JCP contains the following libraries. Please read this for comments on copyright etc.

Chemistry Development Kit, master version as of Fri Jul 27 14:05:35 EEST 2012 (http://cdk.sf.net)
Copyright 1997-2009 The CDK Development Team
License: LGPL v2 (http://www.gnu.org/licenses/old-licenses/gpl-2.0.html)
Download: https://sourceforge.net/projects/cdk/files/
Source available at: http://sourceforge.net/scm/?type=git&group_id=20024

Signatures 1.0 (http://github.com/gilleain/signatures)
Copyright Lars Carlsson and Gilleain Torrance
License: MIT licence (http://github.com/gilleain/signatures/blob/master/LICENCE.txt)
Download: null
Source available at: null


JGraphT 0.6.0 (http://jgrapht.sourceforge.net/)
Copyright 2003-2005, by Barak Naveh and Contributors
License: GNU Lesser General Public License, 2.1 (http://jgrapht.sourceforge.net/LGPL.html)
Download: https://sourceforge.net/projects/jgrapht/files/
Source available at: https://sourceforge.net/scm/?type


XML Pull Parser 1.1.4c (http://www.extreme.indiana.edu/xgws/xsoap/xpp/)
Copyright (c) 2001 Extreme! Lab, Indiana University. All rights reserved.
License: Indiana University Extreme! Lab Software License (http://www.extreme.indiana.edu/viewcvs/~checkout~/XPP3/LICENSE.txt)
Download: http://www.extreme.indiana.edu/xgws/xsoap/xpp/download/old_versions/
Source available at: http://www.extreme.indiana.edu/xgws/xsoap/xpp/download/old_versions/

The author says:
Indiana University Extreme! Lab Software License

Version 1.1.1

Copyright (c) 2002 Extreme! Lab, Indiana University. All rights reserved.

Redistribution and use in source and binary forms, with or without 
modification, are permitted provided that the following conditions 
are met:

1. Redistributions of source code must retain the above copyright notice, 
   this list of conditions and the following disclaimer.

2. Redistributions in binary form must reproduce the above copyright 
   notice, this list of conditions and the following disclaimer in 
   the documentation and/or other materials provided with the distribution.

3. The end-user documentation included with the redistribution, if any, 
   must include the following acknowledgment:

  "This product includes software developed by the Indiana University 
  Extreme! Lab (http://www.extreme.indiana.edu/)."

Alternately, this acknowledgment may appear in the software itself, 
if and wherever such third-party acknowledgments normally appear.

4. The names "Indiana University" and "Indiana University Extreme! Lab" 
must not be used to endorse or promote products derived from this 
software without prior written permission. For written permission, 
please contact http://www.extreme.indiana.edu/.

5. Products derived from this software may not use "Indiana University" 
name nor may "Indiana University" appear in their name, without prior 
written permission of the Indiana University.

THIS SOFTWARE IS PROVIDED "AS IS" AND ANY EXPRESSED OR IMPLIED
WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE AUTHORS, COPYRIGHT HOLDERS OR ITS CONTRIBUTORS
BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Vecmath 1.2-1.14 (null)
Copyright 1997,1998,1999 Kenji Hiranabe, Eiwa System Management, Inc.
License: Custom, MIT-like (null)
Download: null
Source available at: https://sourceforge.net/scm/?type

The author says:
Copyright (C) 1997,1998,1999
Kenji Hiranabe, Eiwa System Management, Inc.

This program is free software.
Implemented by Kenji Hiranabe(hiranabe@esm.co.jp),
conforming to the Java(TM) 3D API specification by Sun Microsystems.

Permission to use, copy, modify, distribute and sell this software
and its documentation for any purpose is hereby granted without fee,
provided that the above copyright notice appear in all copies and
that both that copyright notice and this permission notice appear
in supporting documentation. Kenji Hiranabe and Eiwa System Management,Inc.
makes no representations about the suitability of this software for any
purpose.  It is provided "AS IS" with NO WARRANTY.

XOM 1.1 (http://xom.nu/)
Copyright 2002, 2004 Elliotte Rusty Harold
License: GNU LGPL, 2.1 (http://xom.nu/license.xhtml)
Download: http://www.cafeconleche.org/XOM/xom-1.1.jar
Source available at: https://xom.dev.java.net/source/browse/xom/


Apache Log4J null (null)
Copyright null
License: null (null)
Download: null
Source available at: null

InChI Software 1.03 (http://iupac.org/inchi/)
Copyright null
License: GNU LGPL (null)
Download: null
Source available at: null

JNI-InChI 0.7 (http://jni-inchi.sourceforge.net/)
Copyright null
License: GNU Lesser General Public License (http://jni-inchi.sourceforge.net/license.html)
Download: null
Source available at: null


Apache Commons - CLI 1.0 (http://commons.apache.org/cli/)
Copyright 2001-2002 The Apache Software Foundation
License: Apache License Version 2.0 (http://commons.apache.org/license.html)
Download: http://archive.apache.org/dist/commons/cli/old/v1.0/
Source available at: http://archive.apache.org/dist/commons/cli/old/v1.0/



XML APIs 1.3.02 (http://xml.apache.org/commons/index.html)
Copyright null
License: Apache License, 2.0 (http://xml.apache.org/commons/licenses.html)
Download: http://apache.mirror.rbftpnetworks.com/xml/commons/
Source available at: http://apache.mirror.rbftpnetworks.com/xml/commons/


ANTLR 2.4.0 (http://www.antlr.org)
Copyright (c) 2003-2008, Terence Parr
License: BSD (http://www.antlr.org/license.html)
Download: http://www.antlr2.org/download.html
Source available at: http://www.antlr2.org/download.html

The author says:
Copyright (c) 2003-2008, Terence Parr
All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

    * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
    * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
    * Neither the name of the author nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. 

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 
JavaCC null (http://javacc.java.net/)
Copyright null
License: BSD (null)
Download: null
Source available at: null


A Java Matrix Package 1.0.2 (http://math.nist.gov/javanumerics/jama/)
Copyright This software is a cooperative product of The MathWorks and the National Institute of Standards and Technology (NIST) which has been released to the public domain. Neither The MathWorks nor NIST assumes any responsibility whatsoever for its use by other parties, and makes no guarantees, expressed or implied, about its quality, reliability, or any other characteristic.
License: Public Domain (http://math.nist.gov/javanumerics/jama/)
Download: http://math.nist.gov/javanumerics/jama/
Source available at: http://math.nist.gov/javanumerics/jama/


CML 2.5 XML Schema null (null)
Copyright null
License: Creative Commons BY-ND (null)
Download: null
Source available at: null

CMLXOM 2.5 beta1 (https://sourceforge.net/projects/cml/develop)
Copyright null
License: Artistic License 2.0 (null)
Download: null
Source available at: https://sourceforge.net/scm/?type


Apache Log4J 1.2.15 (http://logging.apache.org/log4j/1.2/index.html)
Copyright 2007 The Apache Software Foundation
License: Apache License, Version 2.0 (http://logging.apache.org/log4j/1.2/license.html)
Download: http://logging.apache.org/log4j/1.2/download.html
Source available at: http://logging.apache.org/log4j/1.2/download.html


Apache Xerces 2.9.0 (http://xerces.apache.org/xerces2-j/)
Copyright null
License: Apache License, 2.0 (http://xerces.apache.org/xerces2-j/)
Download: http://xerces.apache.org/xerces2-j/download.cgi
Source available at: http://xerces.apache.org/xerces2-j/download.cgi


