Macs in Chemistry

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Javascript Molecule Viewers

In the dim and distant past the only option for molecules (particularly biomolecules) was a Unix workstation and specialist software, with the advent of web technologies a number of Java applets were developed that enabled users to visualise proteins etc within the web browser. However, due to security concerns java applets have now been discontinued and a range of javascript based molecular viewers have been developed. This is a list of the viewers that I have come across, please feel free to email me with any I've missed.

3Dmol.js

3Dmol 3Dmol.js is an object-oriented, webGL based JavaScript library for online molecular visualization, jupyterlab_3Dmol is a JupyterLab extension that enables the use of py3Dmol. There is also wizard built on top that allows easy (but limited) use http://www.sbg.bio.ic.ac.uk/ezmol/

License BSD-3-Clause license.
Source code: https://github.com/3dmol/jupyterlab_3Dmol.
Mailing list: https://github.com/3dmol/3Dmol.js/issues

ChemDoodle Web Components

ChemDoodle Web Components library is a pure Javascript chemical graphics and cheminformatics library derived from the ChemDoodle application and produced by iChemLabs.

License GNU General Public License.
Source code:https://web.chemdoodle.com/installation/download/
Mailing list:

IcmJS

IcmJS (formerly known as ActiveIcmJS) is a JavaScript/HTML5 3D molecular viewer which does not require any plug-in or browser extension and runs inside any modern browser. IcmJS brings desktop quality graphics to the web applications. IcmJS is written in ASM.JS which is an optimizable, strictly typed, low level subset of JS. The full ICM shell and graphics have been compiled into JS using Emscripten. MolSoft has developed a special layer which translates OpenGL into WebGl calls which allows the same codebase and delivers high quality graphics.

License Commercial, Free to use
Source code:
Mailing list: https://groups.google.com/forum/#!forum/molsoft-icm-forum

iCn3D

iCn3D is a Javascript/WebGL-based viewer for interactive viewing of three-dimensional macromolecular structures and chemicals on the web

License OpenSource
Source code: https://github.com/ncbi/icn3d
Mailing list: https://github.com/ncbi/icn3d/issues

JSmol

JSmol is the name for the HTML5 canvas version of the Jmol applet. JSmol opens up the use of Jmol in PC, Mac, and Linux systems without Java installed or with Java disabled, as well as tablets and phones (both iOS and Android). No hardware-based graphics acceleration is used, allowing JSmol to run in any web browser that supports HTML5 standards. Jsmol notebook extension This repository contains a Jupyter extension to visualize crystalline structures and molecules in the Jupyter notebook with Jsmol

License free, open source
Source code: https://sourceforge.net/projects/jmol/files/Jmol/ jsmol.zip is contained within Jmol-xx.xx.xx-binary.zip
Mailing list: jmol-users@lists.sourceforge.net

LiteMol

LiteMol is a library/plugin for handling 3D structural molecular data (not only) in the browser. It is written in TypeScript (and compiled to JavaScript). LiteMol features include, but are not limited to, displaying 3D coordinates of molecules and density maps.

License Apache License, Version 2.0
Source code: https://github.com/dsehnal/LiteMol
Mailing list: https://listserver.ebi.ac.uk/mailman/listinfo/litemol

Molmil

Molmil is a WebGL based molecular viewer which can load various formats including PDB, mmCIF and PDBML. Molmil can display small to large structures in high quality as well as scale up to extremely large structures as found in the PDB.

License LGPLv3 licence
Source code: https://github.com/gjbekker/molmil
Mailing list: https://github.com/gjbekker/molmil/issues

Mol*

Mol* is an open collaboration started by PDBe and RCSB PDB to provide a technology stack for the data delivery and analysis tools of macromolecule

License MIT License
Source code: https://github.com/molstar
Mailing list: https://github.com/molstar/molstar.github.io/issues

NGL

NGL Viewer is a web application for molecular visualization. WebGL is employed to display molecules like proteins and DNA/RNA with a variety of representations. There is also a An IPython/Jupyter widget to interactively view molecular structures and trajectories. Utilizes the embeddable NGL Viewer for rendering.

License MIT License
Source code: https://github.com/arose/ngl
Mailing list:https://github.com/arose/ngl/issues

PV

PV is a JavaScript viewer to visualize protein structures directly in the browsers. It's super-fast and and easy to integrate into your website and does not require any plug-ins to be installed.

License MIT License
Source code: https://github.com/biasmv/pv
Mailing list:https://github.com/biasmv/pv/issues

UglyMol

UglyMol is a web-based macromolecular viewer focused on electron density.

License MIT License
Source code: https://github.com/uglymol/uglymol
Mailing list:hhttps://github.com/uglymol/uglymol/issues

There are a couple of other compilations that might be of interest

Cheminformatics Toolkits
Open Source Python Data Science Libraries

Last Updated 4 April 2019