UnityMol Files

Files
-----

* sweetumol_r676beta_src.zip -- gzipped tar archive of the Sweet UnityMol sourcecode of our paper in GlycoBiology, compatible with Unity3D v4.5
* sweetumol_r676beta_mac.zip -- zipped archive containing a beta version MacOS executable of the upcoming Sweet UnityMol v0.9.2
* sweetumol_r676beta_win32.zip -- zipped archive containing a beta version Windows 32 executable of the upcoming Sweet UnityMol v0.9.2
* sweetumol_r676beta_win64.zip -- zipped archive containing a beta version Windows 64 executable of the upcoming Sweet UnityMol v0.9.2
* sweetumol_r676beta_linux.zip -- zipped archive containing a beta version Linux 32 and 64 bit executable of the upcoming Sweet UnityMol v0.9.2
* umol_src080413.tgz -- gzipped tar archive of the UnityMol sourcecode of our paper in PLoS One. Compatible with Unity3D v4.x
*  umol_doc080413.tgz -- gzipped tar archive of the UnityMol development documentation generated with DoxyGen. Courtesy of Axel Viala.
* umolmovie1.m4v -- UnityMol demo movie.
* umol_mac_160413.zip -- current UnityMol MacOS executable (most thoroughly tested version).
* umol_win32_160413.zip -- current UnityMol executable for Windows 32bit.
* umol_win64_160413.zip -- current UnityMol executable for Windows 64bit.
* umol_linux_160413.zip -- current UnityMol 32-bit Linux executable (issue with file open dialog!).
* umol_linux64_160413.zip -- current UnityMol 64-bit Linux executable (issue with file open dialog!).
* umol_web_160413.zip -- current UnityMol webbrowser plugin (Mac and Windows). Can currently be tested at [http://www.shaman.ibpc.fr/umolweb/][umolweb]

[UnityMol][umol] v0.9.1 README
==========================

$Id: README.markdown,v 1.7 2013/04/16 22:42:02 baaden Exp baaden $

UnityMol is a molecular viewer and prototyping platform for the Unity3D game engine developped by Marc Baaden's team in Paris ([Lv et al., 2013][umolpaper]). It includes [HyperBalls][hbpaper]
designed to visualize molecular structures using GPU graphics card capabilities based on shaders (GLSL or Cg).
It can read Protein Data Bank (PDB) files, Cytoscape networks, OpenDX maps and Wavefront OBJ meshes.

More information on <http://unitymol.sourceforge.net>

Features
--------

* Lit sphere artistic texturing of surfaces and HyperBalls
* Screen space effects from Unity (Blur, Glow, ..)
* Animated electric field lines
* (Simple) surfaces with cut planes
* specific representations for carbohydrates and polysaccharides
* description to be completed soon

Citations
---------
* Z. Lv, A. Tek, F. Da Silva, C. Empereur-mot, M. Chavent and M. Baaden: [Game on, Science - how video game technology may help biologists tackle visualization challenges][umolpaper], PLoS ONE (2013) 8(3):e57990.

* S. Perez, T. Tubiana, A. Imberty and M. Baaden: [Three-Dimensional Representations of Complex Carbohydrates and Polysaccharides. SweetUnityMol: A Video Game Based Computer Graphic Software][sweetumolpaper], Glycobiology (2014).

Related work
------------
* M. Chavent, A. Vanel, A. Tek, B. Levy, S. Robert, B. Raffin, M. Baaden: [GPU-accelerated atom and dynamic bond visualization using HyperBalls, a unified algorithm for balls, sticks and hyperboloids][hbpaper]; J Comput Chem (2011) 32, 2924.
* M. Chavent, B. Levy, M. Krone, K. Bidmon, J. P. Nomine, T. Ertl and M. Baaden: [GPU-powered tools boost molecular visualization][gpupaper]; Brief Bioinformatics (2011)

Known Bugs and Issues
---------------------
* Linux version bug: the file open dialog does not allow to choose a file or directory. Investigation of this bug is ongoing. Sorry for the inconvenience.
* Windows version issue: depending on graphics card and windows version you may need to force OpenGL mode for proper representations, in particular of the HyperBalls shaders
* Windows version issue: when both a surface and a hyperballs-shaded structure is present, the depth of the objects is not properly handled.
* this list is to be updated and completed soon

Copyright and License
================================================
This program is under the [CeCill-C licence][cecill], which is compatible with the LGPL licence.



[umol]: http://unitymol.sourceforge.net "http://unitymol.sourceforge.net"
[umolweb]: http://www.shaman.ibpc.fr/umolweb "http://www.shaman.ibpc.fr/umolweb/"
[hb]: http://hyperballs.sourceforge.net "http://hyperballs.sourceforge.net"
[cecill]: http://www.cecill.info/index.en.html "CeCill licence"
[umolpaper]: http://dx.doi.org/10.1371/journal.pone.0057990 "http://dx.doi.org/10.1371/journal.pone.0057990"
[sweetumolpaper]: http://dx.doi.org/10.1093/glycob/cwu133 "http://dx.doi.org/10.1093/glycob/cwu133"
[hbpaper]: http://dx.doi.org/10.1002/jcc.21861 "http://dx.doi.org/10.1002/jcc.21861"
[gpupaper]: http://dx.doi.org/10.1093/bib/bbq089 "http://dx.doi.org/10.1093/bib/bbq089"
[markdown]: http://daringfireball.net/projects/markdown/ "http://daringfireball.net/projects/markdown/"
[cpkwikip]: http://en.wikipedia.org/wiki/CPK_coloring "http://en.wikipedia.org/wiki/CPK_coloring"
[gdbweb]: http://about.gremedy.com "http://about.gremedy.com"