UnityMol Files

Files description

In inverse chronological order, so first entries below are the most up-to-date. Check out the UnityMol website and UnityMol's official twitter page for details about releases.

Read the tutorial !

Check the changelog and the API !

UnityMol releases

• UnityMol-1.1.3 -- Mac, Windows (Desktop & VR) and Linux executables.
• UnityMol-1.1.2 -- Mac and Windows (Desktop & VR).
• UnityMol-1.1.1 -- Mac and Windows (Desktop & VR).
• UnityMol-1.1.0 -- Mac and Windows (Desktop & VR) and Linux executables. Stereo-display version too.
• UnityMol-1.0.39 -- Mac, Windows (Desktop & VR) and Linux executables.
• UnityMol-1.0.37 -- Mac, Windows (Desktop) executables.
• UnityMol-1.0.35 -- Windows (Desktop) executables.
• UnityMol-1.0.34 -- Mac, Windows (Desktop & VR) and Linux executables.
• UnityMol-1.0.33 -- Mac and Windows (Desktop & VR) executables.
• UnityMol-0.9.6 -- Mac, Windows and Linux executables.
• UnityMol-0.9.5 -- Mac, Windows and Linux executables.
• UnityMol-r804 MDDriver (Interactive Molecular Dynamics Simulations, aka 0.9.4) -- Mac, Windows and Linux executables as well as some documentation.
• UnityMol-r676 SweetUnityMol (Sugar Edition, aka 0.9.3) -- Mac, Windows and Linux executables as well as source code.
• UnityMol-r255 (0.9.2 or even earlier) -- Mac, Windows and Linux executables, web player as well as source code and documentation.

HiRE-RNA-VM

• VirtualBox image for the HiRE-RNA Simulator. See tutorials at https://hirerna.galaxy.ibpc.fr/

Other

• umolmovie1.m4v -- UnityMol demo movie.
• OldFiles folder -- really old files :)
• https://www.youtube.com/user/marcbaaden & https://www.youtube.com/channel/UCBH8_6C_nG64RA7L_K7wcbg & https://www.youtube.com/channel/UCBH8_6C_nG64RA7L_K7wcbg

UnityMol 1.1.3 README (current version)

UnityMol is a molecular viewer and prototyping platform, coded in C# with the Unity3D game engine.

It is developed by Marc Baaden's team at the LBT laboratory at the IBPC institute of CNRS in Paris and has been completely redesigned recently to provide a clean code base and new features.

The VR version of UnityMol is based on the VIU framework to support HTC Vive and Oculus headsets. Also tested on Oculus Quest with some minor changes.

UnityMol can currently read PDB, mmCIF, GRO, Mol2, XYZ and SDF files, OpenDX potential maps, XTC trajectory files.

UnityMol includes HyperBalls designed to visualize molecular structures using GPU graphics card capabilities based on shaders (GLSL or Cg).

The current version release uses the SMCRA (Structure/Model/Chain/Residue/Atom) data structure supporting to load several molecules, with a python console, a selection language adapted from MDAnalysis, various molecular representations, a modern UI, and more.

The project is still actively developed and maintained, new releases should keep coming soon.

User friendliness and available features in UnityMol will be further extended.

Please contact us on unitymol@gmail.com

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

Features

• a clean data structure to load several molecules
• VR capabilities with VIU (Oculus/Vive/...) + Leap Motion
• Standard and original representations (hyperballs/cartoon/surface/spheres/hbonds/...)
• IMD, iteractive molecular dynamics
• advanced selection (with MDAnalysis language)
• a python console
• molecular sufaces with EDTSurf and MSMS
• fast implementation of secondary structures
• hydrogen bonds detection based on Schrodinger's criteria
• covalent bonds based on OpenMM topology definition
• realtime object space Ambient Occlusion for Hyperballs and surfaces
• save state, data serialization (in progress, partly done with python commands saved as history)
• a clean code base with a high level API
• some unit tests (parser/selection language)
• some documentation (work in progress)

Data input

• Molecule file parsers: PDB/mmCIF/GRO/MOL2/SDF/XYZ
• Trajectory reader: TRR/XTC, Trajectory smoother built-in
• DX file reader with a Marching Cubes implementation in C# with burst compiler
• Custom bonds parsers: XML/PSF/TOP(preprocessed file using grompp -pp)

Surfaces

• EDTSurf surfaces by default
• MSMS for analytical surfaces
• QuickSES GPU implementation (WIP)
• Object space ambient occlusion (AO)

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, 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, 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; 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; Brief Bioinformatics (2011)
• X. Martinez, M. Krone, M. Baaden: [QuickSES: A Library for Fast Computation of Solvent Excluded Surfaces]; MolVA, EuroVis (2019)
• J. Laureanti, J. Brandi, E. Offor, D. Engel, R. Rallo, B. Ginovska, X. Martinez, M. Baaden, N. A. Baker: [Visualizing biomolecular electrostatics in virtual reality with UnityMol-APBS]; Protein Science (2020)

Known Bugs and Issues

• VRPN support is not finalized yet.
• IDLE mode can cause black screen flash on Mac, disabled for now (Unity bug -> fixed in new Unity version)
• this list is to be updated, please send an email to unitymol@gmail.com

Copyright and License

License defined in detail in LICENSE.markdown, in a nutshell, UnityMol open-source version is licensed under the LGPL-3.0, but check out the license file for the details and also concerning the proprietary version.