aspirincode/faerun-python

A python module for generating interactive views of chemical spaces.

Faerun (Python)

Faerun (Python) is based on the Lore.js 3D WebGL engine for interactive big data rendering and the FUn project. It facilitates the creation of interactive (2D and 3D) HTML plots of chemical data (or chemical spaces). Molecular structures are rendered using SmilesDrawer.

Associated Publication: https://academic.oup.com/bioinformatics/article/34/8/1433/4657075

Installation

pip install faerun

Examples

• Drugbank 3D
• Drugbank 2D

The code of the examples shown above for creating interactive 2D and 3D maps from Drugbank can be found in the examples directory. Following, a simple example of plotting any data:

import numpy as np
from faerun import Faerun

faerun = Faerun(view='free', shader='circle')

t = np.linspace(0, 12.0, 326)
s = np.sin(np.pi * t)
c = np.cos(np.pi * t)
 
faerun.plot({ 'x': t, 'y': s, 'z': c, 'c': t / max(t) })

The code above writes two files to the current directory: index.html and data.js. These files can be used locally or be moved to a (even minimalistic) web server.

TODO

• Add the abilty to draw shapes as well as colours
• Make output templatable

Documentation

Faerun(title='python-faerun', point_size=5, tree_color='#aaaaaa', clear_color='#111111', fog_intensity=2.6, coords=True, coords_color='#888888', view='free', shader='circle')

Parameter	Default	Description
title	'python-faerun'	The title of the HTML document.
point_size	5	The size of the points.
tree_color	'#aaaaaa'	Not yet implemented.
clear_color	'#111111'	The clear colour, or background colour is used to clear the canvas after each rendering step.
fog_intensity	2.6	Fog is used to darken / lighten far away points depending on the clear_color. This is a visual cue helpful for depth perception in orthogonal projections.
coords	True	Whether or not to draw the coordinate axes.
coords_color	'#888888'	The colour used to draw the coordinate axes.
view	'free'	The view mode. Available options: free, front, back, left, right, bottom, top
shader	circle	The name of the shader used to draw the points. Available options: circle, legacyCircle, sphere

Faerun.plot(path, data, x='x', y='y', z='z', c='c', colormap='plasma', smiles='smiles', tree=None)

Parameter	Default	Description
data		A dict or a Pandas DataFrame containing the data.
x	x	The name of the column containing the x-coordinates.
x	y	The name of the column containing the y-coordinates.
x	z	The name of the column containing the z-coordinates.
c	c	The name of the column containing the values by which the points are coloured. Has to be normalized between 0.0 and 1.0
colormap	'plasma'	The colour map to be used. Valid values are matplotlib colormap names.
smiles	smiles	The name of the column containing the SMILES strings with which the points are annotated.
path	''	The path to which the HTML and data files will be written.
tree	None	Not yet implemented.