"Fossies" - the Fresh Open Source Software Archive  

Source code changes of the file "test/README" between
pymol-v2.1.0.tar.bz2 and pymol-open-source-2.2.0.tar.gz

About: PyMOL is a Python-enhanced molecular graphics tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. Open Source version.

README  (pymol-v2.1.0.tar.bz2):README  (pymol-open-source-2.2.0)
PyMOL is Copyright (c) Schrodinger, LLC Test cases are organized by systematic numbering:
PyMOL is an OPEN SOURCE program distributed under the "Python" license.
Please see the LICENSE file for additional information.
See INSTALL for installation instructions
PyMOL has the following external dependencies:
1. OpenGL
2. GLUT library for OpenGL (or freeglut)
3. Python (v 2.1 or better) compiled with threads support
4. libpng (can compiled without it, but image saves won't work)
5. Tcl/Tk (for the external GUI)
6. Numerical Python (technically optional - now using numpy instead)
7. Python megawidgets (Pmw -- only required for the "external" GUI)
8. FreeType2 (if you want nice fonts)
The PyMOL Team:
NOTE: this list has not been updated since Fall 2003. Since then, the <Category Letter><Number><Title>.<extension>
PyMOL effort has grown to such an extent that it is no longer
practical to recognize everyone individually. Fortunately, a public
record of participation exists and can be appreciated on the internet,
and especially via the PyMOL mailing list archives. Suffice it to say
that the PyMOL user community now numbers well into the thousands and
includes scientists, students, and educators worldwide, spread
throughout academia and the biotechnology and pharmaceutical
industries. Though Schrodinger, LLC specifically supports and
maintains the PyMOL code base, the project can only continue to
succeed through the sponsorship and participation of the broader
Founder and Principal Author: ie.
Warren L. DeLano C0002.pml
Major Authors (5000+ lines of code): Categories
Ralf W. Grosse-Kunstleve (SGLite Module -- inactivated as of 2008) C : Automated command line tests
G : Automated graphical tests
Minor Authors (500+ lines of code): T : Manual threading tests
U : Unix tests
Scott Dixon (Metaphorics CEX support) B : PDB-based tests -- require a local copy of the PDB linked from ./pdb
Filipe Maia (Slice Objects) L : Large datafile tests -- requires files too large to fit in distro.
Other Contributors: These are the people who have gone out of
their way to help the project with their ideas, actions,
advice, hardware donations, testing, information, sponsorship,
peer support, or code snippets.
Daan van Aalten
Paul Adams
Stephen Adler
Jun Aishima
Dennis Allison
Ricardo Aparicio
Daniel Appelman
Diosdado "Rey" Banatao
Michael Banck
Ulrich Baumann
Joseph Becker
Balaji Bhyravbhatla
Jeff Bizzaro
Jeff Blaney
Juergen Bosch
Michael Bower
Sarina Bromberg
Axel Brunger
Robert Campbell
Bronwyn Carlisle
Duilio Cascio
Julien Chiron
Shawn Christensen
Scott Classen
David Cooper
Larry Coopet
Jacob Corn
Ben Cornett
Andrew Dalke
Koen van der Drift
Harry Dailey
Byron DeLaBarre
Bill DeGrado
Thomas Earnest
Nathaniel Echols
John Eksterowicz
Erik Evensen
David Fahrney
Tim Fenn
Thierry Fischmann
Michael Ford
Esben Peter Friis
Kevin Gardner
R. Michael Garavito
John Gerig
Jonathan Greene
Michael Goodman
Joel Harp
Reece Hart
Richard Hart
Peter Haebel
Matt Henderson
Douglas Henry
Possu Huang
Uwe Hoffmann
Jenny Hinshaw
Carly Huitema
Bjorn Kauppi
Greg Landrum
Robert Lawrence Kehrer
Tom Lee
Eugen Leitl
Ken Lind
Jules Jacobsen
Luca Jovine
Andrey Khavryuchenko
David Konerding
Greg Landrum
Michael Love
Tadashi Matsushita
Genevieve Matthews
Gerry McDermott
Robert McDowell
Gustavo Mercier
Naveen Michaud-Agrawal
Aaron Miller
Holly Miller
Tim Moore
Kelley Moremen
Hideaki Moriyama
Nigel Moriarty
Geoffrey Mueller
Cameron Mura
Florian Nachon
Hanspeter Niederstrasser
Michael Nilges
Hoa Nguyen
Shoichiro Ono
Chris Oubridge
Andre Padilla
Jay Pandit
Ezequiel "Zac" Panepucci
Robert Phillips
Hans Purkey
Rama Ranganathan
Michael Randal
Daniel Ricklin
Ian Robinson
Eric Ross
Kristian Rother
Marc Saric
Bill Scott
Keana Scott
Denis Shcherbakov
Goede Schueler
Paul Sherwood
Ward Smith
John Somoza
David van der Spoel
Paul Sprengeler
Matt Stephenson
Peter Stogios
John Stone
Charlie Strauss
Michael Summers
Brian Sutton
Hanna and Abraham Szoke
Rod Tweten
Andras Varadi
Scott Walsh
Pat Walters
Mark White
Michael Wilson
Dave Weininger
Chris Wiesmann
Charles Wolfus
Richard Xie
Miscellaneous Code Snippets Lifted From:
Thomas Malik (fast matrix-multiply code)
John E. Grayson (Author of "Python and Tkinter")
Doug Hellmann (Wrote code that JEG later modified.)
Open-Source "Enablers" (essential, but not directly involved):
Brian Paul (Mesa)
Mark Kilgard (GLUT)
Guido van Rossum (Python)
Linus Torvalds (Linux Kernel)
Precision Insight (DRI)
The XFree86 Project (Free Windowing System)
VA Linux (CVS Hosting)
Richard Stallman/Free Software Foundation (GNU Suite)
The unknown authors of EISPACK (Linear Algebra)
Graphics Technology "Enablers" (essential!)
3dfx (RIP)
Specific Acknowledgments (last updated around 2005):
* Thanks to Joni W. Lam for making the business work.
* Thanks to John Stone and John Furr for being such excellent
* Thanks to Ragu Bharadwaj and Marcin Joachimiak for Java expertise
and encouragement.
* Thanks to Apple Computer for continued encouragement, assistance,
and HLAs in support of Mac development. Thanks especially to
Robert Kehrer for creating so many fun opportunities over the years.
* Thanks to Aaron Miller (GlaxoSmithKline) for a continuous stream of
thoughtful opinions and suggestions.
* Thanks to Dave Weininger for suggesting the "roving" feature and for
being such an inspirational friend and mentor.
* Thanks to Matt Hahn and Dave Rogers for proving that it can also be
done, again.
* Thanks to Mick Savage for providing experienced practical advice on
the marketing of scientific software.
* Thanks to Ian Matthew for 3D experience and perspective.
* Thanks for Jeff Blaney for numerous insightful discussions.
* Thanks to Elizabeth Pehrson for making this a team effort.
* Thanks to Erin Bradley for schooling in focus and vision.
* Thanks to Vera Povolona for catalytic clarity and introspection.
* Thanks to Anthony Nichols for proving that it can be done, yet again.
* Thanks to Thompson Doman for timely Open-Source validation.
* Thanks to Manfred Sippl for making it all seem so simple.
* Thanks to Kristian Rother for all his excellent work building on the
PyMOL foundation, and in helping others learn to use the software.
* Thanks to Dave Weininger, Scott Dixon, Roger Sayle, Andrew Dalke,
Anthony Nichols, Dick Cramer, and David Miller, as well as rest of
the Daylight and OpenEye teams for thoughtful discussions on PyMOL
and open-source software during my 2002 pilgrimage to Sante Fe, NM.
* Thanks to Ralf Grosse-Kunstleve for his contribution of the "sglite"
space group and symmetry handling module.
* Thanks to the scientists and management of Sunesis Pharmaceuticals
for supporting PyMOL development since program inception.
* Thanks to the Computational Crystallography Initiative (LBNL)
developers for their encouragement, ideas, and support.
* Thanks to Scott Walsh for being the first individual to provide
financial support for PyMOL.
* Thanks to the hundreds of individuals, companies, and institutions
that have provided financial support for the project.
* Thanks to Brian Paul and the Precision Insight team for development
of Mesa/DRI which greatly assisted in the early development of PyMOL.
* Thanks to Michael Love for the first major outside port of PyMOL
(to GNU-Darwin/OSX) and for believing in the cause.
* Thanks for Paul Sherwood for making a concerted effort to develop
using PyMOL long before the software and vision had matured.
* Thanks to Jay Ponder for thoughtful email discussions on Tinker and
the role of open-source scientific software.
* Thanks to hundreds of PyMOL users for the many forms of feedback,
bug sightings, and encouragement they've provided.
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