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MGLTools License Agreements

by Sargis Dallakyan last modified 2008-07-08 13:39

Please read the following license agreements.

Unless otherwise specified, this software is licensed by Michel F. SANNER and The Scripps Research Institute. Certain pieces of software in this package provide their own licensing scheme which you will find below.
All the components not specifying their own license are under the Mozilla open source license. Although this licensing scheme allows the re-distribution of this software we would appreciate if people using it would download it from our site. This helps us keep track of who is using it which is a strong argument when trying to get money to work on this. Thanks !

If you have any questions please contact Michel SANNER (sanner@scripps.edu).

Packages SOFTWARE LICENSES
ACADEMIC COMMERCIAL
mslib Free for Academic Contact Michel Sanner sanner@scripps.edu
STRIDE
Free for Academic Contact Dmitrij Frishman d.frishman@wzw.tum.de
UTpackages Free for Academic Contact Chandrajit Bajaj bajaj@cs.utexas.edu

MGLTOOLS SOFTWARE LICENSE AGREEMENT

1. Grant Of Limited License; Software Use Restrictions. The programs
received by you will be used only for NON COMMERCIAL purposes.
This license is issued to you as an individual.

For COMMERCIAL use done with the software please contact Michel F.
Sanner for details about commercial usage license agreements.

For any question regarding license agreements, please contact
Michel Sanner:
TSRI, Molecular Biology Department, TCP 26,
10550 North Torrey Pines Road, La Jolla, CA 92037
sanner@scripps.edu
tel (858) 784-7742
fax (858) 784-2341

2. COMMERCIAL USAGE is defined as revenues generating activities. These
include using this software for consulting activities and selling
applications built on top of, or using this software. Scientific
research in an academic environment and teaching are considered
NON COMMERCIAL.

3. Copying Restrictions. You will not sell or otherwise distribute commercially
these programs or derivatives to any other party, whether with or without
consideration.

4. Ownership of Software. You will not obtain, and will not attempt to
obtain copyright coverage thereon without the express purpose written
consent of The Scripps Research Institute and Dr. Sanner.

5. IN NO EVENT SHALL THE AUTHORS OR DISTRIBUTORS BE LIABLE TO ANY PARTY
FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES
ARISING OUT OF THE USE OF THIS SOFTWARE, ITS DOCUMENTATION, OR ANY
DERIVATIVES THEREOF, EVEN IF THE AUTHORS HAVE BEEN ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.

6. THE AUTHORS AND DISTRIBUTORS SPECIFICALLY DISCLAIM ANY WARRANTIES,
INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE, AND NON-INFRINGEMENT. THIS SOFTWARE
IS PROVIDED ON AN "AS IS" BASIS, AND THE AUTHORS AND DISTRIBUTORS HAVE
NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR
MODIFICATIONS.

MOZILLA OPEN SOURCE LICENSE AGREEMENT

Mozilla open source license version 1.1- http://www.opensource.org/licenses/mozilla1.1.php

MSLIB License

The MGLTools uses the MSLIB package to compute molecular surfaces.

FOR COMMERCIAL USE OF MSLIB PLEASE CONTACT Michel SANNER

1. Grant Of Limited License: Software Use Restrictions. You are free to use the program (MSMS) ONLY FOR NON-COMMERCIAL SCIENTIFIC RESEARCH. This license is issued to you as an individual. For institution wide use or commercial use of the software you will have to follow the official registration procedure. To do so you can contact us by e-mail (sanner@scripps.edu), mail (Michel Sanner, TSRI,Molecular Biology Department, MB5, 10666 North Torrey Pines Road, 92037 La Jolla) or fax (858) 784-2860.

2. Credits: WE REQUEST THAT YOU AGREE TO ACKNOWLEDGE THE USE OF THE MSMS SOFTWARE THAT RESULTS IN ANY PUBLISHED WORK, INCLUDING SCIENTIFIC PAPERS, FILMS AND VIDEOTAPES BY CITING THE FOLLOWING REFERENCE:
Sanner, M.F., Spehner, J.-C., and Olson, A.J. (1996) Reduced surface: an efficient way to compute molecular surfaces. Biopolymers, Vol. 38, (3), 305-320.

3. Copying Restrictions: You will not sell or otherwise transfer these programs or derivatives to any other party, whether with or without consideration, for any purpose.

4. Ownership of Software: You will not obtain, and will not attempt to obtain copyright coverage thereon without the express purpose written consent of The Scripps Research Institute.

5. Limitation Of Liability: You will hold harmless from all or any expenses you may incur as a result of or arising from your use, direct or indirect, of these materials. You understand that no other right or license to this program or its derivatives is granted or implied as a result of our transmission of same to you.

STRIDE License

STRIDE: Protein secondary structure assignment from atomic coordinates

Dmitrij Frishman & Patrick Argos

All rights reserved, whether the whole or part of the program is concerned. Permission to use, copy, and modify this software and its documentation is granted for academic use, provided that:

1. This copyright notice appears in all copies of the software and related documentation.

2. The reference given below (Frishman and Argos, 1995) must be cited in any publication of scientific results based in part or completely on the use of the program.

3. Bugs will be reported to the authors. The use of the software in commercial activities is not allowed without a prior written commercial license agreement.

WARNING:

STRIDE is provided 'as-is' and without warranty of any kind, express, implied or otherwise, including without limitation any warranty of merchantability or fitness for a particular purpose. In no event will the authors be liable for any special, incidental, indirect or consequential damages of any kind, or any damages whatsoever resulting from loss of data or profits, whether or not advised of the possibility of damage, and on any theory of liability, arising out of or in connection with the use or performance of this software.

For calculation of the residue solvent accessible area the program NSC is used and was kindly provided by Dr. F.Eisenhaber (EISENHABER@EMBL-HEIDELBERG.DE). Please direct to him all questions concerning specifically accessibility calculations.

Reference:

Frishman,D & Argos,P. (1995) Knowledge-based secondary structure assignment. Proteins: structure, function and genetics, 23, 566-579.

UTPackages License

TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION

1. This software is the copyright of THE UNIVERSITY OF TEXAS AT AUSTIN, 2005.

2. The software is available under multiple licenses.

3. For non commercial educational and non commercial academic use, the software
including source code, interface definitions and compile scripts are freely available.
Any distribution of code, library or executables which contains any modules from this
software should contain, conspicously and appropriately, on each copy, this copyright
and license notice and should be freely distributed.

4. If you wish to incorporate parts of the Library into other free programs whose distribution
conditions are incompatible with these, write to the author to ask for permission.
For software which is copyrighted by the Free Software Foundation, write to the Free Software
Foundation.

5. For any other purpose, including commercial purposes, please contact The University of
Texas at Austin for a different license.

6. Credits:

This software has been developed at the Computational and Visualization center under

Dr Chandrajit Bajaj,
Computational Applied Mathematics Chair in Visualization,
Professor of Computer Sciences,
Director of Center for Computational Visualization,
Department of Computer Sciences & The Institute of Computational Engineering and Sciences,
Center for Computational Visualization,
201 East 24th Street, ACES 2.324A,
1 University Station, C0200,
Austin, TX 78712-0027.

We request that you agree to acknowledge the use of the software that results in any published
work, including scientific papers, films and videotapes by citing the references listed below

For UTblur:

C. Bajaj, V. Siddavanahalli
Fast Feature Adaptive Surfaces and Derivatives Computation for Volumetric Particle Data
ICES and CS technical reports, The University of Texas at Austin, 2005.


For UTisocontour:

C. Bajaj, V. Pascucci, D. Schikore
Accelerated IsoContouring of Scalar Fields
Data Visualization Techniques, edited by C. Bajaj, John Wiley and Sons (1998).

C. Bajaj, V. Pascucci, D. Schikore
Fast Isocontouring for Improved Interactivity
Proceedings: ACM Siggraph/IEEE Symposium on Volume Visualization, ACM Press, (1996),
San Francisco, CA. Pages: 39-46 99


For UTmesh:

Y. Zhang, C. Bajaj
Adaptive and Quality Quadrilateral/Hexahedral Meshing from Volumetric Data
Computer Methods in Applied Mechanics and Engineering (CMAME), in press, 2005.

Y. Zhang, C. Bajaj, B-S. Sohn
3D Finite Element Meshing from Imaging Data
The special issue of Computer Methods in Applied Mechanics and Engineering (CMAME) on Unstructured
Mesh Generation, 194(48-49):5083-5106, 2005.


For UTsdf:

C. Bajaj, V. Siddavanahalli
An Adaptive Grid Based Method for Computing Molecular Surfaces and Properties
ICES and CS Technical Reports, The University of Texas at Austin, 2005.


For UTvolrend:

C. Bajaj, Z. Yu, M. Auer
Volumetric Feature Extraction and Visualization of Tomographic Molecular Imaging.
Journal of Structural Biology, Volume 144, Issues 1-2, October 2003, Pages 132-143


For UTmolderivatives:

C. Bajaj, V. Siddavanahalli
Fast Feature Adaptive Surfaces and Derivatives Computation for Volumetric Particle Data
ICES and CS Technical Reports, The University of Texas at Austin, 2005.

7. No warranty

7a. Because the library is licensed free of charge, there is no warranty for the library,
to the extent permitted by applicable law. except when otherwise stated in writing the copyright
holders and/or other parties provide the library "as is" without warranty of any kind, either
expressed or implied, including, but not limited to, the implied warranties of merchantability and
fitness for a particular purpose. the entire risk as to the quality and performance of the library
is with you. should the library prove defective, you assume the cost of all necessary servicing,
repair or correction.

7b. In no event unless required by applicable law or agreed to in writing will any copyright
holder, or any other party who may modify and/or redistribute the library as permitted above,
be liable to you for damages, including any general, special, incidental or consequential damages
arising out of the use or inability to use the library (including but not limited to loss of data
or data being rendered inaccurate or losses sustained by you or third parties or a failure of the
library to operate with any other software), even if such holder or other party has been advised
of the possibility of such damages.

APBS License

http://apbs.sourceforge.net/doc/license/license.html

Python Imaging Library (PIL) License

http://www.pythonware.com/products/pil/license.htm



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