CBFlib Notices
COPYING
All of the CBFlib 0.7.7 package may be distributed under the terms of the
GNU General Public License (the GPL), see
http://www.gnu.org/licenses/gpl.txt
Alternatively most of the CBFlib 0.7.7 package may be distributed under
the terms of the GNU Lesser General Public License (the LGPL), see
http://www.gnu.org/licenses/lgpl.txt
The portions that may be distributed under the LGPL indentified as such in
the comments of the relevant files, and include the portions constituting
the API, but do not include the documentation nor does it include the
example programs. The documentation and examples may only be distributed
under the GPL.
----------------------------------------------------------------------
----------------------------------------------------------------------
THE FIRST ALTERNATIVE LICENSE FOR ALL OF CBFLIB (GPL)
(Valid for versions of CBFlib starting with release 0.7.5)
========================== GPL STARTS HERE =================================
GNU GENERAL PUBLIC LICENSE
Version 2, June 1991
Copyright (C) 1989, 1991 Free Software Foundation, Inc.
59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
Preamble
The licenses for most software are designed to take away your
freedom to share and change it. By contrast, the GNU General Public
License is intended to guarantee your freedom to share and change free
software--to make sure the software is free for all its users. This
General Public License applies to most of the Free Software
Foundation's software and to any other program whose authors commit to
using it. (Some other Free Software Foundation software is covered by
the GNU Library General Public License instead.) You can apply it to
your programs, too.
When we speak of free software, we are referring to freedom, not
price. Our General Public Licenses are designed to make sure that you
have the freedom to distribute copies of free software (and charge for
this service if you wish), that you receive source code or can get it
if you want it, that you can change the software or use pieces of it
in new free programs; and that you know you can do these things.
To protect your rights, we need to make restrictions that forbid
anyone to deny you these rights or to ask you to surrender the rights.
These restrictions translate to certain responsibilities for you if you
distribute copies of the software, or if you modify it.
For example, if you distribute copies of such a program, whether
gratis or for a fee, you must give the recipients all the rights that
you have. You must make sure that they, too, receive or can get the
source code. And you must show them these terms so they know their
rights.
We protect your rights with two steps: (1) copyright the software, and
(2) offer you this license which gives you legal permission to copy,
distribute and/or modify the software.
Also, for each author's protection and ours, we want to make certain
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The precise terms and conditions for copying, distribution and
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GNU GENERAL PUBLIC LICENSE
TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
0. This License applies to any program or other work which contains
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NO WARRANTY
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Also add information on how to contact you by electronic and paper mail.
If the program is interactive, make it output a short notice like this
when it starts in an interactive mode:
Gnomovision version 69, Copyright (C) year name of author
Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
This is free software, and you are welcome to redistribute it
under certain conditions; type `show c' for details.
The hypothetical commands `show w' and `show c' should show the appropriate
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mouse-clicks or menu items--whatever suits your program.
You should also get your employer (if you work as a programmer) or your
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necessary. Here is a sample; alter the names:
Yoyodyne, Inc., hereby disclaims all copyright interest in the program
`Gnomovision' (which makes passes at compilers) written by James Hacker.
, 1 April 1989
Ty Coon, President of Vice
This General Public License does not permit incorporating your program into
proprietary programs. If your program is a subroutine library, you may
consider it more useful to permit linking proprietary applications with the
library. If this is what you want to do, use the GNU Library General
Public License instead of this License.
=========================== GPL ENDS HERE ==================================
----------------------------------------------------------------------
----------------------------------------------------------------------
THE SECOND ALTERNATIVE LICENSE FOR CERTAIN PORTIONS OF CBFLIB
INCLUDING THE API ITSELF,
BUT NOT THE DOCUMENTATION AND NOT THE EXAMPLES (LGPL)
(Valid for versions of CBFlib starting with release 0.7.5)
========================== LGPL STARTS HERE ================================
GNU LESSER GENERAL PUBLIC LICENSE
Version 2.1, February 1999
Copyright (C) 1991, 1999 Free Software Foundation, Inc.
51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
[This is the first released version of the Lesser GPL. It also counts
as the successor of the GNU Library Public License, version 2, hence
the version number 2.1.]
Preamble
The licenses for most software are designed to take away your
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Licenses are intended to guarantee your freedom to share and change
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This license, the Lesser General Public License, applies to some
specially designated software packages--typically libraries--of the
Free Software Foundation and other authors who decide to use it. You
can use it too, but we suggest you first think carefully about whether
this license or the ordinary General Public License is the better
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That's all there is to it!
=========================== LGPL ENDS HERE =================================
The following notice applies to this work as a whole and to the works
included within it:
* Creative endeavors depend on the lively exchange of ideas. There are
laws and customs which establish rights and responsibilities for
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and conditions of such use.
* Please read the following notice carefully. If you do not understand
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citing this package, its authors and the URL or other source from
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* Some of the software and documents included within this software
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----------------------------------------------------------------------
----------------------------------------------------------------------
Stanford University Notices
for the CBFlib software package that incorporates SLAC software on which
copyright is disclaimed
This software
The term 'this software', as used in these Notices, refers to those
portions of the software package CBFlib that were created by employees of
the Stanford Linear Accelerator Center, Stanford University.
Stanford disclaimer of copyright
Stanford University, owner of the copyright, hereby disclaims its
copyright and all other rights in this software. Hence, anyone may freely
use it for any purpose without restriction.
Acknowledgement of sponsorship
This software was produced by the Stanford Linear Accelerator Center,
Stanford University, under Contract DE-AC03-76SFO0515 with the Department
of Energy.
Government disclaimer of liability
Neither the United States nor the United States Department of Energy, nor
any of their employees, makes any warranty, express or implied, or assumes
any legal liability or responsibility for the accuracy, completeness, or
usefulness of any data, apparatus, product, or process disclosed, or
represents that its use would not infringe privately owned rights.
Stanford disclaimer of liability
Stanford University makes no representations or warranties, express or
implied, nor assumes any liability for the use of this software.
Maintenance of notices
In the interest of clarity regarding the origin and status of this
software, this and all the preceding Stanford University notices are to
remain affixed to any copy or derivative of this software made or
distributed by the recipient and are to be affixed to any copy of software
made or distributed by the recipient that contains a copy or derivative of
this software.
Based on SLAC Software Notices, Set 4 OTT.002a, 2004 FEB 03
----------------------------------------------------------------------
----------------------------------------------------------------------
The IUCr Policy
for the Protection and the Promotion of the STAR File and
CIF Standards for Exchanging and Archiving Electronic Data
Overview
The Crystallographic Information File (CIF)[1] is a standard for
information interchange promulgated by the International Union of
Crystallography (IUCr). CIF (Hall, Allen & Brown, 1991) is the recommended
method for submitting publications to Acta Crystallographica Section C and
reports of crystal structure determinations to other sections of Acta
Crystallographica and many other journals. The syntax of a CIF is a subset
of the more general STAR File[2] format. The CIF and STAR File approaches
are used increasingly in the structural sciences for data exchange and
archiving, and are having a significant influence on these activities in
other fields.
Statement of intent
The IUCr's interest in the STAR File is as a general data interchange
standard for science, and its interest in the CIF, a conformant derivative
of the STAR File, is as a concise data exchange and archival standard for
crystallography and structural science.
Protection of the standards
To protect the STAR File and the CIF as standards for interchanging and
archiving electronic data, the IUCr, on behalf of the scientific
community,
* holds the copyrights on the standards themselves,
* owns the associated trademarks and service marks, and
* holds a patent on the STAR File.
These intellectual property rights relate solely to the interchange
formats, not to the data contained therein, nor to the software used in
the generation, access or manipulation of the data.
Promotion of the standards
The sole requirement that the IUCr, in its protective role, imposes on
software purporting to process STAR File or CIF data is that the following
conditions be met prior to sale or distribution.
* Software claiming to read files written to either the STAR File or the
CIF standard must be able to extract the pertinent data from a file
conformant to the STAR File syntax, or the CIF syntax, respectively.
* Software claiming to write files in either the STAR File, or the CIF,
standard must produce files that are conformant to the STAR File syntax,
or the CIF syntax, respectively.
* Software claiming to read definitions from a specific data dictionary
approved by the IUCr must be able to extract any pertinent definition
which is conformant to the dictionary definition language (DDL)[3]
associated with that dictionary.
The IUCr, through its Committee on CIF Standards, will assist any
developer to verify that software meets these conformance conditions.
Glossary of terms
[1] CIF:
is a data file conformant to the file syntax defined at
http://www.iucr.org/iucr-top/cif/spec/index.html
[2] STAR File:
is a data file conformant to the file syntax defined at
http://www.iucr.org/iucr-top/cif/spec/star/index.html
[3] DDL:
is a language used in a data dictionary to define data items in terms of
"attributes". Dictionaries currently approved by the IUCr, and the DDL
versions used to construct these dictionaries, are listed at
http://www.iucr.org/iucr-top/cif/spec/ddl/index.html
Last modified: 30 September 2000
IUCr Policy Copyright (C) 2000 International Union of Crystallography
----------------------------------------------------------------------
----------------------------------------------------------------------
CBFlib V0.1 Notice
The following Diclaimer Notice applies to CBFlib V0.1, from which this
version is derived.
* The items furnished herewith were developed under the sponsorship of
the U.S. Government. Neither the U.S., nor the U.S. D.O.E., nor the
Leland Stanford Junior University, nor their employees, makes any
warranty, express or implied, or assumes any liability or
responsibility for accuracy, completeness or usefulness of any
information, apparatus, product or process disclosed, or represents
that its use will not infringe privately-owned rights. Mention of any
product, its manufacturer, or suppliers shall not, nor is it intended
to, imply approval, disapproval, or fitness for any particular use.
The U.S. and the University at all times retain the right to use and
disseminate the furnished items for any purpose whatsoever.
* Notice 91 02 01
----------------------------------------------------------------------
----------------------------------------------------------------------
CIFPARSE notice
Portions of this software are loosely based on the CIFPARSE software
package from the NDB at Rutgers university (see
http://ndbserver.rutgers.edu/NDB/mmcif/software). CIFPARSE is part of the
NDBQUERY application, a program component of the Nucleic Acid Database
Project [ H. M. Berman, W. K. Olson, D. L. Beveridge, J. K. Westbrook, A.
Gelbin, T. Demeny, S. H. Shieh, A. R. Srinivasan, and B. Schneider.
(1992). The Nucleic Acid Database: A Comprehensive Relational Database of
Three-Dimensional Structures of Nucleic Acids. Biophys J., 63, 751-759.],
whose cooperation is gratefully acknowledged, especially in the form of
design concepts created by J. Westbrook.
Please be aware of the following notice in the CIFPARSE API:
* This software is provided WITHOUT WARRANTY OF MERCHANTABILITY OR
FITNESS FOR A PARTICULAR PURPOSE OR ANY OTHER WARRANTY, EXPRESS OR
IMPLIED. RUTGERS MAKE NO REPRESENTATION OR WARRANTY THAT THE SOFTWARE
WILL NOT INFRINGE ANY PATENT, COPYRIGHT OR OTHER PROPRIETARY RIGHT.
----------------------------------------------------------------------
----------------------------------------------------------------------
MPACK notice
Portions of this library are adapted from the "mpack/munpack version 1.5"
routines, written by John G. Myers. Mpack and munpack are utilities for
encoding and decoding (respectively) binary files in MIME (Multipurpose
Internet Mail Extensions) format mail messages. The mpack software used is
(C) Copyright 1993,1994 by Carnegie Mellon University, All Rights
Reserved, and is subject to the following notice:
* 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, and that the name of Carnegie Mellon
University not be used in advertising or publicity pertaining to
distribution of the software without specific, written prior
permission. Carnegie Mellon University makes no representations about
the suitability of this software for any purpose. It is provided "as
is" without express or implied warranty.
* CARNEGIE MELLON UNIVERSITY DISCLAIMS ALL WARRANTIES WITH REGARD TO
THIS SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND
FITNESS, IN NO EVENT SHALL CARNEGIE MELLON UNIVERSITY BE LIABLE FOR
ANY SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT
OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
----------------------------------------------------------------------
----------------------------------------------------------------------
MD5 Notice
The following notice applies to the message digest software in md5.h and
md5.c which are optionally used by this library. To that extent, this
library is a work "derived from the RSA Data Security, Inc. MD5
Message-Digest Algorithm".
The software in md5.h and md5.c is Copyright (C) 1991-2, RSA Data
Security, Inc. Created 1991. All rights reserved, and is subject to the
following notice:
* License to copy and use this software is granted provided that it is
identified as the "RSA Data Security, Inc. MD5 Message-Digest
Algorithm" in all material mentioning or referencing this software or
this function.
* License is also granted to make and use derivative works provided that
such works are identified as "derived from the RSA Data Security, Inc.
MD5 Message-Digest Algorithm" in all material mentioning or
referencing the derived work.
* RSA Data Security, Inc. makes no representations concerning either the
merchantability of this software or the suitability of this software
for any particular purpose. It is provided "as is" without express or
implied warranty of any kind.
* These notices must be retained in any copies of any part of this
documentation and/or software.
----------------------------------------------------------------------
----------------------------------------------------------------------
CCP4 Packed Compression Notice
The CBF_PACKED and CBF_PACKED_V2 compression and decompression code
incorporated in CBFlib is derived in large part from the J. P. Abrahams
pack_c.c compression code in CCP4. This code is incorporated in CBFlib
under the GPL and the LGPL with both the permission Jan Pieter Abrahams,
the original author of pack_c.c (email from Jan Pieter Abrahams of 15
January 2007) and of the CCP4 project (email from Martyn Winn on 12
January 2007). The cooperation of J. P. Abrahams and of the CCP4 project
is gratefully acknowledged.
----------------------------------------------------------------------
----------------------------------------------------------------------
Updated 7 April 2007. yaya@bernstein-plus-sons.com
