module" value="io"/></antcall>
      <antcall target="ojdcheck-module"><param name="module" value="ioformats"/></antcall>
      <antcall target="ojdcheck-module"><param name="module" value="iordf"/></antcall>
      <antcall target="ojdcheck-module"><param name="module" value="inchi"/></antcall>
      <antcall target="ojdcheck-module"><param name="module" value="extra"/></antcall>
      <antcall target="ojdcheck-module"><param name="module" value="fingerprint"/></antcall>
      <antcall target="ojdcheck-module"><param name="module" value="formula"/></antcall>
      <antcall target="ojdcheck-module"><param name="module" value="render"/></antcall>
      <antcall target="ojdcheck-module"><param name="module" value="renderextra"/></antcall>
      <antcall target="ojdcheck-module"><param name="module" value="reaction"/></antcall>
      <antcall target="ojdcheck-module"><param name="module" value="libiocml"/></antcall>
      <antcall target="ojdcheck-module"><param name="module" value="libiomd"/></antcall>
      <antcall target="ojdcheck-module"><param name="module" value="log4j"/></antcall>
      <antcall target="ojdcheck-module"><param name="module" value="builder3d"/></antcall>
      <antcall target="ojdcheck-module"><param name="module" value="smiles"/></antcall>
      <antcall target="ojdcheck-module"><param name="module" value="smarts"/></antcall>
      <antcall target="ojdcheck-module"><param name="module" value="sdg"/></antcall>
      <antcall target="ojdcheck-module"><param name="module" value="tautomer"/></antcall>
      <antcall target="ojdcheck-module"><param name="module" value="forcefield"/></antcall>
      <antcall target="ojdcheck-module"><param name="module" value="pdb"/></antcall>
      <antcall target="ojdcheck-module"><param name="module" value="qsar"/></antcall>
      <antcall target="ojdcheck-module"><param name="module" value="qsaratomic"/></antcall>
      <antcall target="ojdcheck-module"><param name="module" value="qsarbond"/></antcall>
      <antcall target="ojdcheck-module"><param name="module" value="qsarionpot"/></antcall>
      <antcall target="ojdcheck-module"><param name="module" value="qsarmolecular"/></antcall>
      <antcall target="ojdcheck-module"><param name="module" value="qsarprotein"/></antcall>
      <antcall target="ojdcheck-module"><param name="module" value="pcore"/></antcall>
      <antcall target="ojdcheck-module"><param name="module" value="structgen"/></antcall>
      <antcall target="ojdcheck-module"><param name="module" value="valencycheck"/></antcall>
      <antcall target="ojdcheck-module"><param name="module" value="charges"/></antcall>
      <antcall target="ojdcheck-module"><param name="module" value="diff"/></antcall>
      <antcall target="ojdcheck-module"><param name="module" value="smsd"/></antcall>
      <antcall target="ojdcheck-module"><param name="module" value="signature"/></antcall>
      <antcall target="ojdcheck-module"><param name="module" value="renderawt"/></antcall>
      <antcall target="ojdcheck-module"><param name="module" value="renderbasic"/></antcall>
    </target>

    <target name="ojdcheck-module">
        <mkdir dir="reports/ojdcheck/"/>
        <mkdir dir="${build}/src/${module}"/>
        <copy todir="${build}/src/${module}">
            <fileset dir="${src}/main">
                <includesfile name="${build}/${module}.javafiles"/>
            </fileset>
        </copy>

        <!-- check for availability for meta info files -->
        <available file="${metainf}/${module}.cdkdepends" property="module.cdkdepends.present"/>
        <available file="${metainf}/${module}.libdepends" property="module.libdepends.present"/>
        <available file="${metainf}/${module}.devellibdepends" property="module.devellibdepends.present"/>

    	<javadoc private="false" public="true">
        	<classpath>
        	    <fileset dir="${dist}/jar" >
        	        <exclude name="**/*" unless="module.cdkdepends.present" />
        	        <includesfile name="${metainf}/${module}.cdkdepends" if="module.cdkdepends.present" />
        	    </fileset>
        	    <fileset dir="${lib}" >
        	        <exclude name="**/*" unless="module.libdepends.present" />
        	        <includesfile name="${metainf}/${module}.libdepends" if="module.libdepends.present" />
        	    </fileset>
        	    <fileset dir="${devellib}">
        	        <exclude name="**/*" unless="module.devellibdepends.present" />
        	        <includesfile name="${metainf}/${module}.devellibdepends" if="module.devellibdepends.present" />
                    </fileset>
        	</classpath>

            <doclet name="com.github.ojdcheck.OpenJavaDocCheck"
                    path="develjar/ojdcheck.jar:src/main">
              <param name="-xhtml"/>
              <param name="-file"
                    value="reports/ojdcheck/${module}.html"/>
              <param name="-tests"
                    value="net.sf.cdk.tools.checkdoctest.MissingGithashTagletTest,net.sf.cdk.tools.checkdoctest.MissingModuleTagletTest,net.sf.cdk.tools.checkdoctest.IncorrectBugNumberTagletTest"/>
            </doclet>
            <sourcepath>
              <pathelement path="${build}/src/${module}"/>
            </sourcepath>
        </javadoc>
    </target>

  <target id="check" name="check">
    <condition property="isMacOsX">
      <and>
        <os family="mac"/>
        <os family="unix"/>
      </and>
    </condition>
  </target>

  <target name="compileTaglets" id="compileTaglets" depends="check, compileTaglets.MacOSX, compileTaglets.Other" />

  <target name="compileTaglets.MacOSX" id="compileTaglets.MacOSX" if="isMacOsX">
    <javac srcdir="src" destdir="src"
           includes="*Taglet.java" debug="on" optimize="off"/>
  </target>

  <target name="compileTaglets.Other" id="compileTaglets.Other" unless="isMacOsX">
    <javac srcdir="src/main" destdir="src/main"
         includes="net/sf/cdk/tools/**/*Taglet.java" debug="on" optimize="off">
      <classpath>
        <fileset dir="jar/">
          <include name="xom-1.1.jar" />
        </fileset>
      </classpath>
    </javac>
  </target>

  <target name="compileDocTests" id="compileDocTests"
       depends="check">
    <javac srcdir="src/main" destdir="src/main"
           includes="net/sf/cdk/tools/checkdoctest/*Test.java"
           debug="on" optimize="off">
      <classpath>
        <fileset dir="develjar/">
          <include name="ojdcheck.jar" />
          <include name="com-sun-*.jar" />
        </fileset>
      </classpath>
    </javac>
  </target>
</project>



Manifest-Version: 1.0
X-COMMENT: Main-Class will be added automatically by build

<?xml version="1.0" encoding="UTF-8"?>
<?eclipse version="3.0"?>
<plugin>

</plugin>
<?xml version="1.0"?>
<project name="CDK" default="pmd" basedir=".">

    <property name="lib" value="develjar" />
    <property name="build" value="build" />
    <property name="src" value="src" />
    <property name="reports.tests" value="reports" />

    <path id="pmd.classpath">
        <pathelement location="${build}"/>
        <fileset dir="${lib}">
          <include name="asm-3.1.jar"/>
          <include name="junit-4.4.jar"/>
          <include name="pmd-4.3.jar"/>
          <include name="jaxen-1.1.1.jar"/>
        </fileset>
    </path>

    <target name="compileRenderer" id="compileRenderer">
        <javac srcdir="pmd" destdir="${build}"
               includes="net/sourceforge/pmd/renderers/SummaryVBHTMLRenderer.java">
            <classpath refid="pmd.classpath" />
        </javac>
    </target>

    <taskdef name="pmd" id="pmd" classname="net.sourceforge.pmd.ant.PMDTask" classpathref="pmd.classpath"/>

    <target name="pmd" id="pmd">
      <!-- the data classes modules -->
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="data"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="datadebug"/></antcall>
      <!-- the other modules -->
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="interfaces"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="core"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="cip"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="standard"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="atomtype"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="io"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="extra"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="formula"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="render"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="renderbasic"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="renderawt"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="renderextra"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="reaction"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="libiocml"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="builder3d"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="smiles"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="smarts"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="tautomer"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="pcore"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="forcefield"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="qsar"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="qsaratomic"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="qsarbond"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="qsarmolecular"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="qsarprotein"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="structgen"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="valencycheck"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="charges"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="diff"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="smsd"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="signature"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating-qm"/><param name="module" value="qm"/></antcall>
      <!-- the test modules -->
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="test-core"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="test-cip"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="test-interfaces"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="test-data"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="test-datadebug"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="test-atomtype"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="test-extra"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="test-forcefield"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="test-io"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="test-reaction"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="test-smiles"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="test-standard"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="test-tautomer"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="test-valencycheck"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="test-charges"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="test-pcore"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="test-qsar"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="test-qsaratomic"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="test-qsarbond"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="test-qsarmolecular"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="test-qsarprotein"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="test-diff"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="test-qm"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="test-smsd"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="test-signature"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="test-render"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="test-renderbasic"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="test-renderawt"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="test-renderextra"/></antcall>
    </target>

    <target id="test-module" name="test-module"
            description="Checks for migrating code updates in the given CDK module.">

      <echo message="Checking for migrating code updates in CDK's ${module} module." />

      <mkdir dir="${reports.tests}/pmd-migrating"/>
      
      <pmd shortFilenames="true" rulesetfiles="pmd/${pmd.test}.xml">
        <formatter type="xml" toFile="${reports.tests}/pmd-migrating/${module}.xml"/>
        <fileset dir="${src}/main">
          <includesfile name="${build}/${module}.javafiles"/>
        </fileset>
        <fileset dir="${src}/test">
          <includesfile name="${build}/${module}.javafiles"/>
        </fileset>
      </pmd>
    </target>

</project>
<?xml version="1.0"?>
<project name="CDK" default="pmd" basedir=".">

    <property name="lib" value="develjar" />
    <property name="build" value="build" />
    <property name="src" value="src" />
    <property name="reports.tests" value="reports" />

    <path id="pmd.classpath">
        <pathelement location="${build}"/>
        <fileset dir="${lib}">
          <include name="asm-3.1.jar"/>
          <include name="junit-4.4.jar"/>
          <include name="pmd-4.3.jar"/>
          <include name="jaxen-1.1.1.jar"/>
        </fileset>
    </path>

    <target name="compileRenderer" id="compileRenderer">
        <javac srcdir="pmd" destdir="${build}"
               includes="net/sourceforge/pmd/renderers/SummaryVBHTMLRenderer.java">
            <classpath refid="pmd.classpath" />
        </javac>
    </target>

    <taskdef name="pmd" id="pmd" classname="net.sourceforge.pmd.ant.PMDTask" classpathref="pmd.classpath"/>

    <target name="pmd" id="pmd">
      <!-- the data classes modules -->
      <antcall target="test-module"><param name="module" value="data"/></antcall>
      <antcall target="test-module"><param name="module" value="datadebug"/></antcall>
      <!-- the other modules -->
      <antcall target="test-module"><param name="module" value="interfaces"/></antcall>
      <antcall target="test-module"><param name="module" value="core"/></antcall>
      <antcall target="test-module"><param name="module" value="cip"/></antcall>
      <antcall target="test-module"><param name="module" value="standard"/></antcall>
      <antcall target="test-module"><param name="module" value="atomtype"/></antcall>
      <antcall target="test-module"><param name="module" value="io"/></antcall>
      <antcall target="test-module"><param name="module" value="extra"/></antcall>
      <antcall target="test-module"><param name="module" value="formula"/></antcall>
      <antcall target="test-module"><param name="module" value="render"/></antcall>
      <antcall target="test-module"><param name="module" value="renderbasic"/></antcall>
      <antcall target="test-module"><param name="module" value="renderawt"/></antcall>
      <antcall target="test-module"><param name="module" value="renderextra"/></antcall>
      <antcall target="test-module"><param name="module" value="reaction"/></antcall>
      <antcall target="test-module"><param name="module" value="libiocml"/></antcall>
      <antcall target="test-module"><param name="module" value="builder3d"/></antcall>
      <antcall target="test-module"><param name="module" value="smiles"/></antcall>
      <antcall target="test-module"><param name="module" value="smarts"/></antcall>
      <antcall target="test-module"><param name="module" value="pcore"/></antcall>
      <antcall target="test-module"><param name="module" value="forcefield"/></antcall>
      <antcall target="test-module"><param name="module" value="qsar"/></antcall>
      <antcall target="test-module"><param name="module" value="qsaratomic"/></antcall>
      <antcall target="test-module"><param name="module" value="qsarbond"/></antcall>
      <antcall target="test-module"><param name="module" value="qsarmolecular"/></antcall>
      <antcall target="test-module"><param name="module" value="qsarprotein"/></antcall>
      <antcall target="test-module"><param name="module" value="structgen"/></antcall>
      <antcall target="test-module"><param name="module" value="tautomer"/></antcall>
      <antcall target="test-module"><param name="module" value="valencycheck"/></antcall>
      <antcall target="test-module"><param name="module" value="charges"/></antcall>
      <antcall target="test-module"><param name="module" value="diff"/></antcall>
      <antcall target="test-module"><param name="module" value="qm"/></antcall>
      <antcall target="test-module"><param name="module" value="smsd"/></antcall>
      <antcall target="test-module"><param name="module" value="iordf"/></antcall>
      <antcall target="test-module"><param name="module" value="signature"/></antcall>
      <!-- the test modules -->
      <antcall target="test-module"><param name="module" value="test-core"/></antcall>
      <antcall target="test-module"><param name="module" value="test-cip"/></antcall>
      <antcall target="test-module"><param name="module" value="test-interfaces"/></antcall>
      <antcall target="test-module"><param name="module" value="test-data"/></antcall>
      <antcall target="test-module"><param name="module" value="test-datadebug"/></antcall>
      <antcall target="test-module"><param name="module" value="test-atomtype"/></antcall>
      <antcall target="test-module"><param name="module" value="test-extra"/></antcall>
      <antcall target="test-module"><param name="module" value="test-forcefield"/></antcall>
      <antcall target="test-module"><param name="module" value="test-io"/></antcall>
      <antcall target="test-module"><param name="module" value="test-reaction"/></antcall>
      <antcall target="test-module"><param name="module" value="test-smiles"/></antcall>
      <antcall target="test-module"><param name="module" value="test-standard"/></antcall>
      <antcall target="test-module"><param name="module" value="test-tautomer"/></antcall>
      <antcall target="test-module"><param name="module" value="test-valencycheck"/></antcall>
      <antcall target="test-module"><param name="module" value="test-charges"/></antcall>
      <antcall target="test-module"><param name="module" value="test-pcore"/></antcall>
      <antcall target="test-module"><param name="module" value="test-qsar"/></antcall>
      <antcall target="test-module"><param name="module" value="test-qsaratomic"/></antcall>
      <antcall target="test-module"><param name="module" value="test-qsarbond"/></antcall>
      <antcall target="test-module"><param name="module" value="test-qsarmolecular"/></antcall>
      <antcall target="test-module"><param name="module" value="test-qsarprotein"/></antcall>
      <antcall target="test-module"><param name="module" value="test-diff"/></antcall>
      <antcall target="test-module"><param name="module" value="test-iordf"/></antcall>
      <antcall target="test-module"><param name="module" value="test-qm"/></antcall>
      <antcall target="test-module"><param name="module" value="test-smsd"/></antcall>
      <antcall target="test-module"><param name="module" value="test-signature"/></antcall>
      <antcall target="test-module"><param name="module" value="test-render"/></antcall>
      <antcall target="test-module"><param name="module" value="test-renderbasic"/></antcall>
      <antcall target="test-module"><param name="module" value="test-renderawt"/></antcall>
      <antcall target="test-module"><param name="module" value="test-renderextra"/></antcall>
    </target>

    <target id="test-module" name="test-module"
            description="Checks for unused code in the given CDK module.">

      <echo message="Checking for unused code in CDK's ${module} module." />

      <mkdir dir="${reports.tests}/pmd-unused"/>
      <pmd shortFilenames="true" rulesetfiles="pmd/unused.xml">
        <formatter type="xml" toFile="${reports.tests}/pmd-unused/${module}.xml"/>
        <fileset dir="${src}/main">
          <includesfile name="${build}/${module}.javafiles"/>
        </fileset>
        <fileset dir="${src}/test">
          <includesfile name="${build}/${module}.javafiles"/>
        </fileset>
      </pmd>
    </target>

</project>
<?xml version="1.0"?>
<project name="CDK" default="pmd" basedir=".">

    <property name="lib" value="develjar" />
    <property name="build" value="build" />
    <property name="src" value="src" />
    <property name="reports.tests" value="reports" />

    <path id="pmd.classpath">
        <pathelement location="${build}"/>
        <fileset dir="${lib}">
          <include name="asm-3.1.jar"/>
          <include name="junit-4.4.jar"/>
          <include name="pmd-4.3.jar"/>
          <include name="jaxen-1.1.1.jar"/>
        </fileset>
    </path>

    <target name="compileRenderer" id="compileRenderer">
        <javac srcdir="pmd" destdir="${build}"
               includes="net/sourceforge/pmd/renderers/SummaryVBHTMLRenderer.java">
            <classpath refid="pmd.classpath" />
        </javac>
    </target>

    <taskdef name="pmd" id="pmd" classname="net.sourceforge.pmd.ant.PMDTask" classpathref="pmd.classpath"/>

    <target name="pmd" id="pmd">
      <!-- the data classes modules -->
      <antcall target="test-module"><param name="pmd.test" value="custom-data"/><param name="module" value="data"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom-data"/><param name="module" value="datadebug"/></antcall>
      <!-- the other modules -->
      <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="interfaces"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="core"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="log4j"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="standard"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="atomtype"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="dict"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="io"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="extra"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="formula"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="render"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="renderbasic"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="renderawt"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="renderextra"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="reaction"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="libiocml"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="libiomd"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="builder3d"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="smiles"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="smarts"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="pcore"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="fingerprint"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="forcefield"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="inchi"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="ioformats"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="pdb"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="qsar"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="qsaratomic"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="qsarbond"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="qsarionpot"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="qsarmolecular"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="qsarprotein"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="structgen"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="sdg"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="tautomer"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="valencycheck"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="charges"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="cip"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="diff"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="smsd"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="iordf"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="signature"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom-qm"/><param name="module" value="qm"/></antcall>
      <!-- the test modules -->
      <antcall target="test-module"><param name="pmd.test" value="custom-test"/><param name="module" value="test-core"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom-test"/><param name="module" value="test-interfaces"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom-test"/><param name="module" value="test-data"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom-test"/><param name="module" value="test-datadebug"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom-test"/><param name="module" value="test-dict"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom-test"/><param name="module" value="test-extra"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom-test"/><param name="module" value="test-forcefield"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom-test"/><param name="module" value="test-atomtype"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom-test"/><param name="module" value="test-io"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom-test"/><param name="module" value="test-reaction"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom-test"/><param name="module" value="test-smiles"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom-test"/><param name="module" value="test-standard"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom-test"/><param name="module" value="test-pcore"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom-test"/><param name="module" value="test-valencycheck"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom-test"/><param name="module" value="test-qsar"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom-test"/><param name="module" value="test-qsaratomic"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom-test"/><param name="module" value="test-qsarbond"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom-test"/><param name="module" value="test-qsarmolecular"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom-test"/><param name="module" value="test-qsarprotein"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom-test"/><param name="module" value="test-charges"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom-test"/><param name="module" value="test-cip"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom-test"/><param name="module" value="test-diff"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom-test"/><param name="module" value="test-qm"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom-test"/><param name="module" value="test-smsd"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom-test"/><param name="module" value="test-tautomer"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom-test"/><param name="module" value="test-log4j"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom-test"/><param name="module" value="test-signature"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom-test"/><param name="module" value="test-iordf"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom-test"/><param name="module" value="test-render"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom-test"/><param name="module" value="test-renderbasic"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom-test"/><param name="module" value="test-renderawt"/></antcall>
      <antcall target="test-module"><param name="pmd.test" value="custom-test"/><param name="module" value="test-renderextra"/></antcall>
    </target>

    <target id="test-module" name="test-module"
            description="Performs a PMD checks for the given CDK module.">

      <echo message="Running PMD checks for CDK's ${module} module." />

      <mkdir dir="${reports.tests}/pmd"/>
      <pmd shortFilenames="true" rulesetfiles="pmd/${pmd.test}.xml">
        <formatter type="xml" toFile="${reports.tests}/pmd/${module}.xml"/>
        <fileset dir="${src}/main">
          <includesfile name="${build}/${module}.javafiles"/>
        </fileset>
        <fileset dir="${src}/test">
          <includesfile name="${build}/${module}.javafiles"/>
        </fileset>
      </pmd>
    </target>

</project>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
  xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
  <modelVersion>4.0.0</modelVersion>
  <groupId>org.openscience.cdk</groupId>
  <artifactId>cdk${dist}</artifactId>
  <version>1.3.6</version>
  <packaging>jar</packaging>
  <name>cdk</name>
   <url>cdk.sourceforge.net</url>
   <distributionManagement>
    <repository>
        <id>ambit-plovdiv</id>
        <url>http://ambit.uni-plovdiv.bg:8083/nexus/content/repositories/thirdparty</url>
    </repository>

  </distributionManagement>
  <inceptionYear>2000</inceptionYear>
 <build>
    <plugins>
      <plugin>
        <groupId>org.jvnet.maven-antrun-extended-plugin</groupId>
        <artifactId>maven-antrun-extended-plugin</artifactId>
        <executions>
          <execution>
            <phase>package</phase>
            <goals>
              <goal>run</goal>
            </goals>
            <configuration>
              <tasks>
                <attachArtifact file="dist/jar/cdk${dist}-${project.version}.jar" />
              </tasks>
            </configuration>
          </execution>
        </executions>
      </plugin>
    </plugins>
    <extensions>
      <extension>
        <groupId>org.jvnet.wagon-svn</groupId>
        <artifactId>wagon-svn</artifactId>
        <version>1.8</version>
      </extension>
    </extensions>
  </build>
  
  <repositories>
    <repository>
      <id>maven2-repository.dev.java.net</id>
      <name>Java.net Repository for Maven</name>
      <url>http://download.java.net/maven/2/</url>
    </repository>
  </repositories>

  <pluginRepositories>
    <pluginRepository>
      <id>maven2-repository.dev.java.net</id>
      <name>Java.net Repository for Maven</name>
      <url>http://download.java.net/maven/2/</url>
    </pluginRepository>
  </pluginRepositories>

 <profiles>
     <profile>
	<id>pure</id>
      <properties>
         <dist>-pure</dist>
      </properties>
  <activation>
        <activeByDefault>false</activeByDefault>
      </activation>

     </profile>
   <profile>
        <id>optional</id>
      <properties>
         <dist>-optional</dist>
      </properties>
    <activation>
        <activeByDefault>false</activeByDefault>
      </activation>

     </profile>
   <profile>
        <id>large</id>
      <activation>
        <activeByDefault>true</activeByDefault>
      </activation>

      <properties>
         <dist></dist>
      </properties>
     </profile>
  <profile>
        <id>test-large</id>
  <activation>
        <activeByDefault>false</activeByDefault>
      </activation>
	
      <properties>
         <dist>-test-large</dist>
      </properties>
     </profile>
 </profiles>  
</project>
@echo off

set CLASSPATH=%CLASSPATH%;dist\jar\cdk-core.jar
set CLASSPATH=%CLASSPATH%;dist\jar\cdk-standard.jar
set CLASSPATH=%CLASSPATH%;dist\jar\cdk-io.jar
set CLASSPATH=%CLASSPATH%;dist\jar\cdk-render.jar
set CLASSPATH=%CLASSPATH%;dist\jar\cdk-extra.jar
set CLASSPATH=%CLASSPATH%;dist\jar\cdk-test.jar
set CLASSPATH=%CLASSPATH%;jar\log4j-core.jar
set CLASSPATH=%CLASSPATH%;jar\log4j.jar
set CLASSPATH=%CLASSPATH%;jar\printf.jar
set CLASSPATH=%CLASSPATH%;jar\vecmath1.2-1.14.jar
set CLASSPATH=%CLASSPATH%;jar\xerces-1.3.0.jar
set CLASSPATH=%CLASSPATH%;jar\baysmith-io.jar
set CLASSPATH=%CLASSPATH%;jar\gnujaxp.jar

java -classpath %CLASSPATH%;jar\junit.jar junit.swingui.TestRunner org.openscience.cdk.test.CDKTests
#! /bin/sh

CLASSPATH=${CLASSPATH}:dist/jar/cdk-core.jar:dist/jar/cdk-standard.jar:dist/jar/cdk-io.jar:dist/jar/cdk-render.jar:dist/jar/cdk-extra.jar:dist/jar/cdk-test.jar:jar/log4j-core.jar:jar/log4j.jar:jar/printf.jar:jar/vecmath1.2-1.14.jar:jar/xerces-1.3.0.jar:jar/baysmith-io.jar:jar/gnujaxp.jar:jar/junit.jar

java -Dcdk.debugging=true -classpath ${CLASSPATH} junit.swingui.TestRunner $*