1========================================================================== 2Licenses of components of MDAnalysis 3========================================================================== 4 5 6 GNU GENERAL PUBLIC LICENSE 7 Version 2, June 1991 8 9 Copyright (C) 1989, 1991 Free Software Foundation, Inc. 10 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA 11 Everyone is permitted to copy and distribute verbatim copies 12 of this license document, but changing it is not allowed. 13 14 Preamble 15 16 The licenses for most software are designed to take away your 17freedom to share and change it. By contrast, the GNU General Public 18License is intended to guarantee your freedom to share and change free 19software--to make sure the software is free for all its users. This 20General Public License applies to most of the Free Software 21Foundation's software and to any other program whose authors commit to 22using it. 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If this is what you want to do, use the GNU Library General 345Public License instead of this License. 346 347 348========================================================================== 349 350Gromacs xdrfile library for reading XTC/TRR trajectories 351 - lib/formats/src/xdrfile.c 352 - lib/formats/src/xdrfile_xtc.c 353 - lib/formats/src/xdrfile_trr.c 354 - lib/formats/include/xdrfile.h 355 - lib/formats/include/xdrfile_xtc.h 356 - lib/formats/include/xdrfile_trr.h 357 358Copyright (c) 2009-2014, Erik Lindahl & David van der Spoel 359All rights reserved. 360 361Redistribution and use in source and binary forms, with or without 362modification, are permitted provided that the following conditions are met: 363 3641. Redistributions of source code must retain the above copyright notice, 365this 366list of conditions and the following disclaimer. 367 3682. Redistributions in binary form must reproduce the above copyright notice, 369this list of conditions and the following disclaimer in the documentation 370and/or other materials provided with the distribution. 371 372THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 373AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 374IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 375ARE 376DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE 377FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL 378DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR 379SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER 380CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, 381OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE 382OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 383 384========================================================================== 385 386CatDCD is released under the UIUC Open Source License: 387http://www.ks.uiuc.edu/Development/MDTools/catdcd/license.html 388 389University of Illinois Open Source License 390Copyright 2003-2007 Theoretical and Computational Biophysics Group, 391All rights reserved. 392 393Developed by: Theoretical and Computational Biophysics Group 394 University of Illinois at Urbana-Champaign 395 http://www.ks.uiuc.edu/ 396 397Permission is hereby granted, free of charge, to any person obtaining a copy of 398this software and associated documentation files (the Software), to deal with 399the Software without restriction, including without limitation the rights to 400use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies 401of the Software, and to permit persons to whom the Software is furnished to 402do so, subject to the following conditions: 403 404Redistributions of source code must retain the above copyright notice, 405this list of conditions and the following disclaimers. 406 407Redistributions in binary form must reproduce the above copyright notice, 408this list of conditions and the following disclaimers in the documentation 409and/or other materials provided with the distribution. 410 411Neither the names of Theoretical and Computational Biophysics Group, 412University of Illinois at Urbana-Champaign, nor the names of its contributors 413may be used to endorse or promote products derived from this Software without 414specific prior written permission. 415 416THE SOFTWARE IS PROVIDED AS IS, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 417IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 418FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL 419THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR 420OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, 421ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR 422OTHER DEALINGS WITH THE SOFTWARE. 423 424========================================================================== 425 426transformations module 427 - transformations.py 428 - transformations.c 429 430Copyright (c) 2006, Christoph Gohlke 431Copyright (c) 2006-2010, The Regents of the University of California 432All rights reserved. 433 434Redistribution and use in source and binary forms, with or without 435modification, are permitted provided that the following conditions are met: 436 437* Redistributions of source code must retain the above copyright 438 notice, this list of conditions and the following disclaimer. 439* Redistributions in binary form must reproduce the above copyright 440 notice, this list of conditions and the following disclaimer in the 441 documentation and/or other materials provided with the distribution. 442* Neither the name of the copyright holders nor the names of any 443 contributors may be used to endorse or promote products derived 444 from this software without specific prior written permission. 445 446THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 447AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 448IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 449ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE 450LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR 451CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF 452SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS 453INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN 454CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 455ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 456POSSIBILITY OF SUCH DAMAGE. 457 458========================================================================== 459 460pyqcprot (src/pyqcprot) is released under the following 'BSD 3-clause' licence: 461 462----------------------------------------------------------------------------- 463PyQCPROT 464 465 Author(s) of Original Implementation: 466 Douglas L. Theobald 467 Department of Biochemistry 468 MS 009 469 Brandeis University 470 415 South St 471 Waltham, MA 02453 472 USA 473 474 dtheobald@brandeis.edu 475 476 Pu Liu 477 Johnson & Johnson Pharmaceutical Research and Development, L.L.C. 478 665 Stockton Drive 479 Exton, PA 19341 480 USA 481 482 pliu24@its.jnj.com 483 484 For the original code written in C see: 485 http://theobald.brandeis.edu/qcp/ 486 487 488 Author of Python Port: 489 Joshua L. Adelman 490 Department of Biological Sciences 491 University of Pittsburgh 492 Pittsburgh, PA 15260 493 494 jla65@pitt.edu 495 496 497 If you use this QCP rotation calculation method in a publication, please 498 reference: 499 500 Douglas L. Theobald (2005) 501 "Rapid calculation of RMSD using a quaternion-based characteristic 502 polynomial." 503 Acta Crystallographica A 61(4):478-480. 504 505 Pu Liu, Dmitris K. Agrafiotis, and Douglas L. Theobald (2010) 506 "Fast determination of the optimal rotational matrix for macromolecular 507 superpositions." 508 J. Comput. Chem. 31, 1561-1563. 509 510 511 Copyright (c) 2009-2010, Pu Liu and Douglas L. Theobald 512 Copyright (c) 2011 Joshua L. Adelman 513 All rights reserved. 514 515 Redistribution and use in source and binary forms, with or without modification, are permitted 516 provided that the following conditions are met: 517 518 * Redistributions of source code must retain the above copyright notice, this list of 519 conditions and the following disclaimer. 520 * Redistributions in binary form must reproduce the above copyright notice, this list 521 of conditions and the following disclaimer in the documentation and/or other materials 522 provided with the distribution. 523 * Neither the name of the <ORGANIZATION> nor the names of its contributors may be used to 524 endorse or promote products derived from this software without specific prior written 525 permission. 526 527 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS 528 "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT 529 LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A 530 PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT 531 HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, 532 SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT 533 LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, 534 DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY 535 THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 536 (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE 537 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 538 539 540========================================================================== 541 542MDAnalysis logo (see doc/sphinx/source/logos) 543 544The MDAnalysis 'Atom' logo was created by Christian Beckstein and is 545 546Copyright (c) 2011 Christian Beckstein 547 548MDAnalysis Logo 'Atom' by Christian Beckstein is licensed under a 549Creative Commons Attribution-NoDerivs 3.0 Unported License. 550To view a copy of this license, visit 551http://creativecommons.org/licenses/by-nd/3.0/ or send a letter to Creative 552Commons, 444 Castro Street, Suite 900, Mountain View, California, 94041, USA. 553 554The logo is contained in the file 'mdanalysis-logo.png'. 555 556Derivatives in the files 'mdanalysis-logo-127x55.png', 557'mdanalysis-logo-200x150.png', 'mdanalysis-logo.ico' were created for 558inclusion in MDAnalysis and on websites related to MDAnalysis. They 559are distributed under the same license as the 'Atom' logo. 560 561========================================================================== 562 563
