imolecule

An embeddable webGL molecule viewer and file format converter. http://patrickfuller.github.io/imolecule/

Examples

• IPython notebook
• metal-organic frameworks

IPython

The IPython notebook is an open-source tool poised to replace MATLAB in many applications. As a scientist of sorts, I'm all about it. Therefore, I made handles to use imolecule with the notebook. Install through pip:

pip install imolecule

Open a new notebook and test the setup by typing:

import imolecule
imolecule.draw("CC1(C(N2C(S1)C(C2=O)NC(=O)CC3=CC=CC=C3)C(=O)O)C")

into a notebook cell. This should convert, optimize and draw the specified SMILES structure (in this case, penicillin) into the notebook.

Note that this requires Open Babel to function. If you do not have Open Babel, see below for installation details.

The drawer can handle any format specified here, and can be set up to better handle different use cases. Check out the docstrings associated with the IPython interface for more.

Server

If you want to run the file format converter on your own computer, install the library with:

pip install imolecule

Then run from the command line with:

imolecule

The default site allows for loading molecules via a simple file drag-and-drop interface. Drag a file to anywhere in the browser and drop to load. This interface communicates with openbabel via websocket, so most file formats should work. Be sure to set the extensions of your files to their data type (ie. "mol", "pdb", etc.) for format inference to work properly.

If you have an existing web server, tornado can be easily switched out for other libraries. If you want to use imolecule as a starting point for a broader user interface, the server is written to be extensible. In both cases, read through the source code - it's surprisingly short.

Javascript

Start by downloading the minified javascript file:

wget https://raw.githubusercontent.com/patrickfuller/imolecule/master/imolecule/js/build/imolecule.min.js

Include this file alongside jQuery in your project, and then use with:

imolecule.create('my-selector');
imolecule.draw(myMolecule);

where 'my-selector' is where you want to place imolecule, and myMolecule is an object. See below for more on the object structure, or just check out the included examples. The imolecule.create() method takes a few optional parameters, specifying a few common drawing and camera types.

options = {
    drawingType: "ball and stick", // Can be "ball and stick", "wireframe", or "space filling"
    cameraType: "perspective", // Can be "perspective" or "orthogonal"
    shader: "toon" // three.js shader to use, can be "toon", "basic", "phong", or "lambert"
};

Molecule Data Format

At its core, imolecule takes input chemical structures as javascript objects. As an example, consider benzene:

{
    atoms: [
        { element: "C", location: [ -0.762160, 1.168557, 0.022754 ] },
        { element: "C", location: [ 0.631044, 1.242862, -0.013022 ] },
        { element: "C", location: [ 1.391783, 0.076397, -0.012244 ] },
        { element: "C", location: [ 0.762101, -1.168506, 0.026080 ] },
        { element: "C", location: [ -0.631044, -1.242903, -0.011791 ] },
        { element: "C", location: [ -1.391806, -0.076430, -0.014083 ] },
    ],
    bonds: [
        { atoms: [ 0, 1 ], order: 2 },
        { atoms: [ 1, 2 ], order: 1 },
        { atoms: [ 2, 3 ], order: 2 },
        { atoms: [ 3, 4 ], order: 1 },
        { atoms: [ 4, 5 ], order: 2 },
        { atoms: [ 0, 5 ], order: 1 }
    ]
}

If you want to make properly formatted JSON, you can use either format_converter.py as a script or run your own imolecule server to convert most chemical file formats to JSON.

Open Babel

Open Babel is an open-source library for interconverting over 100 chemical file formats. imolecule uses Open Babel to convert input formats to JSON before drawing. Therefore, to use imolecule with non-JSON formats, you will need Open Babel.

Open Babel is best installed from source. For more, read through the Open Babel installation instructions.

git clone https://github.com/openbabel/openbabel
mkdir build && cd build
cmake ../openbabel -DPYTHON_BINDINGS=ON
make && make install

Older versions of open babel can be found through standard package managers, and do support most of the functionality of the development version. If you are struggling with building from source, check your package manager for openbabel.