Third Party Software

Sire depends on a lot of third party software, the details and licenses of which can be found below. The software is all bundled with Sire(*), meaning that you don’t need to download or install it yourself. The exact versions used with Sire can be seen in corelib/src/bundled and wrapper/bundled.

Sire is itself distributed under the terms of the GPL version 3.

(*) Well, nearly all. cmake is not bundled and must be installed if you want to compile Sire from scratch.

Qt 5

Sire is built on top of Qt.Core from Qt 5. This is used under the terms of the LGPL 2. Sire does not modify Qt, so this license allows both commercial and non-commercial use without fee. You can find out more about Qt and its license from here.

Python

The Sire C++ library is wrapped up and made available for use within Python 3. This is used under the terms of the PSF license, which is compatible with the GPLv2. The license allows both commercial and non-commercial use without fee. You can find out more about Python and its license from here.

boost

Sire uses many of the component from the boost libraries, in particular the boost::python module that is used to wrap up the C++ code. This is used under the terms of the Boost Software License, which allows both commercial and non-commercial use without fee. This is compatible with the GPL. You can find out more about boost and its license from here.

Py++

Sire uses Py++ to auto-generate all of the C++ python wrappers. Py++ uses either GCCXML or CastXML, and, as it is used as a tool, its license does not affect Sire. You can read more about Py++ from here.

cmake

Sire uses cmake as its build system. As it is used as a tool, its license does not affect Sire. CMake is excellent. You can read more about it from here.

Anaconda

Sire uses Anaconda to simplify the management and installation of Python and the various modules on which Sire depends.

Anaconda (and miniconda) are distributed as open source projects. As Sire does not explicitly link with them, the license is not an issue. You can find out more about Anaconda from here.

Intel Threading Building Blocks (tbb)

Sire uses Intel’s Threading Building Blocks library for within-node parallelisation. This is licensed under the GPLv2 with the libstdc++ runtime exception. The runtime exceptions is;

As a special exception, you may use this file as part 
of a free software library without restriction. Specifically, 
if other files instantiate templates or use macros or inline 
functions from this file, or you compile this file and link 
it with other files to produce an executable, this file does 
not by itself cause the resulting executable to be covered 
by the GNU General Public License. This exception does not 
however invalidate any other reasons why the executable file 
might be covered by the GNU General Public License. 

- See more at: https://www.threadingbuildingblocks.org/Licensing#sthash.g5mwvPjp.dpuf

As Sire does not modify TBB, its use is compatible with the above exception. You can read more about TBB from here.

Gnu Scientific Library (GSL)

Sire uses some of the routines from the Gnu Scientific Library. This is used under the terms of the GPL v3 license. More information about GSL and its license can be found here.

CPUID

Sire uses CPUID to get information about the CPU on which it is running. This is used under a BSD-style license.

 * 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.
 *
 * THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``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 AUTHOR 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.

You can get more information about CPUID from here.

Regress

Sire uses the linear least squares regression library, ‘regress’, for polynomial least squares fitting. This is used under the terms of the GPLv3 license.

The source code for this module can be found here.

eig3

Sire uses the eig3 library for eigenvector/eigenmatrix calculations by Connelly Barnes. This is in the public domain, and is derived itself from the Java matrix library JAMA (also public domain).

Information about this can be found here, with the license within Sire found here.

Mersenne Twister

Sire uses the Mersenne Twister program by Richard Wagner for the generation of random numbers. This is used under a BSD-style license, shown below.

// Mersenne Twister random number generator -- a C++ class MTRand
// Based on code by Makoto Matsumoto, Takuji Nishimura, and Shawn Cokus
// Richard J. Wagner  v1.0  15 May 2003  rjwagner@writeme.com

// The Mersenne Twister is an algorithm for generating random numbers.  It
// was designed with consideration of the flaws in various other generators.
// The period, 2^19937-1, and the order of equidistribution, 623 dimensions,
// are far greater.  The generator is also fast; it avoids multiplication and
// division, and it benefits from caches and pipelines.  For more information
// see the inventors' web page at http://www.math.keio.ac.jp/~matumoto/emt.html

// Reference
// M. Matsumoto and T. Nishimura, "Mersenne Twister: A 623-Dimensionally
// Equidistributed Uniform Pseudo-Random Number Generator", ACM Transactions on
// Modeling and Computer Simulation, Vol. 8, No. 1, January 1998, pp 3-30.

// Copyright (C) 1997 - 2002, Makoto Matsumoto and Takuji Nishimura,
// Copyright (C) 2000 - 2003, Richard J. Wagner
// 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 names of its contributors may not 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.

// The original code included the following notice:
//
//     When you use this, send an email to: matumoto@math.keio.ac.jp
//     with an appropriate reference to your work.
//
// It would be nice to CC: rjwagner@writeme.com and Cokus@math.washington.edu
// when you write.

I must remember to send them an email…

More information about Mersenne Twister can be found here.

sse_mathfun and neon_mathfun

Sire uses sse_mathfun and neon_mathfun for vectorising intrinsic maths functions on processors that support SSE or Neon. These libraries were written by Julien Pommier, and released under the BSD-style zlib license, which is given here.

/* Copyright (C) 2007  Julien Pommier
  This software is provided 'as-is', without any express or implied
  warranty.  In no event will the authors be held liable for any damages
  arising from the use of this software.
  Permission is granted to anyone to use this software for any purpose,
  including commercial applications, and to alter it and redistribute it
  freely, subject to the following restrictions:
  1. The origin of this software must not be misrepresented; you must not
     claim that you wrote the original software. If you use this software
     in a product, an acknowledgment in the product documentation would be
     appreciated but is not required.
  2. Altered source versions must be plainly marked as such, and must not be
     misrepresented as being the original software.
  3. This notice may not be removed or altered from any source distribution.
  (this is the zlib license)
*/

avx_mathfun

This is an AVX library inspired by sse_mathfun, that extends support to processors with AVX instructions. It was written by Giovanni Garberoglio, and is also under a BSD-style zlib license.

  AVX implementation of sin, cos, sincos, exp and log
   Based on "sse_mathfun.h", by Julien Pommier
   http://gruntthepeon.free.fr/ssemath/
   Copyright (C) 2012 Giovanni Garberoglio
   Interdisciplinary Laboratory for Computational Science (LISC)
   Fondazione Bruno Kessler and University of Trento
   via Sommarive, 18
   I-38123 Trento (Italy)
  This software is provided 'as-is', without any express or implied
  warranty.  In no event will the authors be held liable for any damages
  arising from the use of this software.
  Permission is granted to anyone to use this software for any purpose,
  including commercial applications, and to alter it and redistribute it
  freely, subject to the following restrictions:
  1. The origin of this software must not be misrepresented; you must not
     claim that you wrote the original software. If you use this software
     in a product, an acknowledgment in the product documentation would be
     appreciated but is not required.
  2. Altered source versions must be plainly marked as such, and must not be
     misrepresented as being the original software.
  3. This notice may not be removed or altered from any source distribution.
  (this is the zlib license)

BLAS

Sire bundles the reference version of the BLAS library. The license for which is described below (it is ‘freely-available’).

<http://www.netlib.org/blas/faq.html#2>

The reference BLAS is a freely-available software package. 
It is available from netlib via anonymous ftp and the World Wide Web. 
Thus, it can be included in commercial software packages (and has been). 
We only ask that proper credit be given to the authors.

Like all software, it is copyrighted. It is not trademarked, but we do ask the following:

If you modify the source for these routines we ask that you change the name of the 
routine and comment the changes made to the original.

We will gladly answer any questions regarding the software. If a modification is done, 
however, it is the responsibility of the person who modified the routine to provide support.

LAPACK

Sire also bundles a reference LAPACK, the license for which is given below;

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 listed
  in this license in the documentation and/or other materials
  provided with the distribution.
  
- Neither the name of the copyright holders 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.

LINPACK

Sire also bundles some routines from LINPACK. Forum postings indicate that LINPACK is BSD licensed.

LINPACK is a collection of Fortran subroutines that analyze and
solve linear equations and linear least-squares probles.  The
package solves linear systems whose matrices are general, banded,
symmetric indefinite, symmetric positive definite, triangular,
and tridiagonal square.  In addition, the package computes
the QR and singular value decompositions of rectangular matrices
and applies them to least-squares problems.  LINPACK uses
column-oriented algorithms to increase efficiency by preserving
locality of reference.

LINPACK was designed for supercomputers in use in the 1970s and
early 1980s.  LINPACK has been largely superceded by LAPACK
which has been designed to run efficiently on shared-memory, vector
supercomputers.

Developed by Jack Dongarra, Jim Bunch, Cleve Moler and Pete Stewart.
 1 Feb 84

 If you are interested in acquiring the entire LINPACK, it may
 make more sense to talk with NAG. NAG distribute the software
 on a mag tape for a nominal charge.
     NAG
     1400 Opus Place, Suite 200
     Downers Grove, IL  60515-5702
     708-971-2337, FAX 971-2706


===============
See ThirdParty/LAPACK for BSD LAPACK license. Forum postings indicate
that LINPACK is also BSD licensed (e.g. 
<http://icl.cs.utk.edu/lapack-forum/archives/lapack/msg00301.html>)
[Lapack] Linpack license?
From: Jakub Kurzak 
Date: Wed, 11 Jul 2007 09:50:02 -0400
Basically it is BSD.
Jakub

On 7/10/07, Benjamin Collar <benjamin.collar@Domain.Removed> wrote:

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Hello,

I am trying to find out what license Linpack is released under. I
checked the netlib/linpack site, but didn't find the answer there. Do
you know?

Thanks
Benjamin
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.7 (MingW32)
Comment: http://firegpg.tuxfamily.org

iD8DBQFGlE594CA25YTAYOMRAiG8AJ4uLe6DgAIszvyZl7fUdcmdv960MACdF1mA
jfqWri2vpHcKrlsur6Uc1yg=
=Xb40
-----END PGP SIGNATURE-----
_______________________________________________
Lapack mailing list
Lapack@Domain.Removed
http://lists.cs.utk.edu/listinfo/lapack

-------------- next part --------------
An HTML attachment was scrubbed...
URL: 
http://lists.cs.utk.edu/private/lapack/attachments/20070711/cbd659b6/attachment.htm

LAP (Linear Assignment Problem Solver)

Sire implements its own C++ version of the LAP library for solving the linear assignment problem. This is available here.

The original code is Freeware, with more information about it available from here.

MD5

Sire uses the MD5 library written by L. Peter Deutsch. It is used under a BSD-style license, given below.

  Copyright (C) 1999, 2002 Aladdin Enterprises.  All rights reserved.
  This software is provided 'as-is', without any express or implied
  warranty.  In no event will the authors be held liable for any damages
  arising from the use of this software.
  Permission is granted to anyone to use this software for any purpose,
  including commercial applications, and to alter it and redistribute it
  freely, subject to the following restrictions:
  1. The origin of this software must not be misrepresented; you must not
     claim that you wrote the original software. If you use this software
     in a product, an acknowledgment in the product documentation would be
     appreciated but is not required.
  2. Altered source versions must be plainly marked as such, and must not be
     misrepresented as being the original software.
  3. This notice may not be removed or altered from any source distribution.
  L. Peter Deutsch
  ghost@aladdin.com

More information about MD5 libraries in general can be found here.

kabasch fitting

I have written a C++ implementation of the kabasch algorithm for alignment. This was inspired by the calculate_rmsd python script written by Jimmy Charnley Kromann and Lars Bratholm, available https://github.com/charnley/rmsd, and under license;

        =====================
        Copyright (c) 2013, Jimmy Charnley Kromann <jimmy@charnley.dk> & Lars Bratholm
        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.

        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.
        =======================

ap (ascii plot)

Sire bundles the Python “ap” library for drawing ascii graphs. This is available as “Sire.Tools.ap”

Version 0.9 written by M. Fouesneau is included, available freely from github here. The only change I’ve made is running this through Python’s 2to3 program to make this code work with Python 3.

The header documentation reads;

Package that allows you to plot simple graphs in ASCII, a la matplotlib.
This package is a inspired from Imri Goldberg's ASCII-Plotter 1.0
(https://pypi.python.org/pypi/ASCII-Plotter/1.0)
At a time I was enoyed by security not giving me direct access to my computer,
and thus to quickly make figures from python, I looked at how I could make
quick and dirty ASCII figures. But if I were to develop something, I wanted
something that can be used with just python and possible standard-ish packages
(numpy, scipy).
So I came up with this package after many iterations based of ASCII-plotter.
I added the feature to show multiple curves on one plot with different markers.
And I also made the usage, close to matplotlib, such that there is a plot,
hist, hist2d and imshow functions.

TODO:
    imshow does not plot axis yet.
    make a correct documentation