This is a coursework project forked from UnityMol 1.0.36.

UnityMol is based on the game engine Unity.

This version is working on Unity 2019.4.21f1 LTS, tested on Windows/Mac/Linux. Main developpement is done on Windows.

You also need to install the lastest version of NAMD and Open Babel. For our custom modifications to work, remember to add the respective executables to your PATH environment variable.

• Clone the repo with git lfs installed and open the project using the 2019.4.21f1 version of Unity.
• MainUIScene.unity is the main scene for desktop.
• MainScene_VR_Desktop.unity is the Virtual Reality (VR) scene that has a switch to turn VR on/off.

For the VR scene to work, the VR headset must be first configured and functional with SteamVR.

UnityMol uses VRTK 3.x that is limited to the SteamVR plugin version 1.2.3, you must stick to this version (already imported in the project).

The scene lack of a skybox due to the large size of the image file needed. You can find nice examples on this website https://polyhaven.com/. For instance, we usually use this image https://polyhaven.com/a/noon_grass (version 4K).

To add it to the scene:

• Save the chosen image in the Assets folder.
• In the Editor, edit the following parameters in the Inspector view:
  • Shape -> cube
  • Max Size -> 4096
  • Tick Use Crunch Compression
• Choose the texture in the Cubemap option of the skyhdr material (under Assets/Ressources/Materiels)
• Generate LightMaps (Menu Windows->Rendering->Lightning Settings)

• The website of UnityMol is here: http://unitymol.sourceforge.net
• a tutorial can be found here: https://nezix.github.io/
• UnityMol provides a Python API to access functions from the console. The documentation is here: UMolAPI

This is implemented with IronPython, an interpreter for Python 2.7 in C#. You can use most of standard library python modules but not numpy of cython.

UnityMol implements an atom selection language, based on the MDAnalysis one. Please refer to MDAnalysis documentation (here) for a detailed explanation about the language and some examples.

The language is not fully implemented, also some keywords have been added.

To load and display a molecule from a script, use UMol.API.APIPython functions:

using UnityEngine;
using UMol;
using UMol.API;

public class loadMolecule : MonoBehaviour {
	void Start() {
		UnityMolStructure s = APIPython.fetch("1KX2"); //This fetches the file from the PDB
		UnityMolStructure s2 = APIPython.fetch("PDBs/3eam.cif"); //This loads a local file

		UnityMolSelection sel = APIPython.select("3eam and resid 1:10 and chain A", "chainA"); //Create a selection
		APIPython.showSelection("chainA", "hyperball"); //Show the selection as hyperball

		APIPython.delete(s.name); //Remove a loaded molecule

		//Use more APIPython functions here
	}
}

Same commands from the python console:

s = fetch("1KX2")
s2 = load("PDBs/3eam.cif")
sel = select("3eam and resid 1:10 and chain A", "chainA")
showSelection("chainA", "hb")
delete(s.name)

• This version is a snapshot, UnityMol is still in continuous development.
• When loading molecules the LoadedMolecules object will be created if it doesn't exist and all selections of the molecules will be created under it. The global scale is set by changing this LoadedMolecules object.
• In desktop mode, the camera does not move, the mocules are moving!
• For VR: There are a lot of scripts for VR molecular interactions, check [VRTK_Scripts] child objects in the VR scene. Grabbing molecules is based on a custom raycasting implementation (CustomRaycast). The VR camera is different for each HMD type, check [VRTK_SDKManager] object based on the VRTK framework.
• Anti-aliasing is done using SMAA script because hyperball shaders do not support it. You can disable MSAA.
• Raycasting is done using a custom engine without using PhysX that caused a lot of slow downs for medium to large molecules.

The original UnityMol is dual-licensed under the LGPL-3.0 (see under). However, all external assets used in UnityMol are under a permissive open-source license: MIT/Apache-2.0/BSD-3.0

This project follows the lincenses used in the original.